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Reference Library

TrueBlack™ Lipofuscin Autofluorescence Quencher
  1. Wang, Z., Yip, L. Y., Lee, J. H. J., Wu, Z., Chew, H. Y., Chong, P. K. W., … & Ma, S. (2019). Methionine is a metabolic dependency of tumor-initiating cells. Nature Medicine, 25(5), 825. https://doi.org/10.1038/s41591-019-0423-5
1 kb DNA Ladder
  1. Berg, J. A., Merrill, B. D., Breakwell, D. P., Hope, S., & Grose, J. H. (2018). A PCR-based method for distinguishing between two common beehive bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl. Environ. Microbiol., 84(22), e01886-18. https://doi.org/10.1128/AEM.01886-18
  2. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  3. Fischer, M. D., Mgboji, E., & Liu, Z. (2018). Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes. Plant Methods, 14(1), 91.https://doi.org/10.1186/s13007-018-0359-7
  4. Chu, P., Wilson, G. M., Michael, T. P., Vaiciunas, J., Honig, J., & Lam, E. (2018). Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. Plant Molecular Biology, 98(3), 219-231. https://doi.org/10.1007/s11103-018-0774-1
1 kb PLUS™ DNA Ladder
  1. Nacham, O., Clark, K. D., & Anderson, J. L. (2015). Analysis of bacterial plasmid DNA by solid-phase microextraction. Analytical Methods, 7(17), 7202-7207. https://doi.org/10.31274/etd-180810-5204
  2. Clark, K. D., Sorensen, M., Nacham, O., & Anderson, J. L. (2016). Preservation of DNA in nuclease-rich samples using magnetic ionic liquids. RSC Advances, 6(46), 39846–39851. https://doi.org/10.1039/c6ra05932e
  3. Berg, J. A., Merrill, B. D., Breakwell, D. P., Hope, S., & Grose, J. H. (2018). A PCR-based method for distinguishing between two common beehive bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl. Environ. Microbiol., 84(22), e01886-18. https://doi.org/10.1128/AEM.01886-18
  4. Brew-Appiah, R. A., Peracchi, L. M., & Sanguinet, K. A. (2019). Never the two shall mix: robust indel markers to ensure the fidelity of two pivotal and closely-related accessions of Brachypodium distachyon. Plants, 8(6), 153. https://doi.org/10.3390/plants8060153
100 bp DNA Ladder
  1. Fischer, M. D., Mgboji, E., & Liu, Z. (2018). Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes. Plant Methods, 14(1), 91.https://doi.org/10.1186/s13007-018-0359-7
  2. Lang, J. M., DuCharme, E., Ibarra Caballero, J., Luna, E., Hartman, T., Ortiz-Castro, M., … & Leach, J. E. (2017). Detection and characterization of Xanthomonas vasicola pv. vasculorum (Cobb 1894) comb. nov. causing bacterial leaf streak of corn in the United States. Phytopathology, 107(11), 1312-1321. https://doi.org/10.1094/phyto-05-17-0168-r
  3. Shiimori, M., Garrett, S. C., Graveley, B. R., & Terns, M. P. (2018). Cas4 nucleases define the PAM, length, and orientation of DNA fragments integrated at CRISPR loci. Molecular Cell, 70(5), 814-824. https://doi.org/10.1016/j.molcel.2018.05.002
  4. Neyaz, M., Cook, D., & Creamer, R. (2020). Molecular differentiation of Astragalus species and varieties from the western United States: the chloroplast DNA bridge between evolution and molecular systematics. Poisonous Plant Research (PPR), 3(1), 1 https://digitalcommons.usu.edu/poisonousplantresearch/vol3/iss1/1
100 bp PLUS™ DNA Ladder
  1. De Ioannes, P., Leon, V. A., Kuang, Z., Wang, M., Boeke, J. D., Hochwagen, A., & Armache, K. J. (2019). Structure and function of the Orc1 BAH-nucleosome complex. Nature communications, 10(1), 2894. https://doi.org/10.1038/s41467-019-10609-y
  2. Saeidi, S., McKain, M. R., & Kellogg, E. A. (2018). Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens. JoVE (Journal of Visualized Experiments), (133), e56837.https://doi.org/10.3791/56837
2-(4-Methylumbelliferyl)- α-D-N- acetylneuraminic acid sodium salt (4-MU-NANA)
  1. Kongkamnerd, J., Milani, A., Cattoli, G., Terregino, C., Capua, I., Beneduce, L., … De-Eknamkul, W. (2011). A screening assay for neuraminidase inhibitors using neuraminidases N1 and N3 from a baculovirus expression system. Journal of Enzyme Inhibition and Medicinal Chemistry, 27(1), 5–11
    10.3109/14756366.2011.568415
  2. Kongkamnerd, J., Cappelletti, L., Prandi, A., Seneci, P., Rungrotmongkol, T., Jongaroonngamsang, N., … De-Eknamkul, W. (2012). Synthesis and in vitro study of novel neuraminidase inhibitors against avian influenza virus. Bioorganic & Medicinal Chemistry, 20(6), 2152–2157. https://doi.org/10.1016/j.bmc.2012.01.026
  3. Braun, E., Hotter, D., Koepke, L., Zech, F., Groß, R., Sparrer, K. M., … & Sutter, K. (2019). Guanylate-binding proteins 2 and 5 exert broad antiviral activity by inhibiting furin-mediated processing of viral envelope proteins. Cell Reports, 27(7), 2092-2104. https://doi.org/10.1016/j.celrep.2019.04.063
4-Aminophenyl phosphate monosodium salt hydrate
  1. Ahmad, A., & Moore, E. (2012). Electrochemical immunosensor modified with self-assembled monolayer of 11-mercaptoundecanoic acid on gold electrodes for detection of benzo[a]pyrene in water. The Analyst, 137(24), 5839. https://doi.org/10.1039/c2an35236b
  2. Bhimji, A., Zaragoza, A. A., Live, L. S., & Kelley, S. O. (2013). Electrochemical enzyme-linked immunosorbent assay featuring proximal reagent generation: Detection of human immunodeficiency virus antibodies in clinical samples. Analytical Chemistry, 85(14), 6813–6819. https://doi.org/10.1021/ac4009429
  3. Farrow, B., Hong, S. A., Romero, E. C., Lai, B., Coppock, M. B., Deyle, K. M., … & Heath, J. R. (2013). A chemically synthesized capture agent enables the selective, sensitive, and robust electrochemical detection of anthrax protective antigen. ACS Nano, 7(10), 9452-9460. https://doi.org/10.1021/nn404296k
  4. Sung, D., & Yang, S. (2014). Facile method for constructing an effective electron transfer mediating layer using ferrocene-containing multifunctional redox copolymer. Electrochimica Acta, 133, 40-48.https://doi.org/10.1016/j.electacta.2014.03.110
  5. Glavan, A. C., Christodouleas, D. C., Mosadegh, B., Yu, H. D., Smith, B. S., Lessing, J., … & Whitesides, G. M. (2014). Folding analytical devices for electrochemical ELISA in hydrophobic RH paper. Analytical Chemistry, 86(24), 11999-12007. https://doi.org/10.1021/ac5020782
4-Methylumbelliferyl-α- L-fucopyranoside
  1. Pickard, J. M., Maurice, C. F., Kinnebrew, M. A., Abt, M. C., Schenten, D., Golovkina, T. V., … Chervonsky, A. V. (2014). Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness. Nature, 514(7524), 638–641. https://doi.org/10.1038/nature13823
4-Methylumbelliferyl-α- L-iduronic acid cyclohexylammonium salt
  1. Wang, D., Li, J., Song, C. Q., Tran, K., Mou, H., Wu, P. H., … & Su, Q. (2018). Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nature Biotechnology, 36(9), 839.https://doi.org/10.1038/nbt.4219
4-Nitrophenyl phosphate, disodium salt hexahydrate
  1. Henderson, C. F., Bica, I., Long, F. T., Irwin, D. D., Stull, C. H., Baker, B. W., … Lin, J. (2020). Cysteine trisulfide protects E. coli from electrophile-induced death through the generation of cysteine hydropersulfide. Chemical Research in Toxicology, 33(2), 678–686. https://doi.org/10.1021/acs.chemrestox.9b00494
4-Nitrophenyl phosphate, magnesium salt
  1. Meghnani, V., Wagh, A., Indurthi, V. S. K., Koladia, M., Vetter, S. W., Law, B., & Leclerc, E. (2014). The receptor for advanced glycation end products influences the expression of its S100 protein ligands in melanoma tumors. The International Journal of Biochemistry & Cell Biology, 57, 54–62. https://doi.org/10.1016/j.biocel.2014.10.001
4-Nitrophenyl-α-L- fucopyranoside
  1. Garber, J. M., Nothaft, H., Pluvinage, B., Stahl, M., Bian, X., Porfirio, S., … & Line, E. (2020). The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus. Communications Biology, 3(1) https://doi.org/10.1038/s42003-019-0727-5
4-Nitrophenyl-β-D- xylopyranoside
  1. Jordan, D. B., & Braker, J. D. (2015). Rate-limiting steps of a stereochemistry retaining β-d-xylosidase from Geobacillus stearothermophilus acting on four substrates. Archives of Biochemistry and Biophysics, 583, 73–78. https://doi.org/10.1016/j.abb.2015.08.004
  2. Jordan, D. B., Braker, J. D., Wagschal, K., Stoller, J. R., & Lee, C. C. (2016). Isolation and divalent-metal activation of a β-xylosidase, RUM630-BX. Enzyme and Microbial Technology, 82, 158–163. https://doi.org/10.1016/j.enzmictec.2015.10.001
  3. Jordan, D. B., Stoller, J. R., Lee, C. C., Chan, V. J., & Wagschal, K. (2016). Biochemical characterization of a GH43 β-xylosidase from Bacteroides ovatus. Applied Biochemistry and Biotechnology, 182(1), 250–260. https://doi.org/10.1007/s12010-016-2324-0
5-Aminolevulinic acid hydrochloride
  1. Calla, B., Wu, W. ‐Y., Dean, C. A. E., Schuler, M. A., & Berenbaum, M. R. (2019). Substrate‐specificity of cytochrome P450‐mediated detoxification as an evolutionary strategy for specialization on furanocoumarin‐containing hostplants: CYP6AE89 in parsnip webworms. Insect Molecular Biology, 29(1), 112–123. https://doi.org/10.1111/imb.12612
5-Bromo-4-chloro-3-indoxyl-2-acetamido-2-deoxy-β-D-galactopyranoside (X-β-D-GalNAc)
  1. Wu, F., Peacock, S. O., Rao, S., Lemmon, S. K., & Burnstein, K. L. (2012). Novel interaction between the co-chaperone Cdc37 and Rho GTPase exchange factor Vav3 promotes androgen receptor activity and prostate cancer growth. Journal of Biological Chemistry, 288(8), 5463–5474. https://doi.org/10.1074/jbc.m112.390963
5-Bromo-4-chloro-3-indoxyl-β-D-glucuronic acid sodium salt (X-β-D-GlcA·Na)
  1. Lozano‐Sotomayor, P., Chávez Montes, R. A., Silvestre‐Vañó, M., Herrera‐Ubaldo, H., Greco, R., Pablo‐Villa, J., … & Pereira, A. (2016). Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana. The Plant Journal, 88(3), 437-451. https://doi.org/10.1111/tpj.13264
5-Bromo-4-chloro-3-indoxyl-β-D-xylopyranoside
  1. Adelskov, J., & Patel, B. K. (2016). A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor. 3 Biotech, 6(1), 96.https://doi.org/10.1007/s13205-016-0408-8
5-Fluoroorotic acid monohydrate (5-FOA)
  1. Thakker, C., Lin, K., Martini‐Stoica, H., & Bennett, G. N. (2016). Use of transposase and ends of IS608 enables precise and scarless genome modification for modulating gene expression and metabolic engineering applications in Escherichia coli. Biotechnology Journal, 11(1), 80-90. https://doi.org/10.1002/biot.201500205
  2. Standage-Beier, K., Zhang, Q., & Wang, X. (2015). Targeted large-scale deletion of bacterial genomes using CRISPR-nickases. ACS Synthetic Biology, 4(11), 1217–1225. https://doi.org/10.1021/acssynbio.5b00132
  3. Luttgeharm, K. D., Cahoon, E. B., & Markham, J. E. (2016). Substrate specificity, kinetic properties and inhibition by fumonisin B1 of ceramide synthase isoforms from Arabidopsis. Biochemical Journal, 473(5), 593-603. https://doi.org/10.1042/BJ20150824
  4. Burrack, L. S., Hutton, H. F., Matter, K. J., Clancey, S. A., Liachko, I., Plemmons, A. E., … Berman, J. (2016). Neocentromeres provide chromosome segregation accuracy and centromere clustering to multiple loci along a Candida albicans chromosome. PLoS Genetics, 12(9), e1006317. https://doi.org/10.1371/journal.pgen.1006317
5-Hydroxytryptophol
  1. Cecala, C., Rubakhin, S. S., Mitchell, J. W., Gillette, M. U., & Sweedler, J. V. (2012). A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis. The Analyst, 137(13), 2965. https://doi.org/10.1039/c2an35198f
5-Methoxyindole-3-acetic acid
  1. Cecala, C., Rubakhin, S. S., Mitchell, J. W., Gillette, M. U., & Sweedler, J. V. (2012). A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis. The Analyst, 137(13), 2965. https://doi.org/10.1039/c2an35198f
5-Methyl-DL-tryptophan
  1. Lai, W. C., Sun, H. F. S., Lin, P. H., Lin, H., & Shieh, J. C. (2016). A new rapid and efficient system with dominant selection developed to inactivate and conditionally express genes in Candida albicans. Current Genetics, 62(1), 213-235.https://doi.org/10.1007/s00294-015-0526-6
50 bp DNA Ladder
  1. Brew-Appiah, R. A., Peracchi, L. M., & Sanguinet, K. A. (2019). Never the two shall mix: robust indel markers to ensure the fidelity of two pivotal and closely-related accessions of Brachypodium distachyon. Plants, 8(6), 153. https://doi.org/10.3390/plants8060153
  2. Mattiroli, F., Gu, Y., & Luger, K. (2018). Measuring nucleosome assembly activity in vitro with the nucleosome assembly and quantification (NAQ) assay. Bio-protocol, 8(3). https://doi.org/10.21769/bioprotoc.2714
6-Bromo-DL-tryptophan
  1. Ellefson, J. W., Ledbetter, M. P., & Ellington, A. D. (2018). Directed evolution of a synthetic phylogeny of programmable Trp repressors. Nature Chemical Biology, 14(4), 361. https://doi.org/10.1038/s41589-018-0006-7
Acidic FGF (FGF1), Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
AEBSF
  1. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  2. Elsasser S., Shi Y., Finley D. (2012) Binding of ubiquitin conjugates to proteasomes as visualized with native gels. In: Dohmen R., Scheffner M. (eds) Methods in Molecular Biology: Ubiquitin family modifiers and the proteasome. (Vol 832, pp. 403-422) New York, NY: Humana Press https://doi.org/10.1007/978-1-61779-474-2_28
  3. Cardenas-Aguayo, M. del C., Kazim, S. F., Grundke-Iqbal, I., & Iqbal, K. (2013). Neurogenic and neurotrophic effects of BDNF peptides in mouse hippocampal primary neuronal cell cultures. PLoS ONE, 8(1), e53596. https://doi.org/10.1371/journal.pone.0053596
  4. Park, N. J., Wang, X., Diaz, A., Goos-Root, D. M., Bock, C., Vaught, J. D., … & Strom, C. M. (2013). Measurement of cetuximab and panitumumab-unbound serum EGFR extracellular domain using an assay based on slow off-rate modified aptamer (SOMAmer) reagents. PloS one, 8(8), e71703.https://doi.org/10.1371/journal.pone.0071703
  5. Amick, J., Schlanger, S. E., Wachnowsky, C., Moseng, M. A., Emerson, C. C., Dare, M., … & Page, R. C. (2014). Crystal structure of the nucleotide‐binding domain of mortalin, the mitochondrial Hsp70 chaperone. Protein Science, 23(6), 833-842. https://doi.org/10.1002/pro.2466
  6. Baradaran, R., Wang, C., Siliciano, A. F., & Long, S. B. (2018). Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters. Nature, 559(7715), 580. https://doi.org/10.1038/s41586-018-0331-8
  7. Diver, M. M., Pedi, L., Koide, A., Koide, S., & Long, S. B. (2018). Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature, 553(7689), 526. https://doi.org/10.1038/nature25439
  8. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  9. Wacker, D., Wang, S., McCorvy, J. D., Betz, R. M., Venkatakrishnan, A. J., Levit, A., … & Shoichet, B. K. (2017). Crystal structure of an LSD-bound human serotonin receptor. Cell, 168(3), 377-389. https://doi.org/10.1016/j.cell.2016.12.033
  10. Verardi, R., Kim, J. S., Ghirlando, R., & Banerjee, A. (2017). Structural basis for substrate recognition by the ankyrin repeat domain of human DHHC17 palmitoyltransferase. Structure, 25(9), 1337-1347. https://doi.org/10.1016/j.str.2017.06.018
  11. Zinoviev, A., Hellen, C. U., & Pestova, T. V. (2020). In Vitro Characterization of the Activity of the Mammalian RNA Exosome on mRNAs in Ribosomal Translation Complexes. In The Eukaryotic RNA Exosome. Methods In Microbiology (pp. 327-354). Humana, New York, NY. <a “=”” href=”https://doi.org/10.1007/978-1-4939-9822-7_16″ target=”_blank”> https://doi.org/10.1007/978-1-4939-9822-7_16
Agarose LE (Molecular Biology Grade)
  1. Rodriguez, B. V., Pescador, J., Pollok, N., Beall, G. W., Maeder, C., & Lewis, L. K. (2015). Impact of size, secondary structure, and counterions on the binding of small ribonucleic acids to layered double hydroxide nanoparticles. Biointerphases, 10(4), 041007. https://doi.org/10.1116/1.4936393
  2. Ream, J. A., Lewis, L. K., & Lewis, K. A. (2016). Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: RNA interactions. Analytical Biochemistry, 511, 36–41. https://doi.org/10.1016/j.ab.2016.07.027
  3. Kang, W., & Cannon, J. L. (2015). A membrane-based electro-separation method (MBES) for sample clean-up and norovirus concentration. PloS One, 10(10), e0141484. https://doi.org/10.1371/journal.pone.0141484
  4. Zhang, J., Smaga, L. P., Satyavolu, N. S. R., Chan, J., & Lu, Y. (2017). DNA aptamer-based activatable probes for photoacoustic imaging in living mice. Journal of the American Chemical Society, 139(48), 17225-17228. https://doi.org/10.1021/jacs.7b07913
  5. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  6. Chakravarty, A. K., Smejkal, T., Itakura, A. K., Garcia, D. M., & Jarosz, D. F. (2020). A non-amyloid prion particle that activates a heritable gene expression program. Molecular Cell, 77(2), 251-265. https://doi.org/10.1016/j.molcel.2019.10.028
Aminoethyl (Very Low Density) 4% Agarose Beads, Crosslinked
  1. Ashley, G., & Santi, D. V. (2015). U.S. Patent No. 8,946,405 B2. Washington, DC: U.S. Patent and Trademark Office.
Ampicillin (Sodium) 100 mg/mL Solution
  1. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  2. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  3. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
Ampicillin (Sodium) EZ Pak™ for 100 mg/mL Solution
  1. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  2. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  3. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
Ampicillin (Sodium), USP Grade
  1. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  2. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  3. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  4. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  5. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  6. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  7. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  8. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  9. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  10. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  11. Reese, A. T., Pereira, F. C., Schintlmeister, A., Berry, D., Wagner, M., Hale, L. P., … & Premont, R. T. (2018). Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology, 3(12), 1441. https://doi.org/10.1038/s41564-018-0267-7
  12. Smith, C. D. M., Gong, M., Andrew, A. K., Russ, B. N., Ge, Y., Zadeh, M., … & Moore, J. M. (2019). Composition of the gut microbiota transcends genetic determinants of malaria infection severity and influences pregnancy outcome. EBioMedicine 44, 639–655. https://doi.org/10.1016/j.ebiom.2019.05.052
  13. Wright, W. C., Chenge, J., Wang, J., Girvan, H. M., Yang, L., Chai, S. C., Huber, A. D., Wu, J., Oladimeji, P. O., Munro, A. W., & Chen, T. (2020). Clobetasol propionate is a heme-mediated selective inhibitor of human cytochrome P450 3A5. Journal of Medicinal Chemistry, 63(3), 1415–1433. https://doi.org/10.1021/acs.jmedchem.9b02067
  14. Jagessar, K. L., Claxton, D. P., Stein, R. A., & Mchaourab, H. S. (2020). Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter. Proceedings of the National Academy of Sciences, 117(9), 4732–4740. https://doi.org/10.1073/pnas.1917139117
  15. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  16. González, L. M., Mukhitov, N., & Voigt, C. A. (2019). Resilient living materials built by printing bacterial spores. Nature Chemical Biology, 16(2), 126–133. https://doi.org/10.1038/s41589-019-0412-5
  17. Reighard, S. D., Cranert, S. A., Rangel, K. M., Ali, A., Gyurova, I. E., de la Cruz-Lynch, A. T., … Waggoner, S. N. (2020). Therapeutic targeting of follicular T cells with chimeric antigen receptor-expressing natural killer cells. Cell Reports Medicine, 100003. https://doi.org/10.1016/j.xcrm.2020.100003
  18. Song, M., Sukovich, D. J., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, E. A., Tucker, A. C., Gordon, D. B., Marlovits, T. C., & Voigt, C. A. (2017). Control of type III protein secretion using a minimal genetic system. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14737
  19. Kim, W. J., Higashi, D., Goytia, M., Rendón, M. A., Pilligua-Lucas, M., Bronnimann, M., … & So, M. (2019). Commensal Neisseria kill Neisseria gonorrhoeae through a DNA-dependent mechanism. Cell Host & Microbe, 26(2), 228–239.e8. https://doi.org/10.1016/j.chom.2019.07.003
  20. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  21. Staffas, A., da Silva, M. B., Slingerland, A. E., Lazrak, A., Bare, C. J., Holman, C. D., … & Cross, J. R. (2018). Nutritional support from the intestinal microbiota improves hematopoietic reconstitution after bone marrow transplantation in mice. Cell Host & Microbe, 23(4), 447-457. https://doi.org/10.1016/j.chom.2018.03.002
  22. Barton, B., Grinnell, A., & Morgenstein, R. M. (2021). Disruption of the MreB elongasome Is overcome by mutations in the tricarboxylic acid cycle. Frontiers in Microbiology, 12 https://doi.org/10.3389/fmicb.2021.664281
  23. Gao, Y., Cao, D., Pawnikar, S., Akhter, S., Miao, Y., & Liang, B. (2021). Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR protocols, 2(1), 100315. https://doi.org/10.1016/j.xpro.2021.100315
Aprotinin
  1. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  2. Pearce, L. A., Yu, M., Waddington, L. J., Barr, J. A., Scoble, J. A., Crameri, G. S., & McKinstry, W. J. (2015). Structural characterization by transmission electron microscopy and immunoreactivity of recombinant Hendra virus nucleocapsid protein expressed and purified from Escherichia coli. Protein Expression and Purification, 116, 19-29. https://doi.org/10.1016/j.pep.2015.07.008
  3. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  4. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  5. Wacker, D., Wang, S., McCorvy, J. D., Betz, R. M., Venkatakrishnan, A. J., Levit, A., … & Shoichet, B. K. (2017). Crystal structure of an LSD-bound human serotonin receptor. Cell, 168(3), 377-389. https://doi.org/10.1016/j.cell.2016.12.033
Bacterial Cell Lysis Buffer
  1. Li, T., Tong, X., Yang, Q., Giddens, J. P., & Wang, L. X. (2016). Glycosynthase mutants of endoglycosidase S2 show potent transglycosylation activity and remarkably relaxed substrate specificity for antibody glycosylation remodeling. Journal of Biological Chemistry, 291(32), 16508-16518. https://doi.org/10.1074/jbc.m116.738765
Basic FGF (FGF2), Human
  1. Sowmya, S., Chennazhi, K. P., Arzate, H., Jayachandran, P., Nair, S. V., & Jayakumar, R. (2015). Periodontal specific differentiation of dental follicle stem cells into osteoblast, fibroblast, and cementoblast. Tissue Engineering Part C: Methods, 21(10), 1044-1058. https://doi.org/10.1089/ten.tec.2014.0603
  2. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
  3. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  4. Aminuddin, A., Ng, P. Y., Leong, C.-O., & Chua, E. W. (2020). Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64664-3
Basic FGF (FGF2), Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
BCIP
  1. Wang, L., & Liu, D. (2017). Analyses of root-secreted acid phosphatase activity in Arabidopsis. Bio-Protocol, 7(7). https://doi.org/10.21769/bioprotoc.2202
Bialaphos, Sodium Salt
  1. Chung, K. R., & Liao, H. L. (2008). Determination of a transcriptional regulator-like gene involved in biosynthesis of elsinochrome phytotoxin by the citrus scab fungus, Elsinoë fawcettii. Microbiology, 154(11), 3556-3566. https://dx.doi.org/10.1099/mic.0.2008/019414-0
  2. Xu C., Yu W. (2011) Telomere Truncation in Plants. In: Birchler J. (eds) Plant Chromosome Engineering. Methods in Molecular Biology (Methods and Protocols), vol 701 (pp 113-130) https://doi.org/10.1007/978-1-61737-957-4_6
  3. Akbudak, M. A., & Srivastava, V. (2011). Improved FLP recombinase, FLPe, efficiently removes marker gene from transgene locus developed by Cre–lox mediated site-specific gene integration in rice. Molecular Biotechnology, 49(1), 82-89.https://doi.org/10.1007/s12033-011-9381-y
  4. Turgeon B.G., Condon B., Liu J., Zhang N. (2010) Protoplast Transformation of Filamentous Fungi. In: Sharon A. (eds) Protoplast transformation of filamentous fungi. Methods in Molecular Biology (Methods and Protocols), vol 638. (pp. 3-19) https://doi.org/10.1007/978-1-60761-611-5_1
  5. Frame B.R., Paque T., Wang K. (2006) Maize (Zea mays L.). In: Wang K. (eds) Agrobacterium Protocols. Methods in Molecular Biology, vol 343. Humana Press https://doi.org/10.1385/1-59745-130-4:185
  6. Lee, H., & Zhang, Z. J. (2016). Maize (Zea mays) Hi‐II transformation via agrobacterium‐mediated T‐DNA transfer. Current Protocols in Plant Biology, 1(1), 121-137. https://doi.org/10.1002/cppb.20016
Blasticidin S HCl
  1. Leyme, A., Marivin, A., & Garcia-Marcos, M. (2016). GIV/Girdin creates a positive feedback loop that potentiates outside-in integrin signaling in cancer cells. Journal of Biological Chemistry, jbc-M115. https://doi.org/10.1074/jbc.m115.691550
  2. Corcoran, J. A., Jordan, M. D., Carraher, C., & Newcomb, R. D. (2014). A novel method to study insect olfactory receptor function using HEK293 cells. Insect Biochemistry and Molecular Biology, 54, 22-32.https://doi.org/10.1016/j.ibmb.2014.08.005
  3. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  4. Tang, Y., & Gomer, R. H. (2020). An improved shotgun antisense method for mutagenesis and gene identification. BioTechniques, 68(3), 163–165. https://doi.org/10.2144/btn-2019-0123
  5. Santarriaga, S., Haver, H. N., Kanack, A. J., Fikejs, A. S., Sison, S. L., Egner, J. M., … & Ebert, A. D. (2018). SRCP1 conveys resistance to polyglutamine aggregation. Molecular Cell, 71(2), 216-228. https://doi.org/10.1016/j.molcel.2018.07.008
Blazin’ Blue™ Protein Gel Stain
  1. Uppal, S., Liu, T., Poliakov, E., Gentleman, S., & Redmond, T. M. (2019). The dual roles of RPE65 S-palmitoylation in membrane association and visual cycle function. Scientific Reports, 9(1), 5218. https://doi.org/10.1038/s41598-019-41501-w
BLUEstain™ 2 Protein ladder, 5-245 kDa
  1. Ho, J. M., Miller, C. A., Smith, K. A., Mattia, J. R., & Bennett, M. R. (2021). Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway. Nature Communications, 12(1), 1-10. https://doi.org/10.1038/s41467-021-24183-9
BLUEstain™ Protein ladder, 11-245 kDa
  1. Lee, J., Ahn, H., Hong, E. J., An, B. S., Jeung, E. B., & Lee, G. S. (2016). Sulforaphane attenuates activation of NLRP3 and NLRC4 inflammasomes but not AIM2 inflammasome. Cellular Immunology, 306, 53-60.https://doi.org/10.1016/j.cellimm.2016.07.007
  2. Al-Wathiqui, N., Fallon, T. R., South, A., Weng, J. K., & Lewis, S. M. (2016). Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection. Scientific Reports, 6, 38556. https://doi.org/10.1038/srep38556
  3. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
  4. Fiehn, O., Showalter, M. R., & Schaner-Tooley, C. E. (2016). Registered report: the common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. ELife, 5. e12626. https://doi.org/10.7554/elife.12626
Bluo-Gal
  1. Raisch, T., Chang, C. T., Levdansky, Y., Muthukumar, S., Raunser, S., & Valkov, E. (2019). Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation. Nature Communications, 10(1), 3173. https://doi.org/10.1038/s41467-019-11094-z
  2. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  3. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
Bovine Serum Albumin (BSA), Fraction V, Fatty Acid Free for tissue culture
  1. Lewis, A., Dhakal, B., Liu, T., & Mulvey, M. (2016). Histone deacetylase 6 regulates bladder architecture and host susceptibility to uropathogenic Escherichia coli. Pathogens, 5(1), 20. https://doi.org/10.3390/pathogens5010020
  2. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  3. Shin, S. C., Thomas, D., Radhakrishnan, P., & Hollingsworth, M. A. (2020). Invasive phenotype induced by low extracellular pH requires mitochondria dependent metabolic flexibility. Biochemical and Biophysical Research Communications, 525(1), 162–168. https://doi.org/10.1016/j.bbrc.2020.02.018
Bovine Serum Albumin (BSA), Fraction V, Protease Free
  1. Voss, O. H., Lee, H. N., Tian, L., Krzewski, K., & Coligan, J. E. (2018). Liposome preparation for the analysis of lipid‐receptor interaction and efferocytosis. Current Protocols In Immunology, 120(1), 14-44. https://doi.org/10.1002/cpim.43
  2. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  3. Corless, E. I., Mettert, E. L., Kiley, P. J., & Antony, E. (2020). Elevated expression of a functional suf pathway in Escherichia coli BL21 (DE3) enhances recombinant production of an iron-sulfur cluster-containing protein. Journal of Bacteriology, 202(3). https://doi.org/10.1128/JB.00496-19
Carbenicillin (Disodium) 100 mg/mL Solution
  1. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  2. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
Carbenicillin (Disodium) EZ Pak™ for 100 mg/mL Solution
  1. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  2. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
Carbenicillin (Disodium), USP Grade
  1. Kim, J. H., Choi, D. C., Yeon, K. M., Kim, S. R., & Lee, C. H. (2011). Enzyme-immobilized nanofiltration membrane to mitigate biofouling based on quorum quenching. Environmental Science & Technology, 45(4), 1601-1607. https://doi.org/10.1021/es103483j
  2. Mima, T., Schweizer, H. P., & Xu, Z. Q. (2010). In vitro activity of cethromycin against Burkholderia pseudomallei and investigation of mechanism of resistance. Journal of Antimicrobial Chemotherapy, 66(1), 73-78. https://doi.org/10.1093/jac/dkq391
  3. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  4. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
  5. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  6. Bohl, T. E., Shi, K., Lee, J. K., & Aihara, H. (2018). Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nature Communications, 9(1), 377.10.1038/s41467-017-02712-9
  7. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  8. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  9. Liu, X., Schuessler, P. J., Sahoo, A., & Walker, S. E. (2019). Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods. 162–163, 42–53. https://doi.org/10.1016/j.ymeth.2019.03.024
  10. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  11. Shin, J., Zhang, S., Der, B. S., Nielsen, A. A., & Voigt, C. A. (2020). Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16(3). https://doi.org/10.15252/msb.20199401
  12. Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020). Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0468-5
  13. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  14. Pontrelli, S., Fricke, R. C., Teoh, S. T., Laviña, W. A., Putri, S. P., Fitz-Gibbon, S., … & Liao, J. C. (2018). Metabolic repair through emergence of new pathways in Escherichia coli. Nature Chemical Biology, 14(11), 1005-1009. https://doi.org/10.1038/s41589-018-0149-6
  15. English, J. G., Olsen, R. H., Lansu, K., Patel, M., White, K., Cockrell, A. S., … & Roth, B. L. (2019). VEGAS as a platform for facile directed evolution in mammalian cells. Cell, 178(3), 748–761.e17. https://doi.org/10.1016/j.cell.2019.05.051
  16. Guo, M. S., Haakonsen, D. L., Zeng, W., Schumacher, M. A., & Laub, M. T. (2018). A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication. Cell, 175(2), 583-597. https://doi.org/10.1016/j.cell.2018.08.029
  17. Mighell, T. L., Evans-Dutson, S., & O’Roak, B. J. (2018). A saturation mutagenesis approach to understanding PTEN lipid phosphatase activity and genotype-phenotype relationships. The American Journal of Human Genetics, 102(5), 943-955. 10.1016/j.ajhg.2018.03.018
  18. Chen, Y. C., Farzadfard, F., Gharaei, N., Chen, W. C., Cao, J., & Lu, T. K. (2017). Randomized CRISPR-Cas transcriptional perturbation screening reveals protective genes against alpha-synuclein toxicity. Molecular Cell, 68(1), 247-257. https://doi.org/10.1016/j.molcel.2017.09.014
  19. Billon, P., Bryant, E. E., Joseph, S. A., Nambiar, T. S., Hayward, S. B., Rothstein, R., & Ciccia, A. (2017). CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Molecular Cell, 67(6), 1068-1079. https://doi.org/10.1016/j.molcel.2017.08.008
Cefadroxil
  1. Cao, P., & Wall, D. (2019). Direct visualization of a molecular handshake that governs kin recognition and tissue formation in myxobacteria. Nature Communications, 10(1), 3073. https://doi.org/10.1038/s41467-019-11108-w
Cefotaxime (Sodium) 100 mg/mL Solution
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
Cefotaxime (Sodium) EZ Pak™ for 100 mg/mL Solution
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
Cefotaxime (Sodium), USP Grade
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
  2. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  3. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  4. Naim, F., Shand, K., Hayashi, S., O’Brien, M., McGree, J., Johnson, A. A. T., Dugdale, B., & Waterhouse, P. M. (2020). Are the current gRNA ranking prediction algorithms useful for genome editing in plants? PLOS ONE, 15(1), e0227994. https://doi.org/10.1371/journal.pone.0227994
Cefsulodin (SCE-129)
  1. Keilberg, D., Zavros, Y., Shepherd, B., Salama, N. R., & Ottemann, K. M. (2016). Spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection. MBio, 7(5), e01705-16. https://doi.org/10.1128/mBio.01705-16
  2. Fan, Y.-J., Hsu, Y.-C., Gu, B.-C., & Wu, C.-C. (2020). Voltammetric measurement of Escherichia coli concentration through p-APG hydrolysis by endogenous β-galactosidase. Microchemical Journal, 154, 104641. https://doi.org/10.1016/j.microc.2020.104641
CHAPS
  1. Fu, B., Brown, C., & Mäler, L. (2020). Expression and purification of DGD2, a chloroplast outer membrane-associated glycosyltransferase for galactolipid synthesis. Biochemistry, 59(8), 999–1009. https://doi.org/10.1021/acs.biochem.0c00028
Chloramphenicol, USP Grade
  1. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  2. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
  3. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  4. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  5. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  6. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  7. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  8. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  9. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
  10. Walker, L. M., Li, B., Niks, D., Hille, R., & Elliott, S. J. (2019). Deconvolution of reduction potentials of formate dehydrogenase from Cupriavidus necator. JBIC Journal of Biological Inorganic Chemistry. https://doi.org/10.1007/s00775-019-01701-1
  11. Wright, W. C., Chenge, J., Wang, J., Girvan, H. M., Yang, L., Chai, S. C., Huber, A. D., Wu, J., Oladimeji, P. O., Munro, A. W., & Chen, T. (2020). Clobetasol propionate is a heme-mediated selective inhibitor of human cytochrome P450 3A5. Journal of Medicinal Chemistry, 63(3), 1415–1433. https://doi.org/10.1021/acs.jmedchem.9b02067
  12. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  13. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  14. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  15. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  16. Aggarwal, A., Parai, M. K., Shetty, N., Wallis, D., Woolhiser, L., Hastings, C., … & Wakabayashi, S. (2017). Development of a novel lead that targets M. tuberculosis polyketide synthase 13. Cell, 170(2), 249-259. https://doi.org/10.1016/j.cell.2017.06.025
Ciprofloxacin HCl
  1. Ortiz, B. J., Jennings, J., Gross, W. S., Santos, T. M. A., Lin, T.-Y., Weibel, D. B., & Lynn, D. M. (2021). Soft materials that intercept, respond to, and sequester bacterial siderophores. Chemistry of Materials. https://doi.org/10.1021/acs.chemmater.1c01530
Clindamycin Hydrochloride
  1. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
Cobalt Agarose Beads (High Density)
  1. Xu, W., Podoll, J. D., Dong, X., Tumber, A., Oppermann, U., & Wang, X. (2013). Quantitative analysis of histone demethylase probes using fluorescence polarization. Journal of Medicinal Chemistry, 56(12), 5198-5202. https://doi.org/10.1021/jm3018628
  2. Zheng, Y., Xie, J., Huang, X., Dong, J., Park, M. S., & Chan, W. K. (2016). Binding studies using Pichia pastoris expressed human aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator proteins. Protein Expression and Purification, 122, 72-81. https://doi.org/10.1016/j.pep.2016.02.011
  3. Zhu, J., Zhou, X., Huang, X., & Du, Z. (2020). Bacterial expression, purification, and initial characterization of a full-length Cas13b protein from Porphyromonas gingivalis. Protein Expression and Purification, 169, 105588. https://doi.org/10.1016/j.pep.2020.105588
  4. Gao, Y., Cao, D., Pawnikar, S., Akhter, S., Miao, Y., & Liang, B. (2021). Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR protocols, 2(1), 100315. https://doi.org/10.1016/j.xpro.2021.100315
Cobalt HTC Agarose Beads
  1. Block, E., Booker, S. J., Flores‐Penalba, S., George, G. N., Gundala, S., Landgraf, B. J., … & Vattekkatte, A. (2016). Trifluoroselenomethionine: A new unnatural amino acid. ChemBioChem, 17(18), 1738-1751. https://doi.org/10.1002/cbic.201600266
  2. Omattage, N. S., Deng, Z., Pinkner, J. S., Dodson, K. W., Almqvist, F., Yuan, P., & Hultgren, S. J. (2018). Structural basis for usher activation and intramolecular subunit transfer in P pilus biogenesis in Escherichia coli. Nature Microbiology, 3(12), 1362-1368. https://doi.org/10.1038/s41564-018-0255-y
Coelenterazine
  1. Dai, T., Kharkwal, G. B., Zhao, J., Denis, T. G. S., Wu, Q., Xia, Y., … & Hamblin, M. R. (2011). Ultraviolet‐C light for treatment of Candida albicans burn infection in mice. Photochemistry and Photobiology, 87(2), 342-349. https://doi.org/10.1111/j.1751-1097.2011.00886.x
  2. Andreu, N., Zelmer, A., Fletcher, T., Elkington, P. T., Ward, T. H., Ripoll, J., … & Wiles, S. (2010). Optimisation of bioluminescent reporters for use with mycobacteria. PLoS ONE, 5(5), e10777. https://doi.org/10.1371/journal.pone.0010777
  3. Gottschalk, M., Bach, A., Hansen, J. L., Krogsgaard-Larsen, P., Kristensen, A. S., & Strømgaard, K. (2009). Detecting protein–protein interactions in living cells: development of a bioluminescence resonance energy transfer assay to evaluate the PSD-95/NMDA receptor interaction. Neurochemical Research, 34(10), 1729-1737. https://doi.org/10.1007/s11064-009-9998-4
  4. Aird, K. M., Ghanayem, R. B., Peplinski, S., Lyerly, H. K., & Devi, G. R. (2010). X-linked inhibitor of apoptosis protein inhibits apoptosis in inflammatory breast cancer cells with acquired resistance to an ErbB1/2 tyrosine kinase inhibitor. Molecular Cancer Therapeutics, 9(5), 1432-1442 https://doi.org/10.1158/1535-7163.MCT-10-0160
  5. Lin, L., Ibrahim, A. S., Baquir, B., Fu, Y., Applebaum, D., Schwartz, J., … & Spellberg, B. (2010). Safety and efficacy of activated transfected killer cells for neutropenic fungal infections. The Journal of Infectious Diseases, 201(11), 1708-1717. https://doi.org/10.1086/652496
  6. Oki, K., Plonczynski, M. W., Lam, M. L., Gomez-Sanchez, E. P., & Gomez-Sanchez, C. E. (2012). The potassium channel, Kir3. 4 participates in angiotensin II-stimulated aldosterone production by a human adrenocortical cell line. Endocrinology, 153(9), 4328-4335. https://doi.org/10.1210/en.2012-1241
  7. Yamasaki, T., Voshall, A., Kim, E. J., Moriyama, E., Cerutti, H., & Ohama, T. (2013). Complementarity to an mi RNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii. The Plant Journal, 76(6), 1045-1056. https://doi.org/10.1111/tpj.12354
  8. Periasamy, J., Muthuswami, M., Rao, D. B., Tan, P., & Ganesan, K. (2014). Stratification and delineation of gastric cancer signaling by in vitro transcription factor activity profiling and integrative genomics. Cellular Signalling, 26(5), 880-894.10.1016/j.cellsig.2014.01.017
  9. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  10. Freire, F., Ferraresi, C., Jorge, A. O. C., & Hamblin, M. R. (2016). Photodynamic therapy of oral Candida infection in a mouse model. Journal Of Photochemistry And Photobiology B: Biology, 159, 161-168. https://doi.org/10.1016/j.jphotobiol.2016.03.049
  11. Li, Y., Liu, D., Lopez-Paz, C., Olson, B. J., & Umen, J. G. (2016). A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division. Elife, 5, e10767.https://doi.org/10.7554/elife.10767
  12. Ramesh, V., Selvarasu, K., Pandian, J., Myilsamy, S., Shanmugasundaram, C., & Ganesan, K. (2016). NFκB activation demarcates a subset of hepatocellular carcinoma patients for targeted therapy. Cellular Oncology, 39(6), 523-536. https://doi.org/10.1007/s13402-016-0294-4
  13. Kumar, A., Hou, S., Airo, A. M., Limonta, D., Mancinelli, V., Branton, W., … & Hobman, T. C. (2016). Zika virus inhibits type‐I interferon production and downstream signaling. EMBO Reports, 17(12), 1766-1775. https://doi.org/10.15252/embr.201642627
  14. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  15. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  16. Bahat, A., Lahav, O., Plotnikov, A., Leshkowitz, D., & Dikstein, R. (2019). Targeting Spt5-Pol II by small-molecule inhibitors uncouples distinct activities and reveals additional regulatory roles. Molecular Cell, 76(4), 617-631. https://doi.org/10.1016/j.molcel.2019.08.024
  17. FitzPatrick, L. M., Hawkins, K. E., Delhove, J. M., Fernandez, E., Soldati, C., Bullen, L. F., … & McKay, T. R. (2018). NF-κB activity initiates human ESC-derived neural progenitor cell differentiation by inducing a metabolic maturation program. Stem Cell Reports, 10(6), 1766-1781. https://doi.org/10.1016/j.stemcr.2018.03.015
Coelenterazine 400 a
  1. Cheng, Y. H., Ho, M. S., Huang, W. T., Chou, Y. T., & King, K. (2015). Modulation of glucagon-like peptide-1 (GLP-1) potency by endocannabinoid-like lipids represents a novel mode of regulating GLP-1 receptor signaling. Journal of Biological Chemistry, 290(23), 14302-14313. https://doi.org/10.1074/jbc.M115.655662
  2. King, K., Lin, N. P., Cheng, Y. H., Chen, G. H., & Chein, R. J. (2015). Isolation of positive modulator of glucagon-like peptide-1 signaling from Trigonella foenum-graecum (fenugreek) seed. Journal of Biological Chemistry, 290(43), 26235-26248.https://doi.org/10.1074/jbc.M115.672097
  3. Schrage, R., Schmitz, A. L., Gaffal, E., Annala, S., Kehraus, S., Wenzel, D., … & Galandrin, S. (2015). The experimental power of FR900359 to study Gq-regulated biological processes. Nature Communications, 6, 10156.https://doi.org/10.1038/ncomms10156
  4. Mascle, X. H., Gagnon, C., Wahba, H. M., Lussier-Price, M., Cappadocia, L., Sakaguchi, K., & Omichinski, J. G. (2019). Acetylation of SUMO1 alters interactions with the SIMs of PML and Daxx in a protein-specific manner. Structure, 28(2), 157-168. https://doi.org/10.1016/j.str.2019.11.019
  5. Gao, Y., Robertson, M. J., Rahman, S. N., Seven, A. B., Zhang, C., Meyerowitz, J. G., … & Skiniotis, G. (2021). Asymmetric activation of the calcium-sensing receptor homodimer. Nature, 1-5. https://doi.org/10.1038/s41586-021-03691-0
Coomassie Brilliant Blue R-250
  1. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
D-Galactose
  1. Henty-Ridilla, J. L., Rankova, A., Eskin, J. A., Kenny, K., & Goode, B. L. (2016). Accelerated actin filament polymerization from microtubule plus ends. Science, 352(6288), 1004-1009. https://doi.org/10.1126/science.aaf1709
D-Luciferin Firefly, free acid (Proven and Published®)
  1. Thines, B., & Harmon, F. G. (2010). Ambient temperature response establishes ELF3 as a required component of the core Arabidopsis circadian clock. Proceedings of the National Academy of Sciences, 107(7), 3257–3262. https://doi.org/10.1073/pnas.0911006107
  2. Vallera, D. A., Oh, S., Chen, H., Shu, Y., & Frankel, A. E. (2010). Bioengineering a unique deimmunized bispecific targeted toxin that simultaneously recognizes human CD22 and CD19 receptors in a mouse model of B-cell metastases. Molecular Cancer Therapeutics, 9(6), 1872–1883. https://doi.org/10.1158/1535-7163.mct-10-0203
  3. Stish, B. J., Oh, S., & Vallera, D. A. (2008). Anti-glioblastoma effect of a recombinant bispecific cytotoxin cotargeting human IL-13 and EGF receptors in a mouse xenograft model. Journal of Neuro-Oncology, 87(1), 51-61. https://doi.org/10.1007/s11060-007-9499-8
  4. Andreu, N., Zelmer, A., Fletcher, T., Elkington, P. T., Ward, T. H., Ripoll, J., … & Wiles, S. (2010). Optimisation of bioluminescent reporters for use with mycobacteria. PLoS ONE, 5(5), e10777. https://doi.org/10.1371/journal.pone.0010777
  5. Aird, K. M., Ghanayem, R. B., Peplinski, S., Lyerly, H. K., & Devi, G. R. (2010). X-linked inhibitor of apoptosis protein inhibits apoptosis in inflammatory breast cancer cells with acquired resistance to an ErbB1/2 tyrosine kinase inhibitor. Molecular Cancer Therapeutics, 9(5), 1432-1442 https://doi.org/10.1158/1535-7163.MCT-10-0160
  6. Martin, M. D., Carter, K. J., Jean-Philippe, S. R., Chang, M., Mobashery, S., Thiolloy, S., … & Fingleton, B. (2008). Effect of ablation or inhibition of stromal matrix metalloproteinase-9 on lung metastasis in a breast cancer model is dependent on genetic background. Cancer Research, 68(15), 6251-6259 https://doi.org/10.1158/0008-5472.CAN-08-0537
  7. Li, J., Jiang, J., Qian, Q., Xu, Y., Zhang, C., Xiao, J., … & Huang, Y. (2011). Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation. The Plant Cell, 23(2), 628-640. https://doi.org/10.1105/tpc.110.081901
  8. Vallera, D. A., Chen, H., Sicheneder, A. R., Panoskaltsis-Mortari, A., & Taras, E. P. (2009). Genetic alteration of a bispecific ligand-directed toxin targeting human CD19 and CD22 receptors resulting in improved efficacy against systemic B cell malignancy. Leukemia Research, 33(9), 1233-1242. https://doi.org/10.1016/j.leukres.2009.02.006
  9. Bai, X., Yan, Y., Song, Y. H., Seidensticker, M., Rabinovich, B., Metzele, R., … & Alt, E. (2009). Both cultured and freshly isolated adipose tissue-derived stem cells enhance cardiac function after acute myocardial infarction. European Heart Journal, 31(4), 489-501. https://doi.org/10.1093/eurheartj/ehp568
  10. Lam, W., Bussom, S., & Cheng, Y. C. (2009). Effect of hypoxia on the expression of phosphoglycerate kinase and antitumor activity of troxacitabine and gemcitabine in non-small cell lung carcinoma. Molecular Cancer Therapeutics, 8(2), 415-423. https://doi.org/10.1158/1535-7163.MCT-08-0692
  11. Buckley, S. M., Howe, S. J., Rahim, A. A., Buning, H., McIntosh, J., Wong, S. P., … & McKay, T. R. (2008). Luciferin detection after intranasal vector delivery is improved by intranasal rather than intraperitoneal luciferin administration. Human gene therapy, 19(10), 1050-1056. https://doi.org/10.1089/hum.2008.023
  12. Marques, C. P., Cheeran, M. C., Palmquist, J. M., Hu, S., Urban, S. L., & Lokensgard, J. R. (2008). Prolonged microglial cell activation and lymphocyte infiltration following experimental herpes encephalitis. The Journal of Immunology, 181(9), 6417–6426. https://doi.org/10.4049/jimmunol.181.9.6417
  13. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  14. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
D-Luciferin, Potassium Salt (Proven and Published®)
  1. Hashizume, R., Gupta, N., Berger, M. S., Banerjee, A., Prados, M. D., Ayers-Ringler, J., … VandenBerg, S. R. (2010). Morphologic and molecular characterization of ATRT xenografts adapted for orthotopic therapeutic testing. Neuro-Oncology, 12(4), 366–376. https://doi.org/10.1093/neuonc/nop033
  2. Hashizume, R., Ozawa, T., Dinca, E. B., Banerjee, A., Prados, M. D., James, C. D., & Gupta, N. (2010). A human brainstem glioma xenograft model enabled for bioluminescence imaging. Journal of Neuro-Oncology, 96(2), 151-159. https://doi.org/10.1007/s11060-009-9954-9
  3. Kadoch, C., Dinca, E. B., Voicu, R., Chen, L., Nguyen, D., Parikh, S., … & James, C. D. (2009). Pathologic correlates of primary central nervous system lymphoma defined in an orthotopic xenograft model. Clinical Cancer Research, 15(6), 1989-1997. https://doi.org/10.1158/1078-0432.CCR-08-2054
  4. Cawood, R., Wong, S. L., Di, Y., Baban, D. F., & Seymour, L. W. (2011). MicroRNA controlled adenovirus mediates anti-cancer efficacy without affecting endogenous microRNA activity. PloS one, 6(1), e16152. https://doi.org/10.1371/journal.pone.0016152
  5. Amini A., Luo C., Lam E. (2011) Chromatin beacons: global sampling of chromatin physical properties using chromatin charting lines. In: Birchler J. (eds) Plant Chromosome Engineering. Methods in Molecular Biology (Methods and Protocols), vol 701 (pp. 301-314.) https://doi.org/10.1007/978-1-61737-957-4_17
  6. Savellano, M. D., Owusu‐Brackett, N., Son, J., Callier, T., & Savellano, D. H. (2010). Development of an ErbB-overexpressing A-431 optical reporting tumor xenograft model to assess targeted photodynamic therapy regimens. Photochemistry and Photobiology, 86(6), 1379-1389. https://doi.org/10.1111/j.1751-1097.2010.00805.x
  7. Zumsteg, A., Strittmatter, K., Klewe-Nebenius, D., Antoniadis, H., & Christofori, G. (2010). A bioluminescent mouse model of pancreatic β-cell carcinogenesis. Carcinogenesis, 31(8), 1465-1474. https://doi.org/10.1093/carcin/bgq109
  8. Schachtele, S. J., Hu, S., Little, M. R., & Lokensgard, J. R. (2010). Herpes simplex virus induces neural oxidative damage via microglial cell toll-like receptor-2. Journal of Neuroinflammation, 7(1), 35. https://doi.org/10.1186/1742-2094-7-35
  9. Watts, J. C., Giles, K., Grillo, S. K., Lemus, A., DeArmond, S. J., & Prusiner, S. B. (2011). Bioluminescence imaging of Aβ deposition in bigenic mouse models of Alzheimer’s disease. Proceedings of the National Academy of Sciences, 108(6), 2528-2533. https://doi.org/10.1073/pnas.1019034108
  10. Kheirolomoom, A., Kruse, D. E., Qin, S., Watson, K. E., Lai, C. Y., Young, L. J., … & Ferrara, K. W. (2010). Enhanced in vivo bioluminescence imaging using liposomal luciferin delivery system. Journal of Controlled Release, 141(2), 128-136. https://doi.org/10.1016/j.jconrel.2009.08.029
  11. Tafreshi, N. K., Enkemann, S. A., Bui, M. M., Lloyd, M. C., Abrahams, D., Huynh, A. S., … & Gillies, R. J. (2011). A mammaglobin-A targeting agent for noninvasive detection of breast cancer metastasis in lymph nodes. Cancer Research, 71(3), 1050-1059. https://doi.org/10.1158/0008-5472.CAN-10-3091
  12. Tang, X., Sun, Z., Runne, C., Madsen, J., Domann, F., Henry, M., … & Chen, S. (2011). A critical role of Gβγ in tumorigenesis and metastasis of breast cancer. Journal of Biological Chemistry, 286(15), 13244-13254. https://doi.org/10.1074/jbc.M110.206615
  13. Vallera, D. A., Chen, H., Sicheneder, A. R., Panoskaltsis-Mortari, A., & Taras, E. P. (2009). Genetic alteration of a bispecific ligand-directed toxin targeting human CD19 and CD22 receptors resulting in improved efficacy against systemic B cell malignancy. Leukemia Research, 33(9), 1233-1242. https://doi.org/10.1016/j.leukres.2009.02.006
  14. Lam, W., Bussom, S., & Cheng, Y. C. (2009). Effect of hypoxia on the expression of phosphoglycerate kinase and antitumor activity of troxacitabine and gemcitabine in non-small cell lung carcinoma. Molecular Cancer Therapeutics, 8(2), 415-423. https://doi.org/10.1158/1535-7163.MCT-08-0692
  15. Buckley, S. M., Howe, S. J., Rahim, A. A., Buning, H., McIntosh, J., Wong, S. P., … & McKay, T. R. (2008). Luciferin detection after intranasal vector delivery is improved by intranasal rather than intraperitoneal luciferin administration. Human gene therapy, 19(10), 1050-1056. https://doi.org/10.1089/hum.2008.023
  16. Marques, C. P., Cheeran, M. C., Palmquist, J. M., Hu, S., Urban, S. L., & Lokensgard, J. R. (2008). Prolonged microglial cell activation and lymphocyte infiltration following experimental herpes encephalitis. The Journal of Immunology, 181(9), 6417–6426. https://doi.org/10.4049/jimmunol.181.9.6417
  17. Baia, G. S., Dinca, E. B., Ozawa, T., Kimura, E. T., McDermott, M. W., James, C. D., … & Lal, A. (2008). An orthotopic skull base model of malignant meningioma. Brain Pathology, 18(2), 172-179. https://doi.org/10.1111/j.1750-3639.2007.00109.x
  18. Ganapathy-Kanniappan, S., Kunjithapatham, R., Torbenson, M. S., Rao, P. P., Carson, K. A., Buijs, M., … & Geschwind, J. F. H. (2012). Human hepatocellular carcinoma in a mouse model: assessment of tumor response to percutaneous ablation by using glyceraldehyde-3-phosphate dehydrogenase antagonists. Radiology, 262(3), 834-845. https://doi.org/10.1148/radiol.11111569
  19. Niedelman, W., Gold, D. A., Rosowski, E. E., Sprokholt, J. K., Lim, D., Farid Arenas, A., … Saeij, J. P. J. (2012). The rhoptry proteins ROP18 and ROP5 mediate Toxoplasma gondii evasion of the murine, but not the human, interferon-gamma response. PLoS Pathogens, 8(6), e1002784. https://doi.org/10.1371/journal.ppat.1002784
  20. Piotrowska, H., Myszkowski, K., Abraszek, J., Kwiatkowska-Borowczyk, E., Amarowicz, R., Murias, M., … & Jodynis-Liebert, J. (2014). DMU-212 inhibits tumor growth in xenograft model of human ovarian cancer. Biomedicine & Pharmacotherapy, 68(4), 397-400 https://doi.org/10.1016/j.biopha.2014.02.001
  21. Hsu, Y. C., Mildenstein, K., Hunter, K., Tkachenko, O., & Mullen, C. A. (2014). Acute lymphoid leukemia cells with greater stem cell antigen-1 (Ly6a/Sca-1) expression exhibit higher levels of metalloproteinase activity and are more aggressive In vivo. PloS One, 9(2), e88966. https://doi.org/10.1371/journal.pone.0088966
  22. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  23. Thorn, M., Guha, P., Cunetta, M., Espat, N. J., Miller, G., Junghans, R. P., & Katz, S. C. (2016). Tumor-associated GM-CSF overexpression induces immunoinhibitory molecules via STAT3 in myeloid-suppressor cells infiltrating liver metastases. Cancer Gene Therapy, 23(6), 188.https://doi.org/10.1038/cgt.2016.19
  24. Sun, B., Taha, M. S., Ramsey, B., Torregrosa-Allen, S., Elzey, B. D., & Yeo, Y. (2016). Intraperitoneal chemotherapy of ovarian cancer by hydrogel depot of paclitaxel nanocrystals. Journal of Controlled Release, 235, 91-98.https://doi.org/10.1016/j.jconrel.2016.05.056
  25. Burns S.S., Chang LS. (2016) Generation of noninvasive, quantifiable, orthotopic animal models for NF2-associated schwannoma and meningioma. In: Sokolowski B. (eds) Auditory and Vestibular Research. Methods in Molecular Biology, vol 1427 (pp. 59-72.) https://doi.org/10.1007/978-1-4939-3615-1_4
  26. Liu, J., Abshire, C., Carry, C., Sholl, A. B., Mandava, S. H., Datta, A., … & Lai, W. R. (2017). Nanotechnology combined therapy: tyrosine kinase‐bound gold nanorod and laser thermal ablation produce a synergistic higher treatment response of renal cell carcinoma in a murine model. BJU International, 119(2), 342-348. https://doi.org/10.1111/bju.13590
  27. Blackburn, P. R., Hickey, R. D., Nace, R. A., Giama, N. H., Kraft, D. L., Bordner, A. J., … & Torbenson, M. S. (2016). Silent tyrosinemia type I without elevated tyrosine or succinylacetone associated with liver cirrhosis and hepatocellular carcinoma. Human Mutation, 37(10), 1097-1105. https://doi.org/10.1002/humu.23047
  28. Yue, T., Zheng, X., Dou, Y., Zheng, X., Sun, R., Tian, Z., & Wei, H. (2016). Interleukin 12 shows a better curative effect on lung cancer than paclitaxel and cisplatin doublet chemotherapy. BMC Cancer, 16(1), 665. https://doi.org/10.1186/s12885-016-2701-7
  29. Ramesh, V., Selvarasu, K., Pandian, J., Myilsamy, S., Shanmugasundaram, C., & Ganesan, K. (2016). NFκB activation demarcates a subset of hepatocellular carcinoma patients for targeted therapy. Cellular Oncology, 39(6), 523-536. https://doi.org/10.1007/s13402-016-0294-4
  30. Piotrowska-Kempisty, H., Ruciński, M., Borys, S., Kucińska, M., Kaczmarek, M., Zawierucha, P., … & Jodynis-Liebert, J. (2016). 3′-hydroxy-3, 4, 5, 4′-tetramethoxystilbene, the metabolite of resveratrol analogue DMU-212, inhibits ovarian cancer cell growth in vitro and in a mice xenograft model. Scientific Reports, 6, 32627. https://doi.org/10.1038/srep32627
  31. Stading, B. R., Osorio, J. E., Velasco-Villa, A., Smotherman, M., Kingstad-Bakke, B., & Rocke, T. E. (2016). Infectivity of attenuated poxvirus vaccine vectors and immunogenicity of a raccoonpox vectored rabies vaccine in the Brazilian free-tailed bat (Tadarida brasiliensis). Vaccine, 34(44), 5352-5358. https://doi.org/10.1016/j.vaccine.2016.08.088
  32. Matijasevic, Z., Krzywicka-Racka, A., Sluder, G., Gallant, J., & Jones, S. N. (2016). The Zn-finger domain of MdmX suppresses cancer progression by promoting genome stability in p53-mutant cells. Oncogenesis, 5(10), e262. https://doi.org/10.1038/oncsis.2016.62
  33. Kumar, A., Hou, S., Airo, A. M., Limonta, D., Mancinelli, V., Branton, W., … & Hobman, T. C. (2016). Zika virus inhibits type‐I interferon production and downstream signaling. EMBO Reports, 17(12), 1766-1775. https://doi.org/10.15252/embr.201642627
  34. Zhang, J., Yao, T. W., Hashizume, R., Hariono, S., Barkovich, K. J., Fan, Q. W., … & Nicolaides, T. (2017). Combined BRAF V600E and MEK blockade for BRAF V600E-mutant gliomas. Journal of Neuro-Oncology, 131(3), 495-505. https://doi.org/10.1007/s11060-016-2333-4
  35. Ci, L., Yang, X., Gu, X., Li, Q., Guo, Y., Zhou, Z., … & Fei, J. (2017). Cystathionine γ-lyase deficiency exacerbates CCl4-induced acute hepatitis and fibrosis in the mouse liver. Antioxidants & Redox Signaling, 27(3), 133-149. https://doi.org/10.1089/ars.2016.6773
  36. Liu, Z., Wang, Y., Kabraji, S., Xie, S., Pan, P., Liu, Z., … & Zhao, J. J. (2019). Improving orthotopic mouse models of patient-derived breast cancer brain metastases by a modified intracarotid injection method. Scientific Reports, 9(1), 662. https://doi.org/10.1038/s41598-018-36874-3
  37. Drenberg, C. D., Shelat, A., Dang, J., Cotton, A., Orwick, S. J., Li, M., … & Hu, S. (2019). A high-throughput screen indicates gemcitabine and JAK inhibitors may be useful for treating pediatric AML. Nature communications, 10(1), 2189.https://doi.org/10.1038/s41467-019-09917-0
  38. Portillo, S., Zepeda, B. G., Iniguez, E., Olivas, J. J., Karimi, N. H., Moreira, O. C., … & Almeida, I. C. (2019). A prophylactic α-Gal-based glycovaccine effectively protects against murine acute Chagas disease. NPJ vaccines, 4(1), 13. https://doi.org/10.1038/s41541-019-0107-7
  39. de la Cruz Bonilla, M., Stemler, K. M., Taniguchi, C. M., & Piwnica-Worms, H. (2018). Stem cell enriched-epithelial spheroid cultures for rapidly assaying small intestinal radioprotectors and radiosensitizers in vitro. Scientific Reports, 8(1), 15410. https://doi.org/10.1038/s41598-018-33747-7
  40. Tzeng, H. E., Tang, C. H., Wu, S. H., Chen, H. T., Fong, Y. C., Lu, Y. C., … & Wang, S. W. (2018). CCN6-mediated MMP-9 activation enhances metastatic potential of human chondrosarcoma. Cell Death & Disease, 9(10). https://doi.org/10.1038/s41419-018-1008-9
  41. Obermajer, N., Urban, J., Wieckowski, E., Muthuswamy, R., Ravindranathan, R., Bartlett, D. L., & Kalinski, P. (2018). Promoting the accumulation of tumor-specific T cells in tumor tissues by dendritic cell vaccines and chemokine-modulating agents. Nature Protocols, 13(2), 335. https://doi.org/10.1038/nprot.2017.130
  42. Faham, N., Zhao, L., & Welm, A. L. (2018). mTORC1 is a key mediator of RON-dependent breast cancer metastasis with therapeutic potential. NPJ Breast Cancer, 4(1), 36.https://doi.org/10.1038/s41523-018-0091-5
  43. Simandi, Z., Horvath, A., Nagy, P., & Nagy, L. (2016). Prediction and validation of gene regulatory elements activated during retinoic acid induced embryonic stem cell differentiation. JoVE (Journal of Visualized Experiments), (112), e53978. https://doi.org/10.3791/53978
  44. Jang, J. H., Kim, D. H., Lim, J. M., Lee, J. W., Jeong, S. J., Kim, K. P., & Surh, Y. J. (2020). Breast cancer cell–derived soluble CD44 promotes tumor progression by triggering macrophage IL1β production. Cancer Research, 80(6), canres.2288.2019. https://doi.org/10.1158/0008-5472.can-19-2288
  45. Rodriguez-Garcia, A., Watanabe, K., & Guedan, S. (2019). Analysis of antitumor effects of CAR-T cells in mice with solid tumors. In Methods in Molecular Biology (pp. 251–271). Springer US. https://doi.org/10.1007/978-1-0716-0146-4_19
  46. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  47. Poliner, E., Pulman, J. A., Zienkiewicz, K., Childs, K., Benning, C., & Farré, E. M. (2017). A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production. Plant Biotechnology Journal, 16(1), 298–309. https://doi.org/10.1111/pbi.12772
  48. Chambers, L. M., Esakov, E., Braley, C., AlHilli, M., Michener, C., & Reizes, O. (2020). Use of transabdominal ultrasound for the detection of intra-peritoneal tumor engraftment and growth in mouse xenografts of epithelial ovarian cancer. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.20.912402
  49. Rodriguez, F., John, S. F., Iniguez, E., Montalvo, S., Michael, K., White, L., … & Maldonado, R. A. (2020). In vitro and in vivo characterization of potent antileishmanial methionine aminopeptidase-1 inhibitors. Antimicrobial Agents and Chemotherapy. https://doi.org/10.1128/aac.01422-19
  50. Tseng, S.-H., Park, S.-T., Lam, B., Tsai, Y.-C., Cheng, M. A., Farmer, E., Xing, D., & Hung, C.-F. (2020). Novel, genetically induced mouse model that recapitulates the histological morphology and immunosuppressive tumor microenvironment of metastatic peritoneal carcinomatosis. Journal for ImmunoTherapy of Cancer, 8(1), e000480. https://doi.org/10.1136/jitc-2019-000480
  51. Moose, D. L., Krog, B. L., Kim, T. H., Zhao, L., Williams-Perez, S., Burke, G., … & Stipp, C. S. (2020). Cancer cells resist mechanical destruction in circulation via RhoA/actomyosin-dependent mechano-adaptation. Cell Reports, 30(11), 3864–3874.e6. https://doi.org/10.1016/j.celrep.2020.02.080
  52. Zampieri, R. M., Adessi, A., Caldara, F., Codato, A., Furlan, M., Rampazzo, C., … & Dalla Valle, L. (2020). Anti-inflammatory activity of exopolysaccharides from Phormidium sp. ETS05, the most abundant cyanobacterium of the therapeutic euganean thermal muds, using the zebrafish model. Biomolecules, 10(4), 582. https://doi.org/10.3390/biom10040582
  53. Chen, C. C., Li, B., Millman, S. E., Chen, C., Li, X., Morris IV, J. P., … & Qin, W. (2020). Vitamin B6 addiction in acute myeloid leukemia. Cancer Cell, 37(1), 71-84. https://doi.org/10.1016/j.ccell.2019.12.002
  54. Park, S., Brugiolo, M., Akerman, M., Das, S., Urbanski, L., Geier, A., … & Hu, L. (2019). Differential functions of splicing factors in mammary transformation and breast cancer metastasis. Cell Reports, 29(9), 2672-2688.e5. https://doi.org/10.1016/j.celrep.2019.10.110
  55. Liu, C., Meng, Z., Wiggin, T. D., Yu, J., Reed, M. L., Guo, F., … & Griffith, L. C. (2019). A serotonin-modulated circuit controls sleep architecture to regulate cognitive function independent of total sleep in Drosophila. Current Biology, 29(21), 3635-3646. https://doi.org/10.1016/j.cub.2019.08.079
  56. Bahat, A., Lahav, O., Plotnikov, A., Leshkowitz, D., & Dikstein, R. (2019). Targeting Spt5-Pol II by small-molecule inhibitors uncouples distinct activities and reveals additional regulatory roles. Molecular Cell, 76(4), 617-631. https://doi.org/10.1016/j.molcel.2019.08.024
  57. Wang, E., Lu, S. X., Pastore, A., Chen, X., Imig, J., Lee, S. C. W., … & Ki, M. (2019). Targeting an RNA-binding protein network in acute myeloid leukemia. Cancer Cell, 35(3), 369-384. https://doi.org/10.1016/j.ccell.2019.01.010
  58. Ding, L., Wang, S., Song, Z. T., Jiang, Y., Han, J. J., Lu, S. J., … & Liu, J. X. (2018). Two B-box domain proteins, BBX18 and BBX23, interact with ELF3 and regulate thermomorphogenesis in Arabidopsis. Cell Reports, 25(7), 1718-1728.e4. https://doi.org/10.1016/j.celrep.2018.10.060
  59. Somerville, T. D., Xu, Y., Miyabayashi, K., Tiriac, H., Cleary, C. R., Maia-Silva, D., … & Vakoc, C. R. (2018). TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma. Cell Reports, 25(7), 1741-1755.e7. https://doi.org/10.1016/j.celrep.2018.10.051
  60. Rotolo, A., Caputo, V. S., Holubova, M., Baxan, N., Dubois, O., Chaudhry, M. S., … & Kachramanoglou, C. (2018). Enhanced anti-lymphoma activity of CAR19-iNKT cells underpinned by dual CD19 and CD1d targeting. Cancer Cell, 34(4), 596-610. https://doi.org/10.1016/j.ccell.2018.08.017
  61. Mancini, A., Xavier-Magalhães, A., Woods, W. S., Nguyen, K. T., Amen, A. M., Hayes, J. L., … & Jones, L. E. (2018). Disruption of the β1L isoform of GABP reverses glioblastoma replicative immortality in a TERT promoter mutation-dependent manner. Cancer Cell, 34(3), 513-528. https://doi.org/10.1016/j.ccell.2018.08.003
  62. Yang, L., Mo, W., Yu, X., Yao, N., Zhou, Z., Fan, X., … & Lin, C. (2018). Reconstituting Arabidopsis CRY2 signaling pathway in mammalian cells reveals regulation of transcription by direct binding of CRY2 to DNA. Cell Reports, 24(3), 585-593. https://doi.org/10.1016/j.celrep.2018.06.069
  63. Kowalsky, S. J., Liu, Z., Feist, M., Berkey, S. E., Ma, C., Ravindranathan, R., … & Bartlett, D. L. (2018). Superagonist IL-15-armed oncolytic virus elicits potent antitumor immunity and therapy that are enhanced with PD-1 blockade. Molecular Therapy, 26(10), 2476-2486. https://doi.org/10.1016/j.ymthe.2018.07.013
  64. Fan, J., Bai, P., Ning, Y., Wang, J., Shi, X., Xiong, Y., … & Meng, X. (2018). The monocot-specific receptor-like kinase SDS2 controls cell death and immunity in rice. Cell Host & Microbe, 23(4), 498-510. https://doi.org/10.1016/j.chom.2018.03.003
  65. Xu, Y., Milazzo, J. P., Somerville, T. D., Tarumoto, Y., Huang, Y. H., Ostrander, E. L., … & Vakoc, C. R. (2018). A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia. Cancer Cell, 33(1), 13-28. https://doi.org/10.1016/j.ccell.2017.12.002
  66. Zhou, W., Chen, C., Shi, Y., Wu, Q., Gimple, R. C., Fang, X., … & Feng, H. (2017). Targeting glioma stem cell-derived pericytes disrupts the blood-tumor barrier and improves chemotherapeutic efficacy. Cell Stem Cell, 21(5), 591-603. https://doi.org/10.1016/j.stem.2017.10.002
  67. Hartwig, T., Montinaro, A., von Karstedt, S., Sevko, A., Surinova, S., Chakravarthy, A., … & El-Bahrawy, M. A. (2017). The TRAIL-induced cancer secretome promotes a tumor-supportive immune microenvironment via CCR2. Molecular Cell, 65(4), 730-742. https://doi.org/10.1016/j.molcel.2017.01.021
  68. Zhou, Z., Peng, Y., Ai, W., Li, Q., Ye, T., Wu, C., … & Zhang, Y. (2020). Compound Opening Arrow Mixture exerts anti-tumor effects in a mouse model of breast cancer. Scientific Reports, 10(1), 1-8. https://doi.org/10.1038/s41598-020-64561-9
  69. Gao, J., Jung, M., Mayoh, C., Venkat, P., Hannan, K. M., Fletcher, J. I., … Henderson, M. J. (2020). Suppression of ABCE1-mediated mRNA translation limits N-MYC-driven cancer progression. Cancer Research, canres.3914.2019. https://doi.org/10.1158/0008-5472.can-19-3914
D-Luciferin, Sodium Salt (Proven and Published®​)
  1. Swartling, F. J., Grimmer, M. R., Hackett, C. S., Northcott, P. A., Fan, Q. W., Goldenberg, D. D., … & Zhe, X. N. (2010). Pleiotropic role for MYCN in medulloblastoma. Genes & Development, 24(10), 1059-1072. https://doi.org/10.1101/gad.1907510
  2. Rettig G.R., Rice K.G. (2009) Quantitative In Vivo Imaging of Non-viral-Mediated Gene Expression and RNAi-Mediated Knockdown. In: Rich P., Douillet C. (eds) Bioluminescence. Methods in Molecular Biology, vol 574. (pp. 155-171). https://doi.org/10.1007/978-1-60327-321-3_13
  3. Luo, C., Durgin, B. G., Watanabe, N., & Lam, E. (2009). Defining the functional network of epigenetic regulators in Arabidopsis thaliana. Molecular Plant, 2(4), 661–674. https://doi.org/10.1093/mp/ssp017
  4. Zhang, Y., Bressler, J. P., Neal, J., Lal, B., Bhang, H. E. C., Laterra, J., & Pomper, M. G. (2007). ABCG2/BCRP expression modulates d-luciferin–based bioluminescence imaging. Cancer Research, 67(19), 9389-9397. https://doi.org/10.1158/0008-5472.CAN-07-0944
  5. Wiles S., Robertson B.D., Frankel G., Kerton A. (2009) Bioluminescent monitoring of in vivo colonization and clearance dynamics by light-emitting bacteria. In: Rich P., Douillet C. (eds) Bioluminescence. Methods in Molecular Biology (Methods and Protocols), vol 574. (pp. 137-153)https://doi.org/10.1007/978-1-60327-321-3_12
  6. Zhang, Y., Laterra, J., & Pomper, M. G. (2009). Hedgehog pathway inhibitor HhAntag691 is a potent inhibitor of ABCG2/BCRP and ABCB1/Pgp. Neoplasia, 11(1), 96–101. https://doi.org/10.1593/neo.81264
  7. Zhang, Y., Byun, Y., Ren, Y. R., Liu, J. O., Laterra, J., & Pomper, M. G. (2009). Identification of inhibitors of ABCG2 by a bioluminescence imaging–based high-throughput assay. Cancer Research, 69(14), 5867-5875. https://doi.org/10.1158/0008-5472.can-08-4866
  8. Barth, A. S., Kizana, E., Smith, R. R., Terrovitis, J., Dong, P., Leppo, M. K., … Marbán, E. (2008). Lentiviral vectors bearing the cardiac promoter of the Na+-Ca2+ exchanger report cardiogenic differentiation in stem cells Molecular Therapy, 16(5), 957–964. https://doi.org/10.1038/mt.2008.30
  9. Rastegar, F., Gao, J. L., Shenaq, D., Luo, Q., Shi, Q., Kim, S. H., … & Shen, J. (2010). Lysophosphatidic acid acyltransferase β (LPAATβ) promotes the tumor growth of human osteosarcoma. PloS one, 5(12), e14182. https://doi.org/10.1371/journal.pone.0014182
  10. Kargiotis, O., Chetty, C., Gondi, C. S., Tsung, A. J., Dinh, D. H., Gujrati, M., … & Rao, J. S. (2008). Adenovirus-mediated transfer of siRNA against MMP-2 mRNA results in impaired invasion and tumor-induced angiogenesis, induces apoptosis in vitro and inhibits tumor growth in vivo in glioblastoma. Oncogene, 27(35), 4830. https://doi.org/10.1038/onc.2008.122
  11. Mehrotra, S., Languino, L. R., Raskett, C. M., Mercurio, A. M., Dohi, T., & Altieri, D. C. (2010). IAP regulation of metastasis. Cancer Cell, 17(1), 53-64. https://doi.org/10.1016/j.ccr.2009.11.021
  12. Vallera, D. A., Chen, H., Sicheneder, A. R., Panoskaltsis-Mortari, A., & Taras, E. P. (2009). Genetic alteration of a bispecific ligand-directed toxin targeting human CD19 and CD22 receptors resulting in improved efficacy against systemic B cell malignancy. Leukemia Research, 33(9), 1233-1242. https://doi.org/10.1016/j.leukres.2009.02.006
  13. Buckley, S. M., Howe, S. J., Rahim, A. A., Buning, H., McIntosh, J., Wong, S. P., … & McKay, T. R. (2008). Luciferin detection after intranasal vector delivery is improved by intranasal rather than intraperitoneal luciferin administration. Human gene therapy, 19(10), 1050-1056. https://doi.org/10.1089/hum.2008.023
  14. Niedelman, W., Gold, D. A., Rosowski, E. E., Sprokholt, J. K., Lim, D., Farid Arenas, A., … Saeij, J. P. J. (2012). The rhoptry proteins ROP18 and ROP5 mediate Toxoplasma gondii evasion of the murine, but not the human, interferon-gamma response. PLoS Pathogens, 8(6), e1002784. https://doi.org/10.1371/journal.ppat.1002784
  15. Alhasan, M. K., Liu, L., Lewis, M. A., Magnusson, J., & Mason, R. P. (2012). Comparison of optical and power Doppler ultrasound imaging for non-invasive evaluation of arsenic trioxide as a vascular disrupting agent in tumors. PLOS ONE, 7(9), e46106. https://doi.org/10.1371/journal.pone.0046106
  16. Yang, W., Liu, X., Peng, X., Li, P., Wang, T., Tai, G., … Zhou, Y. (2012). Synthesis of novel N-acetylneuraminic acid derivatives as substrates for rapid detection of influenza virus neuraminidase. Carbohydrate Research, 359, 92–96. https://doi.org/j.carres.2012.06.009
  17. Hsu, Y. C., Mildenstein, K., Hunter, K., Tkachenko, O., & Mullen, C. A. (2014). Acute lymphoid leukemia cells with greater stem cell antigen-1 (Ly6a/Sca-1) expression exhibit higher levels of metalloproteinase activity and are more aggressive In vivo. PloS One, 9(2), e88966. https://doi.org/10.1371/journal.pone.0088966
  18. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  19. Malo, C. S., Renner, D. N., Kelcher, A. M. H., Jin, F., Hansen, M. J., Pavelko, K. D., & Johnson, A. J. (2016). The effect of vector silencing during picornavirus vaccination against experimental melanoma and glioma. PloS One, 11(8), e0162064. https://doi.org/10.1371/journal.pone.0162064
  20. Fu, H., Wu, R., Li, Y., Zhang, L., Tang, X., Tu, J., … & Shou, Q. (2016). Safflower yellow prevents pulmonary metastasis of breast cancer by inhibiting tumor cell invadopodia. The American Journal of Chinese Medicine, 44(07), 1491-1506. https://doi.org/10.1142/S0192415X1650083X
  21. Yang, Y., Zhao, X., Li, X., Yan, Z., Liu, Z., & Li, Y. (2017). Effects of anti‑CD44 monoclonal antibody IM7 carried with chitosan polylactic acid-coated nano‑particles on the treatment of ovarian cancer. Oncology Letters, 13(1), 99-104. https://doi.org/10.3892/ol.2016.5413
  22. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  23. Rodriguez-Garcia, A., Watanabe, K., & Guedan, S. (2019). Analysis of antitumor effects of CAR-T cells in mice with solid tumors. In Methods in Molecular Biology (pp. 251–271). Springer US. https://doi.org/10.1007/978-1-0716-0146-4_19
  24. Shu, Y., Wang, Y., Lv, W. Q., Peng, D. Y., Li, J., Zhang, H., … & Chen, Y. H. (2020). ARRB1-promoted NOTCH1 degradation is suppressed by oncomiR miR-223 in T- cell acute lymphoblastic leukemia. Cancer Research, 80(5), 988-998. https://doi.org/10.1158/0008-5472.can-19-1471
  25. Day, E. K., Sosale, N. G., Xiao, A., Zhong, Q., Purow, B., & Lazzara, M. J. (2020). Glioblastoma Cell Resistance to EGFR and MET Inhibition Can Be Overcome via Blockade of FGFR-SPRY2 Bypass Signaling. Cell Reports, 30(10), 3383–3396.e7. https://doi.org/10.1016/j.celrep.2020.02.014
  26. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  27. Poliner, E., Pulman, J. A., Zienkiewicz, K., Childs, K., Benning, C., & Farré, E. M. (2017). A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production. Plant Biotechnology Journal, 16(1), 298–309. https://doi.org/10.1111/pbi.12772
  28. Tseng, S.-H., Park, S.-T., Lam, B., Tsai, Y.-C., Cheng, M. A., Farmer, E., Xing, D., & Hung, C.-F. (2020). Novel, genetically induced mouse model that recapitulates the histological morphology and immunosuppressive tumor microenvironment of metastatic peritoneal carcinomatosis. Journal for ImmunoTherapy of Cancer, 8(1), e000480. https://doi.org/10.1136/jitc-2019-000480
  29. Wang, H., & Zhang, X. (2020). Bone-in-culture array to model bone metastasis in ex vivo condition. Bio-Protocol, 10(2). https://doi.org/10.21769/bioprotoc.3495
  30. Cheng, Q., Wei, T., Farbiak, L., Johnson, L. T., Dilliard, S. A., & Siegwart, D. J. (2020). Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing. Nature Nanotechnology, 15(4), 313–320. https:/doi.org/10.1038/s41565-020-0669-6
  31. Radhakrishnan, S. V., Luetkens, T., Scherer, S. D., Davis, P., Vander Mause, E. R., Olson, M. L., … & Miles, R. R. (2020). CD229 CAR T cells eliminate multiple myeloma and tumor propagating cells without fratricide. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14619-z
  32. De Micheli, A. J., Laurilliard, E. J., Heinke, C. L., Ravichandran, H., Fraczek, P., Soueid-Baumgarten, S., … & Cosgrove, B. D. (2020). Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration. Cell Reports, 30(10), 3583–3595.e5. https://doi.org/10.1016/j.celrep.2020.02.067
  33. Schommers, P., Gruell, H., Abernathy, M. E., Tran, M. K., Dingens, A. S., Gristick, H. B., … & Kreer, C. (2020). Restriction of HIV-1 escape by a highly broad and potent neutralizing antibody. Cell, 180(3), 471-489. https://doi.org/10.1016/j.cell.2020.01.010
  34. Foster, S. R., Hauser, A. S., Vedel, L., Strachan, R. T., Huang, X. P., Gavin, A. C., … & Roth, B. L. (2019). Discovery of human signaling systems: pairing peptides to G protein-coupled receptors. Cell, 179(4), 895–908.e21. https://doi.org/10.1016/j.cell.2019.10.010
  35. Wang, H., Tian, L., Liu, J., Goldstein, A., Bado, I., Zhang, W., Arenkiel, B. R., Li, Z., Yang, M., Du, S., Zhao, H., Rowley, D. R., Wong, S. T. C., Gugala, Z., & Zhang, X. H.-F. (2018). The osteogenic niche is a calcium reservoir of bone micrometastases and confers unexpected therapeutic vulnerability. Cancer Cell, 34(5), 823–839.e7. https://doi.org/10.1016/j.ccell.2018.10.002
  36. Hsu, H. L., Brown, A., Loveland, A. B., Lotun, A., Xu, M., Luo, L., … & Gessler, D. J. (2020). Structural characterization of a novel human adeno-associated virus capsid with neurotropic properties. Nature Communications, 11(1), 1-14. https://doi.org/10.1038/s41467-020-17047-1
D-Raffinose pentahydrate
  1. Henty-Ridilla, J. L., Rankova, A., Eskin, J. A., Kenny, K., & Goode, B. L. (2016). Accelerated actin filament polymerization from microtubule plus ends. Science, 352(6288), 1004-1009. https://doi.org/10.1126/science.aaf1709
Digitonin Special Grade (water soluble)
  1. Taldone, T., Rodina, A., Gomes, E. M. D., Riolo, M., Patel, H. J., Alonso-Sabadell, R., … & Chiosis, G. (2013). Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes. Beilstein Journal of Organic Chemistry, 9, 544–556. https://doi.org/10.3762/bjoc.9.60
  2. Malty, R. H., Aoki, H., Kumar, A., Phanse, S., Amin, S., Zhang, Q., … & Abou-Tok, H. (2017). A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-κB signaling. Cell Systems, 5(6), 564-577. https://doi.org/10.1016/j.cels.2017.10.010
  3. Nowinski, S. M., Solmonson, A., Rusin, S. F., Maschek, J. A., Bensard, C. L., Fogarty, S., … & Rutter, J. (2020). Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria. Elife, 9, e58041.
  4. Ordureau, A., Paulo, J. A., Zhang, J., An, H., Swatek, K. N., Cannon, J. R., … & Harper, J. W. (2020). Global landscape and dynamics of parkin and USP30-dependent ubiquitylomes in iNeurons during mitophagic signaling. Molecular cell, 77(5), 1124-1142.
  5. Pelster, L. N., & Minteer, S. D. (2016). Mitochondrial inner membrane biomimic for the investigation of electron transport chain supercomplex bioelectrocatalysis. Acs Catalysis, 6(8), 4995-4999.
DNase I, Bovine Pancreas (Lysate Tested), >2000 Kunitz U/mg
  1. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  2. Dillard, K. E., Brown, M. W., Johnson, N. V., Xiao, Y., Dolan, A., Hernandez, E., … & Ke, A. (2018). Assembly and translocation of a CRISPR-Cas primed acquisition complex. Cell, 175(4), 934–946.e15. https://doi.org/10.1016/j.cell.2018.09.039
  3. Strohkendl, I., Saifuddin, F. A., Rybarski, J. R., Finkelstein, I. J., & Russell, R. (2018). Kinetic basis for DNA target specificity of CRISPR-Cas12a. Molecular Cell, 71(5), 816-824. https://doi.org/10.1016/j.molcel.2018.06.043
  4. Jung, C., Hawkins, J. A., Jones Jr, S. K., Xiao, Y., Rybarski, J. R., Dillard, K. E., … & Ke, A. (2017). Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips. Cell, 170(1), 35-47. https://doi.org/10.1016/j.cell.2017.05.044
DNase I, Bovine Pancreas (Lysate Tested), >500 Kunitz U/mg
  1. Dao, T. P., Martyniak, B., Canning, A. J., Lei, Y., Colicino, E. G., Cosgrove, M. S., … & Castañeda, C. A. (2019). ALS-linked mutations affect UBQLN2 oligomerization and phase separation in a position-and amino acid-dependent manner. Structure, 27(6), 937-951. https://doi.org/10.1016/j.str.2019.03.012
  2. Dao, T. P., Kolaitis, R. M., Kim, H. J., O’Donovan, K., Martyniak, B., Colicino, E., … & Castañeda, C. A. (2018). Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Molecular Cell, 69(6), 965-978. https://doi.org/10.1016/j.molcel.2018.02.004
Doxycycline Hyclate
  1. Kempton, H. R., Goudy, L. E., Love, K. S., & Qi, L. S. (2020). Multiple input sensing and signal integration using a split Cas12a system. Molecular Cell. https://doi.org/10.1016/j.molcel.2020.01.016
  2. Tang, X., Fu, X., Liu, Y., Yu, D., Cai, S. J., & Yang, C. (2019). Blockade of Glutathione Metabolism in IDH1-Mutated Glioma. Molecular Cancer Therapeutics, 19(1), 221–230. https://doi.org/10.1158/1535-7163.mct-19-0103
DTT (Dithiothreitol) (> 99% pure) Protease free
  1. Tan, A., & Henzl, M. T. (2009). Conformational stabilities of guinea pig OCP1 and OCP2. Biophysical Chemistry, 144(3), 108-118. https://doi.org/10.1016/j.bpc.2009.07.003
  2. Henzl, M. T., Davis, M. E., & Tan, A. (2008). Divalent ion binding properties of the timothy grass allergen, Phl p 7. Biochemistry, 47(30), 7846-7856. https://doi.org/10.1021/bi800620g
  3. Tan, A., Tanner, J. J., & Henzl, M. T. (2008). Energetics of OCP1–OCP2 complex formation. Biophysical Chemistry, 134(1-2), 64-71. https://doi.org/10.1016/j.bpc.2008.01.005
  4. Henzl, M. T., Davis, M. E., & Tan, A. (2010). Polcalcin divalent ion-binding behavior and thermal stability: comparison of Bet v 4, Bra n 1, and Bra n 2 to Phl p 7. Biochemistry, 49(10), 2256–2268. https://doi.org/10.1021/bi902115v
  5. Zhong, Y., Whittington, C. F., & Haynie, D. T. (2007). Stimulated release of small molecules from polyelectrolyte multilayer nanocoatings. Chemical Communications, (14), 1415-1417. https://doi.org/10.1039/b615699a
  6. Swearingen, K. E., Loomis, W. P., Zheng, M., Cookson, B. T., & Dovichi, N. J. (2010). Proteomic profiling of lipopolysaccharide-activated macrophages by isotope coded affinity tagging. Journal of Proteome Research, 9(5), 2412–2421. https://doi.org/10.1021/pr901124u
  7. Rubio, C., Pincus, D., Korennykh, A., Schuck, S., El-Samad, H., & Walter, P. (2011). Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. The Journal of Cell Biology, 193(1), 171-184. https://doi.org/10.1083/jcb.201007077
  8. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L., & Ruoho, A. E. (2007). One-step purification of bacterially expressed recombinant transducin α-subunit and isotopically labeled PDE6 γ-subunit for NMR analysis. Protein Expression and Purification, 51(2), 187-197. https://doi.org/10.1016/j.pep.2006.07.012
  9. Keith, K. E., Killip, L., He, P., Moran, G. R., & Valvano, M. A. (2007). Burkholderia cenocepacia C5424 produces a pigment with antioxidant properties using a homogentisate intermediate. Journal of Bacteriology, 189(24), 9057-9065.https://doi.org/10.1128/JB.00436-07
  10. Norais, C. A., Chitteni-Pattu, S., Wood, E. A., Inman, R. B., & Cox, M. M. (2009). DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. Journal of Biological Chemistry, 284(32), 21402-21411. https://doi.org/10.1074/jbc.M109.010454
  11. Johnson, T. A., & Holyoak, T. (2010). Increasing the conformational entropy of the Ω-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity. Biochemistry, 49(25), 5176-5187.https://doi.org/10.1021/bi100399e
  12. Sandoval, C. M., Baker, S. L., Jansen, K., Metzner, S. I., & Sousa, M. C. (2011). Crystal structure of BamD: an essential component of the β-barrel assembly machinery of gram-negative bacteria. Journal of Molecular Biology, 409(3), 348-357. https://doi.org/10.1016/j.jmb.2011.03.035
  13. Sharma, B., Deo, S. K., Bachas, L. G., & Daunert, S. (2005). Competitive binding assay using fluorescence resonance energy transfer for the identification of calmodulin antagonists. Bioconjugate Chemistry, 16(5), 1257-1263. https://doi.org/10.1021/bc050161y
  14. Lee, K. H., Saleh, L., Anton, B. P., Madinger, C. L., Benner, J. S., Iwig, D. F., … & Booker, S. J. (2009). Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry, 48(42), 10162-10174. https://doi.org/10.1021/bi900939w
  15. Bailey, S. W., & Ayling, J. E. (2009). The extremely slow and variable activity of dihydrofolate reductase in human liver and its implications for high folic acid intake. Proceedings of the National Academy of Sciences, 106(36), 15424-15429. https://doi.org/10.1073/pnas.0902072106
  16. Hasoun, L. Z., Bailey, S. W., Outlaw, K. K., & Ayling, J. E. (2013). Effect of serum folate status on total folate and 5-methyltetrahydrofolate in human skin. The American Journal of Clinical Nutrition, 98(1), 42-48. https://doi.org/10.3945/ajcn.112.057562
  17. Landgraf, B. J., Arcinas, A. J., Lee, K. H., & Booker, S. J. (2013). Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. Journal of the American Chemical Society, 135(41), 15404-15416. https://doi.org/10.1021/ja4048448
  18. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  19. Zhang, B., Zhu, D. W., Hu, X. J., Zhou, M., Shang, P., & Lin, S. X. (2014). Human 3-alpha hydroxysteroid dehydrogenase type 3 (3α-HSD3): the V54L mutation restricting the steroid alternative binding and enhancing the 20α-HSD activity. The Journal of Steroid Biochemistry and Molecular Biology, 141, 135-143.https://doi.org/10.1016/j.jsbmb.2014.01.003
  20. Hentchel, K. L., & Escalante-Semerena, J. C. (2015). In Salmonella enterica, the Gcn5-related acetyltransferase MddA (formerly YncA) acetylates methionine sulfoximine and methionine sulfone, blocking their toxic effects. Journal of Bacteriology, 197(2), 314-325.https://doi.org/10.1128/JB.02311-14
  21. Kitanishi, K., Cracan, V., & Banerjee, R. (2015). Engineered and native coenzyme B12-dependent isovaleryl-CoA/pivalyl-CoA mutase. Journal of Biological Chemistry, 290(33), 20466-20476.https://doi.org/ 10.1074/jbc.M115.646299
  22. Roy, S., Soh, J. H., & Ying, J. Y. (2016). A microarray platform for detecting disease-specific circulating miRNA in human serum. Biosensors and Bioelectronics, 75, 238-246. https://doi.org/10.1016/j.bios.2015.08.039
  23. Balan, M. D., Mcleod, M. J., Lotosky, W. R., Ghaly, M., & Holyoak, T. (2015). Inhibition and allosteric regulation of monomeric phosphoenolpyruvate carboxykinase by 3-mercaptopicolinic acid. Biochemistry, 54(38), 5878-5887.https://doi.org/10.1021/acs.biochem.5b00822
  24. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  25. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  26. Block, E., Booker, S. J., Flores‐Penalba, S., George, G. N., Gundala, S., Landgraf, B. J., … & Vattekkatte, A. (2016). Trifluoroselenomethionine: A new unnatural amino acid. ChemBioChem, 17(18), 1738-1751. https://doi.org/10.1002/cbic.201600266
  27. Bird, J. G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., … & Kaplan, C. D. (2016). The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature, 535(7612), 444. https://doi.org/10.1038/nature18622
  28. Ledwitch, K. V., Gibbs, M. E., Barnes, R. W., & Roberts, A. G. (2016). Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology, 118, 96-108. https://doi.org/10.1016/j.bcp.2016.08.013
  29. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  30. Addington, C. P., Dharmawaj, S., Heffernan, J. M., Sirianni, R. W., & Stabenfeldt, S. E. (2017). Hyaluronic acid-laminin hydrogels increase neural stem cell transplant retention and migratory response to SDF-1α. Matrix Biology, 60, 206-216. https://doi.org/10.1016/j.matbio.2016.09.007
  31. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  32. Rogals, M. J., Greenwood, A. I., Kwon, J., Lu, K. P., & Nicholson, L. K. (2016). Neighboring phosphoSer‐Pro motifs in the undefined domain of IRAK 1 impart bivalent advantage for Pin1 binding. The FEBS Journal, 283(24), 4528-4548. https://doi.org/10.1111/febs.13943
  33. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
  34. Bohl, T. E., Shi, K., Lee, J. K., & Aihara, H. (2018). Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nature Communications, 9(1), 377.10.1038/s41467-017-02712-9
  35. Fassler, R., Edinger, N., Rimon, O., & Reichmann, D. (2018). Defining Hsp33’s redox-regulated chaperone activity and mapping conformational changes on Hsp33 using hydrogen-deuterium exchange mass spectrometry. JoVE (Journal of Visualized Experiments), (136), e57806. https://doi.org/10.3791/57806
  36. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  37. Pisa, R., Cupido, T., Steinman, J. B., Jones, N. H., & Kapoor, T. M. (2019). Analyzing resistance to design selective chemical inhibitors for AAA proteins. Cell Chemical Biology.https://doi.org/10.1016/j.chembiol.2019.06.001
  38. Kim, S., Loeff, L., Colombo, S., Jergic, S., Brouns, S. J. J., & Joo, C. (2020). Selective loading and processing of prespacers for precise CRISPR adaptation. Nature, 579(7797), 141–145. https://doi.org/10.1038/s41586-020-2018-1
  39. Klein, B. J., Cox, K. L., Jang, S. M., Côté, J., Poirier, M. G., & Kutateladze, T. G. (2020). Molecular basis for the PZP domain of BRPF1 association with chromatin. Structure, 28(1), 105–110.e3. https://doi.org/10.1016/j.str.2019.10.014
  40. Cohen, D. T., Wales, T. E., McHenry, M. W., Engen, J. R., & Walensky, L. D. (2020). Site-dependent cysteine lipidation potentiates the activation of proapoptotic BAX. Cell Reports, 30(10), 3229–3239.e6. https://doi.org/10.1016/j.celrep.2020.02.057
  41. Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2020). Modulation of kinesin’s load-bearing capacity by force geometry and the microtubule track. Biophysical Journal, 118(1), 243–253. https://doi.org/10.1016/j.bpj.2019.10.045
  42. Ruetz, M., Kumutima, J., Lewis, B. E., Filipovic, M. R., Lehnert, N., Stemmler, T. L., & Banerjee, R. (2017). A distal ligand mutes the interaction of hydrogen sulfide with human neuroglobin. Journal of Biological Chemistry, 292(16), 6512–6528. https://doi.org/10.1074/jbc.m116.770370
  43. Jin, J., Jung, I. H., Moon, S. H., Jeon, S., Jeong, S. J., Sonn, S. K., … & Kim, S. (2020). CD137 signaling regulates acute colitis via RALDH2-expressing CD11b− CD103+ DCs. Cell Reports, 30(12), 4124-4136. https://doi.org/10.1016/j.celrep.2020.02.103
  44. Grzybowski, A. T., Shah, R. N., Richter, W. F., & Ruthenburg, A. J. (2019). Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nature Protocols, 14(12), 3275–3302. https://doi.org/10.1038/s41596-019-0218-7
  45. Seven, A. B., Hilger, D., Papasergi-Scott, M. M., Zhang, L., Qu, Q., Kobilka, B. K., … & Skiniotis, G. (2020). Structures of Gα proteins in complex with their chaperone reveal quality control mechanisms. Cell Reports, 30(11), 3699–3709.e6. https://doi.org/10.1016/j.celrep.2020.02.086
  46. Qu, X., Kumar, A., Blockus, H., Waites, C., & Bartolini, F. (2019). Activity-dependent nucleation of dynamic microtubules at presynaptic boutons controls neurotransmission. Current Biology, 29(24), 4231-4240.e5. https://doi.org/10.1016/j.cub.2019.10.049
  47. Blus, B. J., Hashimoto, H., Seo, H.-S., Krolak, A., & Debler, E. W. (2019). Substrate affinity and specificity of the ScSth1p bromodomain are fine-tuned for versatile histone recognition. Structure, 27(9), 1460–1468.e3. https://doi.org/10.1016/j.str.2019.06.009
  48. Jia, N., Jones, R., Sukenick, G., & Patel, D. J. (2019). Second messenger cA4 formation within the composite Csm1 palm pocket of type III-A CRISPR-Cas Csm complex and its release path. Molecular cell, 75(5), 933-943. https://doi.org/10.1016/j.molcel.2019.06.013
  49. Jia, N., Jones, R., Yang, G., Ouerfelli, O., & Patel, D. J. (2019). CRISPR-Cas III-A Csm6 CARF domain is a ring nuclease triggering stepwise cA4 cleavage with ApA> p formation terminating RNase activity. Molecular Cell, 75(5), 944-956. https://doi.org/10.1016/j.molcel.2019.06.014
  50. Jia, N., Mo, C. Y., Wang, C., Eng, E. T., Marraffini, L. A., & Patel, D. J. (2019). Type III-A CRISPR-Cas Csm complexes: assembly, periodic RNA cleavage, DNase activity regulation, and autoimmunity. Molecular Cell, 73(2), 264-277.e5. https://doi.org/10.1016/j.molcel.2018.11.007
  51. Li, Y., Zhang, Z., Phoo, W. W., Loh, Y. R., Li, R., Yang, H. Y., … & Luo, D. (2018). Structural insights into the inhibition of Zika virus NS2B-NS3 protease by a small-molecule inhibitor. Structure, 26(4), 555-564. https://doi.org/10.1016/j.str.2018.02.005
  52. Campbell, B. C., Petsko, G. A., & Liu, C. F. (2018). Crystal structure of green fluorescent protein clover and design of clover-based redox sensors. Structure, 26(2), 225-237. https://doi.org/10.1016/j.str.2017.12.006
  53. Martin-Perez, M., & Villén, J. (2017). Determinants and regulation of protein turnover in yeast. Cell Systems, 5(3), 283-294. https://doi.org/10.1016/j.cels.2017.08.008
  54. Li, Y., Zhang, Z., Phoo, W. W., Loh, Y. R., Wang, W., Liu, S., … & Kang, C. (2017). Structural dynamics of Zika virus NS2B-NS3 protease binding to dipeptide inhibitors. Structure, 25(8), 1242-1250. https://doi.org/10.1016/j.str.2017.06.006
  55. Huang, T. L., Wang, H. J., Chang, Y. C., Wang, S. W., & Hsia, K. C. (2020). Promiscuous binding of microprotein Mozart1 to γ-Tubulin complex mediates specific subcellular targeting to control microtubule array formation. Cell Reports, 31(13), 107836. https://doi.org/10.1016/j.celrep.2020.107836
  56. Wieczorek, M., Huang, T. L., Urnavicius, L., Hsia, K. C., & Kapoor, T. M. (2020). MZT proteins form multi-faceted structural modules in the γ-Tubulin ring complex. Cell Reports, 31(13), 107791. https://doi.org/10.1016/j.celrep.2020.107791
E-64
  1. Chaparian, R. R., Tran, M. L., Miller Conrad, L. C., Rusch, D. B., & van Kessel, J. C. (2020). Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. Nucleic Acids Research, 48(1), 171-183.
EDTA Disodium, dihydrate
  1. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
EGF, Human
  1. Kemmerer, Z. A., Ader, N. R., Mulroy, S. S., & Eggler, A. L. (2015). Comparison of human Nrf2 antibodies: a tale of two proteins. Toxicology Letters, 238(2), 83-89.https://doi.org/10.1016/j.toxlet.2015.07.004
  2. Jiang, Y., Zhang, Y., Leung, J. Y., Fan, C., Popov, K. I., Su, S., … & Xiang, Y. (2019). MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression. Nature Communications, 10(1), 1515. https://doi.org/10.1038/s41467-019-09233-7
  3. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
  4. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  5. Hoffman, H. K., Fernandez, M. V., Groves, N. S., Freed, E. O., & van Engelenburg, S. B. (2019). Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. Journal of Biological Chemistry, 294(44), 16266–16281. https://doi.org/10.1074/jbc.ra119.009372
  6. Ali, R. (2019). The Role of Signal Transducer and Activator of Transcription 1 (STAT1) and 3 (STAT3) in Primary and Metastatic Breast Cancer (Doctoral dissertation, Purdue University Graduate School).
  7. Aminuddin, A., Ng, P. Y., Leong, C.-O., & Chua, E. W. (2020). Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64664-3
EGTA
  1. Baradaran, R., Wang, C., Siliciano, A. F., & Long, S. B. (2018). Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters. Nature, 559(7715), 580. https://doi.org/10.1038/s41586-018-0331-8
Erythromycin
  1. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
FGF10/KGF2, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF7/KGF1, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF8, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF9, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
G418 Sulfate
  1. Finnigan, G. C., Ryan, M., & Stevens, T. H. (2011). A genome-wide enhancer screen implicates sphingolipid composition in vacuolar ATPase function in Saccharomyces cerevisiae. Genetics, 187(3), 771-783. https://doi.org/10.1534/genetics.110.125567
  2. Dutta, C., Day, T., Kopp, N., van Bodegom, D., Davids, M. S., Ryan, J., … & Fung, H. (2012). BCL2 suppresses PARP1 function and nonapoptotic cell death. Cancer Research, 72(16), 4193–4203. https://doi.org/10.1158/0008-5472.can-11-4204
  3. Hong, S. W., Jiang, Y., Kim, S., Li, C. J., & Lee, D. (2014). Target gene abundance contributes to the efficiency of siRNA-mediated gene silencing. Nucleic Acid Therapeutics, 24(3), 192–198. https://doi.org/10.1089/nat.2013.0466
  4. Hiemer, S. E., Szymaniak, A. D., & Varelas, X. (2014). The transcriptional regulators TAZ and YAP direct transforming growth factor β-induced tumorigenic phenotypes in breast cancer cells. Journal of Biological Chemistry, 289(19), 13461-13474. https://doi.org/10.1074/jbc.M113.529115
  5. Lawrence, J. E., Steele, C. J., Rovin, R. A., Belton, R. J., & Winn, R. J. (2016). Dexamethasone alone and in combination with desipramine, phenytoin, valproic acid or levetiracetam interferes with 5-ALA-mediated PpIX production and cellular retention in glioblastoma cells. Journal of Neuro-oncology, 127(1), 15-21. https://doi.org/10.1007/s11060-015-2012-x
  6. Keller, J., Nimnual, A. S., Varghese, M. S., VanHeyst, K. A., Hayman, M. J., & Chan, E. L. (2016). A novel EGFR extracellular domain mutant, EGFRΔ768, possesses distinct biological and biochemical properties in neuroblastoma. Molecular Cancer Research, 14(8), 740-752. https://doi.org/10.1158/1541-7786.mcr-15-0477
  7. Abu-Tayeh, H., Weidenfeld, K., Zhilin-Roth, A., Schif-Zuck, S., Thaler, S., Cotarelo, C., … & Sabo, E. (2016). ‘Normalizing’the malignant phenotype of luminal breast cancer cells via alpha (v) beta (3)-integrin. Cell Death & Disease, 7(12), e2491. https://doi.org/10.1038/cddis.2016.387
  8. Mercier, R., Wolmarans, A., Schubert, J., Neuweiler, H., Johnson, J. L., & LaPointe, P. (2019). The conserved NxNNWHW motif in Aha-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation. Nature Communications, 10(1), 1273. https://doi.org/10.1038/s41467-019-09299-3
  9. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  10. Mauldin, I. S., Sheybani, N. D., Young, S. J., Price, R. J., & Slingluff, C. L. (2020). Deconvolution of the immunological contexture of mouse tumors with multiplexed immunohistochemistry. In Methods in Enzymology (pp. 81–93). Elsevier. https://doi.org/10.1016/bs.mie.2019.05.038
  11. Wang, A., Kolhe, J. A., Gioacchini, N., Baade, I., Brieher, W. M., Peterson, C. L., & Freeman, B. C. (2020). Mechanism of long-range chromosome motion triggered by gene activation. Developmental Cell, 52(3), 309–320.e5. https://doi.org/10.1016/j.devcel.2019.12.007
  12. Park, S., Brugiolo, M., Akerman, M., Das, S., Urbanski, L., Geier, A., … & Hu, L. (2019). Differential functions of splicing factors in mammary transformation and breast cancer metastasis. Cell Reports, 29(9), 2672-2688.e5. https://doi.org/10.1016/j.celrep.2019.10.110
GelRed™ Nucleic Acid Gel Stain, 10,000X in Water
  1. Kozakiewicz, C. P., Burridge, C. P., Funk, W. C., Craft, M. E., Crooks, K. R., Fisher, R. N., … Carver, S. (2020). Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development. Evolutionary Applications. https://doi.org/10.1111/eva.12927
  2. Asghari, A., Zare, M., Hatam, G., Shahabi, S., Gholizadeh, F., & Motazedian, M. (2020). Molecular identification and subtypes distribution of Blastocystis sp. isolated from children and adolescent with cancer in Iran: evaluation of possible risk factors and clinical features. Acta Parasitologica. https://doi.org/10.2478/s11686-020-00186-2
Gentamicin Sulfate, USP Grade
  1. Ketelboeter, L. M., & Bardy, S. L. (2015). Methods to inhibit bacterial pyomelanin production and determine the corresponding increase in sensitivity to oxidative stress. JoVE (Journal of Visualized Experiments), (102), e53105. https://doi.org/10.3791/53105
  2. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  3. Moroz, N., & Tanaka, K. (2020). FlgII-28 is a major flagellin-derived defense elicitor in potato. Molecular Plant-Microbe Interactions, 33(2), 247–255. https://doi.org/10.1094/mpmi-06-19-0164-r
  4. Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020). Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0468-5
  5. Gogokhia, L., Buhrke, K., Bell, R., Hoffman, B., Brown, D. G., Hanke-Gogokhia, C., … & Porter, N. (2019). Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host & Microbe, 25(2), 285-299. https://doi.org/10.1016/j.chom.2019.01.008
  6. Yadav, D., Ghosh, K., Basu, S., Roeder, R. G., & Biswas, D. (2019). Multivalent role of human TFIID in recruiting elongation components at the promoter-proximal region for transcriptional control. Cell Reports, 26(5), 1303–1317.e7. https://doi.org/10.1016/j.celrep.2019.01.012
Gibberellic Acid 3 (Quick-Dissolve™)
  1. Pearce, S., Vanzetti, L. S., & Dubcovsky, J. (2013). Exogenous gibberellins induce wheat spike development under short days only in the presence of VERNALIZATION1. Plant Physiology, 163(3), 1433-1445. https://doi.org/10.1104/pp.113.225854
  2. Best, N. B., Hartwig, T., Budka, J. S., Bishop, B. J., Brown, E., Potluri, D. P., … & Schulz, B. (2014). Soilless plant growth media influence the efficacy of phytohormones and phytohormone inhibitors. PloS One, 9(12), e107689.. https://doi.org/10.1371/journal.pone.0107689
  3. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  4. Best, N. B., Wang, X., Brittsan, S., Dean, E., Helfers, S. J., Homburg, R., … & Hasegawa, P. M. (2016). Sunflower ‘Sunspot’ is hyposensitive to GA3 and has a missense mutation in the DELLA motif of HaDella1. Journal of the American Society for Horticultural Science, 141(4), 389-394. https://doi.org/10.21273/JASHS.141.4.389
Glutathione Agarose Resin
  1. Ricketts, M. D., Frederick, B., Hoff, H., Tang, Y., Schultz, D. C., Rai, T. S., … & Marmorstein, R. (2015). Ubinuclein-1 confers histone H3. 3-specific-binding by the HIRA histone chaperone complex. Nature Communications, 6, 7711. https://doi.org/10.1038/ncomms8711
  2. Williams, P. A., Krug, M. S., McMillan, E. A., Peake, J. D., Davis, T. L., Cocklin, S., & Strochlic, T. I. (2016). Phosphorylation of the RNA-binding protein Dazl by MAPKAP kinase 2 regulates spermatogenesis. Molecular Biology of the Cell, 27(15), 2341-2350. https://doi.org/10.1091/mbc.e15-11-0773
  3. Rajavel, M., Orban, T., Xu, M., Hernandez-Sanchez, W., de la Fuente, M., Palczewski, K., & Taylor, D. J. (2016). Dynamic peptides of human TPP1 fulfill diverse functions in telomere maintenance. Nucleic Acids Research, 44(21), 10467-10479. https://doi.org/10.1093/nar/gkw846
  4. Barragan-Iglesias, P., Lou, T. F., Bhat, V. D., Megat, S., Burton, M. D., Price, T. J., & Campbell, Z. T. (2018). Inhibition of Poly (A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice. Nature Communications, 9(1), 10. https://doi.org/10.1038/s41467-017-02449-5
  5. Pisa, R., Cupido, T., Steinman, J. B., Jones, N. H., & Kapoor, T. M. (2019). Analyzing resistance to design selective chemical inhibitors for AAA proteins. Cell Chemical Biology.https://doi.org/10.1016/j.chembiol.2019.06.001
  6. Gorgulla, C., Boeszoermenyi, A., Wang, Z.-F., Fischer, P. D., Coote, P., Padmanabha Das, K. M., … & Arthanari, H. (2020). An open-source drug discovery platform enables ultra-large virtual screens. Nature. https://doi.org/10.1038/s41586-020-2117-z
  7. Holly, R. W., Jones, K., & Prehoda, K. E. (2020). A conserved PDZ-binding motif in aPKC interacts with Par-3 and mediates cortical polarity. Current Biology, 30(5), 893-898.e5. https://doi.org/10.1016/j.cub.2019.12.055
  8. Mayank, A. K., Pandey, V., Vashisht, A. A., Barshop, W. D., Rayatpisheh, S., Sharma, T., … & Wohlschlegel, J. A. (2019). An oxygen-dependent interaction between FBXL5 and the CIA-targeting complex regulates iron homeostasis. Molecular Cell, 75(2), 382–393.e5. https://doi.org/10.1016/j.molcel.2019.05.020
  9. Arceci, A., Bonacci, T., Wang, X., Stewart, K., Damrauer, J. S., Hoadley, K. A., & Emanuele, M. J. (2019). FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell Reports, 26(11), 3076–3086.e6. https://doi.org/10.1016/j.celrep.2019.02.054
GV3101 Agrobacterium Electrocompetent Cells
  1. de Leone, M. J., Hernando, C. E., Romanowski, A., Careno, D. A., Soverna, A. F., Sun, H., Bologna, N. G., Vázquez, M., Schneeberger, K., & Yanovsky, M. J. (2020). Bacterial infection disrupts clock gene expression to attenuate immune responses. Current Biology. https://doi.org/10.1016/j.cub.2020.02.058
HEPES, Free Acid
  1. Pokhrel, A., Lingo, J. C., Wolschendorf, F., & Gray, M. J. (2019). Assaying for inorganic polyphosphate in bacteria. JoVE (Journal of Visualized Experiments), (143), e58818.https://doi.org/10.3791/58818
  2. Schneider, C. R., Lewis, L. C., & Shafaat, H. S. (2019). The good, the neutral, and the positive: buffer identity impacts CO2 reduction activity by nickel(ii) cyclam. Dalton Transactions, 48(42), 15810–15821. https://doi.org/10.1039/c9dt03114f
  3. Ward, C. L., & Linz, T. H. (2020). Characterizing the impact of thermal gels on isotachophoresis in microfluidic devices. Electrophoresis. https://doi.org/10.1002/elps.201900407
  4. Lancaster, C. A., Scholl, W. E., Ticknor, M. A., & Shumaker-Parry, J. S. (2020). Uniting top-down and bottom-up strategies using fabricated nanostructures as hosts for synthesis of Nanomites. The Journal of Physical Chemistry C. https://doi.org/10.1021/acs.jpcc.9b11820
  5. Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2020). Modulation of kinesin’s load-bearing capacity by force geometry and the microtubule track. Biophysical Journal, 118(1), 243–253. https://doi.org/10.1016/j.bpj.2019.10.045
  6. Dai, L., Zhao, T., Bisteau, X., Sun, W., Prabhu, N., Lim, Y. T., … & Nordlund, P. (2018). Modulation of protein-interaction states through the cell cycle. Cell, 173(6), 1481-1494. https://doi.org/10.1016/j.cell.2018.03.065
  7. Dziekan, J. M., Wirjanata, G., Dai, L., Go, K. D., Yu, H., Lim, Y. T., … & Sobota, R. M. (2020). Cellular thermal shift assay for the identification of drug–target interactions in the Plasmodium falciparum proteome. Nature Protocols, 1-41. https://doi.org/10.1038/s41596-020-0310-z
Hygromycin B
  1. Serrano, H., & Blanchard, J. S. (2013). Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry, 52(29), 5009-5015. https://doi.org/10.1021/bi400338f
  2. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  3. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
  4. Lai, W. C., Sun, H. F. S., Lin, P. H., Lin, H., & Shieh, J. C. (2016). A new rapid and efficient system with dominant selection developed to inactivate and conditionally express genes in Candida albicans. Current Genetics, 62(1), 213-235.https://doi.org/10.1007/s00294-015-0526-6
  5. Liang, Y., Zhu, J., Huang, H., Xiang, D., Li, Y., Zhang, D., … & Liu, Z. (2016). SESN2/sestrin 2 induction-mediated autophagy and inhibitory effect of isorhapontigenin (ISO) on human bladder cancers. Autophagy, 12(8), 1229-1239.https://doi.org/10.1080/15548627.2016.1179403
  6. Gallagher, C. M., Garri, C., Cain, E. L., Ang, K. K. H., Wilson, C. G., Chen, S., … & Renslo, A. R. (2016). Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch. Elife, 5, e11878. https://doi.org/10.7554/eLife.11878.001
  7. Garcia, D. M., Dietrich, D., Clardy, J., & Jarosz, D. F. (2016). A common bacterial metabolite elicits prion-based bypass of glucose repression. Elife, 5, e17978. https://doi.org/10.7554/eLife.17978
  8. Li, L., Shemetov, A. A., Baloban, M., Hu, P., Zhu, L., Shcherbakova, D. M., … & Verkhusha, V. V. (2018). Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. Nature Communications, 9(1), 2734. https://doi.org/10.1038/s41467-018-05231-3
  9. Mercier, R., Wolmarans, A., Schubert, J., Neuweiler, H., Johnson, J. L., & LaPointe, P. (2019). The conserved NxNNWHW motif in Aha-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation. Nature Communications, 10(1), 1273. https://doi.org/10.1038/s41467-019-09299-3
  10. Corcoran, J. A., Jordan, M. D., Carraher, C., & Newcomb, R. D. (2014). A novel method to study insect olfactory receptor function using HEK293 cells. Insect Biochemistry and Molecular Biology, 54, 22-32.https://doi.org/10.1016/j.ibmb.2014.08.005
  11. Lai, W.-C., Sun, H. S., & Shieh, J.-C. (2020). Establishment of tetracycline-regulated bimolecular fluorescence complementation assay to detect protein-protein interactions in Candida albicans. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59891-7
  12. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  13. Nambiar, M., & Smith, G. R. (2018). Pericentromere-specific cohesin complex prevents meiotic pericentric DNA double-strand breaks and lethal crossovers. Molecular Cell, 71(4), 540-553. https://doi.org/10.1016/j.molcel.2018.06.035
Hygromycin B EZ Pak™ for 50 mg/mL Solution
  1. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
  2. Lai, W. C., Sun, H. F. S., Lin, P. H., Lin, H., & Shieh, J. C. (2016). A new rapid and efficient system with dominant selection developed to inactivate and conditionally express genes in Candida albicans. Current Genetics, 62(1), 213-235.https://doi.org/10.1007/s00294-015-0526-6
  3. Liang, Y., Zhu, J., Huang, H., Xiang, D., Li, Y., Zhang, D., … & Liu, Z. (2016). SESN2/sestrin 2 induction-mediated autophagy and inhibitory effect of isorhapontigenin (ISO) on human bladder cancers. Autophagy, 12(8), 1229-1239.https://doi.org/10.1080/15548627.2016.1179403
  4. Gallagher, C. M., Garri, C., Cain, E. L., Ang, K. K. H., Wilson, C. G., Chen, S., … & Renslo, A. R. (2016). Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch. Elife, 5, e11878. https://doi.org/10.7554/eLife.11878.001
  5. Garcia, D. M., Dietrich, D., Clardy, J., & Jarosz, D. F. (2016). A common bacterial metabolite elicits prion-based bypass of glucose repression. Elife, 5, e17978. https://doi.org/10.7554/eLife.17978
IAA (Indole-3-Acetic Acid)
  1. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  2. Woodman, J., Hoffman, M., Dzieciatkowska, M., Hansen, K. C., & Megee, P. C. (2015). Phosphorylation of the Scc2 cohesin deposition complex subunit regulates chromosome condensation through cohesin integrity. Molecular Biology of The Cell, 26(21), 3754-3767.https://doi.org/10.1091/mbc.E15-03-0165
IFN-gamma, Murine
  1. Xi, J., Huang, Q., Wang, L., Ma, X., Deng, Q., Kumar, M., … & Zhang, M. (2018). miR-21 depletion in macrophages promotes tumoricidal polarization and enhances PD-1 immunotherapy. Oncogene, 37(23), 3151. https://doi.org/10.1038/s41388-018-0178-3
  2. Shehat, M. G., & Tigno-Aranjuez, J. (2019). Flow cytometric measurement of ROS production in macrophages in response to FcγR cross-linking. JoVE (Journal of Visualized Experiments), (145), e59167. https://doi.org/10.3791/59167
IGF1, Human
  1. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
IL1A (IL-1 alpha), Human
  1. Nawas, A. F., Kanchwala, M., Thomas-Jardin, S. E., Dahl, H., Daescu, K., Bautista, M., … Delk, N. A. (2020). IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival. BMC Cancer, 20(1). https://doi.org/10.1186/s12885-020-6529-9
IL1B (IL-1 beta), Human
  1. Jiang, S. J., Tsai, P. I., Peng, S. Y., Chang, C. C., Chung, Y., Tsao, H. H., … & Hsu, H. J. (2019). A potential peptide derived from cytokine receptors can bind proinflammatory cytokines as a therapeutic strategy for anti-inflammation. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36492-z
  2. Nawas, A. F., Kanchwala, M., Thomas-Jardin, S. E., Dahl, H., Daescu, K., Bautista, M., … Delk, N. A. (2020). IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival. BMC Cancer, 20(1). https://doi.org/10.1186/s12885-020-6529-9
IL1RN (IL-1RA), Murine
  1. Tartey, S., Gurung, P., Karki, R., Burton, A., Hertzog, P., & Kanneganti, T. D. (2020). Ets-2 deletion in myeloid cells attenuates IL-1α-mediated inflammatory disease caused by a Ptpn6 point mutation. Cellular & Molecular Immunology. https://doi.org/10.1038/s41423-020-0398-7
IL3, Murine
  1. Cabal-Hierro, L., van Galen, P., Prado, M. A., Higby, K. J., Togami, K., Mowery, C. T., … Lane, A. A. (2020). Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-15221-z
IL6, Human
  1. Jiang, S. J., Tsai, P. I., Peng, S. Y., Chang, C. C., Chung, Y., Tsao, H. H., … & Hsu, H. J. (2019). A potential peptide derived from cytokine receptors can bind proinflammatory cytokines as a therapeutic strategy for anti-inflammation. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36492-z
IL8, Human (72 a.a.)
  1. Kotha, P. L., Sharma, P., Kolawole, A. O., Yan, R., Alghamri, M. S., Brockman, T. L., … & Excoffon, K. J. (2015). Adenovirus entry from the apical surface of polarized epithelia is facilitated by the host innate immune response. PLoS pathogens, 11(3), e1004696. https://doi.org/10.1371/journal.ppat.1004696
Illumination™ Firefly Luciferase Enhanced Assay Kit
  1. Xiong, Q., Liu, A., Ren, Q., Xue, Y., Yu, X., Ying, Y., … Xu, C. (2020). Cuprous oxide nanoparticles trigger reactive oxygen species-induced apoptosis through activation of erk-dependent autophagy in bladder cancer. Cell Death & Disease, 11(5). https://doi.org/10.1038/s41419-020-2554-5
IPTG
  1. Oppenheimer, M., Pierce, B. S., Crawford, J. A., Ray, K., Helm, R. F., & Sobrado, P. (2010). Recombinant expression, purification, and characterization of ThmD, the oxidoreductase component of tetrahydrofuran monooxygenase. Archives of Biochemistry and Biophysics, 496(2), 123–131. https://doi.org/10.1016/j.abb.2010.02.006
  2. Tan, A., & Henzl, M. T. (2009). Conformational stabilities of guinea pig OCP1 and OCP2. Biophysical Chemistry, 144(3), 108-118. https://doi.org/10.1016/j.bpc.2009.07.003
  3. Kreutzer, D. A., & Essigmann, J. M. (1998). Oxidized, deaminated cytosines are a source of C→ T transitions in vivo . Proceedings of the National Academy of Sciences, 95(7), 3578-3582. https://doi.org/10.1073/pnas.95.7.3578
  4. Fuqua, C., Burbea, M., & Winans, S. C. (1995). Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. Journal of Bacteriology, 177(5), 1367-1373. https://doi.org/10.1128/jb.177.5.1367-1373.1995
  5. Fink, S. P., Reddy, G. R., & Marnett, L. J. (1997). Mutagenicity in Escherichia coli of the major DNA adduct derived from the endogenous mutagen malondialdehyde. Proceedings of the National Academy of Sciences, 94(16), 8652–8657. https://doi.org/10.1073/pnas.94.16.8652
  6. Karunakaran, T., Madden, T., & Kuramitsu, H. (1997). Isolation and characterization of a hemin-regulated gene, hemR , from Porphyromonas gingivalis . Journal of Bacteriology, 179(6), 1898–1908. https://doi.org/10.1128/jb.179.6.1898-1908.1997
  7. VanderVeen, L. A., Hashim, M. F., Nechev, L. V., Harris, T. M., Harris, C. M., & Marnett, L. J. (2001). Evaluation of the mutagenic potential of the principal DNA adduct of acrolein. Journal of Biological Chemistry, 276(12), 9066-9070. https://doi.org/10.1074/jbc.m008900200
  8. O’Sullivan, D. J., Hill, C., & Klaenhammer, T. R. (1993). Effect of increasing the copy number of bacteriophage origins of replication, in trans, on incoming-phage proliferation. Applied and Environmental Microbiology, 59(8), 2449-2456.
  9. Neeley, W. L., Delaney, J. C., Henderson, P. T., & Essigmann, J. M. (2004). In vivo bypass efficiencies and mutational signatures of the guanine oxidation products 2-aminoimidazolone and 5-guanidino-4-nitroimidazole. Journal of Biological Chemistry, 279(42), 43568-43573. https://doi.org/10.1074/jbc.M407117200
  10. Johnson, K. A., Fink, S. P., & Marnett, L. J. (1997). Repair of propanodeoxyguanosine by nucleotide excision repair in vivo and in vitro. Journal of Biological Chemistry, 272(17), 11434-11438. https://doi.org/10.1074/jbc.272.17.11434
  11. Wanyiri, J. W., O’Connor, R., Allison, G., Kim, K., Kane, A., Qiu, J., … & Ward, H. D. (2007). Proteolytic processing of the Cryptosporidium glycoprotein gp40/15 by human furin and by a parasite-derived furin-like protease activity. Infection and Immunity, 75(1), 184-192. https://doi.org/10.1128/iai.00944-06
  12. Henderson, P. T., Delaney, J. C., Gu, F., Tannenbaum, S. R., & Essigmann, J. M. (2002). Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in Vivo. Biochemistry, 41(3), 914–921. https://doi.org/10.1021/bi0156355
  13. Sadler, T. J., Glare, T. R., Ward, V. K., & Kalmakoff, J. (2000). Physical and genetic map of the Wiseana nucleopolyhedrovirus genome. Journal of General Virology, 81(4), 1127-1133. https://doi.org/10.1099/0022-1317-81-4-1127
  14. VanderVeen, L. A., Hashim, M. F., Shyr, Y., & Marnett, L. J. (2003). Induction of frameshift and base pair substitution mutations by the major DNA adduct of the endogenous carcinogen malondialdehyde. Proceedings of the National Academy of Sciences, 100(24), 14247-14252. https://doi.org/10.1073/pnas.2332176100
  15. Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G., & Norris, J. S. (2002). Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. Journal of Virology, 76(11), 5557–5564. https://doi.org/10.1128/jvi.76.11.5557-5564.2002
  16. Bailey, E. A., Iyer, R. S., Stone, M. P., Harris, T. M., & Essigmann, J. M. (1996). Mutational properties of the primary aflatoxin B1-DNA adduct. Proceedings of the National Academy of Sciences, 93(4), 1535–1539. https://doi.org/10.1073/pnas.93.4.1535
  17. Niedernhofer, L. J., Daniels, J. S., Rouzer, C. A., Greene, R. E., & Marnett, L. J. (2003). Malondialdehyde, a product of lipid peroxidation, is mutagenic in human cells. Journal of Biological Chemistry, 278(33), 31426–31433. https://doi.org/10.1074/jbc.m212549200
  18. Fuqua, W. C., & Winans, S. C. (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. Journal of Bacteriology, 176(10), 2796-2806. https://doi.org/10.1128/jb.176.10.2796-2806.1994
  19. Wittmayer, P. K., McKenzie, J. L., & Raines, R. T. (1998). Degenerate DNA recognition by I-PpoI endonuclease. Gene, 206(1), 11–21. https://doi.org/10.1016/s0378-1119(97)00563-5
  20. Chang, M.-Y., Won, S.-J., & Liu, H.-S. (1997). A ribozyme specifically suppresses transformation and tumorigenicity of Ha-ras-oncogene-transformed NIH/3T3 cell lines. Journal of Cancer Research and Clinical Oncology, 123(2), 91–99. https://doi.org/10.1007/bf01269886
  21. Johnson, K. A., Mierzwa, M. L., Fink, S. P., & Marnett, L. J. (1999). MutS recognition of exocyclic DNA adducts that are endogenous products of lipid oxidation. Journal of Biological Chemistry, 274(38), 27112–27118. https://doi.org/10.1074/jbc.274.38.27112
  22. Lough, J., Jackson, M., Morris, R., & Moyer, R. (2001). Bisulfite-induced cytosine deamination rates in E. coli SSB: DNA complexes. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 478(1-2), 191-197. https://doi.org/10.1016/s0027-5107(01)00149-x
  23. Alexander, P., Fahnestock, S., Lee, T., Orban, J., & Bryan, P. (1992). Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures. Biochemistry, 31(14), 3597-3603. https://doi.org/10.1021/bi00129a007
  24. Min, W., Kim, J-K., Lillehoj, H. S., Sohn, E. J., Han, J. Y., Song, K. D., & Lillehoj, E. P. (2001). Characterization of recombinant scFv antibody reactive with an apical antigen of Eimeria acervulina. Biotechnology Letters, 23(12), 949–955. https://doi.org/10.1023/a:1010531019633
  25. Sundberg, E. J., Urrutia, M., Braden, B. C., Isern, J., Tsuchiya, D., Fields, B. A., … Mariuzza, R. A. (2000). Estimation of the hydrophobic effect in an antigen−antibody protein−protein Interface. Biochemistry, 39(50), 15375–15387. https://doi.org/10.1021/bi000704l
  26. Turner, L., Samuel, A. D., Stern, A. S., & Berg, H. C. (1999). Temperature dependence of switching of the bacterial flagellar motor by the protein CheY13DK106YW. Biophysical Journal, 77(1), 597-603. https://doi.org/10.1016/s0006-3495(99)76916-x
  27. Batiza, A. F., Kuo, M. M.-C., Yoshimura, K., & Kung, C. (2002). Gating the bacterial mechanosensitive channel MscL in vivo. Proceedings of the National Academy of Sciences, 99(8), 5643–5648. https://doi.org/10.1073/pnas.082092599
  28. Wolffe, E. J., Katz, E., Weisberg, A., & Moss, B. (1997). The A34R glycoprotein gene is required for induction of specialized actin-containing microvilli and efficient cell-to-cell transmission of vaccinia virus. Journal of Virology, 71(5), 3904-3915.
  29. Parker, A. R., Moore, T. D., Edman, J. C., Schwab, J. M., & Davisson, V. J. (1994). Cloning, sequence analysis and expression of the gene encoding imidazole glycerol phosphate dehydratase in Cryptococcus neoformans. Gene, 145(1), 135-138. https://doi.org/10.1016/0378-1119(94)90336-0
  30. Maldonado-Arocho, F. J., & Bradley, K. A. (2009). Anthrax edema toxin induces maturation of dendritic cells and enhances chemotaxis towards macrophage inflammatory protein 3β. Infection and Immunity, 77(5), 2036-2042. https://doi.org/10.1128/IAI.01329-08
  31. Cooper, K. K., Trinh, H. T., & Songer, J. G. (2009). Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. Veterinary Microbiology, 133(1-2), 92-97. https://doi.org/10.1016/j.vetmic.2008.06.001
  32. Chung, Y. I., Park, D. H., Kim, M., Baker, H., & Joh, T. H. (2001). Immunochemical characterization of brain and pineal tryptophan hydroxylase. Journal of Korean Medical Science, 16(4), 489. https://doi.org/10.3346/jkms.2001.16.4.489
  33. Pieper, U., Hayakawa, K., Li, Z., & Herzberg, O. (1997). Circularly permuted β-lactamase from Staphylococcus aureus PC1. Biochemistry, 36(29), 8767-8774. https://doi.org/10.1021/bi9705117
  34. Klink, T. A., Woycechowsky, K. J., Taylor, K. M., & Raines, R. T. (2000). Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A. European Journal of Biochemistry, 267(2), 566–572. https://doi.org/10.1046/j.1432-1327.2000.01037.x
  35. Glamann, J., Burton, D. R., Parren, P. W., Ditzel, H. J., Kent, K. A., Arnold, C., … & Hirsch, V. M. (1998). Simian immunodeficiency virus (SIV) envelope-specific Fabs with high-level homologous neutralizing activity: recovery from a long-term-nonprogressor SIV-infected macaque. Journal of Virology, 72(1), 585-592.
  36. Li, Y., & Inouye, M. (1994). Autoprocessing of prothiolsubtilisin E in which active-site serine 221 is altered to cysteine. Journal of Biological Chemistry, 269(6), 4169-4174.
  37. McCarter, L. L. (1998). OpaR, a homolog of Vibrio harveyi LuxR, controls opacity of Vibrio parahaemolyticus. Journal of Bacteriology, 180(12), 3166-3173.
  38. Park, K., Kuechle, M. K., Choe, Y., Craik, C. S., Lawrence, O. T., & Presland, R. B. (2006). Expression and characterization of constitutively active human caspase-14. Biochemical and Biophysical Research Communications, 347(4), 941-948. https://doi.org/10.1016/j.bbrc.2006.06.156
  39. Olson, J. W., & Maier, R. J. (2000). Dual roles of Bradyrhizobium japonicum nickelin protein in nickel storage and GTP-dependent Ni mobilization. Journal of Bacteriology, 182(6), 1702–1705. https://doi.org/10.1128/jb.182.6.1702-1705.2000
  40. Tan, A., & Henzl, M. T. (2009). Evidence for a Ca2+-specific conformational change in avian thymic hormone, a high-affinity β-parvalbumin. Biochemistry, 48(18), 3936-3945. https://doi.org/10.1021/bi900029j
  41. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  42. Luo, Y., Cho, H. H., Jones, R. B., Jin, C., & McKeehan, W. L. (2004). Improved production of recombinant fibroblast growth factor 7 (FGF7/KGF) from bacteria in high magnesium chloride. Protein Expression and Purification, 33(2), 326-331. https://doi.org/10.1016/j.pep.2003.10.013
  43. Wanyiri, J. W., Techasintana, P., O’Connor, R. M., Blackman, M. J., Kim, K., & Ward, H. D. (2009). Role of CpSUB1, a subtilisin-like protease, in Cryptosporidium parvum infection in vitro. Eukaryotic Cell, 8(4), 470-477. https://doi.org/10.1128/EC.00306-08
  44. Ye, K., Jin, S., Bratic, K., & Schultz, J. S. (2004). Surface display of a glucose binding protein. Journal of Molecular Catalysis B: Enzymatic, 28(4–6), 201–206. https://doi.org/10.1016/j.molcatb.2003.12.025
  45. Henzl, M. T., Davis, M. E., & Tan, A. (2008). Divalent ion binding properties of the timothy grass allergen, Phl p 7. Biochemistry, 47(30), 7846-7856. https://doi.org/10.1021/bi800620g
  46. Jost, B. H., Songer, J. G., & Billington, S. J. (2001). Cloning, expression, and characterization of a neuraminidase gene from Arcanobacterium pyogenes. Infection and Immunity, 69(7), 4430–4437. https://doi.org/10.1128/iai.69.7.4430-4437.2001
  47. Klem, T. J., Chen, Y., & Davisson, V. J. (2001). Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase. Journal of Bacteriology, 183(3), 989–996. https://doi.org/10.1128/jb.182.3.989-996.2001
  48. Lluis, M., Hoe, W., Schleit, J., & Robertus, J. (2010). Analysis of nucleic acid binding by a recombinant translin–trax complex. Biochemical and Biophysical Research Communications, 396(3), 709-713.https://doi.org/10.1016/j.bbrc.2010.04.166
  49. Tan, A., Tanner, J. J., & Henzl, M. T. (2008). Energetics of OCP1–OCP2 complex formation. Biophysical Chemistry, 134(1-2), 64-71. https://doi.org/10.1016/j.bpc.2008.01.005
  50. Ramachandran, S., Thompson, R. W., Gam, A. A., & Neva, F. A. (1998). Recombinant cDNA clones for immunodiagnosis of strongyloidiasis. The Journal of Infectious Diseases, 177(1), 196–203. https://doi.org/10.1086/513817
  51. Parker, A. R., Moore, J. A., Schwab, J. M., & Davisson, V. J. (1995). Escherichia coli imidazoleglycerol phosphate dehydratase: spectroscopic characterization of the enzymic product and the steric course of the reaction. Journal of the American Chemical Society, 117(43), 10605-10613. https://doi.org/10.1021/ja00148a001
  52. Vazquez, V., Liang, X., Horndahl, J. K., Ganesh, V. K., Smeds, E., Foster, T. J., & Hook, M. (2011). Fibrinogen is a ligand for the S. aureus MSCRAMM Bbp (Bone sialoprotein-binding protein). Journal of Biological Chemistry, 286(34), 29797–29805. https://doi.org/10.1074/jbc.m110.214981
  53. Billington, S. J., Jost, B. H., Cuevas, W. A., Bright, K. R., & Songer, J. G. (1997). The Arcanobacterium (Actinomyces) pyogenes hemolysin, pyolysin, is a novel member of the thiol-activated cytolysin family. Journal of Bacteriology, 179(19), 6100-6106. https://doi.org/10.1128/jb.179.19.6100-6106.1997
  54. Sakowski, S. A., Geddes, T. J., & Kuhn, D. M. (2006). Mouse tryptophan hydroxylase isoform 2 and the role of proline 447 in enzyme function. Journal of Neurochemistry, 96(3), 758–765. https://doi.org/10.1111/j.1471-4159.2005.03604.x
  55. Ramey, J. D., Villareal, V. A., Ng, C., Ward, S. C., Xiong, J. P., Clubb, R. T., & Bradley, K. A. (2010). Anthrax toxin receptor 1/tumor endothelial marker 8: mutation of conserved inserted domain residues overrides cytosolic control of protective antigen binding. Biochemistry, 49(34), 7403-7410. https://doi.org/10.1021/bi100887w
  56. Lahiri, S., Pulakat, L., & Gavini, N. (2008). Functional participation of a nifH–arsA2 chimeric fusion gene in arsenic reduction by Escherichia coli. Biochemical and Biophysical Research Communications, 368(2), 311-317. https://doi.org/10.1016/j.bbrc.2008.01.086
  57. Henzl, M. T., Davis, M. E., & Tan, A. (2010). Polcalcin divalent ion-binding behavior and thermal stability: comparison of Bet v 4, Bra n 1, and Bra n 2 to Phl p 7. Biochemistry, 49(10), 2256–2268. https://doi.org/10.1021/bi902115v
  58. Flores, H., & Ellington, A. D. (2005). A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase. Protein Engineering, Design and Selection, 18(8), 369–377. https://doi.org/10.1093/protein/gzi043
  59. Zawadzke, L. E., Smith, T. J., & Herzberg, O. (1995). An engineered Staphylococcus aureus PCI ß-lactamase that hydrolyses third-generation cephalosporins. Protein Engineering, Design and Selection, 8(12), 1275-1285. https://doi.org/10.1093/protein/8.12.1275
  60. Andi, B., Cook, P. F., & West, A. H. (2006). Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-Å resolution. Cell Biochemistry and Biophysics, 46(1), 17–26. https://doi.org/10.1385/cbb:46:1:17
  61. Smela, M. E., Hamm, M. L., Henderson, P. T., Harris, C. M., Harris, T. M., & Essigmann, J. M. (2002). The aflatoxin B1 formamidopyrimidine adduct plays a major role in causing the types of mutations observed in human hepatocellular carcinoma. Proceedings of the National Academy of Sciences, 99(10), 6655–6660. https://doi.org/10.1073/pnas.102167699
  62. Chou, C. K., Liang, K. H., Tzeng, C. C., Huang, G. C., Chuang, J. I., Chang, T. Y., & Liu, H. S. (2006). Dominant-negative Rac1 suppresses Ras-induced apoptosis possibly through activation of NFκB in Ha-ras oncogene-transformed NIH/3T3 cells. Life Sciences, 78(16), 1823–1829. https://doi.org/10.1016/j.lfs.2005.08.039
  63. Kim, S., Miska, K. B., McElroy, A. P., Jenkins, M. C., Fetterer, R. H., Cox, C. M., … & Dalloul, R. A. (2009). Molecular cloning and functional characterization of avian interleukin-19. Molecular Immunology, 47(2-3), 476-484. https://doi.org/10.1016/j.molimm.2009.08.027
  64. Dall’Acqua, W., Goldman, E. R., Eisenstein, E., & Mariuzza, R. A. (1996). A mutational analysis of the binding of two different proteins to the same antibody. Biochemistry, 35(30), 9667. https://doi.org/10.1021/bi960819i
  65. Veglia, G., Ha, K. N., Shi, L., Verardi, R., & Traaseth, N. J. (2010). What can we learn from a small regulatory membrane protein?. In: Lacapère JJ. (eds) Membrane Protein Structure Determination. Methods in Molecular Biology (Methods and Protocols), vol 654. (pp. 303-319) https://doi.org/10.1007/978-1-60761-762-4_16
  66. Chocklett, S. W., & Sobrado, P. (2010). Aspergillus fumigatus SidA is a highly specific ornithine hydroxylase with bound flavin cofactor. Biochemistry, 49(31), 6777-6783.https://doi.org/10.1021/bi100291n
  67. Kumar, A., Chua, K. L., & Schweizer, H. P. (2006). Method for regulated expression of single-copy efflux pump genes in a surrogate Pseudomonas aeruginosa strain: identification of the BpeEF-OprC chloramphenicol and trimethoprim efflux pump of Burkholderia pseudomallei 1026b. Antimicrobial Agents and Chemotherapy, 50(10), 3460-3463. https://doi.org/10.1128/AAC.00440-06
  68. Angov, E., & Camerini-Otero, R. D. (1994). The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization. Journal of Bacteriology, 176(5), 1405-1412. https://doi.org/10.1128/jb.176.5.1405-1412.1994
  69. Habben, J. E., Moro, G. L., Hunter, B. G., Hamaker, B. R., & Larkins, B. A. (1995). Elongation factor 1 alpha concentration is highly correlated with the lysine content of maize endosperm. Proceedings of the National Academy of Sciences, 92(19), 8640-8644. https://doi.org/10.1073/pnas.92.19.8640
  70. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  71. Ota, I. M., & Mapes, J. (2007). Targeting of PP2C in budding yeast. In Protein Phosphatase Protocols (pp. 309-322). Humana Press https://doi.org/10.1385/1-59745-267-x:309
  72. Richard‐Fogal, C. L., Frawley, E. R., Bonner, E. R., Zhu, H., San Francisco, B., & Kranz, R. G. (2009). A conserved haem redox and trafficking pathway for cofactor attachment. The EMBO Journal, 28(16), 2349-2359. https://doi.org/10.1038/emboj.2009.189
  73. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L., & Ruoho, A. E. (2007). One-step purification of bacterially expressed recombinant transducin α-subunit and isotopically labeled PDE6 γ-subunit for NMR analysis. Protein Expression and Purification, 51(2), 187-197. https://doi.org/10.1016/j.pep.2006.07.012
  74. Norais, C. A., Chitteni-Pattu, S., Wood, E. A., Inman, R. B., & Cox, M. M. (2009). DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. Journal of Biological Chemistry, 284(32), 21402-21411. https://doi.org/10.1074/jbc.M109.010454
  75. Sandoval, C. M., Baker, S. L., Jansen, K., Metzner, S. I., & Sousa, M. C. (2011). Crystal structure of BamD: an essential component of the β-barrel assembly machinery of gram-negative bacteria. Journal of Molecular Biology, 409(3), 348-357. https://doi.org/10.1016/j.jmb.2011.03.035
  76. Larabee, J. L., Maldonado-Arocho, F. J., Pacheco, S., France, B., DeGiusti, K., Shakir, S. M., … & Ballard, J. D. (2011). Gsk-3 activation is important for anthrax edema toxin induced dendritic cell maturation and antxr2 expression in macrophages. Infection and Immunity 79(8) 3302-3308 https://doi.org/10.1128/IAI.05070-11
  77. Matthews, M. L., Krest, C. M., Barr, E. W., Vaillancourt, F. H., Walsh, C. T., Green, M. T., … & Bollinger Jr, J. M. (2009). Substrate-triggered formation and remarkable stability of the C− H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2. Biochemistry, 48(20), 4331-4343.https://doi.org/10.1021/bi900109z
  78. Wang, Y., Fu, T. J., Howard, A., Kothary, M. H., McHugh, T. H., & Zhang, Y. (2013). Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5. Journal of Agricultural and Food Chemistry, 61(7), 1573-1578. https://doi.org/10.1021/jf303861p
  79. Song, L., Huang, Z., Chen, Y., Li, H., Jiang, C., & Li, X. (2014). High-efficiency production of bioactive recombinant human fibroblast growth factor 18 in Escherichia coli and its effects on hair follicle growth. Applied Microbiology and Biotechnology, 98(2), 695-704. https://doi.org/10.1007/s00253-013-4929-3
  80. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  81. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  82. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  83. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  84. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  85. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  86. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  87. Guerra, D., Ballard, K., Truebridge, I., & Vierling, E. (2016). S-nitrosation of conserved cysteines modulates activity and stability of S-nitrosoglutathione reductase (GSNOR). Biochemistry, 55(17), 2452-2464.https://doi.org/10.1021/acs.biochem.5b01373
  88. Sutherland, M. C., Rankin, J. A., & Kranz, R. G. (2016). Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry, 55(22), 3150-3156.https://doi.org/10.1021/acs.biochem.6b00427
  89. Robbins, T., Kapilivsky, J., Cane, D. E., & Khosla, C. (2016). Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry, 55(32), 4476-4484. https://doi.org/10.1021/acs.biochem.6b00639
  90. Inan, K., Sal, F. A., Rahman, A., Putman, R. J., Agblevor, F. A., & Miller, C. D. (2016). Microbubble assisted polyhydroxybutyrate production in Escherichia coli. BMC Research Notes, 9(1), 338. https://doi.org/10.1186/s13104-016-2145-9
  91. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  92. Tanner, J. J., Frey, B. B., Pemberton, T., & Henzl, M. T. (2016). EF5 is the high-affinity Mg2+ site in ALG-2. Biochemistry, 55(36), 5128-5141. https://doi.org/10.1021/acs.biochem.6b00596
  93. Kennedy, E. N., Menon, S. K., & West, A. H. (2016). Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions. FEMS Yeast Research, 16(6) fow068. https://doi.org/10.1093/femsyr/fow068
  94. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  95. Sigala, P. A., Morante, K., Tsumoto, K., Caaveiro, J. M., & Goldberg, D. E. (2016). In-Cell Enzymology To Probe His–Heme Ligation in Heme Oxygenase Catalysis. Biochemistry, 55(34), 4836-4849. https://doi.org/10.1021/acs.biochem.6b00562
  96. Fancher, A. T., Hua, Y., Camarco, D. P., Close, D. A., Strock, C. J., & Johnston, P. A. (2016). Reconfiguring the AR-TIF2 protein–protein interaction HCS assay in prostate cancer cells and characterizing the hits from a LOPAC screen. Assay and Drug Development Technologies, 14(8), 453-477. https://doi.org/10.1089/adt.2016.741
  97. Wang, X., Zhang, Z. T., Wang, Y., & Wang, Y. (2016). Production of polyhydroxybuyrate (PHB) from switchgrass pretreated with a radio frequency-assisted heating process. Biomass and Bioenergy, 94, 220-227. https://doi.org/10.1016/j.biombioe.2016.09.006
  98. Devendran, S., Abdel-Hamid, A. M., Evans, A. F., Iakiviak, M., Kwon, I. H., Mackie, R. I., & Cann, I. (2016). Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Scientific Reports, 6, 35342. https://doi.org/10.1038/srep35342
  99. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  100. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114

View all references

IPTG EZ Pak™ for 1 M Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  3. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  4. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Guerra, D., Ballard, K., Truebridge, I., & Vierling, E. (2016). S-nitrosation of conserved cysteines modulates activity and stability of S-nitrosoglutathione reductase (GSNOR). Biochemistry, 55(17), 2452-2464.https://doi.org/10.1021/acs.biochem.5b01373
  7. Sutherland, M. C., Rankin, J. A., & Kranz, R. G. (2016). Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry, 55(22), 3150-3156.https://doi.org/10.1021/acs.biochem.6b00427
  8. Robbins, T., Kapilivsky, J., Cane, D. E., & Khosla, C. (2016). Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry, 55(32), 4476-4484. https://doi.org/10.1021/acs.biochem.6b00639
  9. Inan, K., Sal, F. A., Rahman, A., Putman, R. J., Agblevor, F. A., & Miller, C. D. (2016). Microbubble assisted polyhydroxybutyrate production in Escherichia coli. BMC Research Notes, 9(1), 338. https://doi.org/10.1186/s13104-016-2145-9
  10. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  11. Tanner, J. J., Frey, B. B., Pemberton, T., & Henzl, M. T. (2016). EF5 is the high-affinity Mg2+ site in ALG-2. Biochemistry, 55(36), 5128-5141. https://doi.org/10.1021/acs.biochem.6b00596
  12. Kennedy, E. N., Menon, S. K., & West, A. H. (2016). Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions. FEMS Yeast Research, 16(6) fow068. https://doi.org/10.1093/femsyr/fow068
  13. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  14. Sigala, P. A., Morante, K., Tsumoto, K., Caaveiro, J. M., & Goldberg, D. E. (2016). In-Cell Enzymology To Probe His–Heme Ligation in Heme Oxygenase Catalysis. Biochemistry, 55(34), 4836-4849. https://doi.org/10.1021/acs.biochem.6b00562
  15. Fancher, A. T., Hua, Y., Camarco, D. P., Close, D. A., Strock, C. J., & Johnston, P. A. (2016). Reconfiguring the AR-TIF2 protein–protein interaction HCS assay in prostate cancer cells and characterizing the hits from a LOPAC screen. Assay and Drug Development Technologies, 14(8), 453-477. https://doi.org/10.1089/adt.2016.741
  16. Wang, X., Zhang, Z. T., Wang, Y., & Wang, Y. (2016). Production of polyhydroxybuyrate (PHB) from switchgrass pretreated with a radio frequency-assisted heating process. Biomass and Bioenergy, 94, 220-227. https://doi.org/10.1016/j.biombioe.2016.09.006
  17. Devendran, S., Abdel-Hamid, A. M., Evans, A. F., Iakiviak, M., Kwon, I. H., Mackie, R. I., & Cann, I. (2016). Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Scientific Reports, 6, 35342. https://doi.org/10.1038/srep35342
  18. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  19. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  20. Fiers, W. D., Dodge, G. J., Sherman, D. H., Smith, J. L., & Aldrich, C. C. (2016). Vinylogous dehydration by a polyketide dehydratase domain in curacin biosynthesis. Journal of the American Chemical Society, 138(49), 16024-16036. https://doi.org/10.1021/jacs.6b09748
  21. Le, C. Q., Oyugi, M., Joseph, E., Nguyen, T., Ullah, M. H., Aubert, J., … & Johnson-Winters, K. (2017). Effects of isoleucine 135 side chain length on the cofactor donor-acceptor distance within F420H2: NADP+ oxidoreductase: a kinetic analysis. Biochemistry and Biophysics Reports, 9, 114-120. https://doi.org/10.1016/j.bbrep.2016.11.012
  22. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate 50 mg/mL Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  3. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  4. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  7. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  8. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  9. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  10. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate EZ Pak™ for 50 mg/mL Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  3. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  4. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  7. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  8. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  9. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  10. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate, USP Grade
  1. Wang, Y., Fu, T. J., Howard, A., Kothary, M. H., McHugh, T. H., & Zhang, Y. (2013). Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5. Journal of Agricultural and Food Chemistry, 61(7), 1573-1578. https://doi.org/10.1021/jf303861p
  2. Rabara, R. C., Tripathi, P., Lin, J., & Rushton, P. J. (2013). Dehydration-induced WRKY genes from tobacco and soybean respond to jasmonic acid treatments in BY-2 cell culture. Biochemical and Biophysical Research Communications, 431(3), 409–414. https://doi.org/10.1016/j.bbrc.2012.12.156
  3. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  4. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  5. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  6. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  9. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  10. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  11. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  12. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
  13. Zhang, K., Xie, Y., Muñoz-Moreno, R., Wang, J., Zhang, L., Esparza, M., … & Ren, Y. (2019). Structural basis for influenza virus NS1 protein block of mRNA nuclear export. Nature Microbiology, 1. https://doi.org/10.1038/s41564-019-0482-x
  14. Heater, B. S., Lee, M. M., & Chan, M. K. (2018). Direct production of a genetically-encoded immobilized biodiesel catalyst. Scientific Reports, 8(1), 12783.https://doi.org/10.1038/s41598-018-31213-y
  15. Howell, M., Daniel, J. J., & Brown, P. J. (2017). Live cell fluorescence microscopy to observe essential processes during microbial cell growth. JoVE (Journal of Visualized Experiments), (129), e56497. https://doi.org/10.3791/56497
  16. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  17. Liu, Z., Sivasankar, P., & Sharma, H. (2019). An improved bioassay to study arabidopsis induced systemic resistance (ISR) against bacterial pathogens and insect pests. Bio-protocol 9 (10): e3236. https://doi.org/10.21769/BioProtoc.3236
  18. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  19. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  20. Karunadasa, S. S., Kurepa, J., Shull, T. E., & Smalle, J. A. (2020). Cytokinin‐induced protein synthesis suppresses growth and osmotic stress tolerance. New Phytologist. https://doi.org/10.1111/nph.16519
  21. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  22. Shin, J., Zhang, S., Der, B. S., Nielsen, A. A., & Voigt, C. A. (2020). Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16(3). https://doi.org/10.15252/msb.20199401
  23. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  24. Parks, T., & Yordanov, Y. S. (2020). Composite plants for a composite plant: an efficient protocol for root studies in the sunflower using composite plants approach. Plant Cell, Tissue and Organ Culture (PCTOC), 140(3), 647–659. https://doi.org/10.1007/s11240-019-01760-x
  25. González, L. M., Mukhitov, N., & Voigt, C. A. (2019). Resilient living materials built by printing bacterial spores. Nature Chemical Biology, 16(2), 126–133. https://doi.org/10.1038/s41589-019-0412-5
  26. Zhou, D., Tanzawa, T., Lin, J., & Gagnon, M. G. (2019). Structural basis for ribosome recycling by RRF and tRNA. Nature Structural & Molecular Biology, 27(1), 25–32. https://doi.org/10.1038/s41594-019-0350-7
  27. Moroz, N., & Tanaka, K. (2020). FlgII-28 is a major flagellin-derived defense elicitor in potato. Molecular Plant-Microbe Interactions, 33(2), 247–255. https://doi.org/10.1094/mpmi-06-19-0164-r
  28. Reighard, S. D., Cranert, S. A., Rangel, K. M., Ali, A., Gyurova, I. E., de la Cruz-Lynch, A. T., … Waggoner, S. N. (2020). Therapeutic targeting of follicular T cells with chimeric antigen receptor-expressing natural killer cells. Cell Reports Medicine, 100003. https://doi.org/10.1016/j.xcrm.2020.100003
  29. Smith, M. D., Robinson, S. L., Molomjamts, M., & Wackett, L. P. (2020). In vivo assay reveals microbial OleA thiolases initiating hydrocarbon and β-lactone biosynthesis. mBio, 11(2). https://doi.org/10.1128/mbio.00111-20
  30. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  31. Song, M., Sukovich, D. J., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, E. A., Tucker, A. C., Gordon, D. B., Marlovits, T. C., & Voigt, C. A. (2017). Control of type III protein secretion using a minimal genetic system. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14737
  32. Silpe, J. E., Bridges, A. A., Huang, X., Coronado, D. R., Duddy, O. P., & Bassler, B. L. (2020). Separating functions of the phage-encoded quorum-sensing-activated antirepressor Qtip. Cell Host & Microbe, 27(4), 629–641.e4. https://doi.org/10.1016/j.chom.2020.01.024
  33. Fukuda, S., Yan, S., Komi, Y., Sun, M., Gabizon, R., & Bustamante, C. (2020). The biogenesis of SRP RNA is modulated by an RNA folding intermediate attained during transcription. Molecular Cell, 77(2), 241–250.e8. https://doi.org/10.1016/j.molcel.2019.10.006
  34. Kim, W. J., Higashi, D., Goytia, M., Rendón, M. A., Pilligua-Lucas, M., Bronnimann, M., … & So, M. (2019). Commensal Neisseria kill Neisseria gonorrhoeae through a DNA-dependent mechanism. Cell Host & Microbe, 26(2), 228–239.e8. https://doi.org/10.1016/j.chom.2019.07.003
  35. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  36. Silpe, J. E., & Bassler, B. L. (2019). A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell, 176(1-2), 268-280.e13. https://doi.org/10.1016/j.cell.2018.10.059
  37. Barton, B., Grinnell, A., & Morgenstein, R. M. (2021). Disruption of the MreB elongasome Is overcome by mutations in the tricarboxylic acid cycle. Frontiers in Microbiology, 12 https://doi.org/10.3389/fmicb.2021.664281
KITLG (SCF), Human
  1. Finch, E. R., Kudva, A. K., Quickel, M. D., Goodfield, L. L., Kennett, M. J., Whelan, J., … & Prabhu, K. S. (2015). Chemopreventive effects of dietary eicosapentaenoic acid supplementation in experimental myeloid leukemia. Cancer Prevention Research, 8(10), 989-999.https://doi.org/10.1158/1940-6207.CAPR-15-0050
L-Albizziine
  1. Deng, L., Yao, P., Li, L., Ji, F., Zhao, S., Xu, C., … & Jiang, P. (2020). p53-mediated control of aspartate-asparagine homeostasis dictates LKB1 activity and modulates cell survival. Nature Communications, 11(1), 1-18. https://doi.org/10.1038/s41467-020-15573-6
L-Arabinose
  1. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  2. Sugihara, J., Sun, L., Yan, N., & Kaback, H. R. (2012). Dynamics of the L-fucose/H+ symporter revealed by fluorescence spectroscopy. Proceedings of the National Academy of Sciences, 109(37), 14847-14851. https://doi.org/10.1073/pnas.1213445109
  3. Köpke, M., Gerth, M. L., Maddock, D. J., Mueller, A. P., Liew, F., Simpson, S. D., & Patrick, W. M. (2014). Reconstruction of an acetogenic 2, 3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase. Applied and Environmental Microbiology, 80(11), 3394–3403.https://doi.org/10.1128/AEM.00301-14
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  10. Kim, S., Loeff, L., Colombo, S., Jergic, S., Brouns, S. J. J., & Joo, C. (2020). Selective loading and processing of prespacers for precise CRISPR adaptation. Nature, 579(7797), 141–145. https://doi.org/10.1038/s41586-020-2018-1
  11. Calla, B., Wu, W. ‐Y., Dean, C. A. E., Schuler, M. A., & Berenbaum, M. R. (2019). Substrate‐specificity of cytochrome P450‐mediated detoxification as an evolutionary strategy for specialization on furanocoumarin‐containing hostplants: CYP6AE89 in parsnip webworms. Insect Molecular Biology, 29(1), 112–123. https://doi.org/10.1111/imb.12612
  12. Manor, M., & Qimron, U. (2017). Selection of genetically modified bacteriophages using the CRISPR-Cas system. Bio-Protocol, 7(15). https://doi.org/10.21769/bioprotoc.2431
  13. Farzadfard, F., Gharaei, N., Higashikuni, Y., Jung, G., Cao, J., & Lu, T. K. (2019). Single-nucleotide-resolution computing and memory in living cells. Molecular Cell, 75(4), 769–780.e4. https://doi.org/10.1016/j.molcel.2019.07.011
L-Glutathione, Reduced
  1. Picarda, E., Bézie, S., Usero, L., Ossart, J., Besnard, M., Halim, H., … & Gras, S. (2019). Cross-reactive donor-specific CD8+ tregs efficiently prevent transplant rejection. Cell Reports, 29(13), 4245-4255. https://doi.org/10.1016/j.celrep.2019.11.106
  2. Huang, T. L., Wang, H. J., Chang, Y. C., Wang, S. W., & Hsia, K. C. (2020). Promiscuous binding of microprotein Mozart1 to γ-Tubulin complex mediates specific subcellular targeting to control microtubule array formation. Cell Reports, 31(13), 107836. https://doi.org/10.1016/j.celrep.2020.107836
  3. Wieczorek, M., Huang, T. L., Urnavicius, L., Hsia, K. C., & Kapoor, T. M. (2020). MZT proteins form multi-faceted structural modules in the γ-Tubulin ring complex. Cell Reports, 31(13), 107791. https://doi.org/10.1016/j.celrep.2020.107791
L-Rhamnose monohydrate
  1. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
Leupeptin Hemisulfate
  1. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  2. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  3. Kang, H., Yang, H. S., Ki, A. Y., Ko, S. B., Kim, K. W., Shim, C. Y., … & Chung, K. Y. (2020). Conformational Dynamics and Functional Implications of Phosphorylated β-Arrestins. Structure.https://doi.org/10.1016/j.str.2019.12.008
  4. Park, J. Y., Qu, C. X., Li, R. R., Yang, F., Yu, X., Tian, Z. M., … & Chung, K. Y. (2019). Structural mechanism of the arrestin-3/JNK3 interaction. Structure, 27(7), 1162–1170.e3. https://doi.org/10.1016/j.str.2019.04.002
Low Melt Agarose
  1. Stoddard, M., Huang, C., Enyedi, B., & Niethammer, P. (2019). Live imaging of leukocyte recruitment in a zebrafish model of chemical liver injury. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36771-9
  2. Schwerdtfeger, L. A., & Tobet, S. A. (2020). Vasoactive intestinal peptide regulates ileal goblet cell production in mice. Physiological Reports, 8(3). https://doi.org/10.14814/phy2.14363
  3. Kinstlinger, I. S., Saxton, S. H., Calderon, G. A., Ruiz, K. V., Yalacki, D. R., Deme, P. R., … & Sazer, D. W. (2020). Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates. Nature Biomedical Engineering, 1-17. https://doi.org/10.1038/s41551-020-0566-1
Luminol, sodium salt
  1. Alshetaiwi, H. S., Balivada, S., Shrestha, T. B., Pyle, M., Basel, M. T., Bossmann, S. H., & Troyer, D. L. (2013). Luminol-based bioluminescence imaging of mouse mammary tumors. Journal of Photochemistry and Photobiology B: Biology, 127, 223-228. https://doi.org/10.1016/j.jphotobiol.2013.08.017
Lysozyme, Egg White
  1. Wang, K. K. A., Ng, T. L., Wang, P., Huang, Z., Balskus, E. P., & van der Donk, W. A. (2018). Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. Nature Communications, 9(1), 3687. https://doi.org/10.1038/s41467-018-06083-7
Magenta-Gal
  1. Kryvoruchko, I. S., Sinharoy, S., Torres-Jerez, I., Sosso, D., Pislariu, C. I., Guan, D., … & Udvardi, M. K. (2016). MtSWEET11, a nodule-specific sucrose transporter of Medicago truncatula. Plant Physiology, 171(1), 554-565. https://doi.org/10.1104/pp.15.01910
Magenta-phos PT
  1. Vize, P. D., McCoy, K. E., & Zhou, X. (2009). Multichannel wholemount fluorescent and fluorescent/chromogenic in situ hybridization in Xenopus embryos. Nature Protocols, 4(6), 975. https://doi.org/10.1038/nprot.2009.69
MOPS Free Acid, Ultra Pure
  1. Schneider, C. R., Lewis, L. C., & Shafaat, H. S. (2019). The good, the neutral, and the positive: buffer identity impacts CO2 reduction activity by nickel(ii) cyclam. Dalton Transactions, 48(42), 15810–15821. https://doi.org/10.1039/c9dt03114f
MUG
  1. Evrard, A., Ndatimana, T., & Eulgem, T. (2009). FORCA, a promoter element that responds to crosstalk between defense and light signaling. BMC Plant Biology, 9(1), 2. https://doi.org/10.11861471-2229-9-2
  2. Stacey, M. G., Osawa, H., Patel, A., Gassmann, W., & Stacey, G. (2006). Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta, 223(2), 291-305. https://doi.org/10.1007/s00425-005-0087-x
  3. Yoo, S. D., Cho, Y. H., & Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protocols, 2(7), 1565. https://doi.org/10.1038/nprot.2007.199
  4. Cohu, C. M., Abdel-Ghany, S. E., Reynolds, K. A. G., Onofrio, A. M., Bodecker, J. R., Kimbrel, J. A., … & Pilon, M. (2009). Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant, 2(6), 1336-1350. https://doi.org/10.1093/mp/ssp084
  5. Kurepa, J., Toh‐e, A., & Smalle, J. A. (2008). 26S proteasome regulatory particle mutants have increased oxidative stress tolerance. The Plant Journal, 53(1), 102-114. https://doi.org/10.1111/j.1365-313X.2007.03322.x
  6. Hymus, G. J., Cai, S., Kohl, E. A., Holtan, H. E., Marion, C. M., Tiwari, S., … & Loida, P. (2013). Application of HB17, an Arabidopsis class II homeodomain-leucine zipper transcription factor, to regulate chloroplast number and photosynthetic capacity. Journal of experimental botany, 64(14), 4479-4490. https://doi.org/10.1093/jxb/ert261
  7. Rice, E. A., Khandelwal, A., Creelman, R. A., Griffith, C., Ahrens, J. E., Taylor, J. P., … & Back, S. L. (2014). Expression of a truncated ATHB17 protein in maize increases ear weight at silking. PLoS One, 9(4), e94238. https://doi.org/10.1371/journal.pone.0094238
  8. Parks, T., & Yordanov, Y. S. (2020). Composite plants for a composite plant: an efficient protocol for root studies in the sunflower using composite plants approach. Plant Cell, Tissue and Organ Culture (PCTOC), 140(3), 647–659. https://doi.org/10.1007/s11240-019-01760-x
n-Dodecyl-B-D-maltoside (DDM)
  1. Mukherjee, D., May, M., & Khomami, B. (2011). Detergent–protein interactions in aqueous buffer suspensions of Photosystem I (PS I). Journal of Colloid and Interface Science, 358(2), 477–484. https://doi.org/10.1016/j.jcis.2011.03.070
  2. Niroomand, H., Venkatesan, G. A., Sarles, S. A., Mukherjee, D., & Khomami, B. (2016). Lipid-detergent phase transitions during detergent-mediated liposome solubilization. The Journal of Membrane Biology, 249(4), 523-538. https://doi.org/10.1007/s00232-016-9894-1
  3. Belardinelli, J. M., Stevens, C. M., Li, W., Tan, Y. Z., Jones, V., Mancia, F., … & Jackson, M. (2019). The MmpL3 interactome reveals a complex crosstalk between cell envelope biosynthesis and cell elongation and division in mycobacteria. Scientific Reports, 9(1), 10728. https://doi.org/10.1038/s41598-019-47159-8
  4. Das, D., Bao, H., Courtney, K. C., Wu, L., & Chapman, E. R. (2020). Resolving kinetic intermediates during the regulated assembly and disassembly of fusion pores. Nature Communications, 11(1), 1-12.https://doi.org/10.1038/s41467-019-14072-7
Nalidixic acid
  1. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
Neomycin Sulfate, USP Grade
  1. Brown, K., Godovannyi, A., Ma, C., Zhang, Y., Ahmadi-Vand, Z., Dai, C., … & Dutz, J. P. (2016). Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice. The ISME Journal, 10(2), 321–332. https://doi.org/10.1038/ismej.2015.114
  2. Godeshala, S., Nitiyanandan, R., Thompson, B., Goklany, S., Nielsen, D. R., & Rege, K. (2016). Folate receptor‐targeted aminoglycoside‐derived polymers for transgene expression in cancer cells. Bioengineering & Translational Medicine, 1(2), 220-231. https://doi.org/10.1002/btm2.10038
  3. Smith, C. D. M., Gong, M., Andrew, A. K., Russ, B. N., Ge, Y., Zadeh, M., … & Moore, J. M. (2019). Composition of the gut microbiota transcends genetic determinants of malaria infection severity and influences pregnancy outcome. EBioMedicine 44, 639–655. https://doi.org/10.1016/j.ebiom.2019.05.052
  4. Mandal, R. K., Denny, J. E., Waide, M. L., Li, Q., Bhutiani, N., Anderson, C. D., … & Schmidt, N. W. (2020). Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility. BMC Biology, 18(1), 1-12. https://doi.org/10.1186/s12915-020-00810-7
Nickel Agarose Beads (High Density)
  1. Armstrong, C. M., Meyers, D. J., Imlay, L. S., Meyers, C. F., & Odom, A. R. (2015). Resistance to the antimicrobial agent fosmidomycin and an FR900098 prodrug through mutations in the deoxyxylulose phosphate reductoisomerase gene (dxr). Antimicrobial Agents and Chemotherapy, 59(9), 5511-5519.https://doi.org/10.1128/AAC.00602-15
  2. Wang, H., Jin, H., & Rapraeger, A. C. (2015). Syndecan-1 and syndecan-4 capture epidermal growth factor receptor family members and the α3β1 integrin via binding sites in their ectodomains: novel synstatins prevent kinase capture and inhibit α6β4-integrin-dependent epithelial cell motility. Journal of Biological Chemistry, 290(43), 26103-26113.https://doi.org/10.1074/jbc.m115.679084
  3. Shen, G., Gan, F., & Bryant, D. A. (2016). The siderophilic cyanobacterium Leptolyngbya sp. strain JSC-1 acclimates to iron starvation by expressing multiple isiA-family genes. Photosynthesis Research, 128(3), 325–340. https://doi.org/10.1007/s11120-016-0257-7
  4. Mullins, M. R., Rajavel, M., Hernandez-Sanchez, W., De La Fuente, M., Biendarra, S. M., Harris, M. E., & Taylor, D. J. (2016). POT1–TPP1 binding and unfolding of telomere DNA discriminates against structural polymorphism. Journal of Molecular Biology, 428(13), 2695-2708. https://doi.org/10.1016/j.jmb.2016.04.031
  5. Rajavel, M., Orban, T., Xu, M., Hernandez-Sanchez, W., de la Fuente, M., Palczewski, K., & Taylor, D. J. (2016). Dynamic peptides of human TPP1 fulfill diverse functions in telomere maintenance. Nucleic Acids Research, 44(21), 10467-10479. https://doi.org/10.1093/nar/gkw846
  6. Kato, M., Yang, Y.-S., Sutter, B. M., Wang, Y., McKnight, S. L., & Tu, B. P. (2019). Redox state controls phase separation of the yeast ataxin-2 protein via reversible oxidation of its methionine-rich low-complexity domain. Cell, 177(3), 711–721.e8. https://doi.org/10.1016/j.cell.2019.02.044
Nickel Agarose Beads (Low Density)
  1. Magaraci, M. S., Veerakumar, A., Qiao, P., Amurthur, A., Lee, J. Y., Miller, J. S., … & Sarkar, C. A. (2014). Engineering Escherichia coli for light-activated cytolysis of mammalian cells. ACS Synthetic Biology, 3(12), 944–948. https://doi.org/10.1021/sb400174s
Nickel HTC Agarose Beads
  1. Block, E., Booker, S. J., Flores‐Penalba, S., George, G. N., Gundala, S., Landgraf, B. J., … & Vattekkatte, A. (2016). Trifluoroselenomethionine: A new unnatural amino acid. ChemBioChem, 17(18), 1738-1751. https://doi.org/10.1002/cbic.201600266
  2. Smathers, C. M., & Robart, A. R. (2020). Transitions between the steps of forward and reverse splicing of group IIC introns. RNA, rna.075044.120. https://doi.org/10.1261/rna.075044.120
Nickel NTA Agarose Beads
  1. Serrano, H., & Blanchard, J. S. (2013). Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry, 52(29), 5009-5015. https://doi.org/10.1021/bi400338f
  2. Landgraf, B. J., Arcinas, A. J., Lee, K. H., & Booker, S. J. (2013). Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. Journal of the American Chemical Society, 135(41), 15404-15416. https://doi.org/10.1021/ja4048448
  3. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  4. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  5. Mahendran, V., Liu, F., Riordan, S. M., Grimm, M. C., Tanaka, M. M., & Zhang, L. (2016). Examination of the effects of Campylobacter concisus zonula occludens toxin on intestinal epithelial cells and macrophages. Gut Pathogens, 8(1), 18. https://doi.org/10.1186/s13099-016-0101-9
  6. Ganguly, A., Manahan, C. C., Top, D., Yee, E. F., Lin, C., Young, M. W., … & Crane, B. R. (2016). Changes in active site histidine hydrogen bonding trigger cryptochrome activation. Proceedings of the National Academy of Sciences, 113(36), 10073-10078. https://doi.org/10.1073/pnas.1606610113
  7. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  8. Wu, X., Paskaleva, E. E., Mehta, K. K., Dordick, J. S., & Kane, R. S. (2016). Wall teichoic acids are involved in the medium-induced loss of function of the autolysin CD11 against Clostridium difficile. Scientific Reports, 6, 35616.https://doi.org/10.1038/srep35616
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  10. Hoffman, H. K., Fernandez, M. V., Groves, N. S., Freed, E. O., & van Engelenburg, S. B. (2019). Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. Journal of Biological Chemistry, 294(44), 16266–16281. https://doi.org/10.1074/jbc.ra119.009372
  11. Dao, T. P., Martyniak, B., Canning, A. J., Lei, Y., Colicino, E. G., Cosgrove, M. S., … & Castañeda, C. A. (2019). ALS-linked mutations affect UBQLN2 oligomerization and phase separation in a position-and amino acid-dependent manner. Structure, 27(6), 937-951. https://doi.org/10.1016/j.str.2019.03.012
  12. Dao, T. P., Kolaitis, R. M., Kim, H. J., O’Donovan, K., Martyniak, B., Colicino, E., … & Castañeda, C. A. (2018). Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Molecular Cell, 69(6), 965-978. https://doi.org/10.1016/j.molcel.2018.02.004
  13. Lee, M., Ghosh, U., Thurber, K. R., Kato, M., & Tycko, R. (2020). Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-19512-3
Nitrotetrazolium blue chloride (NBT)
  1. Paredes, A. J., Naranjo-Palma, T., Alfaro-Valdés, H. M., Barriga, A., Babul, J., & Wilson, C. A. (2017). New visible and selective DNA staining method in gels with tetrazolium salts. Analytical Biochemistry, 517, 31-35. https://doi.org/10.1016/j.ab.2016.11.004
  2. Vatolin, S., Radivoyevitch, T., & Maciejewski, J. P. (2019). New drugs for pharmacological extension of replicative life span in normal and progeroid cells. NPJ Aging and Mechanisms of Disease, 5(1). https://doi.org/10.1038/s41514-018-0032-4
  3. Paredes, A. J., Alfaro-Valdés, H. M., & Wilson, C. A. M. (2018). DNA staining method based on formazan precipitation induced by blue light exposure. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56528
Nourseothricin Sulfate (Streptothricin Sulfate) (NTC or clonNAT)
  1. Shen, M. J., Wu, Y., Yang, K., Li, Y., Xu, H., Zhang, H., … & Mitchell, L. A. (2018). Heterozygous diploid and interspecies SCRaMbLEing. Nature Communications, 9(1), 1934. https://doi.org/10.1038/s41467-018-04157-0
  2. Lin, D. H., Correia, A. R., Cai, S. W., Huber, F. M., Jette, C. A., & Hoelz, A. (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nature Communications, 9(1), 2319. https://doi.org/10.1038/s41467-018-04459-3
  3. Jeong, D., Ye, S., Park, H., & Kim, S. R. (2020). Data for simultaneous fermentation of galacturonic acid and five-carbon sugars by engineered Saccharomyces cerevisiae. Data in Brief, 29, 105359. https://doi.org/10.1016/j.dib.2020.105359
  4. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  5. Rodriguez, F., John, S. F., Iniguez, E., Montalvo, S., Michael, K., White, L., … & Maldonado, R. A. (2020). In vitro and in vivo characterization of potent antileishmanial methionine aminopeptidase-1 inhibitors. Antimicrobial Agents and Chemotherapy. https://doi.org/10.1128/aac.01422-19
  6. Nambiar, M., & Smith, G. R. (2018). Pericentromere-specific cohesin complex prevents meiotic pericentric DNA double-strand breaks and lethal crossovers. Molecular Cell, 71(4), 540-553. https://doi.org/10.1016/j.molcel.2018.06.035
Octylglucoside, Ultra Pure
  1. Zhang, B., Zhu, D. W., Hu, X. J., Zhou, M., Shang, P., & Lin, S. X. (2014). Human 3-alpha hydroxysteroid dehydrogenase type 3 (3α-HSD3): the V54L mutation restricting the steroid alternative binding and enhancing the 20α-HSD activity. The Journal of Steroid Biochemistry and Molecular Biology, 141, 135-143.https://doi.org/10.1016/j.jsbmb.2014.01.003
  2. Fahie, M. A., Yang, B., Mullis, M., Holden, M. A., & Chen, M. (2015). Selective detection of protein homologues in serum using an OmpG nanopore. Analytical Chemistry, 87(21), 11143-11149. https://doi.org/10.1021/acs.analchem.5b03350
  3. Das, D., Bao, H., Courtney, K. C., Wu, L., & Chapman, E. R. (2020). Resolving kinetic intermediates during the regulated assembly and disassembly of fusion pores. Nature Communications, 11(1), 1-12.https://doi.org/10.1038/s41467-019-14072-7
Paclitaxel
  1. Xu, W., Alizadeh, E., & Prasad, A. (2018). Force spectrum microscopy using mitochondrial fluctuations of control and atp-depleted cells. Biophysical Journal, 114(12), 2933-2944. https://doi.org/10.1016/j.bpj.2018.05.002
Paromomycin Sulfate, USP Grade
  1. Godeshala, S., Nitiyanandan, R., Thompson, B., Goklany, S., Nielsen, D. R., & Rege, K. (2016). Folate receptor‐targeted aminoglycoside‐derived polymers for transgene expression in cancer cells. Bioengineering & Translational Medicine, 1(2), 220-231. https://doi.org/10.1002/btm2.10038
PBS (Phosphate Buffered Saline) Tablets
  1. Khan, S. J., Abidi, S. N. F., Tian, Y., Skinner, A., & Smith-Bolton, R. K. (2016). A rapid, gentle and scalable method for dissociation and fluorescent sorting of imaginal disc cells for mRNA sequencing. Fly, 10(2), 73–80. https://doi.org/10.1080/19336934.2016.1173296
  2. Renfrow, J. J., Soike, M. H., West, J. L., Ramkissoon, S. H., Metheny-Barlow, L., Mott, R. T., Kittel, et al. (2020). Attenuating hypoxia driven malignant behavior in glioblastoma with a novel hypoxia-inducible factor 2 alpha inhibitor. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-72290-2
Pectolyase Y-23
  1. Ruzicka, D. R., Kandasamy, M. K., McKinney, E. C., Burgos‐Rivera, B., & Meagher, R. B. (2007). The ancient subclasses of Arabidopsis Actin Depolymerizing Factor, genes exhibit novel and differential expression. The Plant Journal, 52(3), 460-472. https://doi.org/10.1111/j.1365-313X.2007.03257.x
Penicillin G Potassium Salt, USP Grade
  1. Taheri, A. E., Chatterton, S., Foroud, N. A., Gossen, B. D., & McLaren, D. L. (2017). Identification and community dynamics of fungi associated with root, crown, and foot rot of field pea in western Canada. European Journal of Plant Pathology, 147(3), 489-500. https://doi.org/10.1007/s10658-016-1017-4
Penicillin G Sodium Salt, USP Grade
  1. Taheri, A. E., Chatterton, S., Foroud, N. A., Gossen, B. D., & McLaren, D. L. (2017). Identification and community dynamics of fungi associated with root, crown, and foot rot of field pea in western Canada. European Journal of Plant Pathology, 147(3), 489-500. https://doi.org/10.1007/s10658-016-1017-4
  2. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
Pepstatin A
  1. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  2. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  3. Chaparian, R. R., Tran, M. L., Miller Conrad, L. C., Rusch, D. B., & van Kessel, J. C. (2020). Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. Nucleic Acids Research, 48(1), 171-183.
Phenylmethylsulfonyl fluoride (PMSF)
  1. Hillyer, R. L., Sirinvasin, P., Joglekar, M., Sikes, R. A., van Golen, K. L., & Nohe, A. (2012). Differential effects of vitamin D treatment on inflammatory and non-inflammatory breast cancer cell lines. Clinical & Experimental Metastasis, 29(8), 971–979. https://doi.org/10.1007/s10585-012-9486-0
  2. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  3. Zhao, P., Wang, P., Dong, S., Zhou, Z., Cao, Y., Yagita, H., … & Chen, M. (2019). Depletion of PD-1-positive cells ameliorates autoimmune disease. Nature Biomedical Engineering, 3(4), 292–305. https://doi.org/10.1038/s41551-019-0360-0
  4. Andersen, T. K., Huszthy, P. C., Gopalakrishnan, R. P., Jacobsen, J. T., Fauskanger, M., Tveita, A. A., … & Bogen, B. (2019). Enhanced germinal center reaction by targeting vaccine antigen to major histocompatibility complex class II molecules. NPJ Vaccines, 4(1), 9. https://doi.org/10.1038/s41541-019-0101-0
  5. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  6. Grzybowski, A. T., Shah, R. N., Richter, W. F., & Ruthenburg, A. J. (2019). Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nature Protocols, 14(12), 3275–3302. https://doi.org/10.1038/s41596-019-0218-7
Phosphinothricin
  1. Kurepa, J., Karangwa, C., Duke, L. S., & Smalle, J. A. (2010). Arabidopsis sensitivity to protein synthesis inhibitors depends on 26S proteasome activity. Plant Cell Reports, 29(3), 249-259. https://doi.org/10.1007/s00299-010-0818-8
  2. Burgos-Rivera, B., & Dawe, R. K. An Arabidopsis tissue-specific RNAi method for studying genes essential to mitosis. PLOS ONE 7.12 (2012): e51388. https://doi.org/10.1371/journal.pone.0051388
  3. Dalal, J. (2016). Simultaneous Analysis of Multiple Promoters: An Application of the PC-GW Binary Vector Series. In: Hehl R. (eds)Plant Synthetic Promoters Methods in Molecular Biology. vol 1482 (pp. 189–218). https://doi.org/10.1007/978-1-4939-6396-6_13
  4. Gallego-Bartolomé, J., Liu, W., Kuo, P. H., Feng, S., Ghoshal, B., Gardiner, J., … & Jacobsen, S. E. (2019). Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in arabidopsis. Cell, 176(5), 1068–1082.e19. https://doi.org/10.1016/j.cell.2019.01.029
  5. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  6. Powers, S. K., Holehouse, A. S., Korasick, D. A., Schreiber, K. H., Clark, N. M., Jing, H., … & Sozzani, R. (2019). Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana. Molecular Cell, 76(1), 177–190.e5. https://doi.org/10.1016/j.molcel.2019.06.044
  7. Michniewicz, M., Ho, C. H., Enders, T. A., Floro, E., Damodaran, S., Gunther, L. K., … & Strader, L. C. (2019). Transporter of IBA1 links auxin and cytokinin to influence root architecture. Developmental Cell, 50(5), 599-609. https://doi.org/10.1016/j.devcel.2019.06.010
  8. Gallego-Bartolome, J., Liu, W., Kuo, P. H., Feng, S., Ghoshal, B., Gardiner, J., … & Jacobsen, S. E. (2019). Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis. Cell, 176(5), 1068-1082. https://doi.org/10.1016/j.cell.2019.01.029
PNPG (Gus)
  1. Graham, R. J., Ketcham, S., Mohammad, A., Bandaranayake, B. M. B., Cao, T., Ghosh, B., … Madhavarao, C. N. (2019). Zinc supplementation improves the harvest purity of β-glucuronidase from CHO cell culture by suppressing apoptosis. Applied Microbiology and Biotechnology, 104 (3), 1097–1108. https://doi.org/10.1007/s00253-019-10296-1
Polymyxin B Sulfate
  1. Keilberg, D., Zavros, Y., Shepherd, B., Salama, N. R., & Ottemann, K. M. (2016). Spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection. MBio, 7(5), e01705-16. https://doi.org/10.1128/mBio.01705-16
Ponceau S
  1. Wang, X., He, Y., Ye, Y., Zhao, X., Deng, S., He, G., … & Liang, S. (2018). SILAC–based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. Scientific Reports, 8(1), 8441.https://doi.org/10.1038/s41598-018-26262-2
ProBlock™ Gold 2D Protease Inhibitor Cocktail (EDTA Free) [100X]
  1. Kobe, M. J., Neau, D. B., Mitchell, C. E., Bartlett, S. G., & Newcomer, M. E. (2014). The structure of human 15-lipoxygenase-2 with a substrate mimic. Journal of Biological Chemistry, 289(12), 8562-8569. https://doi.org/10.1074/jbc.M113.543777
ProBlock™ Gold Bacterial Protease Inhibitor Cocktail [100X]
  1. Beh, L. Y., Debelouchina, G. T., Clay, D. M., Thompson, R. E., Lindblad, K. A., Hutton, E. R., … & Landweber, L. F. (2019). Identification of a DNA N6-adenine methyltransferase complex and its impact on chromatin organization. Cell, 177(7), 1781-1796. https://doi.org/10.1016/j.cell.2019.04.028
  2. Huang, J. W., Acharya, A., Taglialatela, A., Nambiar, T. S., Cuella-Martin, R., Leuzzi, G., … & Soni, R. K. (2020). MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16718-3
ProBlock™ Gold Mammalian Protease Inhibitor Cocktail [100X]
  1. Santarriaga, S., Haver, H. N., Kanack, A. J., Fikejs, A. S., Sison, S. L., Egner, J. M., … & Ebert, A. D. (2018). SRCP1 conveys resistance to polyglutamine aggregation. Molecular Cell, 71(2), 216-228. https://doi.org/10.1016/j.molcel.2018.07.008
ProBlock™ Gold Protease Inhibitor Cocktail [100X]
  1. Ghaemmaghami, S., Mohaddes, S. M., Hedayati, M., Mohammadi, M. G., & Dehbashi, G. (2013). Resistin and visfatin expression in HCT-116 colorectal cancer cell line. International Journal of Molecular and Cellular Medicine, 2(3), 143.
  2. Kemmerer, Z. A., Ader, N. R., Mulroy, S. S., & Eggler, A. L. (2015). Comparison of human Nrf2 antibodies: a tale of two proteins. Toxicology Letters, 238(2), 83-89.https://doi.org/10.1016/j.toxlet.2015.07.004
  3. Choi, G. C., Zhou, P., Yuen, C. T., Chan, B. K., Xu, F., Bao, S., … & Zheng, Z. (2019). Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nature Methods, 16(8), 722-730.https://doi.org/10.1038/s41592-019-0473-0
  4. Hoffman, H. K., Fernandez, M. V., Groves, N. S., Freed, E. O., & van Engelenburg, S. B. (2019). Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. Journal of Biological Chemistry, 294(44), 16266–16281. https://doi.org/10.1074/jbc.ra119.009372
ProBlock™ Gold Yeast/Fungi Protease Inhibitor Cocktail [100X]
  1. Shattuck, J. E., Paul, K. R., Cascarina, S. M., & Ross, E. D. (2019). The prion-like protein kinase Sky1 is required for efficient stress granule disassembly. Nature Communications, 10(1), 1-11. https://doi.org/10.1038/s41467-019-11550-w
ProBlock™ Protease Inhibitor Cocktail -50, EDTA free
  1. Ravanbod, R., Torkaman, G., Mophid, M., & Mohammadali, F. (2015). Experimental study on the role of intra‐articular injection of MSCs on cartilage regeneration in haemophilia. Haemophilia, 21(5), 693-701.https://doi.org/10.1111/hae.12659
  2. Tomko, N., Kluever, M., Wu, C., Zhu, J., Wang, Y., & Salomon, R. G. (2020). 4-Hydroxy-7-oxo-5-heptenoic acid lactone is a potent inducer of brain cancer cell invasiveness that may contribute to the failure of anti-angiogenic therapies. Free Radical Biology and Medicine, 146, 234–256. https://doi.org/10.1016/j.freeradbiomed.2019.11.009
Protein A Agarose Resin (Pharmaceutical grade for research)
  1. Su, S., Blackwelder, A. J., Grossman, G., Minges, J. T., Yuan, L., Young, S. L., & Wilson, E. M. (2012). Primate-specific melanoma antigen-A11 regulates isoform-specific human progesterone receptor-B transactivation. Journal of Biological Chemistry, 287(41), 34809-34824. https://doi.org/10.1074/jbc.M112.372797
Protein G HTC Agarose Beads
  1. Buttler, C. A., Pezeshkian, N., Fernandez, M. V., Aaron, J., Norman, S., Freed, E. O., & van Engelenburg, S. B. (2018). Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation. Nature Communications, 9(1), 1861. https://doi.org/10.1038/s41467-018-04220-w
Proteinase K, RNase/DNase free
  1. Glynn, C., Sawaya, M. R., Ge, P., Gallagher-Jones, M., Short, C. W., Bowman, R., Apostol, M., Zhou, Z. H., Eisenberg, D. S., & Rodriguez, J. A. (2020). Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nature Structural & Molecular Biology. https://doi.org/10.1038/s41594-020-0403-y
Puromycin Dihydrochloride
  1. Yin, T., & Wu, Y. I. (2015). Optogenetics: optical control of a photoactivatable Rac in living cells. In: Verveer P. (eds) Methods in Molecular Biology (Methods and Protocols): Advanced Fluorescence Microscopy, vol 1251 (pp. 277-289). Humana Press https://doi.org/10.1007/978-1-4939-2080-8_15
  2. Paquin, A., Onabajo, O. O., Tang, W., & Prokunina-Olsson, L. (2016). Comparative functional analysis of 12 mammalian IFN-λ4 orthologs. Journal of Interferon & Cytokine Research, 36(1), 30-36.https://doi.org/10.1089/jir.2015.0096
  3. Leyme, A., Marivin, A., & Garcia-Marcos, M. (2016). GIV/Girdin creates a positive feedback loop that potentiates outside-in integrin signaling in cancer cells. Journal of Biological Chemistry, jbc-M115. https://doi.org/10.1074/jbc.m115.691550
  4. Huang, C. H., Hsu, C. C., Chen, C. P. C., Chow, S. E., Wang, J. S., Shyu, Y. C., & Lu, M. J. (2016). Negative pressure induces p120-catenin–dependent adherens junction disassembly in keratinocytes during wound healing. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1863(9), 2212-2220. https://doi.org/10.1016/j.bbamcr.2016.05.017
  5. An, H., & Harper, J. W. (2018). Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy. Nature Cell Biology, 20(2), 135. https://doi.org/10.1038/s41556-017-0007-x
  6. Dishon, S., Schumacher, A., Fanous, J., Talhami, A., Kassis, I., Karussis, D., … & Nussbaum, G. (2018). Development of a novel backbone cyclic peptide inhibitor of the innate immune TLR/IL1R signaling protein MyD88. Scientific Reports, 8(1), 9476. https://doi.org/10.1038/s41598-018-27773-8
  7. Kempton, H. R., Goudy, L. E., Love, K. S., & Qi, L. S. (2020). Multiple input sensing and signal integration using a split Cas12a system. Molecular Cell. https://doi.org/10.1016/j.molcel.2020.01.016
  8. El-Awaad, E., Pryymachuk, G., Fried, C., Matthes, J., Isensee, J., Hucho, T., … & Pietsch, M. (2019). Direct, gabapentin-insensitive interaction of a soluble form of the calcium channel subunit α2δ-1 with thrombospondin-4. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-52655-y
  9. An, H., Ordureau, A., Körner, M., Paulo, J. A., & Harper, J. W. (2020). Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature, 583(7815), 303–309. https://doi.org/10.1038/s41586-020-2446-y
Rapamycin
  1. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  2. Wang, A., Kolhe, J. A., Gioacchini, N., Baade, I., Brieher, W. M., Peterson, C. L., & Freeman, B. C. (2020). Mechanism of long-range chromosome motion triggered by gene activation. Developmental Cell, 52(3), 309–320.e5. https://doi.org/10.1016/j.devcel.2019.12.007
Rifampicin, Molecular Biology Grade
  1. Moyne, A. L., Harris, L. J., & Marco, M. L. (2013). Assessments of total and viable Escherichia coli O157: H7 on field and laboratory grown lettuce. PloS One, 8(7), e70643. https://doi.org/10.1371/journal.pone.0070643
  2. Sarathy, J. P., Zuccotto, F., Hsinpin, H., Sandberg, L., Via, L. E., Marriner, G. A., … & Dartois, V. (2016). Prediction of drug penetration in tuberculosis lesions. ACS Infectious Diseases, 2(8), 552-563. https://doi.org/10.1021/acsinfecdis.6b00051
  3. Raju, R., Chau, D., Cho, D. S., Park, Y., Verfaillie, C. M., & Hu, W. S. (2017). Cell expansion during directed differentiation of stem cells toward the hepatic lineage. Stem Cells and Development, 26(4), 274-284. https://doi.org/10.1089/scd.2016.0119
  4. Pal, A., Tripathi, K., Pathak, C., & Vernon, B. L. (2019). Plasma-based fast-gelling biohybrid gels for biomedical applications. Scientific Reports, 9(1), 10881. https://doi.org/10.1038/s41598-019-47366-3
  5. Liu, Z., Sivasankar, P., & Sharma, H. (2019). An improved bioassay to study arabidopsis induced systemic resistance (ISR) against bacterial pathogens and insect pests. Bio-protocol 9 (10): e3236. https://doi.org/10.21769/BioProtoc.3236
  6. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  7. Moyne, A., Blessington, T., Williams, T. R., Koike, S. T., Cahn, M. D., Marco, M. L., & Harris, L. J. (2020). Conditions at the time of inoculation influence survival of attenuated Escherichia coli O157:H7 on field-inoculated lettuce. Food Microbiology, 85, 103274. https://doi.org/10.1016/j.fm.2019.103274
  8. Moroz, N., & Tanaka, K. (2020). FlgII-28 is a major flagellin-derived defense elicitor in potato. Molecular Plant-Microbe Interactions, 33(2), 247–255. https://doi.org/10.1094/mpmi-06-19-0164-r
SHH, Murine
  1. Finch, E. R., Kudva, A. K., Quickel, M. D., Goodfield, L. L., Kennett, M. J., Whelan, J., … & Prabhu, K. S. (2015). Chemopreventive effects of dietary eicosapentaenoic acid supplementation in experimental myeloid leukemia. Cancer Prevention Research, 8(10), 989-999.https://doi.org/10.1158/1940-6207.CAPR-15-0050
Simple Stop™ 1 Phosphatase Inhibitor Cocktail
  1. Evelyn, C. R., Biesiada, J., Duan, X., Tang, H., Shang, X., Papoian, R., … & Zheng, Y. (2015). Combined rational design and a high throughput screening platform for identifying chemical inhibitors of a Ras-activating enzyme. Journal of Biological Chemistry, 290(20), 12879-12898. https://doi.org/10.1074/jbc.M114.634493
  2. Mann, B. J., Balchand, S. K., & Wadsworth, P. (2017). Regulation of Kif15 localization and motility by the C-terminus of TPX2 and microtubule dynamics. Molecular Biology of the Cell, 28(1), 65-75. https://doi.org/10.1091/mbc.e16-06-0476
  3. Cai, X., Zheng, Y., & Speck, N. A. (2018). A western blotting protocol for small numbers of hematopoietic stem cells. JoVE (Journal of Visualized Experiments), (138), e56855. https://doi.org/10.3791/56855
  4. Cabello-Arreola, A., Ho, A. M. C., Ozerdem, A., Cuellar-Barboza, A. B., Kucuker, M. U., Heppelmann, C. J., … & Frye, M. A. (2020). Differential dorsolateral prefrontal cortex proteomic profiles of suicide victims with mood disorders. Genes, 11(3), 256. https://doi.org/10.3390/genes11030256
Simple Stop™ 2 Phosphatase Inhibitor Cocktail
  1. Li, S., Lavagnino, Z., Lemacon, D., Kong, L., Ustione, A., Ng, X., … & Vindigni, A. (2019). Ca2+-stimulated AMPK-dependent phosphorylation of exo1 protects stressed replication forks from aberrant resection. Molecular Cell, 74(6), 1123-1137. https://doi.org/10.1016/j.molcel.2019.04.003
Simple Stop™ 3 Phosphatase Inhibitor Cocktail
  1. Cabello-Arreola, A., Ho, A. M. C., Ozerdem, A., Cuellar-Barboza, A. B., Kucuker, M. U., Heppelmann, C. J., … & Frye, M. A. (2020). Differential dorsolateral prefrontal cortex proteomic profiles of suicide victims with mood disorders. Genes, 11(3), 256. https://doi.org/10.3390/genes11030256
Sodium 3-hydroxybutyrate
  1. Jensen, N. J., Nilsson, M., Ingerslev, J. S., Olsen, D. A., Fenger, M., Svart, M., … & Rungby, J. (2020). Effects of β-hydroxybutyrate on cognition in patients with type 2 diabetes. European Journal of Endocrinology, 182(2), 233-242. https://doi.org/10.1530/EJE-19-0710
  2. Lauritzen, E. S., Svart, M. V., Voss, T., Møller, N., & Bjerre, M. (2020). Impact of acutely increased endogenous-and exogenous ketone bodies on FGF21 Levels in humans. Endocrine Research, 1-8. https://doi.org/10.1080/07435800.2020.1831015
Spectinomycin Dihydrochloride Pentahydrate 100 mg/mL Solution
  1. Reifschneider-Wegner, K., Kanygin, A., & Redding, K. E. (2014). Expression of the [FeFe] hydrogenase in the chloroplast of Chlamydomonas reinhardtii. International Journal of Hydrogen Energy, 39(8), 3657–3665. https://doi.org/10.1016/j.ijhydene.2013.12.157
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
Spectinomycin Dihydrochloride Pentahydrate EZ Pak™ for 100 mg/mL Solution
  1. Reifschneider-Wegner, K., Kanygin, A., & Redding, K. E. (2014). Expression of the [FeFe] hydrogenase in the chloroplast of Chlamydomonas reinhardtii. International Journal of Hydrogen Energy, 39(8), 3657–3665. https://doi.org/10.1016/j.ijhydene.2013.12.157
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
Spectinomycin Dihydrochloride Pentahydrate, USP Grade
  1. Reifschneider-Wegner, K., Kanygin, A., & Redding, K. E. (2014). Expression of the [FeFe] hydrogenase in the chloroplast of Chlamydomonas reinhardtii. International Journal of Hydrogen Energy, 39(8), 3657–3665. https://doi.org/10.1016/j.ijhydene.2013.12.157
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  3. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  4. González, L. M., Mukhitov, N., & Voigt, C. A. (2019). Resilient living materials built by printing bacterial spores. Nature Chemical Biology, 16(2), 126–133. https://doi.org/10.1038/s41589-019-0412-5
  5. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  6. Song, M., Sukovich, D. J., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, E. A., Tucker, A. C., Gordon, D. B., Marlovits, T. C., & Voigt, C. A. (2017). Control of type III protein secretion using a minimal genetic system. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14737
  7. Pontrelli, S., Fricke, R. C., Teoh, S. T., Laviña, W. A., Putri, S. P., Fitz-Gibbon, S., … & Liao, J. C. (2018). Metabolic repair through emergence of new pathways in Escherichia coli. Nature Chemical Biology, 14(11), 1005-1009. https://doi.org/10.1038/s41589-018-0149-6
Streptavidin Agarose Resin
  1. Liu, L., & Dong, X. (2014). Complex impacts of PI3K/AKT inhibitors to androgen receptor gene expression in prostate cancer cells. PloS One, 9(10), e108780. https://doi.org/10.1371/journal.pone.0108780
  2. Shen, W., Deng, X., Zou, W., Engelhardt, J. F., Yan, Z., & Qiu, J. (2016). Analysis of cis and trans requirements for DNA replication at the right-end hairpin of the human bocavirus 1 genome. Journal of Virology, 90(17), 7761-7777.https://doi.org/10.1128/JVI.00708-16
Streptomycin Sulfate
  1. Van der Heijden, J., Reynolds, L. A., Deng, W., Mills, A., Scholz, R., Imami, K., … & Finlay, B. B. (2016). Salmonella rapidly regulates membrane permeability to survive oxidative stress. mBio, 7(4), e01238-16. https://doi.org/10.1128/mBio.01238-16
  2. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  3. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  4. Riglar, D. T., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., … & Silver, P. A. (2016). Long-term monitoring of inflammation in the mammalian gut using programmable commensal bacteria. BioRxiv, 075051. https://doi.org/10.1101/075051
  5. Hsu, B. B., Way, J. C., & Silver, P. A. (2020). Stable neutralization of a virulence factor in bacteria using temperate phage in the mammalian gut. mSystems, 5(1). https://doi.org/10.1128/msystems.00013-20
  6. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  7. Nguyen, B. N., & Portnoy, D. A. (2020). An inducible cre-lox system to analyze the role of LLO in Listeria monocytogenes pathogenesis. Toxins, 12(1), 38. https://doi.org/10.3390/toxins12010038
  8. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  9. Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., … & Silver, P. A. (2017). Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nature Biotechnology, 35(7), 653-658. https://doi.org/10.1038/nbt.3879
  10. Hsu, B. B., Plant, I. N., Lyon, L., Anastassacos, F. M., Way, J. C., & Silver, P. A. (2020). In situ reprogramming of gut bacteria by oral delivery. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18614-2
Streptomycin Sulfate 100 mg/mL Solution
  1. Van der Heijden, J., Reynolds, L. A., Deng, W., Mills, A., Scholz, R., Imami, K., … & Finlay, B. B. (2016). Salmonella rapidly regulates membrane permeability to survive oxidative stress. mBio, 7(4), e01238-16. https://doi.org/10.1128/mBio.01238-16
  2. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
Streptomycin Sulfate EZ Pak™ for 100 mg/mL Solution
  1. Van der Heijden, J., Reynolds, L. A., Deng, W., Mills, A., Scholz, R., Imami, K., … & Finlay, B. B. (2016). Salmonella rapidly regulates membrane permeability to survive oxidative stress. mBio, 7(4), e01238-16. https://doi.org/10.1128/mBio.01238-16
  2. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
TCEP HCl
  1. Reyes-Caballero, H., Guerra, A. J., Jacobsen, F. E., Kazmierczak, K. M., Cowart, D., Koppolu, U. M. K., … & Giedroc, D. P. (2010). The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor. Journal of Molecular Biology, 403(2), 197-216.https://doi.org/10.1016/j.jmb.2010.08.030
  2. Hernick M. (2011) Fluorescence-based methods to assay inhibitors of lipopolysaccharide synthesis. In: Holst O. (eds) Microbial Toxins. Methods in Molecular Biology (Methods and Protocols), vol 739 (pp. 123–133). https://doi.org/10.1007/978-1-61779-102-4_11
  3. Hai, Y., Dugery, R. J., Healy, D., & Christianson, D. W. (2013). Formiminoglutamase from Trypanosoma cruzi is an arginase-like manganese metalloenzyme. Biochemistry, 52(51), 9294-9309. https://doi.org/10.1021/bi401352h
  4. Hai, Y., Kerkhoven, E. J., Barrett, M. P., & Christianson, D. W. (2014). Crystal structure of an arginase-like protein from Trypanosoma brucei that evolved without a binuclear manganese cluster. Biochemistry, 54(2), 458-471.https://doi.org/10.1021/bi501366a
  5. Walkup, W. G., Washburn, L., Sweredoski, M. J., Carlisle, H. J., Graham, R. L., Hess, S., & Kennedy, M. B. (2015). Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases. Journal of Biological Chemistry, 290(8), 4908-4927. https://doi.org/10.1074/jbc.M114.614420
  6. Kitanishi, K., Cracan, V., & Banerjee, R. (2015). Engineered and native coenzyme B12-dependent isovaleryl-CoA/pivalyl-CoA mutase. Journal of Biological Chemistry, 290(33), 20466-20476.https://doi.org/ 10.1074/jbc.M115.646299
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  9. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  10. Kim, Y. B., Zhao, K. T., Thompson, D. B., & Liu, D. R. (2019). An anionic human protein mediates cationic liposome delivery of genome editing proteins into mammalian cells. Nature Communications, 10(1), 2905. https://doi.org/10.1038/s41467-019-10828-3
  11. Bessen, J. L., Afeyan, L. K., Dančík, V., Koblan, L. W., Thompson, D. B., Leichner, C., … & Liu, D. R. (2019). High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases. Nature Communications, 10(1), 1937.https://doi.org/10.1038/s41467-019-09987-0
  12. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  13. Mattiroli, F., Gu, Y., & Luger, K. (2018). Measuring nucleosome assembly activity in vitro with the nucleosome assembly and quantification (NAQ) assay. Bio-protocol, 8(3). https://doi.org/10.21769/bioprotoc.2714
  14. Pisa, R., Cupido, T., Steinman, J. B., Jones, N. H., & Kapoor, T. M. (2019). Analyzing resistance to design selective chemical inhibitors for AAA proteins. Cell Chemical Biology.https://doi.org/10.1016/j.chembiol.2019.06.001
  15. Radford, D. C., Yang, J., Doan, M. C., Li, L., Dixon, A. S., Owen, S. C., & Kopeček, J. (2020). Multivalent HER2-binding polymer conjugates facilitate rapid endocytosis and enhance intracellular drug delivery. Journal of Controlled Release, 319, 285–299. https://doi.org/10.1016/j.jconrel.2019.12.049
  16. Fu, B., Brown, C., & Mäler, L. (2020). Expression and purification of DGD2, a chloroplast outer membrane-associated glycosyltransferase for galactolipid synthesis. Biochemistry, 59(8), 999–1009. https://doi.org/10.1021/acs.biochem.0c00028
  17. Kang, H., Yang, H. S., Ki, A. Y., Ko, S. B., Kim, K. W., Shim, C. Y., … & Chung, K. Y. (2020). Conformational Dynamics and Functional Implications of Phosphorylated β-Arrestins. Structure.https://doi.org/10.1016/j.str.2019.12.008
  18. Rodgers, J. T., & Jones, J. P. (2019). Numerical analysis of time-dependent inhibition by MDMA. Drug Metabolism and Disposition, 48(1), 1–7. https://doi.org/10.1124/dmd.119.089268
  19. Surewicz, W., & Babinchak, W. (2020). Studying protein aggregation in the context of liquid-liquid phase separation using fluorescence and atomic force microscopy, fluorescence and turbidity assays, and FRAP. Bio-Protocol, 10(2). https://doi.org/10.21769/bioprotoc.3489
  20. Sloutsky, R., Dziedzic, N., Dunn, M. J., Bates, R., Torres-Ocampo, A. P., Boopathy, S., … & Stratton, M. M. (2019). Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation. Cold Spring Harbor Laboratory. https://doi.org/10.1101/721589
  21. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  22. Dutka, P., Mukherjee, S., Gao, X., Kang, Y., de Waal, P. W., Wang, L., … & Kossiakoff, A. A. (2019). Development of “plug and play” fiducial marks for structural studies of GPCR signaling complexes by single-particle Cryo-EM. Structure, 27(12), 1862–1874.e7. https://doi.org/10.1016/j.str.2019.10.004
  23. Lin King, J. V., Emrick, J. J., Kelly, M. J. S., Herzig, V., King, G. F., Medzihradszky, K. F., & Julius, D. (2019). A cell-penetrating scorpion toxin enables mode-specific modulation of TRPA1 and pain. Cell, 178(6), 1362–1374.e16. https://doi.org/10.1016/j.cell.2019.07.014″
  24. Park, J. Y., Qu, C. X., Li, R. R., Yang, F., Yu, X., Tian, Z. M., … & Chung, K. Y. (2019). Structural mechanism of the arrestin-3/JNK3 interaction. Structure, 27(7), 1162–1170.e3. https://doi.org/10.1016/j.str.2019.04.002
  25. Maji, B., Gangopadhyay, S. A., Lee, M., Shi, M., Wu, P., Heler, R., … & Dančík, V. (2019). A high-throughput platform to identify small-molecule inhibitors of CRISPR-Cas9. Cell, 177(4), 1067-1079. https://doi.org/10.1016/j.cell.2019.04.009
  26. Verardi, R., Kim, J. S., Ghirlando, R., & Banerjee, A. (2017). Structural basis for substrate recognition by the ankyrin repeat domain of human DHHC17 palmitoyltransferase. Structure, 25(9), 1337-1347. https://doi.org/10.1016/j.str.2017.06.018
  27. Chojnacki, M., Mansour, W., Hameed, D. S., Singh, R. K., El Oualid, F., Rosenzweig, R., … & Fushman, D. (2017). Polyubiquitin-photoactivatable crosslinking reagents for mapping ubiquitin interactome identify Rpn1 as a proteasome ubiquitin-associating subunit. Cell Chemical Biology, 24(4), 443-457. https://doi.org/10.1016/j.chembiol.2017.02.013
  28. An, H., Ordureau, A., Körner, M., Paulo, J. A., & Harper, J. W. (2020). Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature, 583(7815), 303–309. https://doi.org/10.1038/s41586-020-2446-y
Tetracycline Hydrochloride
  1. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  2. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  3. Butterwick, J. A., del Mármol, J., Kim, K. H., Kahlson, M. A., Rogow, J. A., Walz, T., & Ruta, V. (2018). Cryo-EM structure of the insect olfactory receptor Orco. Nature, 560(7719), 447.https://doi.org/10.1038/s41586-018-0420-8
  4. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
  5. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  6. Nguyen, B. N., & Portnoy, D. A. (2020). An inducible cre-lox system to analyze the role of LLO in Listeria monocytogenes pathogenesis. Toxins, 12(1), 38. https://doi.org/10.3390/toxins12010038
  7. Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020). Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0468-5
  8. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
Thiazolyl Blue Tetrazolium Bromide (MTT)
  1. Song, L., Huang, Z., Chen, Y., Li, H., Jiang, C., & Li, X. (2014). High-efficiency production of bioactive recombinant human fibroblast growth factor 18 in Escherichia coli and its effects on hair follicle growth. Applied Microbiology and Biotechnology, 98(2), 695-704. https://doi.org/10.1007/s00253-013-4929-3
  2. Yi, S., Yang, J., Huang, J., Guan, L., Du, L., Guo, Y., … & Li, H. (2015). Expression of bioactive recombinant human fibroblast growth factor 9 in oil bodies of Arabidopsis thaliana. Protein Expression and Purification, 116, 127-132. https://doi.org/10.1016/j.pep.2015.08.006
  3. Huang, J., Yang, J., Guan, L., Yi, S., Du, L., Tian, H., … & Li, X. (2017). Expression of bioactive recombinant human fibroblast growth factor 10 in Carthamus tinctorius L. seeds. Protein Expression and Purification, 138, 7-12.https://doi.org/10.1016/j.pep.2015.09.016
  4. Lee, S. I., Jeong, Y. J., Yu, A. R., Kwak, H. J., Cha, J. Y., Kang, I., & Yeo, E. J. (2019). Carfilzomib enhances cisplatin-induced apoptosis in SK-N-BE (2)-M17 human neuroblastoma cells. Scientific Reports, 9(1), 5039. https://doi.org/10.1038/s41598-019-41527-0
  5. Guven, M. N., Demirci, G., Altuncu, S., Gulyuz, U., Okay, O., Acar, H. Y., & Avci, D. (2020). Alendronate-functionalized poly (amido amine) cryogels of high-toughness for biomedical applications. Polymer, 190, 122248. https://doi.org/10.1016/j.polymer.2020.122248
  6. Chen, C.-H., Hsieh, Y.-C., Yang, P.-M., Liu, Y.-R., & Cho, E.-C. (2020). Dicoumarol suppresses HMGA2-mediated oncogenic capacities and inhibits cell proliferation by inducing apoptosis in colon cancer. Biochemical and Biophysical Research Communications, 524(4), 1003–1009. https://doi.org/10.1016/j.bbrc.2020.01.147
  7. Lo, P.-Y., Lee, G.-Y., Zheng, J.-H., Huang, J.-H., Cho, E.-C., & Lee, K.-C. (2020). Intercalating pyrene with polypeptide as a novel self-assembly nano-carrier for colon cancer suppression in vitro and in vivo. Materials Science and Engineering: C, 109, 110593. https://doi.org/10.1016/j.msec.2019.110593
Timentin™ Ticarcillin/Clavulanate (15/1)
  1. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
  2. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  3. Naim, F., Shand, K., Hayashi, S., O’Brien, M., McGree, J., Johnson, A. A. T., Dugdale, B., & Waterhouse, P. M. (2020). Are the current gRNA ranking prediction algorithms useful for genome editing in plants? PLOS ONE, 15(1), e0227994. https://doi.org/10.1371/journal.pone.0227994
Timentin™ Ticarcillin/Clavulanate (15/1) 100 mg/mL Solution
  1. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
Timentin™ Ticarcillin/Clavulanate (15/1)EZ Pak™ for 100 mg/mL Solution
  1. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
Tissue Cell Lysis Buffer
  1. Tomasz, S., Dominika, S., Iwona, K. S., Jodok, F., Bronisława, S. P., Marcin, K., … & Marek, M. (2015). Long-term Effect of Ileal Transposition on Adipokine Serum Level in Zucker (Orl)-Lepr fa Fatty Rats. Obesity Surgery, 25(10), 1848-1857. https://doi.org/10.1007/s11695-015-1618-6
  2. Tomko, N., Kluever, M., Wu, C., Zhu, J., Wang, Y., & Salomon, R. G. (2020). 4-Hydroxy-7-oxo-5-heptenoic acid lactone is a potent inducer of brain cancer cell invasiveness that may contribute to the failure of anti-angiogenic therapies. Free Radical Biology and Medicine, 146, 234–256. https://doi.org/10.1016/j.freeradbiomed.2019.11.009
TNF-α, Human
  1. Anusree, S. S., Nisha, V. M., Priyanka, A., & Raghu, K. G. (2015). Insulin resistance by TNF-α is associated with mitochondrial dysfunction in 3T3-L1 adipocytes and is ameliorated by punicic acid, a PPARγ agonist. Molecular and Cellular Endocrinology, 413, 120-128. https://doi.org/10.1016/j.mce.2015.06.018
  2. Yeo, K. S., Tan, M. C., Wong, W. Y., Loh, S. W., Lam, Y. L., Tan, C. L., … & Ea, C. K. (2016). JMJD8 is a positive regulator of TNF-induced NF-κB signaling. Scientific Reports, 6, 34125. https://doi.org/10.1038/srep34125
trans-Zeatin
  1. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
trans-Zeatin-riboside
  1. Marutani-Hert, M., Bowman, K. D., McCollum, G. T., Mirkov, T. E., Evens, T. J., & Niedz, R. P. (2012). A dark incubation period is important for agrobacterium-mediated transformation of mature internode explants of sweet orange, grapefruit, citron, and a citrange rootstock. PLOS ONE, 7(10), e47426. https://doi.org/
    10.1371/journal.pone.0047426
Tris (Tris Base)
  1. Moinpour, M., Barker, N. K., Guzman, L. E., Jewett, J. C., Langlais, P. R., & Schwartz, J. C. (2020). Discriminating changes to protein structure using PTAD conjugation to tyrosine. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.02.04.934406
  2. Picarda, E., Bézie, S., Usero, L., Ossart, J., Besnard, M., Halim, H., … & Gras, S. (2019). Cross-reactive donor-specific CD8+ tregs efficiently prevent transplant rejection. Cell Reports, 29(13), 4245-4255. https://doi.org/10.1016/j.celrep.2019.11.106
Tris HCl
  1. Desai, M., Di, R., & Fan, H. (2019). Application of Biolayer Interferometry (BLI) for Studying Protein-Protein Interactions in Transcription. Journal of visualized experiments: JoVE, (149). e59687 https://doi.org/10.3791/59687
Validamycin A
  1. Boudreau, B. A., Larson, T. M., Brown, D. W., Busman, M., Roberts, E. S., Kendra, D. F., & McQuade, K. L. (2013). Impact of temperature stress and validamycin A on compatible solutes and fumonisin production in F. verticillioides: role of trehalose-6-phosphate synthase. Fungal Genetics and Biology, 57, 1-10.https://doi.org/10.1016/j.fgb.2013.06.001
Vancomycin Hydrochloride EZ Pak™ for 100 mg/mL Solution
  1. Thangamani, S., Younis, W., & Seleem, M. N. (2015). Repurposing ebselen for treatment of multidrug-resistant staphylococcal infections. Scientific Reports, 5, 11596. https://doi.org/10.1038/srep11596
  2. Thangamani, S., Nepal, M., Chmielewski, J., & Seleem, M. N. (2015). Antibacterial activity and therapeutic efficacy of Fl-PRPRPL-5, a cationic amphiphilic polyproline helix, in a mouse model of staphylococcal skin infection. Drug Design, Development and Therapy, 9, 5749.https://doi.org/10.2147/DDDT.S94505
  3. Thangamani, S., Mohammad, H., Abushahba, M. F., Sobreira, T. J., Hedrick, V. E., Paul, L. N., & Seleem, M. N. (2016). Antibacterial activity and mechanism of action of auranofin against multi-drug resistant bacterial pathogens. Scientific Reports, 6, 22571. https://doi.org/10.1038/srep22571
  4. Abushahba, M. F., Mohammad, H., & Seleem, M. N. (2016). Targeting multidrug-resistant staphylococci with an anti-rpoA peptide nucleic acid conjugated to the HIV-1 TAT cell penetrating peptide. Molecular Therapy-Nucleic Acids, 5, e339. https://doi.org/10.1038/mtna.2016.53
  5. Keilberg, D., Zavros, Y., Shepherd, B., Salama, N. R., & Ottemann, K. M. (2016). Spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection. MBio, 7(5), e01705-16. https://doi.org/10.1128/mBio.01705-16
Vancomycin Hydrochloride, USP Grade
  1. Olson, K. M., Starks, C. M., Williams, R. B., O’Neil-Johnson, M., Huang, Z., Ellis, M., … & Eldridge, G. R. (2011). Novel pentadecenyl tetrazole enhances susceptibility of methicillin-resistant Staphylococcus aureus biofilms to gentamicin. Antimicrobial Agents and Chemotherapy, 55(8), 3691-3695.https://doi.org/10.1128/AAC.00302-11
  2. Sande, L., Sanchez, M., Montes, J., Wolf, A. J., Morgan, M. A., Omri, A., & Liu, G. Y. (2012). Liposomal encapsulation of vancomycin improves killing of methicillin-resistant Staphylococcus aureus in a murine infection model. Journal of Antimicrobial Chemotherapy, 67(9), 2191-2194. https://doi.org/10.1093/jac/dks212
  3. Thangamani, S., Younis, W., & Seleem, M. N. (2015). Repurposing ebselen for treatment of multidrug-resistant staphylococcal infections. Scientific Reports, 5, 11596. https://doi.org/10.1038/srep11596
  4. Thangamani, S., Nepal, M., Chmielewski, J., & Seleem, M. N. (2015). Antibacterial activity and therapeutic efficacy of Fl-PRPRPL-5, a cationic amphiphilic polyproline helix, in a mouse model of staphylococcal skin infection. Drug Design, Development and Therapy, 9, 5749.https://doi.org/10.2147/DDDT.S94505
  5. Thangamani, S., Mohammad, H., Abushahba, M. F., Sobreira, T. J., Hedrick, V. E., Paul, L. N., & Seleem, M. N. (2016). Antibacterial activity and mechanism of action of auranofin against multi-drug resistant bacterial pathogens. Scientific Reports, 6, 22571. https://doi.org/10.1038/srep22571
  6. Abushahba, M. F., Mohammad, H., & Seleem, M. N. (2016). Targeting multidrug-resistant staphylococci with an anti-rpoA peptide nucleic acid conjugated to the HIV-1 TAT cell penetrating peptide. Molecular Therapy-Nucleic Acids, 5, e339. https://doi.org/10.1038/mtna.2016.53
  7. Keilberg, D., Zavros, Y., Shepherd, B., Salama, N. R., & Ottemann, K. M. (2016). Spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection. MBio, 7(5), e01705-16. https://doi.org/10.1128/mBio.01705-16
  8. AbdelKhalek, A., Abutaleb, N. S., Elmagarmid, K. A., & Seleem, M. N. (2018). Repurposing auranofin as an intestinal decolonizing agent for vancomycin-resistant enterococci. Scientific Reports, 8(1), 8353. https://doi.org/10.1038/s41598-018-26674-0
  9. Smith, C. D. M., Gong, M., Andrew, A. K., Russ, B. N., Ge, Y., Zadeh, M., … & Moore, J. M. (2019). Composition of the gut microbiota transcends genetic determinants of malaria infection severity and influences pregnancy outcome. EBioMedicine 44, 639–655. https://doi.org/10.1016/j.ebiom.2019.05.052
  10. Touré, A. M., Landry, M., Souchkova, O., Kembel, S. W., & Pilon, N. (2019). Gut microbiota-mediated gene-environment interaction in the TashT mouse model of Hirschsprung disease. Scientific Reports, 9(1), 492. https://doi.org/10.1038/s41598-018-36967-z
  11. Buchta Rosean, C., Bostic, R. R., Ferey, J. C. M., Feng, T.-Y., Azar, F. N., Tung, K. S., Dozmorov, M. G., Smirnova, E., Bos, P. D., & Rutkowski, M. R. (2019). Preexisting commensal dysbiosis is a host-intrinsic regulator of tissue inflammation and tumor cell dissemination in hormone receptor–positive breast cancer. Cancer Research, 79(14), 3662–3675. https://doi.org/10.1158/0008-5472.can-18-3464
  12. Karau, M. J., Zhang, C., Mandrekar, J. N., Kohrs, N. J., Puleo, D. A., van Wijnen, A. J., Patel, R., Boyce, T. G., Larson, A. N., & Milbrandt, T. A. (2020). Topical vancomycin for treatment of methicillin-resistant Staphylococcus epidermidis infection in a rat spinal implant model. Spine Deformity. https://doi.org/10.1007/s43390-020-00087-4
  13. Pal, R., & Seleem, M. N. (2020). Screening of natural products and approved oncology drug libraries for activity against Clostridioides difficile. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-63029-0
  14. AbdelKhalek, A., Mohammad, H., Mayhoub, A. S., & Seleem, M. N. (2020). Screening for potent and selective anticlostridial leads among FDA-approved drugs. The Journal of Antibiotics. https://doi.org/10.1038/s41429-020-0288-3
  15. Jin, C., Lagoudas, G. K., Zhao, C., Bullman, S., Bhutkar, A., Hu, B., … & Whary, M. T. (2019). Commensal microbiota promote lung cancer development via γδ T cells. Cell, 176(5), 998-1013. https://doi.org/10.1016/j.cell.2018.12.040
  16. Kamimura, Y., & Lanier, L. L. (2015). Homeostatic control of memory cell progenitors in the natural killer cell lineage. Cell Reports, 10(2), 280-291. https://doi.org/10.1016/j.celrep.2014.12.025
VEGF164, Murine
  1. Graaf, M. D., Marquez, B. V., Yeh, N. H., Lapi, S. E., & Moeller, K. D. (2016). New methods for the site-selective placement of peptides on a microelectrode array: probing VEGF–v107 binding as proof of concept. ACS Chemical Biology, 11(10), 2829-2837. https://doi.org/10.1021/acschembio.6b00685
VEGF165, Human
  1. Graaf, M. D., Marquez, B. V., Yeh, N. H., Lapi, S. E., & Moeller, K. D. (2016). New methods for the site-selective placement of peptides on a microelectrode array: probing VEGF–v107 binding as proof of concept. ACS Chemical Biology, 11(10), 2829-2837. https://doi.org/10.1021/acschembio.6b00685
VersaLadder™, 100-10,000 bp
  1. O’Halloran, D. M., Uriagereka-Herburger, I., & Bode, K. (2017). STITCHER 2.0: primer design for overlapping PCR applications. Scientific Reports, 7(1). https://doi.org/10.1038/srep45349
X-Gal
  1. Cromie, M. J., & Groisman, E. A. (2009). Promoter and riboswitch control of the Mg2+ transporter MgtA from Salmonella enterica. Journal of Bacteriology, 192(2), 604–607. https://doi.org/10.1128/jb.01239-09
  2. Day, K., Shefer, G., Shearer, A., & Yablonka-Reuveni, Z. (2010). The depletion of skeletal muscle satellite cells with age is concomitant with reduced capacity of single progenitors to produce reserve progeny. Developmental Biology, 340(2), 330-343. https://doi.org/10.1016/j.ydbio.2010.01.006
  3. Phalke, S., Nickel, O., Walluscheck, D., Hortig, F., Onorati, M. C., & Reuter, G. (2009). Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nature Genetics, 41(6), 696–702. https://doi.org/10.1038/ng.360
  4. Ourmanov, I., Kuwata, T., Goeken, R., Goldstein, S., Iyengar, R., Buckler-White, A., … Hirsch, V. M. (2009). Improved survival in rhesus macaques immunized with modified vaccinia virus Ankara recombinants expressing simian immunodeficiency virus envelope correlates with reduction in memory CD4+ T-cell loss and higher titers of neutralizing antibody. Journal of Virology, 83(11), 5388–5400. https://doi.org/10.1128/jvi.02598-08
  5. Kreutzer, D. A., & Essigmann, J. M. (1998). Oxidized, deaminated cytosines are a source of C→ T transitions in vivo . Proceedings of the National Academy of Sciences, 95(7), 3578-3582. https://doi.org/10.1073/pnas.95.7.3578
  6. Fuqua, C., Burbea, M., & Winans, S. C. (1995). Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. Journal of Bacteriology, 177(5), 1367-1373. https://doi.org/10.1128/jb.177.5.1367-1373.1995
  7. Trimboli, A. J., Fukino, K., de Bruin, A., Wei, G., Shen, L., Tanner, S. M., … & Ostrowski, M. C. (2008). Direct evidence for epithelial-mesenchymal transitions in breast cancer. Cancer Research, 68(3), 937-945. https://doi.org/10.1158/0008-5472.CAN-07-2148
  8. Schmidt, M., Katano, H., Bossis, I., & Chiorini, J. A. (2004). Cloning and characterization of a bovine adeno-associated virus. Journal of Virology, 78(12), 6509-6516. https://doi.org/10.1128/jvi.78.12.6509-6516.2004
  9. Bosch, A., Mccray, P. B., Chang, S. M., Ulich, T. R., Simonet, W. S., Jolly, D. J., & Davidson, B. L. (1996). Proliferation induced by keratinocyte growth factor enhances in vivo retroviral-mediated gene transfer to mouse hepatocytes. The Journal of Clinical Investigation, 98(12), 2683-2687. https://doi.org/10.1172/JCI119091
  10. Fink, S. P., Reddy, G. R., & Marnett, L. J. (1997). Mutagenicity in Escherichia coli of the major DNA adduct derived from the endogenous mutagen malondialdehyde. Proceedings of the National Academy of Sciences, 94(16), 8652–8657. https://doi.org/10.1073/pnas.94.16.8652
  11. Karunakaran, T., Madden, T., & Kuramitsu, H. (1997). Isolation and characterization of a hemin-regulated gene, hemR , from Porphyromonas gingivalis . Journal of Bacteriology, 179(6), 1898–1908. https://doi.org/10.1128/jb.179.6.1898-1908.1997
  12. Bosch, A., McCray, P. B., Jr., Walters, K. S., Bodner, M., Jolly, D. J., van Es, H. H. G., … & Davidson, B. L. (1998). Effects of keratinocyte and hepatocyte growth factor in vivo: implications for retrovirus-mediated gene transfer to liver. Human Gene Therapy, 9(12), 1747–1754. https://doi.org/10.1089/hum.1998.9.12-1747
  13. Parikh, M. R., Greene, D. N., Woods, K. K., & Matsumura, I. (2006). Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E. coli. Protein Engineering Design and Selection, 19(3), 113-119. https://doi.org/10.1093/protein/gzj010
  14. Dollé, M. E., Martus, H. J., Novak, M., Van Orsouw, N. J., & Vijg, J. (1999) Characterization of color mutants in lacZ plasmid-based transgenic mice, as detected by positive selection, Mutagenesis, 14(3), 287–293. https://doi.org/10.1093/mutage/14.3.287
  15. Wang, G., Slepushkin, V. A., Bodner, M., Zabner, J., Van Es, H. H., Thomas, P., … & McCray Jr, P. B. (1999). Keratinocyte growth factor induced epithelial proliferation facilitates retroviral–mediated gene transfer to distal lung epithelia in vivo . The Journal of Gene Medicine, 1(1), 22-30.
  16. VanderVeen, L. A., Hashim, M. F., Nechev, L. V., Harris, T. M., Harris, C. M., & Marnett, L. J. (2001). Evaluation of the mutagenic potential of the principal DNA adduct of acrolein. Journal of Biological Chemistry, 276(12), 9066-9070. https://doi.org/10.1074/jbc.m008900200
  17. Mantis, N. J., & Winans, S. C. (1993). The chromosomal response regulatory gene chvI of Agrobacterium tumefaciens complements an Escherichia coli phoB mutation and is required for virulence. Journal of Bacteriology, 175(20), 6626–6636. https://doi.org/10.1128/jb.175.20.6626-6636.1993
  18. Wang, Y.-H., Chen, C.-P., Chan, M.-H., Chang, M., Hou, Y.-W., Chen, H.-H., … Lee, H.-J. (2006). Arginine-rich intracellular delivery peptides noncovalently transport protein into living cells. Biochemical and Biophysical Research Communications, 346(3), 758–767. https://doi.org/10.1016/j.bbrc.2006.05.205
  19. Peterson, J. J., Rayburn, H. B., Lager, D. J., Raife, T. J., Kealey, G. P., Rosenberg, R. D., & Lentz, S. R. (1999). Expression of thrombomodulin and consequences of thrombomodulin deficiency during healing of cutaneous wounds. The American Journal of Pathology, 155(5), 1569-1575. https://doi.org/10.1016/S0002-9440(10)65473-9
  20. Guo, X., Hutcheon, A. E., & Zieske, J. D. (2004). Transduction of functionally active TAT fusion proteins into cornea. Experimental Eye Research, 78(5), 997–1005. https://doi.org/10.1016/j.exer.2003.12.010
  21. Kloser, A. W., Laird, M. W., & Misra, R. (1996). asmB, a suppressor locus for assembly-defective OmpF mutants of Escherichia coli, is allelic to envA (lpxC). Journal of Bacteriology, 178(17), 5138-5143. https://doi.org/10.1128/jb.178.17.5138-5143.1996
  22. Easter, C. L., Sobecky, P. A., & Helinski, D. R. (1997). Contribution of different segments of the par region to stable maintenance of the broad-host-range plasmid RK2. Journal of Bacteriology, 179(20), 6472–6479. https://doi.org/10.1128/jb.179.20.6472-6479.1997
  23. Low, H. P., Gréco, B., Tanahashi, Y., Gallant, J., Jones, S. N., Billings-Gagliardi, S., … & Schwartz, W. J. (2009). Embryonic stem cell rescue of tremor and ataxia in myelin-deficient shiverer mice. Journal of the Neurological Sciences, 276(1–2), 133–137. https://doi.org/10.1016/j.jns.2008.09.037
  24. Jasnow, A. M., Rainnie, D. G., Maguschak, K. A., Chhatwal, J. P., & Ressler, K. J. (2009). Construction of cell-type specific promoter lentiviruses for optically guiding electrophysiological recordings and for targeted gene delivery. In Viral Applications of Green Fluorescent Protein (pp. 199-213). Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-559-6_13
  25. Keil, D. J., Burns, E. H., Jr., Kisker, W. R., Bemis, D., & Fenwick, B. (1999). Cloning and immunologic characterization of a truncated Bordetella bronchiseptica filamentous hemagglutinin fusion protein. Vaccine, 18(9–10), 860–867. https://doi.org/10.1016/s0264-410x(99)00322-9
  26. O’Sullivan, D. J., Hill, C., & Klaenhammer, T. R. (1993). Effect of increasing the copy number of bacteriophage origins of replication, in trans, on incoming-phage proliferation. Applied and Environmental Microbiology, 59(8), 2449-2456.
  27. Gaur, T., Rich, L., Lengner, C. J., Hussain, S., Trevant, B., Ayers, D., … Lian, J. B. (2006). Secreted frizzled related protein 1 regulates Wnt signaling for BMP2 induced chondrocyte differentiation. Journal of Cellular Physiology, 208(1), 87-96.https://doi.org/10.1002/jcp.20637
  28. Callahan, S. M., Ming, X., Lu, S. K., Brunner, L. J., & Croyle, M. A. (2005). Considerations for use of recombinant adenoviral vectors: dose effect on hepatic cytochromes P450. Journal of Pharmacology and Experimental Therapeutics, 312(2), 492-501. https://doi.org/10.1124/jpet.104.075374
  29. Neeley, W. L., Delaney, J. C., Henderson, P. T., & Essigmann, J. M. (2004). In vivo bypass efficiencies and mutational signatures of the guanine oxidation products 2-aminoimidazolone and 5-guanidino-4-nitroimidazole. Journal of Biological Chemistry, 279(42), 43568-43573. https://doi.org/10.1074/jbc.M407117200
  30. Johnson, K. A., Fink, S. P., & Marnett, L. J. (1997). Repair of propanodeoxyguanosine by nucleotide excision repair in vivo and in vitro. Journal of Biological Chemistry, 272(17), 11434-11438. https://doi.org/10.1074/jbc.272.17.11434
  31. Kasus-Jacobi, A., Ou, J., Birch, D. G., Locke, K. G., Shelton, J. M., Richardson, J. A., … & Edwards, A. O. (2005). Functional characterization of mouse RDH11 as a retinol dehydrogenase involved in dark adaptation in Vivo. Journal of Biological Chemistry, 280(21), 20413-20420. https://doi.org/10.1074/jbc.m413789200
  32. Chang, M., Chou, J.-C., Chen, C.-P., Liu, B. R., & Lee, H.-J. (2007). Noncovalent protein transduction in plant cells by macropinocytosis. New Phytologist, 174(1), 46–56. https://doi.org/10.1111/j.1469-8137.2007.01977.x
  33. Henderson, P. T., Delaney, J. C., Gu, F., Tannenbaum, S. R., & Essigmann, J. M. (2002). Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in Vivo. Biochemistry, 41(3), 914–921. https://doi.org/10.1021/bi0156355
  34. Sadler, T. J., Glare, T. R., Ward, V. K., & Kalmakoff, J. (2000). Physical and genetic map of the Wiseana nucleopolyhedrovirus genome. Journal of General Virology, 81(4), 1127-1133. https://doi.org/10.1099/0022-1317-81-4-1127
  35. Mark, M. D., Liu, Y., Wong, S. T., Hinds, T. R., & Storm, D. R. (1995). Stimulation of neurite outgrowth in PC12 cells by EGF and KCl depolarization: a Ca (2+)-independent phenomenon. The Journal of Cell Biology, 130(3), 701-710. https://doi.org/10.1083/jcb.130.3.701
  36. VanderVeen, L. A., Hashim, M. F., Shyr, Y., & Marnett, L. J. (2003). Induction of frameshift and base pair substitution mutations by the major DNA adduct of the endogenous carcinogen malondialdehyde. Proceedings of the National Academy of Sciences, 100(24), 14247-14252. https://doi.org/10.1073/pnas.2332176100
  37. Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G., & Norris, J. S. (2002). Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. Journal of Virology, 76(11), 5557–5564. https://doi.org/10.1128/jvi.76.11.5557-5564.2002
  38. Katano, H., Kok, M. R., Cotrim, A. P., Yamano, S., Schmidt, M., Afione, S., … Chiorini, J. A. (2006). Enhanced transduction of mouse salivary glands with AAV5-based vectors. Gene Therapy, 13(7), 594. https://doi.org/10.1038/sj.gt.3302691
  39. Smith, A., Collaco, R., & Trempe, J. P. (2004). AAV vector delivery to cells in culture. In Gene delivery to mammalian cells (pp. 167–178). Humana Press. https://doi.org/10.1385/1-59259-650-9:167
  40. Zawistowski, J. S., Serebriiskii, I. G., Lee, M. F., Golemis, E. A., & Marchuk, D. A. (2002). KRIT1 association with the integrin-binding protein ICAP-1: a new direction in the elucidation of cerebral cavernous malformations (CCM1) pathogenesis. Human Molecular Genetics, 11(4), 389–396. https://doi.org/10.1093/hmg/11.4.389
  41. Jain, P. T., & Gewirtz, D. A. (1998). Estradiol enhances gene delivery to human breast tumor cells. Journal of Molecular Medicine, 76(10), 709–714. https://doi.org/10.1007/s001090050271
  42. Kasman, L., London, L., London, S., & Pilgrim, M. (2009). A mouse model linking viral hepatitis and salivary gland dysfunction. Oral Diseases, 15(8), 587–595. https://doi.org/10.1111/j.1601-0825.2009.01600.x
  43. Noya, F., Chien, W.-M., Wu, X., Banerjee, N. S., Kappes, J. C., Broker, T. R., & Chow, L. T. (2002). The promoter of the human proliferating cell nuclear antigen gene is not sufficient for cell cycle-dependent regulation in organotypic cultures of keratinocytes. Journal of Biological Chemistry, 277(19), 17271–17280. https://doi.org/10.1074/jbc.m112441200
  44. Lei, Y., Huang, S., Sharif-Kashani, P., Chen, Y., Kavehpour, P., & Segura, T. (2010). Incorporation of active DNA/cationic polymer polyplexes into hydrogel scaffolds. Biomaterials, 31(34), 9106-9116. https://doi.org/10.1016/j.biomaterials.2010.08.016
  45. Nou, X., Braaten, B., Kaltenbach, L., & Low, D. A. (1995). Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli. The EMBO Journal, 14(23), 5785–5797. https://doi.org/10.1002/j.1460-2075.1995.tb00267.x
  46. Howard, B. D., Kalthoff, H., & Fong, T. C. (1999). Ablation of tumor cells in vivo by direct injection of HSV‐thymidine kinase retroviral vector and ganciclovir therapy. Annals of the New York Academy of Sciences, 880(1), 352-365. https://doi.org/10.1111/j.1749-6632.1999.tb09538.x
  47. Bailey, E. A., Iyer, R. S., Stone, M. P., Harris, T. M., & Essigmann, J. M. (1996). Mutational properties of the primary aflatoxin B1-DNA adduct. Proceedings of the National Academy of Sciences, 93(4), 1535–1539. https://doi.org/10.1073/pnas.93.4.1535
  48. Niedernhofer, L. J., Daniels, J. S., Rouzer, C. A., Greene, R. E., & Marnett, L. J. (2003). Malondialdehyde, a product of lipid peroxidation, is mutagenic in human cells. Journal of Biological Chemistry, 278(33), 31426–31433. https://doi.org/10.1074/jbc.m212549200
  49. Boerrigter, M. E. (2004). Mutagenicity of the peroxisome proliferators clofibrate, Wyeth 14,643 and di-2-ethylhexyl phthalate in the lacZ plasmid-based transgenic mouse mutation assay. Journal of Carcinogenesis, 3(1), 7. https://doi.org/10.1186/1477-3163-3-7
  50. Kuroda, H., Kutner, R. H., Bazan, N. G., & Reiser, J. (2009). Simplified lentivirus vector production in protein-free media using polyethylenimine-mediated transfection. Journal of Virological Methods, 157(2), 113-121. https://doi.org/10.1016/j.jviromet.2008.11.021
  51. Newmark, K. G., O’Reilly, E. K., Pohlhaus, J. R., & Kreuzer, K. N. (2005). Genetic analysis of the requirements for SOS induction by nalidixic acid in Escherichia coli. Gene, 356, 69-76. https://doi.org/10.1016/j.gene.2005.04.029
  52. Li, Z., Wang, X., Chen, F., & Kim, H. J. (2007). Chemical changes and overexpressed genes in sweet basil (Ocimum basilicum L.) upon methyl jasmonate treatment. Journal of Agricultural and Food Chemistry, 55(3), 706-713.https://doi.org/10.1021/jf062481x
  53. Di, X., Gennings, C., Bear, H. D., Graham, L. J., Sheth, C. M., White, K. L., & Gewirtz, D. A. (2010). Influence of the phosphodiesterase-5 inhibitor, sildenafil, on sensitivity to chemotherapy in breast tumor cells. Breast Cancer Research and Treatment, 124(2), 349–360. https://doi.org/10.1007/s10549-010-0765-7
  54. Mitome, M., Low, H. P., van den Pol, A., Nunnari, J. J., Wolf, M. K., Billings-Gagliardi, S., & Schwartz, W. J. (2001). Towards the reconstruction of central nervous system white matter using neural precursor cells. Brain, 124(11), 2147–2161. https://doi.org/10.1093/brain/124.11.2147
  55. DeMasters, G., Di, X., Newsham, I., Shiu, R., & Gewirtz, D. A. (2006). Potentiation of radiation sensitivity in breast tumor cells by the vitamin D3 analogue, EB 1089, through promotion of autophagy and interference with proliferative recovery. Molecular Cancer Therapeutics, 5(11), 2786-2797. https://doi.org/10.1158/1535-7163.MCT-06-0316
  56. López, C. M., Rholl, D. A., Trunck, L. A., & Schweizer, H. P. (2009). Versatile dual-technology system for markerless allele replacement in Burkholderia pseudomallei. Applied and Environmental Microbiology, 75(20), 6496–6503. https://doi.org/10.1128/aem.01669-09
  57. Di, X., Shiu, R. P., Newsham, I. F., & Gewirtz, D. A. (2009). Apoptosis, autophagy, accelerated senescence and reactive oxygen in the response of human breast tumor cells to Adriamycin. Biochemical Pharmacology, 77(7), 1139–1150. https://doi.org/10.1016/j.bcp.2008.12.016
  58. Lei, P., & Andreadis, S. T. (2005). Stoichiometric limitations in assembly of active recombinant retrovirus. Biotechnology and Bioengineering, 90(7), 781–792. https://doi.org/10.1002/bit.20468
    https://doi.org/10.1002/bit.20468
  59. Zhang, L., Wang, H., Liu, D., Liddington, R., & Fu, H. (1997). Raf-1 kinase and exoenzyme S interact with 14-3-3ζ through a common site involving lysine 49. Journal of Biological Chemistry, 272(21), 13717–13724. https://doi.org/10.1074/jbc.272.21.13717
  60. Fuqua, W. C., & Winans, S. C. (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. Journal of Bacteriology, 176(10), 2796-2806. https://doi.org/10.1128/jb.176.10.2796-2806.1994
  61. O’Reilly, E. K., & Kreuzer, K. N. (2004). Isolation of SOS constitutive mutants of Escherichia coli. Journal of Bacteriology, 186(21), 7149–7160. https://doi.org/10.1128/jb.186.21.7149-7160.2004
  62. Wang, H., Zhang, L., Liddington, R., & Fu, H. (1998). Mutations in the hydrophobic surface of an amphipathic groove of 14-3-3ζ disrupt its interaction with Raf-1 kinase. Journal of Biological Chemistry, 273(26), 16297-16304. https://doi.org/10.1074/jbc.273.26.16297
  63. Harvie, P. D., Filippova, M., & Bryant, P. J. (1998). Genes expressed in the ring gland, the major endocrine organ of Drosophila melanogaster. Genetics, 149(1), 217-231. http://www.genetics.org/content/genetics/149/1/217.full.pdf
  64. Johnson, K. A., Mierzwa, M. L., Fink, S. P., & Marnett, L. J. (1999). MutS recognition of exocyclic DNA adducts that are endogenous products of lipid oxidation. Journal of Biological Chemistry, 274(38), 27112–27118. https://doi.org/10.1074/jbc.274.38.27112
  65. Lu, B. Y., Ma, J., & Eissenberg, J. C. (1998). Developmental regulation of heterochromatin-mediated gene silencing in Drosophila. Development, 125(12), 2223-2234.
  66. Garcia, A. M., Busuttil, R. A., Rodriguez, A., Cabrera, C., Lundell, M., Dollé, M. E., & Vijg, J. (2007). Detection and analysis of somatic mutations at a lacZ reporter locus in higher organisms. In: Tollefsbol T.O. (eds) Biological Aging. Methods in Molecular Biology™, vol 371. (pp. 267-287). Humana Press. https://doi.org/10.1007/978-1-59745-361-5_20
  67. Kuroda, H., Kutner, R. H., Bazan, N. G., & Reiser, J. (2008). A comparative analysis of constitutive and cell‐specific promoters in the adult mouse hippocampus using lentivirus vector‐mediated gene transfer. The Journal of Gene Medicine, 10(11), 1163-1175. https://doi.org/10.1002/jgm.1249
  68. Eliason, S. L., Stein, C. S., Mao, Q., Tecedor, L., Ding, S. L., Gaines, D. M., & Davidson, B. L. (2007). A knock-in reporter model of Batten disease. Journal of Neuroscience, 27(37), 9826-9834. https://doi.org/10.1523/JNEUROSCI.1710-07.2007
  69. Cao, S., Siriwardana, C. L., Kumimoto, R. W., & Holt, B. F. (2011). Construction of high quality Gateway™ entry libraries and their application to yeast two-hybrid for the monocot model plant Brachypodium distachyon. BMC Biotechnology, 11(1), 53. https://doi.org/10.1186/1472-6750-11-53
  70. Lei, Y., Rahim, M., Ng, Q., & Segura, T. (2011). Hyaluronic acid and fibrin hydrogels with concentrated DNA/PEI polyplexes for local gene delivery. Journal of Controlled Release, 153(3), 255-261.https://doi.org/10.1016/j.jconrel.2011.01.028
  71. Lough, J., Jackson, M., Morris, R., & Moyer, R. (2001). Bisulfite-induced cytosine deamination rates in E. coli SSB: DNA complexes. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 478(1-2), 191-197. https://doi.org/10.1016/s0027-5107(01)00149-x
  72. Voutetakis, A., Zheng, C., Mineshiba, F., Cotrim, A. P., Goldsmith, C. M., Schmidt, M., … & Chiorini, J. A. (2007). Adeno-associated virus serotype 2-mediated gene transfer to the parotid glands of nonhuman primates. Human Gene Therapy, 18(2), 142-150. https://doi.org/10.1089/hum.2006.154
  73. Smela, M. E., Hamm, M. L., Henderson, P. T., Harris, C. M., Harris, T. M., & Essigmann, J. M. (2002). The aflatoxin B1 formamidopyrimidine adduct plays a major role in causing the types of mutations observed in human hepatocellular carcinoma. Proceedings of the National Academy of Sciences, 99(10), 6655–6660. https://doi.org/10.1073/pnas.102167699
  74. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  75. Kanisicak, O., Mendez, J. J., Yamamoto, S., Yamamoto, M., & Goldhamer, D. J. (2009). Progenitors of skeletal muscle satellite cells express the muscle determination gene, MyoD. Developmental Biology, 332(1), 131-141. https://doi.org/10.1016/j.ydbio.2009.05.554
  76. Suttipanta, N., Pattanaik, S., Gunjan, S., Xie, C. H., Littleton, J., & Yuan, L. (2007). Promoter analysis of the Catharanthus roseus geraniol 10-hydroxylase gene involved in terpenoid indole alkaloid biosynthesis. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression, 1769(2), 139-148. https://doi.org/10.1016/j.bbaexp.2007.01.006
  77. Demelash, A., Pfannenstiel, L. W., Tannenbaum, C. S., Li, X., Kalady, M. F., DeVecchio, J., & Gastman, B. R. (2015). Structure-function analysis of the Mcl-1 protein identifies a novel senescence-regulating domain. Journal of Biological Chemistry, 290(36), 21962-21975.https://doi.org/10.1074/jbc.M115.663898
  78. Ingram, N. T., Khankan, R. R., & Phelps, P. E. (2016). Olfactory ensheathing cells express α7 integrin to mediate their migration on laminin. PloS One, 11(4), e0153394. https://doi.org/10.1371/journal.pone.0153394
  79. Sidiq, F., Hoostal, M., & Rogers, S. O. (2016). Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses. BMC Research Notes, 9(1), 293. https://doi.org/10.1186/s13104-016-2097-0
  80. Mucka, P., Levonyak, N., Geretti, E., Zwaans, B. M., Li, X., Adini, I., … & Bielenberg, D. R. (2016). Inflammation and lymphedema are exacerbated and prolonged by neuropilin 2 deficiency. The American Journal of Pathology, 186(11), 2803-2812. https://doi.org/10.1016/j.ajpath.2016.07.022
  81. McBride, T. J., Schneider, J. E., Floyd, R. A., & Loeb, L. A. (1992). Mutations induced by methylene blue plus light in single-stranded M13mp2. Proceedings of the National Academy of Sciences, 89(15), 6866–6870. https://doi.org/10.1073/pnas.89.15.6866
  82. Harrell, R. L., Rajanayagam, M. S., Doanes, A. M., Guzman, R. J., Hirschowitz, E. A., Crystal, R. G., … & Finkel, T. (1997). Inhibition of vascular smooth muscle cell proliferation and neointimal accumulation by adenovirus-mediated gene transfer of cytosine deaminase. Circulation, 96(2), 621-627. https://doi.org/10.1161/01.CIR.96.2.621
  83. Owens, T. W., Taylor, R. J., Pahil, K. S., Bertani, B. R., Ruiz, N., Kruse, A. C., & Kahne, D. (2019). Structural basis of unidirectional export of lipopolysaccharide to the cell surface. Nature, 567(7749), 550. https://doi.org/10.1038/s41586-019-1039-0
  84. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  85. Chirakul, S., Norris, M. H., Pagdepanichkit, S., Somprasong, N., Randall, L. B., Shirley, J. F., … & Schweizer, H. P. (2018). Transcriptional and post-transcriptional regulation of PenA β-lactamase in acquired Burkholderia pseudomallei β-lactam resistance. Scientific Reports, 8(1) https://doi.org/10.1038/s41598-018-28843-7
  86. Wang, Q. A., Song, A., Chen, W., Schwalie, P. C., Zhang, F., Vishvanath, L., … & Gupta, R. K. (2018). Reversible de-differentiation of mature white adipocytes into preadipocyte-like precursors during lactation. Cell Metabolism, 28(2), 282-288. https://doi.org/10.1016/j.cmet.2018.05.022
  87. Briscoe, S. D., Albertin, C. B., Rowell, J. J., & Ragsdale, C. W. (2018). Neocortical association cell types in the forebrain of birds and alligators. Current Biology, 28(5), 686-696. https://doi.org/10.1016/j.cub.2018.01.036
X-gluc (CHX salt)
  1. Tan, X., Meyers, B. C., Kozik, A., West, M. A., Morgante, M., St Clair, D. A., … Michelmore, R. W. (2007). Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biology, 7(1), 56. https://doi.org/10.1186/1471-2229-7-56
  2. DeMason, D. A., & Polowick, P. L. (2009). Patterns of DR5::GUS expression in organs of pea (Pisum sativum). International Journal of Plant Sciences, 170(1), 1–11. https://doi.org/10.1086/593046
  3. Ourmanov, I., Kuwata, T., Goeken, R., Goldstein, S., Iyengar, R., Buckler-White, A., … Hirsch, V. M. (2009). Improved survival in rhesus macaques immunized with modified vaccinia virus Ankara recombinants expressing simian immunodeficiency virus envelope correlates with reduction in memory CD4+ T-cell loss and higher titers of neutralizing antibody. Journal of Virology, 83(11), 5388–5400. https://doi.org/10.1128/jvi.02598-08
  4. Yuan, S., & Dean, J. F. D. (2010). Differential responses of the promoters from nearly identical paralogs of loblolly pine (Pinus taeda L.) ACC oxidase to biotic and abiotic stresses in transgenic Arabidopsis thaliana. Planta, 232(4), 873–886. https://doi.org/10.1007/s00425-010-1224-8
  5. Fuqua, C., Burbea, M., & Winans, S. C. (1995). Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. Journal of Bacteriology, 177(5), 1367-1373. https://doi.org/10.1128/jb.177.5.1367-1373.1995
  6. López, C. M., Rholl, D. A., Trunck, L. A., & Schweizer, H. P. (2009). Versatile dual-technology system for markerless allele replacement in Burkholderia pseudomallei. Applied and Environmental Microbiology, 75(20), 6496–6503. https://doi.org/10.1128/aem.01669-09
  7. Fuqua, W. C., & Winans, S. C. (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. Journal of Bacteriology, 176(10), 2796-2806. https://doi.org/10.1128/jb.176.10.2796-2806.1994
  8. Marchant, R., Power, J. B., Lucas, J. A., & Davey, M. R. (1998). Biolistic transformation of rose (Rosa hybrida L.). Annals of Botany, 81(1), 109-114. https://doi.org/10.1006/anbo.1997.0538
  9. Cho, M. J., Choi, H. W., Buchanan, B. B., & Lemaux, P. G. (1999). Inheritance of tissue-specific expression of barley hordein promoter-uidA fusions in transgenic barley plants. Theoretical and Applied Genetics, 98(8), 1253–1262. https://doi.org/10.1007/s001220051191
  10. Matsumura, I., Wallingford, J. B., Surana, N. K., Vize, P. D., & Ellington, A. D. (1999). Directed evolution of the surface chemistry of the reporter enzyme β-glucuronidase. Nature Biotechnology, 17(7), 696. https://doi.org/10.1038/10910
  11. Cho, M.J., Jiang, W., & Lemaux, P. G. (1999). High-frequency transformation of oat via microprojectile bombardment of seed-derived highly regenerative cultures. Plant Science, 148(1), 9–17. https://doi.org/10.1016/s0168-9452(99)00082-5
  12. Ingram, H. M., Power, J. B., Lowe, K. C., & Davey, M. R. (1999). Optimisation of procedures for microprojectile bombardment of microspore-derived embryos in wheat. Plant Cell, Tissue and Organ Culture, 57(3), 207–210. https://doi.org/10.1023/a:1006384525513
  13. Sripaoraya, S., Marchant, R., Power, J. B., & Davey, M. R. (2001). Herbicide-tolerant transgenic pineapple (Ananas comosus) produced by microprojectile bombardment. Annals of Botany, 88(4), 597–603. https://doi.org/10.1006/anbo.2001.1502
  14. Bartel, B., & Fink, G. R. (1994). Differential regulation of an auxin-producing nitrilase gene family in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 91(14), 6649-6653. https://doi.org/10.1073/pnas.91.14.6649
  15. Micallef, M. C., Austin, S., & Bingham, E. T. (1995). Improvement of transgenic alfalfa by backcrossing. In Vitro Cellular & Developmental Biology-Plant, 31(4), 187-192. https://doi.org/10.1007/BF02632019
  16. Yang, Z., Rogers, L. M., Song, Y., Guo, W., & Kolattukudy, P. E. (2005). Homoserine and asparagine are host signals that trigger in planta expression of a pathogenesis gene in Nectria haematococca. Proceedings of the National Academy of Sciences, 102(11), 4197-4202. https://doi.org/10.1073/pnas.0500312102
  17. Southgate, E. M., Davey, M. R., Power, J. B., & Westcott, R. J. (1998). A comparison of methods for direct gene transfer into maize (Zea mays L.). In Vitro Cellular & Developmental Biology – Plant, 34(3), 218–224. https://doi.org/10.1007/bf02822711
  18. Ketchum, R. E., Wherland, L., & Croteau, R. B. (2007). Stable transformation and long-term maintenance of transgenic Taxus cell suspension cultures. Plant Cell Reports, 26(7), 1025-1033. https://doi.org/10.1007/s00299-007-0323-x
  19. Coque, L., Neogi, P., Pislariu, C., Wilson, K. A., Catalano, C., Avadhani, M., … & Dickstein, R. (2008). Transcription of ENOD8 in Medicago truncatula nodules directs ENOD8 esterase to developing and mature symbiosomes. Molecular Plant-Microbe Interactions, 21(4), 404-410. https://doi.org/10.1094/MPMI-21-4-0404
  20. Basu, C., Luo, H., Kausch, A. P., & Chandlee, J. M. (2003). Transient reporter gene (GUS) expression in creeping bentgrass (Agrostis palustris) is affected by in vivo nucleolytic activity. Biotechnology Letters, 25(12), 939-944. https://doi.org/10.1023/A:1024050720199
    https://doi.org/10.1023/A:1024050720199
  21. Kim, H., & Woloshuk, C. P. (2008). Role of AREA, a regulator of nitrogen metabolism, during colonization of maize kernels and fumonisin biosynthesis in Fusarium verticillioides. Fungal Genetics and Biology, 45(6), 947–953. https://doi.org/10.1016/j.fgb.2008.03.007
  22. Li, S., De-gang, Z., Yong-jun, W., & Yi, L. (2008). Transient expression of chicken alpha interferon gene in lettuce. Journal of Zhejiang University Science B, 9(5), 351–355. https://doi.org/10.1631/jzus.b0710596
  23. Vahling, C. M., & McIver, K. S. (2006). Domains required for transcriptional activation show conservation in the MGA family of virulence gene regulators. Journal of Bacteriology, 188(3), 863-873. https://doi.org/10.1128/jb.188.3.863-873.2006
  24. Krizek, B. A., Prost, V., Joshi, R. M., Stoming, T., & Glenn, T. C. (2003). Developing transgenic arabidopsis plants to be metal-specific bioindicators. Environmental Toxicology and Chemistry, 22(1), 175–181. https://doi.org/10.1002/etc.5620220123
  25. Geddie, M. L., & Matsumura, I. (2007). Antibody-induced oligomerization and activation of an engineered reporter enzyme. Journal of Molecular Biology, 369(4), 1052-1059. https://doi.org/10.1016/j.jmb.2007.03.076
  26. Annis, S. L., Velasquez, L., Xu, H., Hammerschmidt, R., Linz, J., & Trail, F. (2000). Novel procedure for identification of compounds inhibitory to transcription of genes involved in mycotoxin biosynthesis. Journal of Agricultural and Food Chemistry, 48(10), 4656–4660. https://doi.org/10.1021/jf0005115
  27. Ward, D. E., Van Der Weijden, C. C., Van Der Merwe, M. J., Westerhoff, H. V., Claiborne, A., & Snoep, J. L. (2000). Branched-chain alpha -keto acid catabolism via the gene products of the bkd Operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink. Journal of Bacteriology, 182(11), 3239–3246. https://doi.org/10.1128/jb.182.11.3239-3246.2000
  28. Tovkach, A., Zeevi, V., & Tzfira, T. (2010). Validation and expression of zinc finger nucleases in plant cells. In Engineered Zinc Finger Proteins (pp. 315-336). Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-753-2_20
  29. Ha, C. D., Lemaux, P. G., & Cho, M.-J. (2001). Stable transformation of a recalcitrant kentucky bluegrass (Poa pratensis L.) cultivar using mature seed-derived highly regenerative tissues. In Vitro Cellular & Developmental Biology – Plant, 37(1), 6–11. https://doi.org/10.1007/s11627-001-0002-5
  30. O’Loughlin, T. L., & Matsumura, I. (2006). HIV protease-activated molecular switches based on beta-glucuronidase and alkaline phosphatase. Combinatorial Chemistry & High Throughput Screening, 9(4), 313-320. https://doi.org/10.2174/138620706776843219
  31. Kale S.D., Tyler B.M. (2011) Assaying Effector Function in Planta Using Double-Barreled Particle Bombardment. In: McDowell J. (eds) Plant Immunity. Methods in Molecular Biology, vol 712. (pp. 153-172) https://doi.org/10.1007/978-1-61737-998-7_13
  32. Bosacchi, M. (2008). Selective plant growth using D-amino acids (Doctoral dissertation, Rutgers University-Graduate School-New Brunswick). Retrieved from: https://doi.org/10.7282/t3p84c8q
  33. Kim, K.-W., Franceschi, V. R., Davin, L. B., & Lewis, N. G. (2006). β-Glucuronidase as Reporter Gene: Advantages and Limitations. In Arabidopsis Protocols (pp. 263–274). Humana Press. New York City. https://doi.org/10.1385/1-59745-003-0:263
  34. Stacey, M. G., Osawa, H., Patel, A., Gassmann, W., & Stacey, G. (2006). Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta, 223(2), 291-305. https://doi.org/10.1007/s00425-005-0087-x
  35. Curtis, I.S., Power, J. B., Hedden, P., Phillips, A., Lowe, K. C., Ward, D. A., & Davey, M. R. (2000). Transformation and characterization of transgenic plants of Solanum dulcamara L.—incidence of transgene silencing. Annals of Botany, 86(1), 63–71. https://doi.org/10.1006/anbo.2000.1159
  36. Liu, Z., & Kearney, C. M. (2010). A tobamovirus expression vector for agroinfection of legumes and Nicotiana. Journal of Biotechnology, 147(3–4), 151–159. https://doi.org/10.1016/j.jbiotec.2010.03.021
  37. Foster, J., Lee, Y. H., & Tegeder, M. (2008). Distinct expression of members of the LHT amino acid transporter family in flowers indicates specific roles in plant reproduction. Sexual Plant Reproduction, 21(2), 143-152. https://doi.org/10.1007/s00497-008-0074-z
  38. Kim, Y.-H., Bae, J. M., & Huh, G.-H. (2010). Transcriptional regulation of the cinnamyl alcohol dehydrogenase gene from sweetpotato in response to plant developmental stage and environmental stress. Plant Cell Reports, 29(7), 779–791. https://doi.org/10.1007/s00299-010-0864-2
  39. Bondino, H. G., & Valle, E. M. (2009). A small intergenic region drives exclusive tissue-specific expression of the adjacent genes in Arabidopsis thaliana. BMC Molecular Biology, 10(1), 95. https://doi.org/10.1186/1471-2199-10-95
  40. Becnel, J., Natarajan, M., Kipp, A., & Braam, J. (2006). Developmental expression patterns of arabidopsis XTH genes reported by transgenes and genevestigator. Plant Molecular Biology, 61(3), 451-467. https://doi.org/10.1007/s11103-006-0021-z
  41. Wang, X. (2008). Functions of the Tobacco mosaic virus helicase domain: regulating formation of the virus replication complex and altering the activity of a host-encoded transcription factor (Doctoral dissertation, University of Maryland). Retrieved from: http://hdl.handle.net/1903/8124
  42. Sieburth, L. E., & Meyerowitz, E. M. (1997). Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. The Plant Cell, 9(3), 355-365. https://doi.org/10.1105/tpc.9.3.355
  43. Mason, M. G., Li, J., Mathews, D. E., Kieber, J. J., & Schaller, G. E. (2004). Type-B response regulators display overlapping expression patterns in Arabidopsis. Plant Physiology, 135(2), 927-937. https://doi.org/10.1104/pp.103.038109
  44. Scarpeci, T. E., Zanor, M. I., Carrillo, N., Mueller-Roeber, B., & Valle, E. M. (2008). Generation of superoxide anion in chloroplasts of Arabidopsis thaliana during active photosynthesis: a focus on rapidly induced genes. Plant Molecular Biology, 66(4), 361-378. https://doi.org/10.1007/s11103-007-9274-4
  45. Mima, T., & Schweizer, H. P. (2010). The BpeAB-OprB efflux pump of Burkholderia pseudomallei 1026b does not play a role in quorum sensing, virulence factor production, or extrusion of aminoglycosides but is a broad-spectrum drug efflux system. Antimicrobial Agents and Chemotherapy, 54(8), 3113-3120. https://doi.org/10.1128/AAC.01803-09
  46. Cohu, C. M., Abdel-Ghany, S. E., Reynolds, K. A. G., Onofrio, A. M., Bodecker, J. R., Kimbrel, J. A., … & Pilon, M. (2009). Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant, 2(6), 1336-1350. https://doi.org/10.1093/mp/ssp084
  47. Zhu, W., Zhang, D., Lu, X., Zhang, L., Yu, Z., Lv, H., & Zhang, H. (2014). Characterisation of an SKn-type dehydrin promoter from wheat and its responsiveness to various abiotic and biotic stresses. Plant Molecular Biology Reporter, 32(3), 664-678. https://doi.org/10.1007/s11105-013-0681-1
  48. Klauser, D., Desurmont, G. A., Glauser, G., Vallat, A., Flury, P., Boller, T., … & Bartels, S. (2015). The Arabidopsis Pep-PEPR system is induced by herbivore feeding and contributes to JA-mediated plant defence against herbivory. Journal of Experimental Botany, 66(17), 5327-5336. https://doi.org/10.1093/jxb/erv250
  49. Kryvoruchko, I. S., Sinharoy, S., Torres-Jerez, I., Sosso, D., Pislariu, C. I., Guan, D., … & Udvardi, M. K. (2016). MtSWEET11, a nodule-specific sucrose transporter of Medicago truncatula. Plant Physiology, 171(1), 554-565. https://doi.org/10.1104/pp.15.01910
  50. Owens, D. K., Alerding, A. B., Crosby, K. C., Bandara, A. B., Westwood, J. H., & Winkel, B. S. (2008). Functional analysis of a predicted flavonol synthase gene family in Arabidopsis. Plant Physiology, 147(3), 1046-1061. https://doi.org/10.1104/pp.108.117457
  51. Karunadasa, S. S., Kurepa, J., Shull, T. E., & Smalle, J. A. (2020). Cytokinin‐induced protein synthesis suppresses growth and osmotic stress tolerance. New Phytologist. https://doi.org/10.1111/nph.16519
  52. Chirakul, S., Norris, M. H., Pagdepanichkit, S., Somprasong, N., Randall, L. B., Shirley, J. F., … & Schweizer, H. P. (2018). Transcriptional and post-transcriptional regulation of PenA β-lactamase in acquired Burkholderia pseudomallei β-lactam resistance. Scientific Reports, 8(1) https://doi.org/10.1038/s41598-018-28843-7
  53. Polko, J. K., Barnes, W. J., Voiniciuc, C., Doctor, S., Steinwand, B., Hill Jr, J. L., … & Kieber, J. J. (2018). SHOU4 proteins regulate trafficking of cellulose synthase complexes to the plasma membrane. Current Biology, 28(19), 3174-3182. 10.1016/j.cub.2018.07.076
X-α-Gal
  1. Feurtado, J. A., Huang, D., Wicki-Stordeur, L., Hemstock, L. E., Potentier, M. S., Tsang, E. W., & Cutler, A. J. (2011). The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation. The Plant Cell, 23(5), 1772-1794. https://doi.org/10.1105/tpc.111.085134
  2. Galletta, B. J., Jacobs, K. C., Fagerstrom, C. J., & Rusan, N. M. (2016). Asterless is required for centriole length control and sperm development. The Journal of Cell Biology, 213(4), 435–450. https://doi.org/10.1083/jcb.201501120
  3. Galletta, B. J., Fagerstrom, C. J., Schoborg, T. A., McLamarrah, T. A., Ryniawec, J. M., Buster, D. W., … Rusan, N. M. (2016). A centrosome interactome provides insight into organelle assembly and reveals a non-duplication role for Plk4. Nature Communications, 7(1). https://doi.org/10.1038/ncomms12476
  4. Sheng, Y., Song, Y., Li, Z., Wang, Y., Lin, H., Cheng, H., & Zhou, R. (2018). RAB37 interacts directly with ATG5 and promotes autophagosome formation via regulating ATG5-12-16 complex assembly. Cell Death & Differentiation, 25(5), 918. https://doi.org/10.1038/s41418-017-0023-1
  5. Galletta, B. J., Guillen, R. X., Fagerstrom, C. J., Brownlee, C. W., Lerit, D. A., Megraw, T. L., … & Rusan, N. M. (2014). Drosophila pericentrin requires interaction with calmodulin for its function at centrosomes and neuronal basal bodies but not at sperm basal bodies. Molecular Biology of the Cell, 25(18), 2682-2694. https://doi.org/10.1091/mbc.e13-10-0617
4-Aminophenyl phosphate monosodium salt hydrate
  1. Ahmad, A., & Moore, E. (2012). Electrochemical immunosensor modified with self-assembled monolayer of 11-mercaptoundecanoic acid on gold electrodes for detection of benzo[a]pyrene in water. The Analyst, 137(24), 5839. https://doi.org/10.1039/c2an35236b
  2. Bhimji, A., Zaragoza, A. A., Live, L. S., & Kelley, S. O. (2013). Electrochemical enzyme-linked immunosorbent assay featuring proximal reagent generation: Detection of human immunodeficiency virus antibodies in clinical samples. Analytical Chemistry, 85(14), 6813–6819. https://doi.org/10.1021/ac4009429
  3. Farrow, B., Hong, S. A., Romero, E. C., Lai, B., Coppock, M. B., Deyle, K. M., … & Heath, J. R. (2013). A chemically synthesized capture agent enables the selective, sensitive, and robust electrochemical detection of anthrax protective antigen. ACS Nano, 7(10), 9452-9460. https://doi.org/10.1021/nn404296k
  4. Sung, D., & Yang, S. (2014). Facile method for constructing an effective electron transfer mediating layer using ferrocene-containing multifunctional redox copolymer. Electrochimica Acta, 133, 40-48.https://doi.org/10.1016/j.electacta.2014.03.110
  5. Glavan, A. C., Christodouleas, D. C., Mosadegh, B., Yu, H. D., Smith, B. S., Lessing, J., … & Whitesides, G. M. (2014). Folding analytical devices for electrochemical ELISA in hydrophobic RH paper. Analytical Chemistry, 86(24), 11999-12007. https://doi.org/10.1021/ac5020782
5-Aminolevulinic acid hydrochloride
  1. Calla, B., Wu, W. ‐Y., Dean, C. A. E., Schuler, M. A., & Berenbaum, M. R. (2019). Substrate‐specificity of cytochrome P450‐mediated detoxification as an evolutionary strategy for specialization on furanocoumarin‐containing hostplants: CYP6AE89 in parsnip webworms. Insect Molecular Biology, 29(1), 112–123. https://doi.org/10.1111/imb.12612
AEBSF
  1. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  2. Elsasser S., Shi Y., Finley D. (2012) Binding of ubiquitin conjugates to proteasomes as visualized with native gels. In: Dohmen R., Scheffner M. (eds) Methods in Molecular Biology: Ubiquitin family modifiers and the proteasome. (Vol 832, pp. 403-422) New York, NY: Humana Press https://doi.org/10.1007/978-1-61779-474-2_28
  3. Cardenas-Aguayo, M. del C., Kazim, S. F., Grundke-Iqbal, I., & Iqbal, K. (2013). Neurogenic and neurotrophic effects of BDNF peptides in mouse hippocampal primary neuronal cell cultures. PLoS ONE, 8(1), e53596. https://doi.org/10.1371/journal.pone.0053596
  4. Park, N. J., Wang, X., Diaz, A., Goos-Root, D. M., Bock, C., Vaught, J. D., … & Strom, C. M. (2013). Measurement of cetuximab and panitumumab-unbound serum EGFR extracellular domain using an assay based on slow off-rate modified aptamer (SOMAmer) reagents. PloS one, 8(8), e71703.https://doi.org/10.1371/journal.pone.0071703
  5. Amick, J., Schlanger, S. E., Wachnowsky, C., Moseng, M. A., Emerson, C. C., Dare, M., … & Page, R. C. (2014). Crystal structure of the nucleotide‐binding domain of mortalin, the mitochondrial Hsp70 chaperone. Protein Science, 23(6), 833-842. https://doi.org/10.1002/pro.2466
  6. Baradaran, R., Wang, C., Siliciano, A. F., & Long, S. B. (2018). Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters. Nature, 559(7715), 580. https://doi.org/10.1038/s41586-018-0331-8
  7. Diver, M. M., Pedi, L., Koide, A., Koide, S., & Long, S. B. (2018). Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature, 553(7689), 526. https://doi.org/10.1038/nature25439
  8. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  9. Wacker, D., Wang, S., McCorvy, J. D., Betz, R. M., Venkatakrishnan, A. J., Levit, A., … & Shoichet, B. K. (2017). Crystal structure of an LSD-bound human serotonin receptor. Cell, 168(3), 377-389. https://doi.org/10.1016/j.cell.2016.12.033
  10. Verardi, R., Kim, J. S., Ghirlando, R., & Banerjee, A. (2017). Structural basis for substrate recognition by the ankyrin repeat domain of human DHHC17 palmitoyltransferase. Structure, 25(9), 1337-1347. https://doi.org/10.1016/j.str.2017.06.018
  11. Zinoviev, A., Hellen, C. U., & Pestova, T. V. (2020). In Vitro Characterization of the Activity of the Mammalian RNA Exosome on mRNAs in Ribosomal Translation Complexes. In The Eukaryotic RNA Exosome. Methods In Microbiology (pp. 327-354). Humana, New York, NY. <a “=”” href=”https://doi.org/10.1007/978-1-4939-9822-7_16″ target=”_blank”> https://doi.org/10.1007/978-1-4939-9822-7_16
Agarose LE (Molecular Biology Grade)
  1. Rodriguez, B. V., Pescador, J., Pollok, N., Beall, G. W., Maeder, C., & Lewis, L. K. (2015). Impact of size, secondary structure, and counterions on the binding of small ribonucleic acids to layered double hydroxide nanoparticles. Biointerphases, 10(4), 041007. https://doi.org/10.1116/1.4936393
  2. Ream, J. A., Lewis, L. K., & Lewis, K. A. (2016). Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: RNA interactions. Analytical Biochemistry, 511, 36–41. https://doi.org/10.1016/j.ab.2016.07.027
  3. Kang, W., & Cannon, J. L. (2015). A membrane-based electro-separation method (MBES) for sample clean-up and norovirus concentration. PloS One, 10(10), e0141484. https://doi.org/10.1371/journal.pone.0141484
  4. Zhang, J., Smaga, L. P., Satyavolu, N. S. R., Chan, J., & Lu, Y. (2017). DNA aptamer-based activatable probes for photoacoustic imaging in living mice. Journal of the American Chemical Society, 139(48), 17225-17228. https://doi.org/10.1021/jacs.7b07913
  5. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  6. Chakravarty, A. K., Smejkal, T., Itakura, A. K., Garcia, D. M., & Jarosz, D. F. (2020). A non-amyloid prion particle that activates a heritable gene expression program. Molecular Cell, 77(2), 251-265. https://doi.org/10.1016/j.molcel.2019.10.028
Aminoethyl (Very Low Density) 4% Agarose Beads, Crosslinked
  1. Ashley, G., & Santi, D. V. (2015). U.S. Patent No. 8,946,405 B2. Washington, DC: U.S. Patent and Trademark Office.
Ampicillin (Sodium) 100 mg/mL Solution
  1. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  2. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  3. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
Ampicillin (Sodium) EZ Pak™ for 100 mg/mL Solution
  1. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  2. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  3. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
Ampicillin (Sodium), USP Grade
  1. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  2. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  3. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  4. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  5. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  6. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  7. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  8. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  9. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  10. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  11. Reese, A. T., Pereira, F. C., Schintlmeister, A., Berry, D., Wagner, M., Hale, L. P., … & Premont, R. T. (2018). Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology, 3(12), 1441. https://doi.org/10.1038/s41564-018-0267-7
  12. Smith, C. D. M., Gong, M., Andrew, A. K., Russ, B. N., Ge, Y., Zadeh, M., … & Moore, J. M. (2019). Composition of the gut microbiota transcends genetic determinants of malaria infection severity and influences pregnancy outcome. EBioMedicine 44, 639–655. https://doi.org/10.1016/j.ebiom.2019.05.052
  13. Wright, W. C., Chenge, J., Wang, J., Girvan, H. M., Yang, L., Chai, S. C., Huber, A. D., Wu, J., Oladimeji, P. O., Munro, A. W., & Chen, T. (2020). Clobetasol propionate is a heme-mediated selective inhibitor of human cytochrome P450 3A5. Journal of Medicinal Chemistry, 63(3), 1415–1433. https://doi.org/10.1021/acs.jmedchem.9b02067
  14. Jagessar, K. L., Claxton, D. P., Stein, R. A., & Mchaourab, H. S. (2020). Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter. Proceedings of the National Academy of Sciences, 117(9), 4732–4740. https://doi.org/10.1073/pnas.1917139117
  15. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  16. González, L. M., Mukhitov, N., & Voigt, C. A. (2019). Resilient living materials built by printing bacterial spores. Nature Chemical Biology, 16(2), 126–133. https://doi.org/10.1038/s41589-019-0412-5
  17. Reighard, S. D., Cranert, S. A., Rangel, K. M., Ali, A., Gyurova, I. E., de la Cruz-Lynch, A. T., … Waggoner, S. N. (2020). Therapeutic targeting of follicular T cells with chimeric antigen receptor-expressing natural killer cells. Cell Reports Medicine, 100003. https://doi.org/10.1016/j.xcrm.2020.100003
  18. Song, M., Sukovich, D. J., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, E. A., Tucker, A. C., Gordon, D. B., Marlovits, T. C., & Voigt, C. A. (2017). Control of type III protein secretion using a minimal genetic system. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14737
  19. Kim, W. J., Higashi, D., Goytia, M., Rendón, M. A., Pilligua-Lucas, M., Bronnimann, M., … & So, M. (2019). Commensal Neisseria kill Neisseria gonorrhoeae through a DNA-dependent mechanism. Cell Host & Microbe, 26(2), 228–239.e8. https://doi.org/10.1016/j.chom.2019.07.003
  20. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  21. Staffas, A., da Silva, M. B., Slingerland, A. E., Lazrak, A., Bare, C. J., Holman, C. D., … & Cross, J. R. (2018). Nutritional support from the intestinal microbiota improves hematopoietic reconstitution after bone marrow transplantation in mice. Cell Host & Microbe, 23(4), 447-457. https://doi.org/10.1016/j.chom.2018.03.002
  22. Barton, B., Grinnell, A., & Morgenstein, R. M. (2021). Disruption of the MreB elongasome Is overcome by mutations in the tricarboxylic acid cycle. Frontiers in Microbiology, 12 https://doi.org/10.3389/fmicb.2021.664281
  23. Gao, Y., Cao, D., Pawnikar, S., Akhter, S., Miao, Y., & Liang, B. (2021). Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR protocols, 2(1), 100315. https://doi.org/10.1016/j.xpro.2021.100315
Aprotinin
  1. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  2. Pearce, L. A., Yu, M., Waddington, L. J., Barr, J. A., Scoble, J. A., Crameri, G. S., & McKinstry, W. J. (2015). Structural characterization by transmission electron microscopy and immunoreactivity of recombinant Hendra virus nucleocapsid protein expressed and purified from Escherichia coli. Protein Expression and Purification, 116, 19-29. https://doi.org/10.1016/j.pep.2015.07.008
  3. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  4. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  5. Wacker, D., Wang, S., McCorvy, J. D., Betz, R. M., Venkatakrishnan, A. J., Levit, A., … & Shoichet, B. K. (2017). Crystal structure of an LSD-bound human serotonin receptor. Cell, 168(3), 377-389. https://doi.org/10.1016/j.cell.2016.12.033
IPTG EZ Pak™ for 1 M Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  3. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  4. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Guerra, D., Ballard, K., Truebridge, I., & Vierling, E. (2016). S-nitrosation of conserved cysteines modulates activity and stability of S-nitrosoglutathione reductase (GSNOR). Biochemistry, 55(17), 2452-2464.https://doi.org/10.1021/acs.biochem.5b01373
  7. Sutherland, M. C., Rankin, J. A., & Kranz, R. G. (2016). Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry, 55(22), 3150-3156.https://doi.org/10.1021/acs.biochem.6b00427
  8. Robbins, T., Kapilivsky, J., Cane, D. E., & Khosla, C. (2016). Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry, 55(32), 4476-4484. https://doi.org/10.1021/acs.biochem.6b00639
  9. Inan, K., Sal, F. A., Rahman, A., Putman, R. J., Agblevor, F. A., & Miller, C. D. (2016). Microbubble assisted polyhydroxybutyrate production in Escherichia coli. BMC Research Notes, 9(1), 338. https://doi.org/10.1186/s13104-016-2145-9
  10. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  11. Tanner, J. J., Frey, B. B., Pemberton, T., & Henzl, M. T. (2016). EF5 is the high-affinity Mg2+ site in ALG-2. Biochemistry, 55(36), 5128-5141. https://doi.org/10.1021/acs.biochem.6b00596
  12. Kennedy, E. N., Menon, S. K., & West, A. H. (2016). Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions. FEMS Yeast Research, 16(6) fow068. https://doi.org/10.1093/femsyr/fow068
  13. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  14. Sigala, P. A., Morante, K., Tsumoto, K., Caaveiro, J. M., & Goldberg, D. E. (2016). In-Cell Enzymology To Probe His–Heme Ligation in Heme Oxygenase Catalysis. Biochemistry, 55(34), 4836-4849. https://doi.org/10.1021/acs.biochem.6b00562
  15. Fancher, A. T., Hua, Y., Camarco, D. P., Close, D. A., Strock, C. J., & Johnston, P. A. (2016). Reconfiguring the AR-TIF2 protein–protein interaction HCS assay in prostate cancer cells and characterizing the hits from a LOPAC screen. Assay and Drug Development Technologies, 14(8), 453-477. https://doi.org/10.1089/adt.2016.741
  16. Wang, X., Zhang, Z. T., Wang, Y., & Wang, Y. (2016). Production of polyhydroxybuyrate (PHB) from switchgrass pretreated with a radio frequency-assisted heating process. Biomass and Bioenergy, 94, 220-227. https://doi.org/10.1016/j.biombioe.2016.09.006
  17. Devendran, S., Abdel-Hamid, A. M., Evans, A. F., Iakiviak, M., Kwon, I. H., Mackie, R. I., & Cann, I. (2016). Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Scientific Reports, 6, 35342. https://doi.org/10.1038/srep35342
  18. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  19. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  20. Fiers, W. D., Dodge, G. J., Sherman, D. H., Smith, J. L., & Aldrich, C. C. (2016). Vinylogous dehydration by a polyketide dehydratase domain in curacin biosynthesis. Journal of the American Chemical Society, 138(49), 16024-16036. https://doi.org/10.1021/jacs.6b09748
  21. Le, C. Q., Oyugi, M., Joseph, E., Nguyen, T., Ullah, M. H., Aubert, J., … & Johnson-Winters, K. (2017). Effects of isoleucine 135 side chain length on the cofactor donor-acceptor distance within F420H2: NADP+ oxidoreductase: a kinetic analysis. Biochemistry and Biophysics Reports, 9, 114-120. https://doi.org/10.1016/j.bbrep.2016.11.012
  22. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
L-Albizziine
  1. Deng, L., Yao, P., Li, L., Ji, F., Zhao, S., Xu, C., … & Jiang, P. (2020). p53-mediated control of aspartate-asparagine homeostasis dictates LKB1 activity and modulates cell survival. Nature Communications, 11(1), 1-18. https://doi.org/10.1038/s41467-020-15573-6
L-Arabinose
  1. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  2. Sugihara, J., Sun, L., Yan, N., & Kaback, H. R. (2012). Dynamics of the L-fucose/H+ symporter revealed by fluorescence spectroscopy. Proceedings of the National Academy of Sciences, 109(37), 14847-14851. https://doi.org/10.1073/pnas.1213445109
  3. Köpke, M., Gerth, M. L., Maddock, D. J., Mueller, A. P., Liew, F., Simpson, S. D., & Patrick, W. M. (2014). Reconstruction of an acetogenic 2, 3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase. Applied and Environmental Microbiology, 80(11), 3394–3403.https://doi.org/10.1128/AEM.00301-14
  4. Maddock, D. J., Patrick, W. M., & Gerth, M. L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design & Selection, 28(8), 251-258. https://doi.org/10.1093/protein/gzv028
  5. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  6. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  10. Kim, S., Loeff, L., Colombo, S., Jergic, S., Brouns, S. J. J., & Joo, C. (2020). Selective loading and processing of prespacers for precise CRISPR adaptation. Nature, 579(7797), 141–145. https://doi.org/10.1038/s41586-020-2018-1
  11. Calla, B., Wu, W. ‐Y., Dean, C. A. E., Schuler, M. A., & Berenbaum, M. R. (2019). Substrate‐specificity of cytochrome P450‐mediated detoxification as an evolutionary strategy for specialization on furanocoumarin‐containing hostplants: CYP6AE89 in parsnip webworms. Insect Molecular Biology, 29(1), 112–123. https://doi.org/10.1111/imb.12612
  12. Manor, M., & Qimron, U. (2017). Selection of genetically modified bacteriophages using the CRISPR-Cas system. Bio-Protocol, 7(15). https://doi.org/10.21769/bioprotoc.2431
  13. Farzadfard, F., Gharaei, N., Higashikuni, Y., Jung, G., Cao, J., & Lu, T. K. (2019). Single-nucleotide-resolution computing and memory in living cells. Molecular Cell, 75(4), 769–780.e4. https://doi.org/10.1016/j.molcel.2019.07.011
Low Melt Agarose
  1. Stoddard, M., Huang, C., Enyedi, B., & Niethammer, P. (2019). Live imaging of leukocyte recruitment in a zebrafish model of chemical liver injury. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36771-9
  2. Schwerdtfeger, L. A., & Tobet, S. A. (2020). Vasoactive intestinal peptide regulates ileal goblet cell production in mice. Physiological Reports, 8(3). https://doi.org/10.14814/phy2.14363
  3. Kinstlinger, I. S., Saxton, S. H., Calderon, G. A., Ruiz, K. V., Yalacki, D. R., Deme, P. R., … & Sazer, D. W. (2020). Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates. Nature Biomedical Engineering, 1-17. https://doi.org/10.1038/s41551-020-0566-1
Streptavidin Agarose Resin
  1. Liu, L., & Dong, X. (2014). Complex impacts of PI3K/AKT inhibitors to androgen receptor gene expression in prostate cancer cells. PloS One, 9(10), e108780. https://doi.org/10.1371/journal.pone.0108780
  2. Shen, W., Deng, X., Zou, W., Engelhardt, J. F., Yan, Z., & Qiu, J. (2016). Analysis of cis and trans requirements for DNA replication at the right-end hairpin of the human bocavirus 1 genome. Journal of Virology, 90(17), 7761-7777.https://doi.org/10.1128/JVI.00708-16
Streptomycin Sulfate
  1. Van der Heijden, J., Reynolds, L. A., Deng, W., Mills, A., Scholz, R., Imami, K., … & Finlay, B. B. (2016). Salmonella rapidly regulates membrane permeability to survive oxidative stress. mBio, 7(4), e01238-16. https://doi.org/10.1128/mBio.01238-16
  2. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  3. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  4. Riglar, D. T., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., Kotula, J. W., … & Silver, P. A. (2016). Long-term monitoring of inflammation in the mammalian gut using programmable commensal bacteria. BioRxiv, 075051. https://doi.org/10.1101/075051
  5. Hsu, B. B., Way, J. C., & Silver, P. A. (2020). Stable neutralization of a virulence factor in bacteria using temperate phage in the mammalian gut. mSystems, 5(1). https://doi.org/10.1128/msystems.00013-20
  6. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  7. Nguyen, B. N., & Portnoy, D. A. (2020). An inducible cre-lox system to analyze the role of LLO in Listeria monocytogenes pathogenesis. Toxins, 12(1), 38. https://doi.org/10.3390/toxins12010038
  8. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  9. Riglar, D. T., Giessen, T. W., Baym, M., Kerns, S. J., Niederhuber, M. J., Bronson, R. T., … & Silver, P. A. (2017). Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nature Biotechnology, 35(7), 653-658. https://doi.org/10.1038/nbt.3879
  10. Hsu, B. B., Plant, I. N., Lyon, L., Anastassacos, F. M., Way, J. C., & Silver, P. A. (2020). In situ reprogramming of gut bacteria by oral delivery. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18614-2
5-Bromo-4-chloro-3-indoxyl-2-acetamido-2-deoxy-β-D-galactopyranoside (X-β-D-GalNAc)
  1. Wu, F., Peacock, S. O., Rao, S., Lemmon, S. K., & Burnstein, K. L. (2012). Novel interaction between the co-chaperone Cdc37 and Rho GTPase exchange factor Vav3 promotes androgen receptor activity and prostate cancer growth. Journal of Biological Chemistry, 288(8), 5463–5474. https://doi.org/10.1074/jbc.m112.390963
5-Bromo-4-chloro-3-indoxyl-β-D-glucuronic acid sodium salt (X-β-D-GlcA·Na)
  1. Lozano‐Sotomayor, P., Chávez Montes, R. A., Silvestre‐Vañó, M., Herrera‐Ubaldo, H., Greco, R., Pablo‐Villa, J., … & Pereira, A. (2016). Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana. The Plant Journal, 88(3), 437-451. https://doi.org/10.1111/tpj.13264
5-Bromo-4-chloro-3-indoxyl-β-D-xylopyranoside
  1. Adelskov, J., & Patel, B. K. (2016). A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor. 3 Biotech, 6(1), 96.https://doi.org/10.1007/s13205-016-0408-8
6-Bromo-DL-tryptophan
  1. Ellefson, J. W., Ledbetter, M. P., & Ellington, A. D. (2018). Directed evolution of a synthetic phylogeny of programmable Trp repressors. Nature Chemical Biology, 14(4), 361. https://doi.org/10.1038/s41589-018-0006-7
Bacterial Cell Lysis Buffer
  1. Li, T., Tong, X., Yang, Q., Giddens, J. P., & Wang, L. X. (2016). Glycosynthase mutants of endoglycosidase S2 show potent transglycosylation activity and remarkably relaxed substrate specificity for antibody glycosylation remodeling. Journal of Biological Chemistry, 291(32), 16508-16518. https://doi.org/10.1074/jbc.m116.738765
Basic FGF (FGF2), Human
  1. Sowmya, S., Chennazhi, K. P., Arzate, H., Jayachandran, P., Nair, S. V., & Jayakumar, R. (2015). Periodontal specific differentiation of dental follicle stem cells into osteoblast, fibroblast, and cementoblast. Tissue Engineering Part C: Methods, 21(10), 1044-1058. https://doi.org/10.1089/ten.tec.2014.0603
  2. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
  3. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  4. Aminuddin, A., Ng, P. Y., Leong, C.-O., & Chua, E. W. (2020). Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64664-3
BCIP
  1. Wang, L., & Liu, D. (2017). Analyses of root-secreted acid phosphatase activity in Arabidopsis. Bio-Protocol, 7(7). https://doi.org/10.21769/bioprotoc.2202
Bialaphos, Sodium Salt
  1. Chung, K. R., & Liao, H. L. (2008). Determination of a transcriptional regulator-like gene involved in biosynthesis of elsinochrome phytotoxin by the citrus scab fungus, Elsinoë fawcettii. Microbiology, 154(11), 3556-3566. https://dx.doi.org/10.1099/mic.0.2008/019414-0
  2. Xu C., Yu W. (2011) Telomere Truncation in Plants. In: Birchler J. (eds) Plant Chromosome Engineering. Methods in Molecular Biology (Methods and Protocols), vol 701 (pp 113-130) https://doi.org/10.1007/978-1-61737-957-4_6
  3. Akbudak, M. A., & Srivastava, V. (2011). Improved FLP recombinase, FLPe, efficiently removes marker gene from transgene locus developed by Cre–lox mediated site-specific gene integration in rice. Molecular Biotechnology, 49(1), 82-89.https://doi.org/10.1007/s12033-011-9381-y
  4. Turgeon B.G., Condon B., Liu J., Zhang N. (2010) Protoplast Transformation of Filamentous Fungi. In: Sharon A. (eds) Protoplast transformation of filamentous fungi. Methods in Molecular Biology (Methods and Protocols), vol 638. (pp. 3-19) https://doi.org/10.1007/978-1-60761-611-5_1
  5. Frame B.R., Paque T., Wang K. (2006) Maize (Zea mays L.). In: Wang K. (eds) Agrobacterium Protocols. Methods in Molecular Biology, vol 343. Humana Press https://doi.org/10.1385/1-59745-130-4:185
  6. Lee, H., & Zhang, Z. J. (2016). Maize (Zea mays) Hi‐II transformation via agrobacterium‐mediated T‐DNA transfer. Current Protocols in Plant Biology, 1(1), 121-137. https://doi.org/10.1002/cppb.20016
Blasticidin S HCl
  1. Leyme, A., Marivin, A., & Garcia-Marcos, M. (2016). GIV/Girdin creates a positive feedback loop that potentiates outside-in integrin signaling in cancer cells. Journal of Biological Chemistry, jbc-M115. https://doi.org/10.1074/jbc.m115.691550
  2. Corcoran, J. A., Jordan, M. D., Carraher, C., & Newcomb, R. D. (2014). A novel method to study insect olfactory receptor function using HEK293 cells. Insect Biochemistry and Molecular Biology, 54, 22-32.https://doi.org/10.1016/j.ibmb.2014.08.005
  3. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  4. Tang, Y., & Gomer, R. H. (2020). An improved shotgun antisense method for mutagenesis and gene identification. BioTechniques, 68(3), 163–165. https://doi.org/10.2144/btn-2019-0123
  5. Santarriaga, S., Haver, H. N., Kanack, A. J., Fikejs, A. S., Sison, S. L., Egner, J. M., … & Ebert, A. D. (2018). SRCP1 conveys resistance to polyglutamine aggregation. Molecular Cell, 71(2), 216-228. https://doi.org/10.1016/j.molcel.2018.07.008
Blazin’ Blue™ Protein Gel Stain
  1. Uppal, S., Liu, T., Poliakov, E., Gentleman, S., & Redmond, T. M. (2019). The dual roles of RPE65 S-palmitoylation in membrane association and visual cycle function. Scientific Reports, 9(1), 5218. https://doi.org/10.1038/s41598-019-41501-w
BLUEstain™ 2 Protein ladder, 5-245 kDa
  1. Ho, J. M., Miller, C. A., Smith, K. A., Mattia, J. R., & Bennett, M. R. (2021). Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway. Nature Communications, 12(1), 1-10. https://doi.org/10.1038/s41467-021-24183-9
BLUEstain™ Protein ladder, 11-245 kDa
  1. Lee, J., Ahn, H., Hong, E. J., An, B. S., Jeung, E. B., & Lee, G. S. (2016). Sulforaphane attenuates activation of NLRP3 and NLRC4 inflammasomes but not AIM2 inflammasome. Cellular Immunology, 306, 53-60.https://doi.org/10.1016/j.cellimm.2016.07.007
  2. Al-Wathiqui, N., Fallon, T. R., South, A., Weng, J. K., & Lewis, S. M. (2016). Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection. Scientific Reports, 6, 38556. https://doi.org/10.1038/srep38556
  3. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
  4. Fiehn, O., Showalter, M. R., & Schaner-Tooley, C. E. (2016). Registered report: the common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. ELife, 5. e12626. https://doi.org/10.7554/elife.12626
Bluo-Gal
  1. Raisch, T., Chang, C. T., Levdansky, Y., Muthukumar, S., Raunser, S., & Valkov, E. (2019). Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation. Nature Communications, 10(1), 3173. https://doi.org/10.1038/s41467-019-11094-z
  2. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  3. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
Bovine Serum Albumin (BSA), Fraction V, Fatty Acid Free for tissue culture
  1. Lewis, A., Dhakal, B., Liu, T., & Mulvey, M. (2016). Histone deacetylase 6 regulates bladder architecture and host susceptibility to uropathogenic Escherichia coli. Pathogens, 5(1), 20. https://doi.org/10.3390/pathogens5010020
  2. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  3. Shin, S. C., Thomas, D., Radhakrishnan, P., & Hollingsworth, M. A. (2020). Invasive phenotype induced by low extracellular pH requires mitochondria dependent metabolic flexibility. Biochemical and Biophysical Research Communications, 525(1), 162–168. https://doi.org/10.1016/j.bbrc.2020.02.018
Bovine Serum Albumin (BSA), Fraction V, Protease Free
  1. Voss, O. H., Lee, H. N., Tian, L., Krzewski, K., & Coligan, J. E. (2018). Liposome preparation for the analysis of lipid‐receptor interaction and efferocytosis. Current Protocols In Immunology, 120(1), 14-44. https://doi.org/10.1002/cpim.43
  2. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  3. Corless, E. I., Mettert, E. L., Kiley, P. J., & Antony, E. (2020). Elevated expression of a functional suf pathway in Escherichia coli BL21 (DE3) enhances recombinant production of an iron-sulfur cluster-containing protein. Journal of Bacteriology, 202(3). https://doi.org/10.1128/JB.00496-19
Carbenicillin (Disodium) 100 mg/mL Solution
  1. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  2. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
Carbenicillin (Disodium) EZ Pak™ for 100 mg/mL Solution
  1. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  2. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
Carbenicillin (Disodium), USP Grade
  1. Kim, J. H., Choi, D. C., Yeon, K. M., Kim, S. R., & Lee, C. H. (2011). Enzyme-immobilized nanofiltration membrane to mitigate biofouling based on quorum quenching. Environmental Science & Technology, 45(4), 1601-1607. https://doi.org/10.1021/es103483j
  2. Mima, T., Schweizer, H. P., & Xu, Z. Q. (2010). In vitro activity of cethromycin against Burkholderia pseudomallei and investigation of mechanism of resistance. Journal of Antimicrobial Chemotherapy, 66(1), 73-78. https://doi.org/10.1093/jac/dkq391
  3. Choi, D. C., Won, Y. J., Lee, C. H., Lee, S., Lee, M. H., & Khang, D. Y. (2013). Tunable pore size micro/submicron-sieve membranes by soft lithography. Journal of Materials Chemistry A, 1(40), 12448-12454. https://doi.org/10.1039/C3TA12490H
  4. Won, Y. J., Choi, D. C., Jang, J. H., Lee, J. W., Chae, H. R., Kim, I., … & Kim, I. C. (2014). Factors affecting pattern fidelity and performance of a patterned membrane. Journal of Membrane Science, 462, 1-8. https://doi.org/10.1016/j.memsci.2014.03.012
  5. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  6. Bohl, T. E., Shi, K., Lee, J. K., & Aihara, H. (2018). Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nature Communications, 9(1), 377.10.1038/s41467-017-02712-9
  7. Sierra-Valdez, F. J., Stein, R. A., Velissety, P., Vasquez, V., & Cordero-Morales, J. F. (2018). Purification and reconstitution of TRPV1 for spectroscopic analysis. JoVE (Journal of Visualized Experiments), (137), e57796.https://doi.org/10.3791/57796
  8. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  9. Liu, X., Schuessler, P. J., Sahoo, A., & Walker, S. E. (2019). Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes. Methods. 162–163, 42–53. https://doi.org/10.1016/j.ymeth.2019.03.024
  10. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  11. Shin, J., Zhang, S., Der, B. S., Nielsen, A. A., & Voigt, C. A. (2020). Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16(3). https://doi.org/10.15252/msb.20199401
  12. Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020). Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0468-5
  13. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  14. Pontrelli, S., Fricke, R. C., Teoh, S. T., Laviña, W. A., Putri, S. P., Fitz-Gibbon, S., … & Liao, J. C. (2018). Metabolic repair through emergence of new pathways in Escherichia coli. Nature Chemical Biology, 14(11), 1005-1009. https://doi.org/10.1038/s41589-018-0149-6
  15. English, J. G., Olsen, R. H., Lansu, K., Patel, M., White, K., Cockrell, A. S., … & Roth, B. L. (2019). VEGAS as a platform for facile directed evolution in mammalian cells. Cell, 178(3), 748–761.e17. https://doi.org/10.1016/j.cell.2019.05.051
  16. Guo, M. S., Haakonsen, D. L., Zeng, W., Schumacher, M. A., & Laub, M. T. (2018). A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication. Cell, 175(2), 583-597. https://doi.org/10.1016/j.cell.2018.08.029
  17. Mighell, T. L., Evans-Dutson, S., & O’Roak, B. J. (2018). A saturation mutagenesis approach to understanding PTEN lipid phosphatase activity and genotype-phenotype relationships. The American Journal of Human Genetics, 102(5), 943-955. 10.1016/j.ajhg.2018.03.018
  18. Chen, Y. C., Farzadfard, F., Gharaei, N., Chen, W. C., Cao, J., & Lu, T. K. (2017). Randomized CRISPR-Cas transcriptional perturbation screening reveals protective genes against alpha-synuclein toxicity. Molecular Cell, 68(1), 247-257. https://doi.org/10.1016/j.molcel.2017.09.014
  19. Billon, P., Bryant, E. E., Joseph, S. A., Nambiar, T. S., Hayward, S. B., Rothstein, R., & Ciccia, A. (2017). CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Molecular Cell, 67(6), 1068-1079. https://doi.org/10.1016/j.molcel.2017.08.008
Cefadroxil
  1. Cao, P., & Wall, D. (2019). Direct visualization of a molecular handshake that governs kin recognition and tissue formation in myxobacteria. Nature Communications, 10(1), 3073. https://doi.org/10.1038/s41467-019-11108-w
Cefotaxime (Sodium) 100 mg/mL Solution
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
Cefotaxime (Sodium) EZ Pak™ for 100 mg/mL Solution
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
Cefotaxime (Sodium), USP Grade
  1. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
  2. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  3. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  4. Naim, F., Shand, K., Hayashi, S., O’Brien, M., McGree, J., Johnson, A. A. T., Dugdale, B., & Waterhouse, P. M. (2020). Are the current gRNA ranking prediction algorithms useful for genome editing in plants? PLOS ONE, 15(1), e0227994. https://doi.org/10.1371/journal.pone.0227994
Cefsulodin (SCE-129)
  1. Keilberg, D., Zavros, Y., Shepherd, B., Salama, N. R., & Ottemann, K. M. (2016). Spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection. MBio, 7(5), e01705-16. https://doi.org/10.1128/mBio.01705-16
  2. Fan, Y.-J., Hsu, Y.-C., Gu, B.-C., & Wu, C.-C. (2020). Voltammetric measurement of Escherichia coli concentration through p-APG hydrolysis by endogenous β-galactosidase. Microchemical Journal, 154, 104641. https://doi.org/10.1016/j.microc.2020.104641
CHAPS
  1. Fu, B., Brown, C., & Mäler, L. (2020). Expression and purification of DGD2, a chloroplast outer membrane-associated glycosyltransferase for galactolipid synthesis. Biochemistry, 59(8), 999–1009. https://doi.org/10.1021/acs.biochem.0c00028
Chloramphenicol, USP Grade
  1. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  2. Carey, S. B., Payton, A. C., & McDaniel, S. F. (2015). A method for eliminating bacterial contamination from in vitro moss cultures. Applications in Plant Sciences, 3(1), 1400086.https://doi.org/10.3732/apps.1400086
  3. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  4. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  5. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  6. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  7. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  8. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  9. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
  10. Walker, L. M., Li, B., Niks, D., Hille, R., & Elliott, S. J. (2019). Deconvolution of reduction potentials of formate dehydrogenase from Cupriavidus necator. JBIC Journal of Biological Inorganic Chemistry. https://doi.org/10.1007/s00775-019-01701-1
  11. Wright, W. C., Chenge, J., Wang, J., Girvan, H. M., Yang, L., Chai, S. C., Huber, A. D., Wu, J., Oladimeji, P. O., Munro, A. W., & Chen, T. (2020). Clobetasol propionate is a heme-mediated selective inhibitor of human cytochrome P450 3A5. Journal of Medicinal Chemistry, 63(3), 1415–1433. https://doi.org/10.1021/acs.jmedchem.9b02067
  12. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  13. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  14. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  15. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  16. Aggarwal, A., Parai, M. K., Shetty, N., Wallis, D., Woolhiser, L., Hastings, C., … & Wakabayashi, S. (2017). Development of a novel lead that targets M. tuberculosis polyketide synthase 13. Cell, 170(2), 249-259. https://doi.org/10.1016/j.cell.2017.06.025
Ciprofloxacin HCl
  1. Ortiz, B. J., Jennings, J., Gross, W. S., Santos, T. M. A., Lin, T.-Y., Weibel, D. B., & Lynn, D. M. (2021). Soft materials that intercept, respond to, and sequester bacterial siderophores. Chemistry of Materials. https://doi.org/10.1021/acs.chemmater.1c01530
Clindamycin Hydrochloride
  1. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
Cobalt Agarose Beads (High Density)
  1. Xu, W., Podoll, J. D., Dong, X., Tumber, A., Oppermann, U., & Wang, X. (2013). Quantitative analysis of histone demethylase probes using fluorescence polarization. Journal of Medicinal Chemistry, 56(12), 5198-5202. https://doi.org/10.1021/jm3018628
  2. Zheng, Y., Xie, J., Huang, X., Dong, J., Park, M. S., & Chan, W. K. (2016). Binding studies using Pichia pastoris expressed human aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator proteins. Protein Expression and Purification, 122, 72-81. https://doi.org/10.1016/j.pep.2016.02.011
  3. Zhu, J., Zhou, X., Huang, X., & Du, Z. (2020). Bacterial expression, purification, and initial characterization of a full-length Cas13b protein from Porphyromonas gingivalis. Protein Expression and Purification, 169, 105588. https://doi.org/10.1016/j.pep.2020.105588
  4. Gao, Y., Cao, D., Pawnikar, S., Akhter, S., Miao, Y., & Liang, B. (2021). Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR protocols, 2(1), 100315. https://doi.org/10.1016/j.xpro.2021.100315
Cobalt HTC Agarose Beads
  1. Block, E., Booker, S. J., Flores‐Penalba, S., George, G. N., Gundala, S., Landgraf, B. J., … & Vattekkatte, A. (2016). Trifluoroselenomethionine: A new unnatural amino acid. ChemBioChem, 17(18), 1738-1751. https://doi.org/10.1002/cbic.201600266
  2. Omattage, N. S., Deng, Z., Pinkner, J. S., Dodson, K. W., Almqvist, F., Yuan, P., & Hultgren, S. J. (2018). Structural basis for usher activation and intramolecular subunit transfer in P pilus biogenesis in Escherichia coli. Nature Microbiology, 3(12), 1362-1368. https://doi.org/10.1038/s41564-018-0255-y
Coelenterazine
  1. Dai, T., Kharkwal, G. B., Zhao, J., Denis, T. G. S., Wu, Q., Xia, Y., … & Hamblin, M. R. (2011). Ultraviolet‐C light for treatment of Candida albicans burn infection in mice. Photochemistry and Photobiology, 87(2), 342-349. https://doi.org/10.1111/j.1751-1097.2011.00886.x
  2. Andreu, N., Zelmer, A., Fletcher, T., Elkington, P. T., Ward, T. H., Ripoll, J., … & Wiles, S. (2010). Optimisation of bioluminescent reporters for use with mycobacteria. PLoS ONE, 5(5), e10777. https://doi.org/10.1371/journal.pone.0010777
  3. Gottschalk, M., Bach, A., Hansen, J. L., Krogsgaard-Larsen, P., Kristensen, A. S., & Strømgaard, K. (2009). Detecting protein–protein interactions in living cells: development of a bioluminescence resonance energy transfer assay to evaluate the PSD-95/NMDA receptor interaction. Neurochemical Research, 34(10), 1729-1737. https://doi.org/10.1007/s11064-009-9998-4
  4. Aird, K. M., Ghanayem, R. B., Peplinski, S., Lyerly, H. K., & Devi, G. R. (2010). X-linked inhibitor of apoptosis protein inhibits apoptosis in inflammatory breast cancer cells with acquired resistance to an ErbB1/2 tyrosine kinase inhibitor. Molecular Cancer Therapeutics, 9(5), 1432-1442 https://doi.org/10.1158/1535-7163.MCT-10-0160
  5. Lin, L., Ibrahim, A. S., Baquir, B., Fu, Y., Applebaum, D., Schwartz, J., … & Spellberg, B. (2010). Safety and efficacy of activated transfected killer cells for neutropenic fungal infections. The Journal of Infectious Diseases, 201(11), 1708-1717. https://doi.org/10.1086/652496
  6. Oki, K., Plonczynski, M. W., Lam, M. L., Gomez-Sanchez, E. P., & Gomez-Sanchez, C. E. (2012). The potassium channel, Kir3. 4 participates in angiotensin II-stimulated aldosterone production by a human adrenocortical cell line. Endocrinology, 153(9), 4328-4335. https://doi.org/10.1210/en.2012-1241
  7. Yamasaki, T., Voshall, A., Kim, E. J., Moriyama, E., Cerutti, H., & Ohama, T. (2013). Complementarity to an mi RNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii. The Plant Journal, 76(6), 1045-1056. https://doi.org/10.1111/tpj.12354
  8. Periasamy, J., Muthuswami, M., Rao, D. B., Tan, P., & Ganesan, K. (2014). Stratification and delineation of gastric cancer signaling by in vitro transcription factor activity profiling and integrative genomics. Cellular Signalling, 26(5), 880-894.10.1016/j.cellsig.2014.01.017
  9. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  10. Freire, F., Ferraresi, C., Jorge, A. O. C., & Hamblin, M. R. (2016). Photodynamic therapy of oral Candida infection in a mouse model. Journal Of Photochemistry And Photobiology B: Biology, 159, 161-168. https://doi.org/10.1016/j.jphotobiol.2016.03.049
  11. Li, Y., Liu, D., Lopez-Paz, C., Olson, B. J., & Umen, J. G. (2016). A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division. Elife, 5, e10767.https://doi.org/10.7554/elife.10767
  12. Ramesh, V., Selvarasu, K., Pandian, J., Myilsamy, S., Shanmugasundaram, C., & Ganesan, K. (2016). NFκB activation demarcates a subset of hepatocellular carcinoma patients for targeted therapy. Cellular Oncology, 39(6), 523-536. https://doi.org/10.1007/s13402-016-0294-4
  13. Kumar, A., Hou, S., Airo, A. M., Limonta, D., Mancinelli, V., Branton, W., … & Hobman, T. C. (2016). Zika virus inhibits type‐I interferon production and downstream signaling. EMBO Reports, 17(12), 1766-1775. https://doi.org/10.15252/embr.201642627
  14. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  15. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  16. Bahat, A., Lahav, O., Plotnikov, A., Leshkowitz, D., & Dikstein, R. (2019). Targeting Spt5-Pol II by small-molecule inhibitors uncouples distinct activities and reveals additional regulatory roles. Molecular Cell, 76(4), 617-631. https://doi.org/10.1016/j.molcel.2019.08.024
  17. FitzPatrick, L. M., Hawkins, K. E., Delhove, J. M., Fernandez, E., Soldati, C., Bullen, L. F., … & McKay, T. R. (2018). NF-κB activity initiates human ESC-derived neural progenitor cell differentiation by inducing a metabolic maturation program. Stem Cell Reports, 10(6), 1766-1781. https://doi.org/10.1016/j.stemcr.2018.03.015
Coelenterazine 400 a
  1. Cheng, Y. H., Ho, M. S., Huang, W. T., Chou, Y. T., & King, K. (2015). Modulation of glucagon-like peptide-1 (GLP-1) potency by endocannabinoid-like lipids represents a novel mode of regulating GLP-1 receptor signaling. Journal of Biological Chemistry, 290(23), 14302-14313. https://doi.org/10.1074/jbc.M115.655662
  2. King, K., Lin, N. P., Cheng, Y. H., Chen, G. H., & Chein, R. J. (2015). Isolation of positive modulator of glucagon-like peptide-1 signaling from Trigonella foenum-graecum (fenugreek) seed. Journal of Biological Chemistry, 290(43), 26235-26248.https://doi.org/10.1074/jbc.M115.672097
  3. Schrage, R., Schmitz, A. L., Gaffal, E., Annala, S., Kehraus, S., Wenzel, D., … & Galandrin, S. (2015). The experimental power of FR900359 to study Gq-regulated biological processes. Nature Communications, 6, 10156.https://doi.org/10.1038/ncomms10156
  4. Mascle, X. H., Gagnon, C., Wahba, H. M., Lussier-Price, M., Cappadocia, L., Sakaguchi, K., & Omichinski, J. G. (2019). Acetylation of SUMO1 alters interactions with the SIMs of PML and Daxx in a protein-specific manner. Structure, 28(2), 157-168. https://doi.org/10.1016/j.str.2019.11.019
  5. Gao, Y., Robertson, M. J., Rahman, S. N., Seven, A. B., Zhang, C., Meyerowitz, J. G., … & Skiniotis, G. (2021). Asymmetric activation of the calcium-sensing receptor homodimer. Nature, 1-5. https://doi.org/10.1038/s41586-021-03691-0
Coomassie Brilliant Blue R-250
  1. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
GV3101 Agrobacterium Electrocompetent Cells
  1. de Leone, M. J., Hernando, C. E., Romanowski, A., Careno, D. A., Soverna, A. F., Sun, H., Bologna, N. G., Vázquez, M., Schneeberger, K., & Yanovsky, M. J. (2020). Bacterial infection disrupts clock gene expression to attenuate immune responses. Current Biology. https://doi.org/10.1016/j.cub.2020.02.058
1 kb DNA Ladder
  1. Berg, J. A., Merrill, B. D., Breakwell, D. P., Hope, S., & Grose, J. H. (2018). A PCR-based method for distinguishing between two common beehive bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl. Environ. Microbiol., 84(22), e01886-18. https://doi.org/10.1128/AEM.01886-18
  2. Chorba, J. S., Galvan, A. M., & Shokat, K. M. (2018). A high-throughput luciferase assay to evaluate proteolysis of the single-turnover protease PCSK9. JoVE (Journal of Visualized Experiments), (138), e58265. https://doi.org/10.3791/58265
  3. Fischer, M. D., Mgboji, E., & Liu, Z. (2018). Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes. Plant Methods, 14(1), 91.https://doi.org/10.1186/s13007-018-0359-7
  4. Chu, P., Wilson, G. M., Michael, T. P., Vaiciunas, J., Honig, J., & Lam, E. (2018). Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. Plant Molecular Biology, 98(3), 219-231. https://doi.org/10.1007/s11103-018-0774-1
1 kb PLUS™ DNA Ladder
  1. Nacham, O., Clark, K. D., & Anderson, J. L. (2015). Analysis of bacterial plasmid DNA by solid-phase microextraction. Analytical Methods, 7(17), 7202-7207. https://doi.org/10.31274/etd-180810-5204
  2. Clark, K. D., Sorensen, M., Nacham, O., & Anderson, J. L. (2016). Preservation of DNA in nuclease-rich samples using magnetic ionic liquids. RSC Advances, 6(46), 39846–39851. https://doi.org/10.1039/c6ra05932e
  3. Berg, J. A., Merrill, B. D., Breakwell, D. P., Hope, S., & Grose, J. H. (2018). A PCR-based method for distinguishing between two common beehive bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl. Environ. Microbiol., 84(22), e01886-18. https://doi.org/10.1128/AEM.01886-18
  4. Brew-Appiah, R. A., Peracchi, L. M., & Sanguinet, K. A. (2019). Never the two shall mix: robust indel markers to ensure the fidelity of two pivotal and closely-related accessions of Brachypodium distachyon. Plants, 8(6), 153. https://doi.org/10.3390/plants8060153
100 bp DNA Ladder
  1. Fischer, M. D., Mgboji, E., & Liu, Z. (2018). Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes. Plant Methods, 14(1), 91.https://doi.org/10.1186/s13007-018-0359-7
  2. Lang, J. M., DuCharme, E., Ibarra Caballero, J., Luna, E., Hartman, T., Ortiz-Castro, M., … & Leach, J. E. (2017). Detection and characterization of Xanthomonas vasicola pv. vasculorum (Cobb 1894) comb. nov. causing bacterial leaf streak of corn in the United States. Phytopathology, 107(11), 1312-1321. https://doi.org/10.1094/phyto-05-17-0168-r
  3. Shiimori, M., Garrett, S. C., Graveley, B. R., & Terns, M. P. (2018). Cas4 nucleases define the PAM, length, and orientation of DNA fragments integrated at CRISPR loci. Molecular Cell, 70(5), 814-824. https://doi.org/10.1016/j.molcel.2018.05.002
  4. Neyaz, M., Cook, D., & Creamer, R. (2020). Molecular differentiation of Astragalus species and varieties from the western United States: the chloroplast DNA bridge between evolution and molecular systematics. Poisonous Plant Research (PPR), 3(1), 1 https://digitalcommons.usu.edu/poisonousplantresearch/vol3/iss1/1
100 bp PLUS™ DNA Ladder
  1. De Ioannes, P., Leon, V. A., Kuang, Z., Wang, M., Boeke, J. D., Hochwagen, A., & Armache, K. J. (2019). Structure and function of the Orc1 BAH-nucleosome complex. Nature communications, 10(1), 2894. https://doi.org/10.1038/s41467-019-10609-y
  2. Saeidi, S., McKain, M. R., & Kellogg, E. A. (2018). Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens. JoVE (Journal of Visualized Experiments), (133), e56837.https://doi.org/10.3791/56837
50 bp DNA Ladder
  1. Brew-Appiah, R. A., Peracchi, L. M., & Sanguinet, K. A. (2019). Never the two shall mix: robust indel markers to ensure the fidelity of two pivotal and closely-related accessions of Brachypodium distachyon. Plants, 8(6), 153. https://doi.org/10.3390/plants8060153
  2. Mattiroli, F., Gu, Y., & Luger, K. (2018). Measuring nucleosome assembly activity in vitro with the nucleosome assembly and quantification (NAQ) assay. Bio-protocol, 8(3). https://doi.org/10.21769/bioprotoc.2714
D-Luciferin, Sodium Salt (Proven and Published®​)
  1. Swartling, F. J., Grimmer, M. R., Hackett, C. S., Northcott, P. A., Fan, Q. W., Goldenberg, D. D., … & Zhe, X. N. (2010). Pleiotropic role for MYCN in medulloblastoma. Genes & Development, 24(10), 1059-1072. https://doi.org/10.1101/gad.1907510
  2. Rettig G.R., Rice K.G. (2009) Quantitative In Vivo Imaging of Non-viral-Mediated Gene Expression and RNAi-Mediated Knockdown. In: Rich P., Douillet C. (eds) Bioluminescence. Methods in Molecular Biology, vol 574. (pp. 155-171). https://doi.org/10.1007/978-1-60327-321-3_13
  3. Luo, C., Durgin, B. G., Watanabe, N., & Lam, E. (2009). Defining the functional network of epigenetic regulators in Arabidopsis thaliana. Molecular Plant, 2(4), 661–674. https://doi.org/10.1093/mp/ssp017
  4. Zhang, Y., Bressler, J. P., Neal, J., Lal, B., Bhang, H. E. C., Laterra, J., & Pomper, M. G. (2007). ABCG2/BCRP expression modulates d-luciferin–based bioluminescence imaging. Cancer Research, 67(19), 9389-9397. https://doi.org/10.1158/0008-5472.CAN-07-0944
  5. Wiles S., Robertson B.D., Frankel G., Kerton A. (2009) Bioluminescent monitoring of in vivo colonization and clearance dynamics by light-emitting bacteria. In: Rich P., Douillet C. (eds) Bioluminescence. Methods in Molecular Biology (Methods and Protocols), vol 574. (pp. 137-153)https://doi.org/10.1007/978-1-60327-321-3_12
  6. Zhang, Y., Laterra, J., & Pomper, M. G. (2009). Hedgehog pathway inhibitor HhAntag691 is a potent inhibitor of ABCG2/BCRP and ABCB1/Pgp. Neoplasia, 11(1), 96–101. https://doi.org/10.1593/neo.81264
  7. Zhang, Y., Byun, Y., Ren, Y. R., Liu, J. O., Laterra, J., & Pomper, M. G. (2009). Identification of inhibitors of ABCG2 by a bioluminescence imaging–based high-throughput assay. Cancer Research, 69(14), 5867-5875. https://doi.org/10.1158/0008-5472.can-08-4866
  8. Barth, A. S., Kizana, E., Smith, R. R., Terrovitis, J., Dong, P., Leppo, M. K., … Marbán, E. (2008). Lentiviral vectors bearing the cardiac promoter of the Na+-Ca2+ exchanger report cardiogenic differentiation in stem cells Molecular Therapy, 16(5), 957–964. https://doi.org/10.1038/mt.2008.30
  9. Rastegar, F., Gao, J. L., Shenaq, D., Luo, Q., Shi, Q., Kim, S. H., … & Shen, J. (2010). Lysophosphatidic acid acyltransferase β (LPAATβ) promotes the tumor growth of human osteosarcoma. PloS one, 5(12), e14182. https://doi.org/10.1371/journal.pone.0014182
  10. Kargiotis, O., Chetty, C., Gondi, C. S., Tsung, A. J., Dinh, D. H., Gujrati, M., … & Rao, J. S. (2008). Adenovirus-mediated transfer of siRNA against MMP-2 mRNA results in impaired invasion and tumor-induced angiogenesis, induces apoptosis in vitro and inhibits tumor growth in vivo in glioblastoma. Oncogene, 27(35), 4830. https://doi.org/10.1038/onc.2008.122
  11. Mehrotra, S., Languino, L. R., Raskett, C. M., Mercurio, A. M., Dohi, T., & Altieri, D. C. (2010). IAP regulation of metastasis. Cancer Cell, 17(1), 53-64. https://doi.org/10.1016/j.ccr.2009.11.021
  12. Vallera, D. A., Chen, H., Sicheneder, A. R., Panoskaltsis-Mortari, A., & Taras, E. P. (2009). Genetic alteration of a bispecific ligand-directed toxin targeting human CD19 and CD22 receptors resulting in improved efficacy against systemic B cell malignancy. Leukemia Research, 33(9), 1233-1242. https://doi.org/10.1016/j.leukres.2009.02.006
  13. Buckley, S. M., Howe, S. J., Rahim, A. A., Buning, H., McIntosh, J., Wong, S. P., … & McKay, T. R. (2008). Luciferin detection after intranasal vector delivery is improved by intranasal rather than intraperitoneal luciferin administration. Human gene therapy, 19(10), 1050-1056. https://doi.org/10.1089/hum.2008.023
  14. Niedelman, W., Gold, D. A., Rosowski, E. E., Sprokholt, J. K., Lim, D., Farid Arenas, A., … Saeij, J. P. J. (2012). The rhoptry proteins ROP18 and ROP5 mediate Toxoplasma gondii evasion of the murine, but not the human, interferon-gamma response. PLoS Pathogens, 8(6), e1002784. https://doi.org/10.1371/journal.ppat.1002784
  15. Alhasan, M. K., Liu, L., Lewis, M. A., Magnusson, J., & Mason, R. P. (2012). Comparison of optical and power Doppler ultrasound imaging for non-invasive evaluation of arsenic trioxide as a vascular disrupting agent in tumors. PLOS ONE, 7(9), e46106. https://doi.org/10.1371/journal.pone.0046106
  16. Yang, W., Liu, X., Peng, X., Li, P., Wang, T., Tai, G., … Zhou, Y. (2012). Synthesis of novel N-acetylneuraminic acid derivatives as substrates for rapid detection of influenza virus neuraminidase. Carbohydrate Research, 359, 92–96. https://doi.org/j.carres.2012.06.009
  17. Hsu, Y. C., Mildenstein, K., Hunter, K., Tkachenko, O., & Mullen, C. A. (2014). Acute lymphoid leukemia cells with greater stem cell antigen-1 (Ly6a/Sca-1) expression exhibit higher levels of metalloproteinase activity and are more aggressive In vivo. PloS One, 9(2), e88966. https://doi.org/10.1371/journal.pone.0088966
  18. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  19. Malo, C. S., Renner, D. N., Kelcher, A. M. H., Jin, F., Hansen, M. J., Pavelko, K. D., & Johnson, A. J. (2016). The effect of vector silencing during picornavirus vaccination against experimental melanoma and glioma. PloS One, 11(8), e0162064. https://doi.org/10.1371/journal.pone.0162064
  20. Fu, H., Wu, R., Li, Y., Zhang, L., Tang, X., Tu, J., … & Shou, Q. (2016). Safflower yellow prevents pulmonary metastasis of breast cancer by inhibiting tumor cell invadopodia. The American Journal of Chinese Medicine, 44(07), 1491-1506. https://doi.org/10.1142/S0192415X1650083X
  21. Yang, Y., Zhao, X., Li, X., Yan, Z., Liu, Z., & Li, Y. (2017). Effects of anti‑CD44 monoclonal antibody IM7 carried with chitosan polylactic acid-coated nano‑particles on the treatment of ovarian cancer. Oncology Letters, 13(1), 99-104. https://doi.org/10.3892/ol.2016.5413
  22. Che, T., Majumdar, S., Zaidi, S. A., Ondachi, P., McCorvy, J. D., Wang, S., … & Han, G. W. (2018). Structure of the nanobody-stabilized active state of the kappa opioid receptor. Cell, 172(1-2), 55-67. e15. https://doi.org/10.1016/j.cell.2017.12.011
  23. Rodriguez-Garcia, A., Watanabe, K., & Guedan, S. (2019). Analysis of antitumor effects of CAR-T cells in mice with solid tumors. In Methods in Molecular Biology (pp. 251–271). Springer US. https://doi.org/10.1007/978-1-0716-0146-4_19
  24. Shu, Y., Wang, Y., Lv, W. Q., Peng, D. Y., Li, J., Zhang, H., … & Chen, Y. H. (2020). ARRB1-promoted NOTCH1 degradation is suppressed by oncomiR miR-223 in T- cell acute lymphoblastic leukemia. Cancer Research, 80(5), 988-998. https://doi.org/10.1158/0008-5472.can-19-1471
  25. Day, E. K., Sosale, N. G., Xiao, A., Zhong, Q., Purow, B., & Lazzara, M. J. (2020). Glioblastoma Cell Resistance to EGFR and MET Inhibition Can Be Overcome via Blockade of FGFR-SPRY2 Bypass Signaling. Cell Reports, 30(10), 3383–3396.e7. https://doi.org/10.1016/j.celrep.2020.02.014
  26. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  27. Poliner, E., Pulman, J. A., Zienkiewicz, K., Childs, K., Benning, C., & Farré, E. M. (2017). A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production. Plant Biotechnology Journal, 16(1), 298–309. https://doi.org/10.1111/pbi.12772
  28. Tseng, S.-H., Park, S.-T., Lam, B., Tsai, Y.-C., Cheng, M. A., Farmer, E., Xing, D., & Hung, C.-F. (2020). Novel, genetically induced mouse model that recapitulates the histological morphology and immunosuppressive tumor microenvironment of metastatic peritoneal carcinomatosis. Journal for ImmunoTherapy of Cancer, 8(1), e000480. https://doi.org/10.1136/jitc-2019-000480
  29. Wang, H., & Zhang, X. (2020). Bone-in-culture array to model bone metastasis in ex vivo condition. Bio-Protocol, 10(2). https://doi.org/10.21769/bioprotoc.3495
  30. Cheng, Q., Wei, T., Farbiak, L., Johnson, L. T., Dilliard, S. A., & Siegwart, D. J. (2020). Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing. Nature Nanotechnology, 15(4), 313–320. https:/doi.org/10.1038/s41565-020-0669-6
  31. Radhakrishnan, S. V., Luetkens, T., Scherer, S. D., Davis, P., Vander Mause, E. R., Olson, M. L., … & Miles, R. R. (2020). CD229 CAR T cells eliminate multiple myeloma and tumor propagating cells without fratricide. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14619-z
  32. De Micheli, A. J., Laurilliard, E. J., Heinke, C. L., Ravichandran, H., Fraczek, P., Soueid-Baumgarten, S., … & Cosgrove, B. D. (2020). Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration. Cell Reports, 30(10), 3583–3595.e5. https://doi.org/10.1016/j.celrep.2020.02.067
  33. Schommers, P., Gruell, H., Abernathy, M. E., Tran, M. K., Dingens, A. S., Gristick, H. B., … & Kreer, C. (2020). Restriction of HIV-1 escape by a highly broad and potent neutralizing antibody. Cell, 180(3), 471-489. https://doi.org/10.1016/j.cell.2020.01.010
  34. Foster, S. R., Hauser, A. S., Vedel, L., Strachan, R. T., Huang, X. P., Gavin, A. C., … & Roth, B. L. (2019). Discovery of human signaling systems: pairing peptides to G protein-coupled receptors. Cell, 179(4), 895–908.e21. https://doi.org/10.1016/j.cell.2019.10.010
  35. Wang, H., Tian, L., Liu, J., Goldstein, A., Bado, I., Zhang, W., Arenkiel, B. R., Li, Z., Yang, M., Du, S., Zhao, H., Rowley, D. R., Wong, S. T. C., Gugala, Z., & Zhang, X. H.-F. (2018). The osteogenic niche is a calcium reservoir of bone micrometastases and confers unexpected therapeutic vulnerability. Cancer Cell, 34(5), 823–839.e7. https://doi.org/10.1016/j.ccell.2018.10.002
  36. Hsu, H. L., Brown, A., Loveland, A. B., Lotun, A., Xu, M., Luo, L., … & Gessler, D. J. (2020). Structural characterization of a novel human adeno-associated virus capsid with neurotropic properties. Nature Communications, 11(1), 1-14. https://doi.org/10.1038/s41467-020-17047-1
Digitonin Special Grade (water soluble)
  1. Taldone, T., Rodina, A., Gomes, E. M. D., Riolo, M., Patel, H. J., Alonso-Sabadell, R., … & Chiosis, G. (2013). Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes. Beilstein Journal of Organic Chemistry, 9, 544–556. https://doi.org/10.3762/bjoc.9.60
  2. Malty, R. H., Aoki, H., Kumar, A., Phanse, S., Amin, S., Zhang, Q., … & Abou-Tok, H. (2017). A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-κB signaling. Cell Systems, 5(6), 564-577. https://doi.org/10.1016/j.cels.2017.10.010
  3. Nowinski, S. M., Solmonson, A., Rusin, S. F., Maschek, J. A., Bensard, C. L., Fogarty, S., … & Rutter, J. (2020). Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria. Elife, 9, e58041.
  4. Ordureau, A., Paulo, J. A., Zhang, J., An, H., Swatek, K. N., Cannon, J. R., … & Harper, J. W. (2020). Global landscape and dynamics of parkin and USP30-dependent ubiquitylomes in iNeurons during mitophagic signaling. Molecular cell, 77(5), 1124-1142.
  5. Pelster, L. N., & Minteer, S. D. (2016). Mitochondrial inner membrane biomimic for the investigation of electron transport chain supercomplex bioelectrocatalysis. Acs Catalysis, 6(8), 4995-4999.
DNase I, Bovine Pancreas (Lysate Tested), >2000 Kunitz U/mg
  1. Zubcevic, L., Hsu, A. L., Borgnia, M. J., & Lee, S.-Y. (2019). Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. eLife, 8. https://doi.org/10.7554/elife.45779
  2. Dillard, K. E., Brown, M. W., Johnson, N. V., Xiao, Y., Dolan, A., Hernandez, E., … & Ke, A. (2018). Assembly and translocation of a CRISPR-Cas primed acquisition complex. Cell, 175(4), 934–946.e15. https://doi.org/10.1016/j.cell.2018.09.039
  3. Strohkendl, I., Saifuddin, F. A., Rybarski, J. R., Finkelstein, I. J., & Russell, R. (2018). Kinetic basis for DNA target specificity of CRISPR-Cas12a. Molecular Cell, 71(5), 816-824. https://doi.org/10.1016/j.molcel.2018.06.043
  4. Jung, C., Hawkins, J. A., Jones Jr, S. K., Xiao, Y., Rybarski, J. R., Dillard, K. E., … & Ke, A. (2017). Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips. Cell, 170(1), 35-47. https://doi.org/10.1016/j.cell.2017.05.044
DNase I, Bovine Pancreas (Lysate Tested), >500 Kunitz U/mg
  1. Dao, T. P., Martyniak, B., Canning, A. J., Lei, Y., Colicino, E. G., Cosgrove, M. S., … & Castañeda, C. A. (2019). ALS-linked mutations affect UBQLN2 oligomerization and phase separation in a position-and amino acid-dependent manner. Structure, 27(6), 937-951. https://doi.org/10.1016/j.str.2019.03.012
  2. Dao, T. P., Kolaitis, R. M., Kim, H. J., O’Donovan, K., Martyniak, B., Colicino, E., … & Castañeda, C. A. (2018). Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Molecular Cell, 69(6), 965-978. https://doi.org/10.1016/j.molcel.2018.02.004
Doxycycline Hyclate
  1. Kempton, H. R., Goudy, L. E., Love, K. S., & Qi, L. S. (2020). Multiple input sensing and signal integration using a split Cas12a system. Molecular Cell. https://doi.org/10.1016/j.molcel.2020.01.016
  2. Tang, X., Fu, X., Liu, Y., Yu, D., Cai, S. J., & Yang, C. (2019). Blockade of Glutathione Metabolism in IDH1-Mutated Glioma. Molecular Cancer Therapeutics, 19(1), 221–230. https://doi.org/10.1158/1535-7163.mct-19-0103
DTT (Dithiothreitol) (> 99% pure) Protease free
  1. Tan, A., & Henzl, M. T. (2009). Conformational stabilities of guinea pig OCP1 and OCP2. Biophysical Chemistry, 144(3), 108-118. https://doi.org/10.1016/j.bpc.2009.07.003
  2. Henzl, M. T., Davis, M. E., & Tan, A. (2008). Divalent ion binding properties of the timothy grass allergen, Phl p 7. Biochemistry, 47(30), 7846-7856. https://doi.org/10.1021/bi800620g
  3. Tan, A., Tanner, J. J., & Henzl, M. T. (2008). Energetics of OCP1–OCP2 complex formation. Biophysical Chemistry, 134(1-2), 64-71. https://doi.org/10.1016/j.bpc.2008.01.005
  4. Henzl, M. T., Davis, M. E., & Tan, A. (2010). Polcalcin divalent ion-binding behavior and thermal stability: comparison of Bet v 4, Bra n 1, and Bra n 2 to Phl p 7. Biochemistry, 49(10), 2256–2268. https://doi.org/10.1021/bi902115v
  5. Zhong, Y., Whittington, C. F., & Haynie, D. T. (2007). Stimulated release of small molecules from polyelectrolyte multilayer nanocoatings. Chemical Communications, (14), 1415-1417. https://doi.org/10.1039/b615699a
  6. Swearingen, K. E., Loomis, W. P., Zheng, M., Cookson, B. T., & Dovichi, N. J. (2010). Proteomic profiling of lipopolysaccharide-activated macrophages by isotope coded affinity tagging. Journal of Proteome Research, 9(5), 2412–2421. https://doi.org/10.1021/pr901124u
  7. Rubio, C., Pincus, D., Korennykh, A., Schuck, S., El-Samad, H., & Walter, P. (2011). Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. The Journal of Cell Biology, 193(1), 171-184. https://doi.org/10.1083/jcb.201007077
  8. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L., & Ruoho, A. E. (2007). One-step purification of bacterially expressed recombinant transducin α-subunit and isotopically labeled PDE6 γ-subunit for NMR analysis. Protein Expression and Purification, 51(2), 187-197. https://doi.org/10.1016/j.pep.2006.07.012
  9. Keith, K. E., Killip, L., He, P., Moran, G. R., & Valvano, M. A. (2007). Burkholderia cenocepacia C5424 produces a pigment with antioxidant properties using a homogentisate intermediate. Journal of Bacteriology, 189(24), 9057-9065.https://doi.org/10.1128/JB.00436-07
  10. Norais, C. A., Chitteni-Pattu, S., Wood, E. A., Inman, R. B., & Cox, M. M. (2009). DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. Journal of Biological Chemistry, 284(32), 21402-21411. https://doi.org/10.1074/jbc.M109.010454
  11. Johnson, T. A., & Holyoak, T. (2010). Increasing the conformational entropy of the Ω-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity. Biochemistry, 49(25), 5176-5187.https://doi.org/10.1021/bi100399e
  12. Sandoval, C. M., Baker, S. L., Jansen, K., Metzner, S. I., & Sousa, M. C. (2011). Crystal structure of BamD: an essential component of the β-barrel assembly machinery of gram-negative bacteria. Journal of Molecular Biology, 409(3), 348-357. https://doi.org/10.1016/j.jmb.2011.03.035
  13. Sharma, B., Deo, S. K., Bachas, L. G., & Daunert, S. (2005). Competitive binding assay using fluorescence resonance energy transfer for the identification of calmodulin antagonists. Bioconjugate Chemistry, 16(5), 1257-1263. https://doi.org/10.1021/bc050161y
  14. Lee, K. H., Saleh, L., Anton, B. P., Madinger, C. L., Benner, J. S., Iwig, D. F., … & Booker, S. J. (2009). Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry, 48(42), 10162-10174. https://doi.org/10.1021/bi900939w
  15. Bailey, S. W., & Ayling, J. E. (2009). The extremely slow and variable activity of dihydrofolate reductase in human liver and its implications for high folic acid intake. Proceedings of the National Academy of Sciences, 106(36), 15424-15429. https://doi.org/10.1073/pnas.0902072106
  16. Hasoun, L. Z., Bailey, S. W., Outlaw, K. K., & Ayling, J. E. (2013). Effect of serum folate status on total folate and 5-methyltetrahydrofolate in human skin. The American Journal of Clinical Nutrition, 98(1), 42-48. https://doi.org/10.3945/ajcn.112.057562
  17. Landgraf, B. J., Arcinas, A. J., Lee, K. H., & Booker, S. J. (2013). Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. Journal of the American Chemical Society, 135(41), 15404-15416. https://doi.org/10.1021/ja4048448
  18. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  19. Zhang, B., Zhu, D. W., Hu, X. J., Zhou, M., Shang, P., & Lin, S. X. (2014). Human 3-alpha hydroxysteroid dehydrogenase type 3 (3α-HSD3): the V54L mutation restricting the steroid alternative binding and enhancing the 20α-HSD activity. The Journal of Steroid Biochemistry and Molecular Biology, 141, 135-143.https://doi.org/10.1016/j.jsbmb.2014.01.003
  20. Hentchel, K. L., & Escalante-Semerena, J. C. (2015). In Salmonella enterica, the Gcn5-related acetyltransferase MddA (formerly YncA) acetylates methionine sulfoximine and methionine sulfone, blocking their toxic effects. Journal of Bacteriology, 197(2), 314-325.https://doi.org/10.1128/JB.02311-14
  21. Kitanishi, K., Cracan, V., & Banerjee, R. (2015). Engineered and native coenzyme B12-dependent isovaleryl-CoA/pivalyl-CoA mutase. Journal of Biological Chemistry, 290(33), 20466-20476.https://doi.org/ 10.1074/jbc.M115.646299
  22. Roy, S., Soh, J. H., & Ying, J. Y. (2016). A microarray platform for detecting disease-specific circulating miRNA in human serum. Biosensors and Bioelectronics, 75, 238-246. https://doi.org/10.1016/j.bios.2015.08.039
  23. Balan, M. D., Mcleod, M. J., Lotosky, W. R., Ghaly, M., & Holyoak, T. (2015). Inhibition and allosteric regulation of monomeric phosphoenolpyruvate carboxykinase by 3-mercaptopicolinic acid. Biochemistry, 54(38), 5878-5887.https://doi.org/10.1021/acs.biochem.5b00822
  24. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  25. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  26. Block, E., Booker, S. J., Flores‐Penalba, S., George, G. N., Gundala, S., Landgraf, B. J., … & Vattekkatte, A. (2016). Trifluoroselenomethionine: A new unnatural amino acid. ChemBioChem, 17(18), 1738-1751. https://doi.org/10.1002/cbic.201600266
  27. Bird, J. G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., … & Kaplan, C. D. (2016). The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature, 535(7612), 444. https://doi.org/10.1038/nature18622
  28. Ledwitch, K. V., Gibbs, M. E., Barnes, R. W., & Roberts, A. G. (2016). Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology, 118, 96-108. https://doi.org/10.1016/j.bcp.2016.08.013
  29. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  30. Addington, C. P., Dharmawaj, S., Heffernan, J. M., Sirianni, R. W., & Stabenfeldt, S. E. (2017). Hyaluronic acid-laminin hydrogels increase neural stem cell transplant retention and migratory response to SDF-1α. Matrix Biology, 60, 206-216. https://doi.org/10.1016/j.matbio.2016.09.007
  31. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  32. Rogals, M. J., Greenwood, A. I., Kwon, J., Lu, K. P., & Nicholson, L. K. (2016). Neighboring phosphoSer‐Pro motifs in the undefined domain of IRAK 1 impart bivalent advantage for Pin1 binding. The FEBS Journal, 283(24), 4528-4548. https://doi.org/10.1111/febs.13943
  33. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
  34. Bohl, T. E., Shi, K., Lee, J. K., & Aihara, H. (2018). Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Nature Communications, 9(1), 377.10.1038/s41467-017-02712-9
  35. Fassler, R., Edinger, N., Rimon, O., & Reichmann, D. (2018). Defining Hsp33’s redox-regulated chaperone activity and mapping conformational changes on Hsp33 using hydrogen-deuterium exchange mass spectrometry. JoVE (Journal of Visualized Experiments), (136), e57806. https://doi.org/10.3791/57806
  36. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  37. Pisa, R., Cupido, T., Steinman, J. B., Jones, N. H., & Kapoor, T. M. (2019). Analyzing resistance to design selective chemical inhibitors for AAA proteins. Cell Chemical Biology.https://doi.org/10.1016/j.chembiol.2019.06.001
  38. Kim, S., Loeff, L., Colombo, S., Jergic, S., Brouns, S. J. J., & Joo, C. (2020). Selective loading and processing of prespacers for precise CRISPR adaptation. Nature, 579(7797), 141–145. https://doi.org/10.1038/s41586-020-2018-1
  39. Klein, B. J., Cox, K. L., Jang, S. M., Côté, J., Poirier, M. G., & Kutateladze, T. G. (2020). Molecular basis for the PZP domain of BRPF1 association with chromatin. Structure, 28(1), 105–110.e3. https://doi.org/10.1016/j.str.2019.10.014
  40. Cohen, D. T., Wales, T. E., McHenry, M. W., Engen, J. R., & Walensky, L. D. (2020). Site-dependent cysteine lipidation potentiates the activation of proapoptotic BAX. Cell Reports, 30(10), 3229–3239.e6. https://doi.org/10.1016/j.celrep.2020.02.057
  41. Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2020). Modulation of kinesin’s load-bearing capacity by force geometry and the microtubule track. Biophysical Journal, 118(1), 243–253. https://doi.org/10.1016/j.bpj.2019.10.045
  42. Ruetz, M., Kumutima, J., Lewis, B. E., Filipovic, M. R., Lehnert, N., Stemmler, T. L., & Banerjee, R. (2017). A distal ligand mutes the interaction of hydrogen sulfide with human neuroglobin. Journal of Biological Chemistry, 292(16), 6512–6528. https://doi.org/10.1074/jbc.m116.770370
  43. Jin, J., Jung, I. H., Moon, S. H., Jeon, S., Jeong, S. J., Sonn, S. K., … & Kim, S. (2020). CD137 signaling regulates acute colitis via RALDH2-expressing CD11b− CD103+ DCs. Cell Reports, 30(12), 4124-4136. https://doi.org/10.1016/j.celrep.2020.02.103
  44. Grzybowski, A. T., Shah, R. N., Richter, W. F., & Ruthenburg, A. J. (2019). Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nature Protocols, 14(12), 3275–3302. https://doi.org/10.1038/s41596-019-0218-7
  45. Seven, A. B., Hilger, D., Papasergi-Scott, M. M., Zhang, L., Qu, Q., Kobilka, B. K., … & Skiniotis, G. (2020). Structures of Gα proteins in complex with their chaperone reveal quality control mechanisms. Cell Reports, 30(11), 3699–3709.e6. https://doi.org/10.1016/j.celrep.2020.02.086
  46. Qu, X., Kumar, A., Blockus, H., Waites, C., & Bartolini, F. (2019). Activity-dependent nucleation of dynamic microtubules at presynaptic boutons controls neurotransmission. Current Biology, 29(24), 4231-4240.e5. https://doi.org/10.1016/j.cub.2019.10.049
  47. Blus, B. J., Hashimoto, H., Seo, H.-S., Krolak, A., & Debler, E. W. (2019). Substrate affinity and specificity of the ScSth1p bromodomain are fine-tuned for versatile histone recognition. Structure, 27(9), 1460–1468.e3. https://doi.org/10.1016/j.str.2019.06.009
  48. Jia, N., Jones, R., Sukenick, G., & Patel, D. J. (2019). Second messenger cA4 formation within the composite Csm1 palm pocket of type III-A CRISPR-Cas Csm complex and its release path. Molecular cell, 75(5), 933-943. https://doi.org/10.1016/j.molcel.2019.06.013
  49. Jia, N., Jones, R., Yang, G., Ouerfelli, O., & Patel, D. J. (2019). CRISPR-Cas III-A Csm6 CARF domain is a ring nuclease triggering stepwise cA4 cleavage with ApA> p formation terminating RNase activity. Molecular Cell, 75(5), 944-956. https://doi.org/10.1016/j.molcel.2019.06.014
  50. Jia, N., Mo, C. Y., Wang, C., Eng, E. T., Marraffini, L. A., & Patel, D. J. (2019). Type III-A CRISPR-Cas Csm complexes: assembly, periodic RNA cleavage, DNase activity regulation, and autoimmunity. Molecular Cell, 73(2), 264-277.e5. https://doi.org/10.1016/j.molcel.2018.11.007
  51. Li, Y., Zhang, Z., Phoo, W. W., Loh, Y. R., Li, R., Yang, H. Y., … & Luo, D. (2018). Structural insights into the inhibition of Zika virus NS2B-NS3 protease by a small-molecule inhibitor. Structure, 26(4), 555-564. https://doi.org/10.1016/j.str.2018.02.005
  52. Campbell, B. C., Petsko, G. A., & Liu, C. F. (2018). Crystal structure of green fluorescent protein clover and design of clover-based redox sensors. Structure, 26(2), 225-237. https://doi.org/10.1016/j.str.2017.12.006
  53. Martin-Perez, M., & Villén, J. (2017). Determinants and regulation of protein turnover in yeast. Cell Systems, 5(3), 283-294. https://doi.org/10.1016/j.cels.2017.08.008
  54. Li, Y., Zhang, Z., Phoo, W. W., Loh, Y. R., Wang, W., Liu, S., … & Kang, C. (2017). Structural dynamics of Zika virus NS2B-NS3 protease binding to dipeptide inhibitors. Structure, 25(8), 1242-1250. https://doi.org/10.1016/j.str.2017.06.006
  55. Huang, T. L., Wang, H. J., Chang, Y. C., Wang, S. W., & Hsia, K. C. (2020). Promiscuous binding of microprotein Mozart1 to γ-Tubulin complex mediates specific subcellular targeting to control microtubule array formation. Cell Reports, 31(13), 107836. https://doi.org/10.1016/j.celrep.2020.107836
  56. Wieczorek, M., Huang, T. L., Urnavicius, L., Hsia, K. C., & Kapoor, T. M. (2020). MZT proteins form multi-faceted structural modules in the γ-Tubulin ring complex. Cell Reports, 31(13), 107791. https://doi.org/10.1016/j.celrep.2020.107791
n-Dodecyl-B-D-maltoside (DDM)
  1. Mukherjee, D., May, M., & Khomami, B. (2011). Detergent–protein interactions in aqueous buffer suspensions of Photosystem I (PS I). Journal of Colloid and Interface Science, 358(2), 477–484. https://doi.org/10.1016/j.jcis.2011.03.070
  2. Niroomand, H., Venkatesan, G. A., Sarles, S. A., Mukherjee, D., & Khomami, B. (2016). Lipid-detergent phase transitions during detergent-mediated liposome solubilization. The Journal of Membrane Biology, 249(4), 523-538. https://doi.org/10.1007/s00232-016-9894-1
  3. Belardinelli, J. M., Stevens, C. M., Li, W., Tan, Y. Z., Jones, V., Mancia, F., … & Jackson, M. (2019). The MmpL3 interactome reveals a complex crosstalk between cell envelope biosynthesis and cell elongation and division in mycobacteria. Scientific Reports, 9(1), 10728. https://doi.org/10.1038/s41598-019-47159-8
  4. Das, D., Bao, H., Courtney, K. C., Wu, L., & Chapman, E. R. (2020). Resolving kinetic intermediates during the regulated assembly and disassembly of fusion pores. Nature Communications, 11(1), 1-12.https://doi.org/10.1038/s41467-019-14072-7
VersaLadder™, 100-10,000 bp
  1. O’Halloran, D. M., Uriagereka-Herburger, I., & Bode, K. (2017). STITCHER 2.0: primer design for overlapping PCR applications. Scientific Reports, 7(1). https://doi.org/10.1038/srep45349
E-64
  1. Chaparian, R. R., Tran, M. L., Miller Conrad, L. C., Rusch, D. B., & van Kessel, J. C. (2020). Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. Nucleic Acids Research, 48(1), 171-183.
EDTA Disodium, dihydrate
  1. Case, H., & Dickenson, N. (2018). Kinetic characterization of the shigella type three secretion system ATPase spa47 using α-32P ATP. Bio-Protocol, 8(21): e3074. https://doi.org/10.21769/bioprotoc.3074
EGF, Human
  1. Kemmerer, Z. A., Ader, N. R., Mulroy, S. S., & Eggler, A. L. (2015). Comparison of human Nrf2 antibodies: a tale of two proteins. Toxicology Letters, 238(2), 83-89.https://doi.org/10.1016/j.toxlet.2015.07.004
  2. Jiang, Y., Zhang, Y., Leung, J. Y., Fan, C., Popov, K. I., Su, S., … & Xiang, Y. (2019). MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression. Nature Communications, 10(1), 1515. https://doi.org/10.1038/s41467-019-09233-7
  3. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
  4. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  5. Hoffman, H. K., Fernandez, M. V., Groves, N. S., Freed, E. O., & van Engelenburg, S. B. (2019). Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. Journal of Biological Chemistry, 294(44), 16266–16281. https://doi.org/10.1074/jbc.ra119.009372
  6. Ali, R. (2019). The Role of Signal Transducer and Activator of Transcription 1 (STAT1) and 3 (STAT3) in Primary and Metastatic Breast Cancer (Doctoral dissertation, Purdue University Graduate School).
  7. Aminuddin, A., Ng, P. Y., Leong, C.-O., & Chua, E. W. (2020). Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64664-3
EGTA
  1. Baradaran, R., Wang, C., Siliciano, A. F., & Long, S. B. (2018). Cryo-EM structures of fungal and metazoan mitochondrial calcium uniporters. Nature, 559(7715), 580. https://doi.org/10.1038/s41586-018-0331-8
Erythromycin
  1. Park, E. J., Hussain, M. S., Wei, S., Kwon, M., & Oh, D. H. (2019). Genotypic and phenotypic characteristics of biofilm formation of emetic toxin producing Bacillus cereus, strains. Food Control, 96, 527-534.https://doi.org/10.1016/j.foodcont.2018.10.008
5-Fluoroorotic acid monohydrate (5-FOA)
  1. Thakker, C., Lin, K., Martini‐Stoica, H., & Bennett, G. N. (2016). Use of transposase and ends of IS608 enables precise and scarless genome modification for modulating gene expression and metabolic engineering applications in Escherichia coli. Biotechnology Journal, 11(1), 80-90. https://doi.org/10.1002/biot.201500205
  2. Standage-Beier, K., Zhang, Q., & Wang, X. (2015). Targeted large-scale deletion of bacterial genomes using CRISPR-nickases. ACS Synthetic Biology, 4(11), 1217–1225. https://doi.org/10.1021/acssynbio.5b00132
  3. Luttgeharm, K. D., Cahoon, E. B., & Markham, J. E. (2016). Substrate specificity, kinetic properties and inhibition by fumonisin B1 of ceramide synthase isoforms from Arabidopsis. Biochemical Journal, 473(5), 593-603. https://doi.org/10.1042/BJ20150824
  4. Burrack, L. S., Hutton, H. F., Matter, K. J., Clancey, S. A., Liachko, I., Plemmons, A. E., … Berman, J. (2016). Neocentromeres provide chromosome segregation accuracy and centromere clustering to multiple loci along a Candida albicans chromosome. PLoS Genetics, 12(9), e1006317. https://doi.org/10.1371/journal.pgen.1006317
Acidic FGF (FGF1), Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
Basic FGF (FGF2), Human
  1. Sowmya, S., Chennazhi, K. P., Arzate, H., Jayachandran, P., Nair, S. V., & Jayakumar, R. (2015). Periodontal specific differentiation of dental follicle stem cells into osteoblast, fibroblast, and cementoblast. Tissue Engineering Part C: Methods, 21(10), 1044-1058. https://doi.org/10.1089/ten.tec.2014.0603
  2. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
  3. Spina, R., Voss, D. M., Asnaghi, L., Sloan, A., & Bar, E. E. (2018). Flow cytometry-based drug screening system for the identification of small molecules that promote cellular differentiation of glioblastoma stem cells. Journal of Visualized Experiments, 131. https://doi.org/10.3791/56176
  4. Aminuddin, A., Ng, P. Y., Leong, C.-O., & Chua, E. W. (2020). Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64664-3
Basic FGF (FGF2), Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF10/KGF2, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF7/KGF1, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF8, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
FGF9, Murine
  1. Wu, J., Zhang, M., Zhang, Y., Zeng, Y., Zhang, L., & Zhao, X. (2016). Anticoagulant and FGF/FGFR signal activating activities of the heparinoid propylene glycol alginate sodium sulfate and its oligosaccharides. Carbohydrate Polymers, 136, 641–648. https://doi.org/10.1016/j.carbpol.2015.09.059
  2. Hou, N., Zhang, M., Xu, Y., Sun, Z., Wang, J., Zhang, L., & Zhang, Q. (2017). Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities. International Journal of Biological Macromolecules, 105, 1511–1518. https://doi.org/10.1016/j.ijbiomac.2017.06.042
D-Galactose
  1. Henty-Ridilla, J. L., Rankova, A., Eskin, J. A., Kenny, K., & Goode, B. L. (2016). Accelerated actin filament polymerization from microtubule plus ends. Science, 352(6288), 1004-1009. https://doi.org/10.1126/science.aaf1709
G418 Sulfate
  1. Finnigan, G. C., Ryan, M., & Stevens, T. H. (2011). A genome-wide enhancer screen implicates sphingolipid composition in vacuolar ATPase function in Saccharomyces cerevisiae. Genetics, 187(3), 771-783. https://doi.org/10.1534/genetics.110.125567
  2. Dutta, C., Day, T., Kopp, N., van Bodegom, D., Davids, M. S., Ryan, J., … & Fung, H. (2012). BCL2 suppresses PARP1 function and nonapoptotic cell death. Cancer Research, 72(16), 4193–4203. https://doi.org/10.1158/0008-5472.can-11-4204
  3. Hong, S. W., Jiang, Y., Kim, S., Li, C. J., & Lee, D. (2014). Target gene abundance contributes to the efficiency of siRNA-mediated gene silencing. Nucleic Acid Therapeutics, 24(3), 192–198. https://doi.org/10.1089/nat.2013.0466
  4. Hiemer, S. E., Szymaniak, A. D., & Varelas, X. (2014). The transcriptional regulators TAZ and YAP direct transforming growth factor β-induced tumorigenic phenotypes in breast cancer cells. Journal of Biological Chemistry, 289(19), 13461-13474. https://doi.org/10.1074/jbc.M113.529115
  5. Lawrence, J. E., Steele, C. J., Rovin, R. A., Belton, R. J., & Winn, R. J. (2016). Dexamethasone alone and in combination with desipramine, phenytoin, valproic acid or levetiracetam interferes with 5-ALA-mediated PpIX production and cellular retention in glioblastoma cells. Journal of Neuro-oncology, 127(1), 15-21. https://doi.org/10.1007/s11060-015-2012-x
  6. Keller, J., Nimnual, A. S., Varghese, M. S., VanHeyst, K. A., Hayman, M. J., & Chan, E. L. (2016). A novel EGFR extracellular domain mutant, EGFRΔ768, possesses distinct biological and biochemical properties in neuroblastoma. Molecular Cancer Research, 14(8), 740-752. https://doi.org/10.1158/1541-7786.mcr-15-0477
  7. Abu-Tayeh, H., Weidenfeld, K., Zhilin-Roth, A., Schif-Zuck, S., Thaler, S., Cotarelo, C., … & Sabo, E. (2016). ‘Normalizing’the malignant phenotype of luminal breast cancer cells via alpha (v) beta (3)-integrin. Cell Death & Disease, 7(12), e2491. https://doi.org/10.1038/cddis.2016.387
  8. Mercier, R., Wolmarans, A., Schubert, J., Neuweiler, H., Johnson, J. L., & LaPointe, P. (2019). The conserved NxNNWHW motif in Aha-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation. Nature Communications, 10(1), 1273. https://doi.org/10.1038/s41467-019-09299-3
  9. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  10. Mauldin, I. S., Sheybani, N. D., Young, S. J., Price, R. J., & Slingluff, C. L. (2020). Deconvolution of the immunological contexture of mouse tumors with multiplexed immunohistochemistry. In Methods in Enzymology (pp. 81–93). Elsevier. https://doi.org/10.1016/bs.mie.2019.05.038
  11. Wang, A., Kolhe, J. A., Gioacchini, N., Baade, I., Brieher, W. M., Peterson, C. L., & Freeman, B. C. (2020). Mechanism of long-range chromosome motion triggered by gene activation. Developmental Cell, 52(3), 309–320.e5. https://doi.org/10.1016/j.devcel.2019.12.007
  12. Park, S., Brugiolo, M., Akerman, M., Das, S., Urbanski, L., Geier, A., … & Hu, L. (2019). Differential functions of splicing factors in mammary transformation and breast cancer metastasis. Cell Reports, 29(9), 2672-2688.e5. https://doi.org/10.1016/j.celrep.2019.10.110
GelRed™ Nucleic Acid Gel Stain, 10,000X in Water
  1. Kozakiewicz, C. P., Burridge, C. P., Funk, W. C., Craft, M. E., Crooks, K. R., Fisher, R. N., … Carver, S. (2020). Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development. Evolutionary Applications. https://doi.org/10.1111/eva.12927
  2. Asghari, A., Zare, M., Hatam, G., Shahabi, S., Gholizadeh, F., & Motazedian, M. (2020). Molecular identification and subtypes distribution of Blastocystis sp. isolated from children and adolescent with cancer in Iran: evaluation of possible risk factors and clinical features. Acta Parasitologica. https://doi.org/10.2478/s11686-020-00186-2
Gentamicin Sulfate, USP Grade
  1. Ketelboeter, L. M., & Bardy, S. L. (2015). Methods to inhibit bacterial pyomelanin production and determine the corresponding increase in sensitivity to oxidative stress. JoVE (Journal of Visualized Experiments), (102), e53105. https://doi.org/10.3791/53105
  2. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  3. Moroz, N., & Tanaka, K. (2020). FlgII-28 is a major flagellin-derived defense elicitor in potato. Molecular Plant-Microbe Interactions, 33(2), 247–255. https://doi.org/10.1094/mpmi-06-19-0164-r
  4. Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020). Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nature Biotechnology. https://doi.org/10.1038/s41587-020-0468-5
  5. Gogokhia, L., Buhrke, K., Bell, R., Hoffman, B., Brown, D. G., Hanke-Gogokhia, C., … & Porter, N. (2019). Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host & Microbe, 25(2), 285-299. https://doi.org/10.1016/j.chom.2019.01.008
  6. Yadav, D., Ghosh, K., Basu, S., Roeder, R. G., & Biswas, D. (2019). Multivalent role of human TFIID in recruiting elongation components at the promoter-proximal region for transcriptional control. Cell Reports, 26(5), 1303–1317.e7. https://doi.org/10.1016/j.celrep.2019.01.012
Gibberellic Acid 3 (Quick-Dissolve™)
  1. Pearce, S., Vanzetti, L. S., & Dubcovsky, J. (2013). Exogenous gibberellins induce wheat spike development under short days only in the presence of VERNALIZATION1. Plant Physiology, 163(3), 1433-1445. https://doi.org/10.1104/pp.113.225854
  2. Best, N. B., Hartwig, T., Budka, J. S., Bishop, B. J., Brown, E., Potluri, D. P., … & Schulz, B. (2014). Soilless plant growth media influence the efficacy of phytohormones and phytohormone inhibitors. PloS One, 9(12), e107689.. https://doi.org/10.1371/journal.pone.0107689
  3. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  4. Best, N. B., Wang, X., Brittsan, S., Dean, E., Helfers, S. J., Homburg, R., … & Hasegawa, P. M. (2016). Sunflower ‘Sunspot’ is hyposensitive to GA3 and has a missense mutation in the DELLA motif of HaDella1. Journal of the American Society for Horticultural Science, 141(4), 389-394. https://doi.org/10.21273/JASHS.141.4.389
Glutathione Agarose Resin
  1. Ricketts, M. D., Frederick, B., Hoff, H., Tang, Y., Schultz, D. C., Rai, T. S., … & Marmorstein, R. (2015). Ubinuclein-1 confers histone H3. 3-specific-binding by the HIRA histone chaperone complex. Nature Communications, 6, 7711. https://doi.org/10.1038/ncomms8711
  2. Williams, P. A., Krug, M. S., McMillan, E. A., Peake, J. D., Davis, T. L., Cocklin, S., & Strochlic, T. I. (2016). Phosphorylation of the RNA-binding protein Dazl by MAPKAP kinase 2 regulates spermatogenesis. Molecular Biology of the Cell, 27(15), 2341-2350. https://doi.org/10.1091/mbc.e15-11-0773
  3. Rajavel, M., Orban, T., Xu, M., Hernandez-Sanchez, W., de la Fuente, M., Palczewski, K., & Taylor, D. J. (2016). Dynamic peptides of human TPP1 fulfill diverse functions in telomere maintenance. Nucleic Acids Research, 44(21), 10467-10479. https://doi.org/10.1093/nar/gkw846
  4. Barragan-Iglesias, P., Lou, T. F., Bhat, V. D., Megat, S., Burton, M. D., Price, T. J., & Campbell, Z. T. (2018). Inhibition of Poly (A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice. Nature Communications, 9(1), 10. https://doi.org/10.1038/s41467-017-02449-5
  5. Pisa, R., Cupido, T., Steinman, J. B., Jones, N. H., & Kapoor, T. M. (2019). Analyzing resistance to design selective chemical inhibitors for AAA proteins. Cell Chemical Biology.https://doi.org/10.1016/j.chembiol.2019.06.001
  6. Gorgulla, C., Boeszoermenyi, A., Wang, Z.-F., Fischer, P. D., Coote, P., Padmanabha Das, K. M., … & Arthanari, H. (2020). An open-source drug discovery platform enables ultra-large virtual screens. Nature. https://doi.org/10.1038/s41586-020-2117-z
  7. Holly, R. W., Jones, K., & Prehoda, K. E. (2020). A conserved PDZ-binding motif in aPKC interacts with Par-3 and mediates cortical polarity. Current Biology, 30(5), 893-898.e5. https://doi.org/10.1016/j.cub.2019.12.055
  8. Mayank, A. K., Pandey, V., Vashisht, A. A., Barshop, W. D., Rayatpisheh, S., Sharma, T., … & Wohlschlegel, J. A. (2019). An oxygen-dependent interaction between FBXL5 and the CIA-targeting complex regulates iron homeostasis. Molecular Cell, 75(2), 382–393.e5. https://doi.org/10.1016/j.molcel.2019.05.020
  9. Arceci, A., Bonacci, T., Wang, X., Stewart, K., Damrauer, J. S., Hoadley, K. A., & Emanuele, M. J. (2019). FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell Reports, 26(11), 3076–3086.e6. https://doi.org/10.1016/j.celrep.2019.02.054
L-Glutathione, Reduced
  1. Picarda, E., Bézie, S., Usero, L., Ossart, J., Besnard, M., Halim, H., … & Gras, S. (2019). Cross-reactive donor-specific CD8+ tregs efficiently prevent transplant rejection. Cell Reports, 29(13), 4245-4255. https://doi.org/10.1016/j.celrep.2019.11.106
  2. Huang, T. L., Wang, H. J., Chang, Y. C., Wang, S. W., & Hsia, K. C. (2020). Promiscuous binding of microprotein Mozart1 to γ-Tubulin complex mediates specific subcellular targeting to control microtubule array formation. Cell Reports, 31(13), 107836. https://doi.org/10.1016/j.celrep.2020.107836
  3. Wieczorek, M., Huang, T. L., Urnavicius, L., Hsia, K. C., & Kapoor, T. M. (2020). MZT proteins form multi-faceted structural modules in the γ-Tubulin ring complex. Cell Reports, 31(13), 107791. https://doi.org/10.1016/j.celrep.2020.107791
ProBlock™ Gold Bacterial Protease Inhibitor Cocktail [100X]
  1. Beh, L. Y., Debelouchina, G. T., Clay, D. M., Thompson, R. E., Lindblad, K. A., Hutton, E. R., … & Landweber, L. F. (2019). Identification of a DNA N6-adenine methyltransferase complex and its impact on chromatin organization. Cell, 177(7), 1781-1796. https://doi.org/10.1016/j.cell.2019.04.028
  2. Huang, J. W., Acharya, A., Taglialatela, A., Nambiar, T. S., Cuella-Martin, R., Leuzzi, G., … & Soni, R. K. (2020). MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16718-3
ProBlock™ Gold Mammalian Protease Inhibitor Cocktail [100X]
  1. Santarriaga, S., Haver, H. N., Kanack, A. J., Fikejs, A. S., Sison, S. L., Egner, J. M., … & Ebert, A. D. (2018). SRCP1 conveys resistance to polyglutamine aggregation. Molecular Cell, 71(2), 216-228. https://doi.org/10.1016/j.molcel.2018.07.008
Simple Stop™ 2 Phosphatase Inhibitor Cocktail
  1. Li, S., Lavagnino, Z., Lemacon, D., Kong, L., Ustione, A., Ng, X., … & Vindigni, A. (2019). Ca2+-stimulated AMPK-dependent phosphorylation of exo1 protects stressed replication forks from aberrant resection. Molecular Cell, 74(6), 1123-1137. https://doi.org/10.1016/j.molcel.2019.04.003
X-gluc (CHX salt)
  1. Tan, X., Meyers, B. C., Kozik, A., West, M. A., Morgante, M., St Clair, D. A., … Michelmore, R. W. (2007). Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biology, 7(1), 56. https://doi.org/10.1186/1471-2229-7-56
  2. DeMason, D. A., & Polowick, P. L. (2009). Patterns of DR5::GUS expression in organs of pea (Pisum sativum). International Journal of Plant Sciences, 170(1), 1–11. https://doi.org/10.1086/593046
  3. Ourmanov, I., Kuwata, T., Goeken, R., Goldstein, S., Iyengar, R., Buckler-White, A., … Hirsch, V. M. (2009). Improved survival in rhesus macaques immunized with modified vaccinia virus Ankara recombinants expressing simian immunodeficiency virus envelope correlates with reduction in memory CD4+ T-cell loss and higher titers of neutralizing antibody. Journal of Virology, 83(11), 5388–5400. https://doi.org/10.1128/jvi.02598-08
  4. Yuan, S., & Dean, J. F. D. (2010). Differential responses of the promoters from nearly identical paralogs of loblolly pine (Pinus taeda L.) ACC oxidase to biotic and abiotic stresses in transgenic Arabidopsis thaliana. Planta, 232(4), 873–886. https://doi.org/10.1007/s00425-010-1224-8
  5. Fuqua, C., Burbea, M., & Winans, S. C. (1995). Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. Journal of Bacteriology, 177(5), 1367-1373. https://doi.org/10.1128/jb.177.5.1367-1373.1995
  6. López, C. M., Rholl, D. A., Trunck, L. A., & Schweizer, H. P. (2009). Versatile dual-technology system for markerless allele replacement in Burkholderia pseudomallei. Applied and Environmental Microbiology, 75(20), 6496–6503. https://doi.org/10.1128/aem.01669-09
  7. Fuqua, W. C., & Winans, S. C. (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. Journal of Bacteriology, 176(10), 2796-2806. https://doi.org/10.1128/jb.176.10.2796-2806.1994
  8. Marchant, R., Power, J. B., Lucas, J. A., & Davey, M. R. (1998). Biolistic transformation of rose (Rosa hybrida L.). Annals of Botany, 81(1), 109-114. https://doi.org/10.1006/anbo.1997.0538
  9. Cho, M. J., Choi, H. W., Buchanan, B. B., & Lemaux, P. G. (1999). Inheritance of tissue-specific expression of barley hordein promoter-uidA fusions in transgenic barley plants. Theoretical and Applied Genetics, 98(8), 1253–1262. https://doi.org/10.1007/s001220051191
  10. Matsumura, I., Wallingford, J. B., Surana, N. K., Vize, P. D., & Ellington, A. D. (1999). Directed evolution of the surface chemistry of the reporter enzyme β-glucuronidase. Nature Biotechnology, 17(7), 696. https://doi.org/10.1038/10910
  11. Cho, M.J., Jiang, W., & Lemaux, P. G. (1999). High-frequency transformation of oat via microprojectile bombardment of seed-derived highly regenerative cultures. Plant Science, 148(1), 9–17. https://doi.org/10.1016/s0168-9452(99)00082-5
  12. Ingram, H. M., Power, J. B., Lowe, K. C., & Davey, M. R. (1999). Optimisation of procedures for microprojectile bombardment of microspore-derived embryos in wheat. Plant Cell, Tissue and Organ Culture, 57(3), 207–210. https://doi.org/10.1023/a:1006384525513
  13. Sripaoraya, S., Marchant, R., Power, J. B., & Davey, M. R. (2001). Herbicide-tolerant transgenic pineapple (Ananas comosus) produced by microprojectile bombardment. Annals of Botany, 88(4), 597–603. https://doi.org/10.1006/anbo.2001.1502
  14. Bartel, B., & Fink, G. R. (1994). Differential regulation of an auxin-producing nitrilase gene family in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 91(14), 6649-6653. https://doi.org/10.1073/pnas.91.14.6649
  15. Micallef, M. C., Austin, S., & Bingham, E. T. (1995). Improvement of transgenic alfalfa by backcrossing. In Vitro Cellular & Developmental Biology-Plant, 31(4), 187-192. https://doi.org/10.1007/BF02632019
  16. Yang, Z., Rogers, L. M., Song, Y., Guo, W., & Kolattukudy, P. E. (2005). Homoserine and asparagine are host signals that trigger in planta expression of a pathogenesis gene in Nectria haematococca. Proceedings of the National Academy of Sciences, 102(11), 4197-4202. https://doi.org/10.1073/pnas.0500312102
  17. Southgate, E. M., Davey, M. R., Power, J. B., & Westcott, R. J. (1998). A comparison of methods for direct gene transfer into maize (Zea mays L.). In Vitro Cellular & Developmental Biology – Plant, 34(3), 218–224. https://doi.org/10.1007/bf02822711
  18. Ketchum, R. E., Wherland, L., & Croteau, R. B. (2007). Stable transformation and long-term maintenance of transgenic Taxus cell suspension cultures. Plant Cell Reports, 26(7), 1025-1033. https://doi.org/10.1007/s00299-007-0323-x
  19. Coque, L., Neogi, P., Pislariu, C., Wilson, K. A., Catalano, C., Avadhani, M., … & Dickstein, R. (2008). Transcription of ENOD8 in Medicago truncatula nodules directs ENOD8 esterase to developing and mature symbiosomes. Molecular Plant-Microbe Interactions, 21(4), 404-410. https://doi.org/10.1094/MPMI-21-4-0404
  20. Basu, C., Luo, H., Kausch, A. P., & Chandlee, J. M. (2003). Transient reporter gene (GUS) expression in creeping bentgrass (Agrostis palustris) is affected by in vivo nucleolytic activity. Biotechnology Letters, 25(12), 939-944. https://doi.org/10.1023/A:1024050720199
    https://doi.org/10.1023/A:1024050720199
  21. Kim, H., & Woloshuk, C. P. (2008). Role of AREA, a regulator of nitrogen metabolism, during colonization of maize kernels and fumonisin biosynthesis in Fusarium verticillioides. Fungal Genetics and Biology, 45(6), 947–953. https://doi.org/10.1016/j.fgb.2008.03.007
  22. Li, S., De-gang, Z., Yong-jun, W., & Yi, L. (2008). Transient expression of chicken alpha interferon gene in lettuce. Journal of Zhejiang University Science B, 9(5), 351–355. https://doi.org/10.1631/jzus.b0710596
  23. Vahling, C. M., & McIver, K. S. (2006). Domains required for transcriptional activation show conservation in the MGA family of virulence gene regulators. Journal of Bacteriology, 188(3), 863-873. https://doi.org/10.1128/jb.188.3.863-873.2006
  24. Krizek, B. A., Prost, V., Joshi, R. M., Stoming, T., & Glenn, T. C. (2003). Developing transgenic arabidopsis plants to be metal-specific bioindicators. Environmental Toxicology and Chemistry, 22(1), 175–181. https://doi.org/10.1002/etc.5620220123
  25. Geddie, M. L., & Matsumura, I. (2007). Antibody-induced oligomerization and activation of an engineered reporter enzyme. Journal of Molecular Biology, 369(4), 1052-1059. https://doi.org/10.1016/j.jmb.2007.03.076
  26. Annis, S. L., Velasquez, L., Xu, H., Hammerschmidt, R., Linz, J., & Trail, F. (2000). Novel procedure for identification of compounds inhibitory to transcription of genes involved in mycotoxin biosynthesis. Journal of Agricultural and Food Chemistry, 48(10), 4656–4660. https://doi.org/10.1021/jf0005115
  27. Ward, D. E., Van Der Weijden, C. C., Van Der Merwe, M. J., Westerhoff, H. V., Claiborne, A., & Snoep, J. L. (2000). Branched-chain alpha -keto acid catabolism via the gene products of the bkd Operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink. Journal of Bacteriology, 182(11), 3239–3246. https://doi.org/10.1128/jb.182.11.3239-3246.2000
  28. Tovkach, A., Zeevi, V., & Tzfira, T. (2010). Validation and expression of zinc finger nucleases in plant cells. In Engineered Zinc Finger Proteins (pp. 315-336). Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-753-2_20
  29. Ha, C. D., Lemaux, P. G., & Cho, M.-J. (2001). Stable transformation of a recalcitrant kentucky bluegrass (Poa pratensis L.) cultivar using mature seed-derived highly regenerative tissues. In Vitro Cellular & Developmental Biology – Plant, 37(1), 6–11. https://doi.org/10.1007/s11627-001-0002-5
  30. O’Loughlin, T. L., & Matsumura, I. (2006). HIV protease-activated molecular switches based on beta-glucuronidase and alkaline phosphatase. Combinatorial Chemistry & High Throughput Screening, 9(4), 313-320. https://doi.org/10.2174/138620706776843219
  31. Kale S.D., Tyler B.M. (2011) Assaying Effector Function in Planta Using Double-Barreled Particle Bombardment. In: McDowell J. (eds) Plant Immunity. Methods in Molecular Biology, vol 712. (pp. 153-172) https://doi.org/10.1007/978-1-61737-998-7_13
  32. Bosacchi, M. (2008). Selective plant growth using D-amino acids (Doctoral dissertation, Rutgers University-Graduate School-New Brunswick). Retrieved from: https://doi.org/10.7282/t3p84c8q
  33. Kim, K.-W., Franceschi, V. R., Davin, L. B., & Lewis, N. G. (2006). β-Glucuronidase as Reporter Gene: Advantages and Limitations. In Arabidopsis Protocols (pp. 263–274). Humana Press. New York City. https://doi.org/10.1385/1-59745-003-0:263
  34. Stacey, M. G., Osawa, H., Patel, A., Gassmann, W., & Stacey, G. (2006). Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta, 223(2), 291-305. https://doi.org/10.1007/s00425-005-0087-x
  35. Curtis, I.S., Power, J. B., Hedden, P., Phillips, A., Lowe, K. C., Ward, D. A., & Davey, M. R. (2000). Transformation and characterization of transgenic plants of Solanum dulcamara L.—incidence of transgene silencing. Annals of Botany, 86(1), 63–71. https://doi.org/10.1006/anbo.2000.1159
  36. Liu, Z., & Kearney, C. M. (2010). A tobamovirus expression vector for agroinfection of legumes and Nicotiana. Journal of Biotechnology, 147(3–4), 151–159. https://doi.org/10.1016/j.jbiotec.2010.03.021
  37. Foster, J., Lee, Y. H., & Tegeder, M. (2008). Distinct expression of members of the LHT amino acid transporter family in flowers indicates specific roles in plant reproduction. Sexual Plant Reproduction, 21(2), 143-152. https://doi.org/10.1007/s00497-008-0074-z
  38. Kim, Y.-H., Bae, J. M., & Huh, G.-H. (2010). Transcriptional regulation of the cinnamyl alcohol dehydrogenase gene from sweetpotato in response to plant developmental stage and environmental stress. Plant Cell Reports, 29(7), 779–791. https://doi.org/10.1007/s00299-010-0864-2
  39. Bondino, H. G., & Valle, E. M. (2009). A small intergenic region drives exclusive tissue-specific expression of the adjacent genes in Arabidopsis thaliana. BMC Molecular Biology, 10(1), 95. https://doi.org/10.1186/1471-2199-10-95
  40. Becnel, J., Natarajan, M., Kipp, A., & Braam, J. (2006). Developmental expression patterns of arabidopsis XTH genes reported by transgenes and genevestigator. Plant Molecular Biology, 61(3), 451-467. https://doi.org/10.1007/s11103-006-0021-z
  41. Wang, X. (2008). Functions of the Tobacco mosaic virus helicase domain: regulating formation of the virus replication complex and altering the activity of a host-encoded transcription factor (Doctoral dissertation, University of Maryland). Retrieved from: http://hdl.handle.net/1903/8124
  42. Sieburth, L. E., & Meyerowitz, E. M. (1997). Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. The Plant Cell, 9(3), 355-365. https://doi.org/10.1105/tpc.9.3.355
  43. Mason, M. G., Li, J., Mathews, D. E., Kieber, J. J., & Schaller, G. E. (2004). Type-B response regulators display overlapping expression patterns in Arabidopsis. Plant Physiology, 135(2), 927-937. https://doi.org/10.1104/pp.103.038109
  44. Scarpeci, T. E., Zanor, M. I., Carrillo, N., Mueller-Roeber, B., & Valle, E. M. (2008). Generation of superoxide anion in chloroplasts of Arabidopsis thaliana during active photosynthesis: a focus on rapidly induced genes. Plant Molecular Biology, 66(4), 361-378. https://doi.org/10.1007/s11103-007-9274-4
  45. Mima, T., & Schweizer, H. P. (2010). The BpeAB-OprB efflux pump of Burkholderia pseudomallei 1026b does not play a role in quorum sensing, virulence factor production, or extrusion of aminoglycosides but is a broad-spectrum drug efflux system. Antimicrobial Agents and Chemotherapy, 54(8), 3113-3120. https://doi.org/10.1128/AAC.01803-09
  46. Cohu, C. M., Abdel-Ghany, S. E., Reynolds, K. A. G., Onofrio, A. M., Bodecker, J. R., Kimbrel, J. A., … & Pilon, M. (2009). Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant, 2(6), 1336-1350. https://doi.org/10.1093/mp/ssp084
  47. Zhu, W., Zhang, D., Lu, X., Zhang, L., Yu, Z., Lv, H., & Zhang, H. (2014). Characterisation of an SKn-type dehydrin promoter from wheat and its responsiveness to various abiotic and biotic stresses. Plant Molecular Biology Reporter, 32(3), 664-678. https://doi.org/10.1007/s11105-013-0681-1
  48. Klauser, D., Desurmont, G. A., Glauser, G., Vallat, A., Flury, P., Boller, T., … & Bartels, S. (2015). The Arabidopsis Pep-PEPR system is induced by herbivore feeding and contributes to JA-mediated plant defence against herbivory. Journal of Experimental Botany, 66(17), 5327-5336. https://doi.org/10.1093/jxb/erv250
  49. Kryvoruchko, I. S., Sinharoy, S., Torres-Jerez, I., Sosso, D., Pislariu, C. I., Guan, D., … & Udvardi, M. K. (2016). MtSWEET11, a nodule-specific sucrose transporter of Medicago truncatula. Plant Physiology, 171(1), 554-565. https://doi.org/10.1104/pp.15.01910
  50. Owens, D. K., Alerding, A. B., Crosby, K. C., Bandara, A. B., Westwood, J. H., & Winkel, B. S. (2008). Functional analysis of a predicted flavonol synthase gene family in Arabidopsis. Plant Physiology, 147(3), 1046-1061. https://doi.org/10.1104/pp.108.117457
  51. Karunadasa, S. S., Kurepa, J., Shull, T. E., & Smalle, J. A. (2020). Cytokinin‐induced protein synthesis suppresses growth and osmotic stress tolerance. New Phytologist. https://doi.org/10.1111/nph.16519
  52. Chirakul, S., Norris, M. H., Pagdepanichkit, S., Somprasong, N., Randall, L. B., Shirley, J. F., … & Schweizer, H. P. (2018). Transcriptional and post-transcriptional regulation of PenA β-lactamase in acquired Burkholderia pseudomallei β-lactam resistance. Scientific Reports, 8(1) https://doi.org/10.1038/s41598-018-28843-7
  53. Polko, J. K., Barnes, W. J., Voiniciuc, C., Doctor, S., Steinwand, B., Hill Jr, J. L., … & Kieber, J. J. (2018). SHOU4 proteins regulate trafficking of cellulose synthase complexes to the plasma membrane. Current Biology, 28(19), 3174-3182. 10.1016/j.cub.2018.07.076
5-Hydroxytryptophol
  1. Cecala, C., Rubakhin, S. S., Mitchell, J. W., Gillette, M. U., & Sweedler, J. V. (2012). A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis. The Analyst, 137(13), 2965. https://doi.org/10.1039/c2an35198f
HEPES, Free Acid
  1. Pokhrel, A., Lingo, J. C., Wolschendorf, F., & Gray, M. J. (2019). Assaying for inorganic polyphosphate in bacteria. JoVE (Journal of Visualized Experiments), (143), e58818.https://doi.org/10.3791/58818
  2. Schneider, C. R., Lewis, L. C., & Shafaat, H. S. (2019). The good, the neutral, and the positive: buffer identity impacts CO2 reduction activity by nickel(ii) cyclam. Dalton Transactions, 48(42), 15810–15821. https://doi.org/10.1039/c9dt03114f
  3. Ward, C. L., & Linz, T. H. (2020). Characterizing the impact of thermal gels on isotachophoresis in microfluidic devices. Electrophoresis. https://doi.org/10.1002/elps.201900407
  4. Lancaster, C. A., Scholl, W. E., Ticknor, M. A., & Shumaker-Parry, J. S. (2020). Uniting top-down and bottom-up strategies using fabricated nanostructures as hosts for synthesis of Nanomites. The Journal of Physical Chemistry C. https://doi.org/10.1021/acs.jpcc.9b11820
  5. Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2020). Modulation of kinesin’s load-bearing capacity by force geometry and the microtubule track. Biophysical Journal, 118(1), 243–253. https://doi.org/10.1016/j.bpj.2019.10.045
  6. Dai, L., Zhao, T., Bisteau, X., Sun, W., Prabhu, N., Lim, Y. T., … & Nordlund, P. (2018). Modulation of protein-interaction states through the cell cycle. Cell, 173(6), 1481-1494. https://doi.org/10.1016/j.cell.2018.03.065
  7. Dziekan, J. M., Wirjanata, G., Dai, L., Go, K. D., Yu, H., Lim, Y. T., … & Sobota, R. M. (2020). Cellular thermal shift assay for the identification of drug–target interactions in the Plasmodium falciparum proteome. Nature Protocols, 1-41. https://doi.org/10.1038/s41596-020-0310-z
Hygromycin B
  1. Serrano, H., & Blanchard, J. S. (2013). Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry, 52(29), 5009-5015. https://doi.org/10.1021/bi400338f
  2. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  3. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
  4. Lai, W. C., Sun, H. F. S., Lin, P. H., Lin, H., & Shieh, J. C. (2016). A new rapid and efficient system with dominant selection developed to inactivate and conditionally express genes in Candida albicans. Current Genetics, 62(1), 213-235.https://doi.org/10.1007/s00294-015-0526-6
  5. Liang, Y., Zhu, J., Huang, H., Xiang, D., Li, Y., Zhang, D., … & Liu, Z. (2016). SESN2/sestrin 2 induction-mediated autophagy and inhibitory effect of isorhapontigenin (ISO) on human bladder cancers. Autophagy, 12(8), 1229-1239.https://doi.org/10.1080/15548627.2016.1179403
  6. Gallagher, C. M., Garri, C., Cain, E. L., Ang, K. K. H., Wilson, C. G., Chen, S., … & Renslo, A. R. (2016). Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch. Elife, 5, e11878. https://doi.org/10.7554/eLife.11878.001
  7. Garcia, D. M., Dietrich, D., Clardy, J., & Jarosz, D. F. (2016). A common bacterial metabolite elicits prion-based bypass of glucose repression. Elife, 5, e17978. https://doi.org/10.7554/eLife.17978
  8. Li, L., Shemetov, A. A., Baloban, M., Hu, P., Zhu, L., Shcherbakova, D. M., … & Verkhusha, V. V. (2018). Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. Nature Communications, 9(1), 2734. https://doi.org/10.1038/s41467-018-05231-3
  9. Mercier, R., Wolmarans, A., Schubert, J., Neuweiler, H., Johnson, J. L., & LaPointe, P. (2019). The conserved NxNNWHW motif in Aha-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation. Nature Communications, 10(1), 1273. https://doi.org/10.1038/s41467-019-09299-3
  10. Corcoran, J. A., Jordan, M. D., Carraher, C., & Newcomb, R. D. (2014). A novel method to study insect olfactory receptor function using HEK293 cells. Insect Biochemistry and Molecular Biology, 54, 22-32.https://doi.org/10.1016/j.ibmb.2014.08.005
  11. Lai, W.-C., Sun, H. S., & Shieh, J.-C. (2020). Establishment of tetracycline-regulated bimolecular fluorescence complementation assay to detect protein-protein interactions in Candida albicans. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-59891-7
  12. Poliner, E., Clark, E., Cummings, C., Benning, C., & Farre, E. M. (2020). A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, 101664. https://doi.org/10.1016/j.algal.2019.101664
  13. Nambiar, M., & Smith, G. R. (2018). Pericentromere-specific cohesin complex prevents meiotic pericentric DNA double-strand breaks and lethal crossovers. Molecular Cell, 71(4), 540-553. https://doi.org/10.1016/j.molcel.2018.06.035
Hygromycin B EZ Pak™ for 50 mg/mL Solution
  1. Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., … & Qi, Y. (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiology, 169(2), 971-985.https://doi.org/10.1104/pp.15.00636
  2. Lai, W. C., Sun, H. F. S., Lin, P. H., Lin, H., & Shieh, J. C. (2016). A new rapid and efficient system with dominant selection developed to inactivate and conditionally express genes in Candida albicans. Current Genetics, 62(1), 213-235.https://doi.org/10.1007/s00294-015-0526-6
  3. Liang, Y., Zhu, J., Huang, H., Xiang, D., Li, Y., Zhang, D., … & Liu, Z. (2016). SESN2/sestrin 2 induction-mediated autophagy and inhibitory effect of isorhapontigenin (ISO) on human bladder cancers. Autophagy, 12(8), 1229-1239.https://doi.org/10.1080/15548627.2016.1179403
  4. Gallagher, C. M., Garri, C., Cain, E. L., Ang, K. K. H., Wilson, C. G., Chen, S., … & Renslo, A. R. (2016). Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch. Elife, 5, e11878. https://doi.org/10.7554/eLife.11878.001
  5. Garcia, D. M., Dietrich, D., Clardy, J., & Jarosz, D. F. (2016). A common bacterial metabolite elicits prion-based bypass of glucose repression. Elife, 5, e17978. https://doi.org/10.7554/eLife.17978
IL1A (IL-1 alpha), Human
  1. Nawas, A. F., Kanchwala, M., Thomas-Jardin, S. E., Dahl, H., Daescu, K., Bautista, M., … Delk, N. A. (2020). IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival. BMC Cancer, 20(1). https://doi.org/10.1186/s12885-020-6529-9
Nickel Agarose Beads (High Density)
  1. Armstrong, C. M., Meyers, D. J., Imlay, L. S., Meyers, C. F., & Odom, A. R. (2015). Resistance to the antimicrobial agent fosmidomycin and an FR900098 prodrug through mutations in the deoxyxylulose phosphate reductoisomerase gene (dxr). Antimicrobial Agents and Chemotherapy, 59(9), 5511-5519.https://doi.org/10.1128/AAC.00602-15
  2. Wang, H., Jin, H., & Rapraeger, A. C. (2015). Syndecan-1 and syndecan-4 capture epidermal growth factor receptor family members and the α3β1 integrin via binding sites in their ectodomains: novel synstatins prevent kinase capture and inhibit α6β4-integrin-dependent epithelial cell motility. Journal of Biological Chemistry, 290(43), 26103-26113.https://doi.org/10.1074/jbc.m115.679084
  3. Shen, G., Gan, F., & Bryant, D. A. (2016). The siderophilic cyanobacterium Leptolyngbya sp. strain JSC-1 acclimates to iron starvation by expressing multiple isiA-family genes. Photosynthesis Research, 128(3), 325–340. https://doi.org/10.1007/s11120-016-0257-7
  4. Mullins, M. R., Rajavel, M., Hernandez-Sanchez, W., De La Fuente, M., Biendarra, S. M., Harris, M. E., & Taylor, D. J. (2016). POT1–TPP1 binding and unfolding of telomere DNA discriminates against structural polymorphism. Journal of Molecular Biology, 428(13), 2695-2708. https://doi.org/10.1016/j.jmb.2016.04.031
  5. Rajavel, M., Orban, T., Xu, M., Hernandez-Sanchez, W., de la Fuente, M., Palczewski, K., & Taylor, D. J. (2016). Dynamic peptides of human TPP1 fulfill diverse functions in telomere maintenance. Nucleic Acids Research, 44(21), 10467-10479. https://doi.org/10.1093/nar/gkw846
  6. Kato, M., Yang, Y.-S., Sutter, B. M., Wang, Y., McKnight, S. L., & Tu, B. P. (2019). Redox state controls phase separation of the yeast ataxin-2 protein via reversible oxidation of its methionine-rich low-complexity domain. Cell, 177(3), 711–721.e8. https://doi.org/10.1016/j.cell.2019.02.044
Nickel NTA Agarose Beads
  1. Serrano, H., & Blanchard, J. S. (2013). Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry, 52(29), 5009-5015. https://doi.org/10.1021/bi400338f
  2. Landgraf, B. J., Arcinas, A. J., Lee, K. H., & Booker, S. J. (2013). Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. Journal of the American Chemical Society, 135(41), 15404-15416. https://doi.org/10.1021/ja4048448
  3. Plucinski, L., Gartia, M. R., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., … & Das, A. (2016). Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays. Biosensors and Bioelectronics, 75, 337-346.https://doi.org/10.1016/j.bios.2015.07.041
  4. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  5. Mahendran, V., Liu, F., Riordan, S. M., Grimm, M. C., Tanaka, M. M., & Zhang, L. (2016). Examination of the effects of Campylobacter concisus zonula occludens toxin on intestinal epithelial cells and macrophages. Gut Pathogens, 8(1), 18. https://doi.org/10.1186/s13099-016-0101-9
  6. Ganguly, A., Manahan, C. C., Top, D., Yee, E. F., Lin, C., Young, M. W., … & Crane, B. R. (2016). Changes in active site histidine hydrogen bonding trigger cryptochrome activation. Proceedings of the National Academy of Sciences, 113(36), 10073-10078. https://doi.org/10.1073/pnas.1606610113
  7. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  8. Wu, X., Paskaleva, E. E., Mehta, K. K., Dordick, J. S., & Kane, R. S. (2016). Wall teichoic acids are involved in the medium-induced loss of function of the autolysin CD11 against Clostridium difficile. Scientific Reports, 6, 35616.https://doi.org/10.1038/srep35616
  9. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  10. Hoffman, H. K., Fernandez, M. V., Groves, N. S., Freed, E. O., & van Engelenburg, S. B. (2019). Genomic tagging of endogenous human ESCRT-I complex preserves ESCRT-mediated membrane-remodeling functions. Journal of Biological Chemistry, 294(44), 16266–16281. https://doi.org/10.1074/jbc.ra119.009372
  11. Dao, T. P., Martyniak, B., Canning, A. J., Lei, Y., Colicino, E. G., Cosgrove, M. S., … & Castañeda, C. A. (2019). ALS-linked mutations affect UBQLN2 oligomerization and phase separation in a position-and amino acid-dependent manner. Structure, 27(6), 937-951. https://doi.org/10.1016/j.str.2019.03.012
  12. Dao, T. P., Kolaitis, R. M., Kim, H. J., O’Donovan, K., Martyniak, B., Colicino, E., … & Castañeda, C. A. (2018). Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Molecular Cell, 69(6), 965-978. https://doi.org/10.1016/j.molcel.2018.02.004
  13. Lee, M., Ghosh, U., Thurber, K. R., Kato, M., & Tycko, R. (2020). Molecular structure and interactions within amyloid-like fibrils formed by a low-complexity protein sequence from FUS. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-19512-3
Sodium 3-hydroxybutyrate
  1. Jensen, N. J., Nilsson, M., Ingerslev, J. S., Olsen, D. A., Fenger, M., Svart, M., … & Rungby, J. (2020). Effects of β-hydroxybutyrate on cognition in patients with type 2 diabetes. European Journal of Endocrinology, 182(2), 233-242. https://doi.org/10.1530/EJE-19-0710
  2. Lauritzen, E. S., Svart, M. V., Voss, T., Møller, N., & Bjerre, M. (2020). Impact of acutely increased endogenous-and exogenous ketone bodies on FGF21 Levels in humans. Endocrine Research, 1-8. https://doi.org/10.1080/07435800.2020.1831015
IAA (Indole-3-Acetic Acid)
  1. Shao, M., Michno, J. M., Hotton, S. K., Blechl, A., & Thomson, J. (2015). A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. Plant Cell Reports, 34(10), 1707-1716. https://doi.org/10.1007/s00299-015-1818-5
  2. Woodman, J., Hoffman, M., Dzieciatkowska, M., Hansen, K. C., & Megee, P. C. (2015). Phosphorylation of the Scc2 cohesin deposition complex subunit regulates chromosome condensation through cohesin integrity. Molecular Biology of The Cell, 26(21), 3754-3767.https://doi.org/10.1091/mbc.E15-03-0165
IFN-gamma, Murine
  1. Xi, J., Huang, Q., Wang, L., Ma, X., Deng, Q., Kumar, M., … & Zhang, M. (2018). miR-21 depletion in macrophages promotes tumoricidal polarization and enhances PD-1 immunotherapy. Oncogene, 37(23), 3151. https://doi.org/10.1038/s41388-018-0178-3
  2. Shehat, M. G., & Tigno-Aranjuez, J. (2019). Flow cytometric measurement of ROS production in macrophages in response to FcγR cross-linking. JoVE (Journal of Visualized Experiments), (145), e59167. https://doi.org/10.3791/59167
IGF1, Human
  1. Pouraghaei, S., Moztarzadeh, F., Chen, C., Ansari, S., & Moshaverinia, A. (2020). Microenvironment can induce development of auditory progenitor cells from human gingival mesenchymal stem cells. ACS Biomaterials Science & Engineering. https://doi.org/10.1021/acsbiomaterials.9b01795
IL1B (IL-1 beta), Human
  1. Jiang, S. J., Tsai, P. I., Peng, S. Y., Chang, C. C., Chung, Y., Tsao, H. H., … & Hsu, H. J. (2019). A potential peptide derived from cytokine receptors can bind proinflammatory cytokines as a therapeutic strategy for anti-inflammation. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36492-z
  2. Nawas, A. F., Kanchwala, M., Thomas-Jardin, S. E., Dahl, H., Daescu, K., Bautista, M., … Delk, N. A. (2020). IL-1-conferred gene expression pattern in ERα+ BCa and AR+ PCa cells is intrinsic to ERα− BCa and AR− PCa cells and promotes cell survival. BMC Cancer, 20(1). https://doi.org/10.1186/s12885-020-6529-9
IL1RN (IL-1RA), Murine
  1. Tartey, S., Gurung, P., Karki, R., Burton, A., Hertzog, P., & Kanneganti, T. D. (2020). Ets-2 deletion in myeloid cells attenuates IL-1α-mediated inflammatory disease caused by a Ptpn6 point mutation. Cellular & Molecular Immunology. https://doi.org/10.1038/s41423-020-0398-7
IL3, Murine
  1. Cabal-Hierro, L., van Galen, P., Prado, M. A., Higby, K. J., Togami, K., Mowery, C. T., … Lane, A. A. (2020). Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-15221-z
IL6, Human
  1. Jiang, S. J., Tsai, P. I., Peng, S. Y., Chang, C. C., Chung, Y., Tsao, H. H., … & Hsu, H. J. (2019). A potential peptide derived from cytokine receptors can bind proinflammatory cytokines as a therapeutic strategy for anti-inflammation. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36492-z
IL8, Human (72 a.a.)
  1. Kotha, P. L., Sharma, P., Kolawole, A. O., Yan, R., Alghamri, M. S., Brockman, T. L., … & Excoffon, K. J. (2015). Adenovirus entry from the apical surface of polarized epithelia is facilitated by the host innate immune response. PLoS pathogens, 11(3), e1004696. https://doi.org/10.1371/journal.ppat.1004696
Illumination™ Firefly Luciferase Enhanced Assay Kit
  1. Xiong, Q., Liu, A., Ren, Q., Xue, Y., Yu, X., Ying, Y., … Xu, C. (2020). Cuprous oxide nanoparticles trigger reactive oxygen species-induced apoptosis through activation of erk-dependent autophagy in bladder cancer. Cell Death & Disease, 11(5). https://doi.org/10.1038/s41419-020-2554-5
IPTG
  1. Oppenheimer, M., Pierce, B. S., Crawford, J. A., Ray, K., Helm, R. F., & Sobrado, P. (2010). Recombinant expression, purification, and characterization of ThmD, the oxidoreductase component of tetrahydrofuran monooxygenase. Archives of Biochemistry and Biophysics, 496(2), 123–131. https://doi.org/10.1016/j.abb.2010.02.006
  2. Tan, A., & Henzl, M. T. (2009). Conformational stabilities of guinea pig OCP1 and OCP2. Biophysical Chemistry, 144(3), 108-118. https://doi.org/10.1016/j.bpc.2009.07.003
  3. Kreutzer, D. A., & Essigmann, J. M. (1998). Oxidized, deaminated cytosines are a source of C→ T transitions in vivo . Proceedings of the National Academy of Sciences, 95(7), 3578-3582. https://doi.org/10.1073/pnas.95.7.3578
  4. Fuqua, C., Burbea, M., & Winans, S. C. (1995). Activity of the Agrobacterium Ti plasmid conjugal transfer regulator TraR is inhibited by the product of the traM gene. Journal of Bacteriology, 177(5), 1367-1373. https://doi.org/10.1128/jb.177.5.1367-1373.1995
  5. Fink, S. P., Reddy, G. R., & Marnett, L. J. (1997). Mutagenicity in Escherichia coli of the major DNA adduct derived from the endogenous mutagen malondialdehyde. Proceedings of the National Academy of Sciences, 94(16), 8652–8657. https://doi.org/10.1073/pnas.94.16.8652
  6. Karunakaran, T., Madden, T., & Kuramitsu, H. (1997). Isolation and characterization of a hemin-regulated gene, hemR , from Porphyromonas gingivalis . Journal of Bacteriology, 179(6), 1898–1908. https://doi.org/10.1128/jb.179.6.1898-1908.1997
  7. VanderVeen, L. A., Hashim, M. F., Nechev, L. V., Harris, T. M., Harris, C. M., & Marnett, L. J. (2001). Evaluation of the mutagenic potential of the principal DNA adduct of acrolein. Journal of Biological Chemistry, 276(12), 9066-9070. https://doi.org/10.1074/jbc.m008900200
  8. O’Sullivan, D. J., Hill, C., & Klaenhammer, T. R. (1993). Effect of increasing the copy number of bacteriophage origins of replication, in trans, on incoming-phage proliferation. Applied and Environmental Microbiology, 59(8), 2449-2456.
  9. Neeley, W. L., Delaney, J. C., Henderson, P. T., & Essigmann, J. M. (2004). In vivo bypass efficiencies and mutational signatures of the guanine oxidation products 2-aminoimidazolone and 5-guanidino-4-nitroimidazole. Journal of Biological Chemistry, 279(42), 43568-43573. https://doi.org/10.1074/jbc.M407117200
  10. Johnson, K. A., Fink, S. P., & Marnett, L. J. (1997). Repair of propanodeoxyguanosine by nucleotide excision repair in vivo and in vitro. Journal of Biological Chemistry, 272(17), 11434-11438. https://doi.org/10.1074/jbc.272.17.11434
  11. Wanyiri, J. W., O’Connor, R., Allison, G., Kim, K., Kane, A., Qiu, J., … & Ward, H. D. (2007). Proteolytic processing of the Cryptosporidium glycoprotein gp40/15 by human furin and by a parasite-derived furin-like protease activity. Infection and Immunity, 75(1), 184-192. https://doi.org/10.1128/iai.00944-06
  12. Henderson, P. T., Delaney, J. C., Gu, F., Tannenbaum, S. R., & Essigmann, J. M. (2002). Oxidation of 7,8-dihydro-8-oxoguanine affords lesions that are potent sources of replication errors in Vivo. Biochemistry, 41(3), 914–921. https://doi.org/10.1021/bi0156355
  13. Sadler, T. J., Glare, T. R., Ward, V. K., & Kalmakoff, J. (2000). Physical and genetic map of the Wiseana nucleopolyhedrovirus genome. Journal of General Virology, 81(4), 1127-1133. https://doi.org/10.1099/0022-1317-81-4-1127
  14. VanderVeen, L. A., Hashim, M. F., Shyr, Y., & Marnett, L. J. (2003). Induction of frameshift and base pair substitution mutations by the major DNA adduct of the endogenous carcinogen malondialdehyde. Proceedings of the National Academy of Sciences, 100(24), 14247-14252. https://doi.org/10.1073/pnas.2332176100
  15. Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G., & Norris, J. S. (2002). Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. Journal of Virology, 76(11), 5557–5564. https://doi.org/10.1128/jvi.76.11.5557-5564.2002
  16. Bailey, E. A., Iyer, R. S., Stone, M. P., Harris, T. M., & Essigmann, J. M. (1996). Mutational properties of the primary aflatoxin B1-DNA adduct. Proceedings of the National Academy of Sciences, 93(4), 1535–1539. https://doi.org/10.1073/pnas.93.4.1535
  17. Niedernhofer, L. J., Daniels, J. S., Rouzer, C. A., Greene, R. E., & Marnett, L. J. (2003). Malondialdehyde, a product of lipid peroxidation, is mutagenic in human cells. Journal of Biological Chemistry, 278(33), 31426–31433. https://doi.org/10.1074/jbc.m212549200
  18. Fuqua, W. C., & Winans, S. C. (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. Journal of Bacteriology, 176(10), 2796-2806. https://doi.org/10.1128/jb.176.10.2796-2806.1994
  19. Wittmayer, P. K., McKenzie, J. L., & Raines, R. T. (1998). Degenerate DNA recognition by I-PpoI endonuclease. Gene, 206(1), 11–21. https://doi.org/10.1016/s0378-1119(97)00563-5
  20. Chang, M.-Y., Won, S.-J., & Liu, H.-S. (1997). A ribozyme specifically suppresses transformation and tumorigenicity of Ha-ras-oncogene-transformed NIH/3T3 cell lines. Journal of Cancer Research and Clinical Oncology, 123(2), 91–99. https://doi.org/10.1007/bf01269886
  21. Johnson, K. A., Mierzwa, M. L., Fink, S. P., & Marnett, L. J. (1999). MutS recognition of exocyclic DNA adducts that are endogenous products of lipid oxidation. Journal of Biological Chemistry, 274(38), 27112–27118. https://doi.org/10.1074/jbc.274.38.27112
  22. Lough, J., Jackson, M., Morris, R., & Moyer, R. (2001). Bisulfite-induced cytosine deamination rates in E. coli SSB: DNA complexes. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 478(1-2), 191-197. https://doi.org/10.1016/s0027-5107(01)00149-x
  23. Alexander, P., Fahnestock, S., Lee, T., Orban, J., & Bryan, P. (1992). Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures. Biochemistry, 31(14), 3597-3603. https://doi.org/10.1021/bi00129a007
  24. Min, W., Kim, J-K., Lillehoj, H. S., Sohn, E. J., Han, J. Y., Song, K. D., & Lillehoj, E. P. (2001). Characterization of recombinant scFv antibody reactive with an apical antigen of Eimeria acervulina. Biotechnology Letters, 23(12), 949–955. https://doi.org/10.1023/a:1010531019633
  25. Sundberg, E. J., Urrutia, M., Braden, B. C., Isern, J., Tsuchiya, D., Fields, B. A., … Mariuzza, R. A. (2000). Estimation of the hydrophobic effect in an antigen−antibody protein−protein Interface. Biochemistry, 39(50), 15375–15387. https://doi.org/10.1021/bi000704l
  26. Turner, L., Samuel, A. D., Stern, A. S., & Berg, H. C. (1999). Temperature dependence of switching of the bacterial flagellar motor by the protein CheY13DK106YW. Biophysical Journal, 77(1), 597-603. https://doi.org/10.1016/s0006-3495(99)76916-x
  27. Batiza, A. F., Kuo, M. M.-C., Yoshimura, K., & Kung, C. (2002). Gating the bacterial mechanosensitive channel MscL in vivo. Proceedings of the National Academy of Sciences, 99(8), 5643–5648. https://doi.org/10.1073/pnas.082092599
  28. Wolffe, E. J., Katz, E., Weisberg, A., & Moss, B. (1997). The A34R glycoprotein gene is required for induction of specialized actin-containing microvilli and efficient cell-to-cell transmission of vaccinia virus. Journal of Virology, 71(5), 3904-3915.
  29. Parker, A. R., Moore, T. D., Edman, J. C., Schwab, J. M., & Davisson, V. J. (1994). Cloning, sequence analysis and expression of the gene encoding imidazole glycerol phosphate dehydratase in Cryptococcus neoformans. Gene, 145(1), 135-138. https://doi.org/10.1016/0378-1119(94)90336-0
  30. Maldonado-Arocho, F. J., & Bradley, K. A. (2009). Anthrax edema toxin induces maturation of dendritic cells and enhances chemotaxis towards macrophage inflammatory protein 3β. Infection and Immunity, 77(5), 2036-2042. https://doi.org/10.1128/IAI.01329-08
  31. Cooper, K. K., Trinh, H. T., & Songer, J. G. (2009). Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. Veterinary Microbiology, 133(1-2), 92-97. https://doi.org/10.1016/j.vetmic.2008.06.001
  32. Chung, Y. I., Park, D. H., Kim, M., Baker, H., & Joh, T. H. (2001). Immunochemical characterization of brain and pineal tryptophan hydroxylase. Journal of Korean Medical Science, 16(4), 489. https://doi.org/10.3346/jkms.2001.16.4.489
  33. Pieper, U., Hayakawa, K., Li, Z., & Herzberg, O. (1997). Circularly permuted β-lactamase from Staphylococcus aureus PC1. Biochemistry, 36(29), 8767-8774. https://doi.org/10.1021/bi9705117
  34. Klink, T. A., Woycechowsky, K. J., Taylor, K. M., & Raines, R. T. (2000). Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A. European Journal of Biochemistry, 267(2), 566–572. https://doi.org/10.1046/j.1432-1327.2000.01037.x
  35. Glamann, J., Burton, D. R., Parren, P. W., Ditzel, H. J., Kent, K. A., Arnold, C., … & Hirsch, V. M. (1998). Simian immunodeficiency virus (SIV) envelope-specific Fabs with high-level homologous neutralizing activity: recovery from a long-term-nonprogressor SIV-infected macaque. Journal of Virology, 72(1), 585-592.
  36. Li, Y., & Inouye, M. (1994). Autoprocessing of prothiolsubtilisin E in which active-site serine 221 is altered to cysteine. Journal of Biological Chemistry, 269(6), 4169-4174.
  37. McCarter, L. L. (1998). OpaR, a homolog of Vibrio harveyi LuxR, controls opacity of Vibrio parahaemolyticus. Journal of Bacteriology, 180(12), 3166-3173.
  38. Park, K., Kuechle, M. K., Choe, Y., Craik, C. S., Lawrence, O. T., & Presland, R. B. (2006). Expression and characterization of constitutively active human caspase-14. Biochemical and Biophysical Research Communications, 347(4), 941-948. https://doi.org/10.1016/j.bbrc.2006.06.156
  39. Olson, J. W., & Maier, R. J. (2000). Dual roles of Bradyrhizobium japonicum nickelin protein in nickel storage and GTP-dependent Ni mobilization. Journal of Bacteriology, 182(6), 1702–1705. https://doi.org/10.1128/jb.182.6.1702-1705.2000
  40. Tan, A., & Henzl, M. T. (2009). Evidence for a Ca2+-specific conformational change in avian thymic hormone, a high-affinity β-parvalbumin. Biochemistry, 48(18), 3936-3945. https://doi.org/10.1021/bi900029j
  41. Richard-Fogal, C., & Kranz, R. G. (2010). The CcmC: heme: CcmE complex in heme trafficking and cytochrome c biosynthesis. Journal of Molecular Biology, 401(3), 350-362. https://doi.org/10.1016/j.jmb.2010.06.041
  42. Luo, Y., Cho, H. H., Jones, R. B., Jin, C., & McKeehan, W. L. (2004). Improved production of recombinant fibroblast growth factor 7 (FGF7/KGF) from bacteria in high magnesium chloride. Protein Expression and Purification, 33(2), 326-331. https://doi.org/10.1016/j.pep.2003.10.013
  43. Wanyiri, J. W., Techasintana, P., O’Connor, R. M., Blackman, M. J., Kim, K., & Ward, H. D. (2009). Role of CpSUB1, a subtilisin-like protease, in Cryptosporidium parvum infection in vitro. Eukaryotic Cell, 8(4), 470-477. https://doi.org/10.1128/EC.00306-08
  44. Ye, K., Jin, S., Bratic, K., & Schultz, J. S. (2004). Surface display of a glucose binding protein. Journal of Molecular Catalysis B: Enzymatic, 28(4–6), 201–206. https://doi.org/10.1016/j.molcatb.2003.12.025
  45. Henzl, M. T., Davis, M. E., & Tan, A. (2008). Divalent ion binding properties of the timothy grass allergen, Phl p 7. Biochemistry, 47(30), 7846-7856. https://doi.org/10.1021/bi800620g
  46. Jost, B. H., Songer, J. G., & Billington, S. J. (2001). Cloning, expression, and characterization of a neuraminidase gene from Arcanobacterium pyogenes. Infection and Immunity, 69(7), 4430–4437. https://doi.org/10.1128/iai.69.7.4430-4437.2001
  47. Klem, T. J., Chen, Y., & Davisson, V. J. (2001). Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase. Journal of Bacteriology, 183(3), 989–996. https://doi.org/10.1128/jb.182.3.989-996.2001
  48. Lluis, M., Hoe, W., Schleit, J., & Robertus, J. (2010). Analysis of nucleic acid binding by a recombinant translin–trax complex. Biochemical and Biophysical Research Communications, 396(3), 709-713.https://doi.org/10.1016/j.bbrc.2010.04.166
  49. Tan, A., Tanner, J. J., & Henzl, M. T. (2008). Energetics of OCP1–OCP2 complex formation. Biophysical Chemistry, 134(1-2), 64-71. https://doi.org/10.1016/j.bpc.2008.01.005
  50. Ramachandran, S., Thompson, R. W., Gam, A. A., & Neva, F. A. (1998). Recombinant cDNA clones for immunodiagnosis of strongyloidiasis. The Journal of Infectious Diseases, 177(1), 196–203. https://doi.org/10.1086/513817
  51. Parker, A. R., Moore, J. A., Schwab, J. M., & Davisson, V. J. (1995). Escherichia coli imidazoleglycerol phosphate dehydratase: spectroscopic characterization of the enzymic product and the steric course of the reaction. Journal of the American Chemical Society, 117(43), 10605-10613. https://doi.org/10.1021/ja00148a001
  52. Vazquez, V., Liang, X., Horndahl, J. K., Ganesh, V. K., Smeds, E., Foster, T. J., & Hook, M. (2011). Fibrinogen is a ligand for the S. aureus MSCRAMM Bbp (Bone sialoprotein-binding protein). Journal of Biological Chemistry, 286(34), 29797–29805. https://doi.org/10.1074/jbc.m110.214981
  53. Billington, S. J., Jost, B. H., Cuevas, W. A., Bright, K. R., & Songer, J. G. (1997). The Arcanobacterium (Actinomyces) pyogenes hemolysin, pyolysin, is a novel member of the thiol-activated cytolysin family. Journal of Bacteriology, 179(19), 6100-6106. https://doi.org/10.1128/jb.179.19.6100-6106.1997
  54. Sakowski, S. A., Geddes, T. J., & Kuhn, D. M. (2006). Mouse tryptophan hydroxylase isoform 2 and the role of proline 447 in enzyme function. Journal of Neurochemistry, 96(3), 758–765. https://doi.org/10.1111/j.1471-4159.2005.03604.x
  55. Ramey, J. D., Villareal, V. A., Ng, C., Ward, S. C., Xiong, J. P., Clubb, R. T., & Bradley, K. A. (2010). Anthrax toxin receptor 1/tumor endothelial marker 8: mutation of conserved inserted domain residues overrides cytosolic control of protective antigen binding. Biochemistry, 49(34), 7403-7410. https://doi.org/10.1021/bi100887w
  56. Lahiri, S., Pulakat, L., & Gavini, N. (2008). Functional participation of a nifH–arsA2 chimeric fusion gene in arsenic reduction by Escherichia coli. Biochemical and Biophysical Research Communications, 368(2), 311-317. https://doi.org/10.1016/j.bbrc.2008.01.086
  57. Henzl, M. T., Davis, M. E., & Tan, A. (2010). Polcalcin divalent ion-binding behavior and thermal stability: comparison of Bet v 4, Bra n 1, and Bra n 2 to Phl p 7. Biochemistry, 49(10), 2256–2268. https://doi.org/10.1021/bi902115v
  58. Flores, H., & Ellington, A. D. (2005). A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase. Protein Engineering, Design and Selection, 18(8), 369–377. https://doi.org/10.1093/protein/gzi043
  59. Zawadzke, L. E., Smith, T. J., & Herzberg, O. (1995). An engineered Staphylococcus aureus PCI ß-lactamase that hydrolyses third-generation cephalosporins. Protein Engineering, Design and Selection, 8(12), 1275-1285. https://doi.org/10.1093/protein/8.12.1275
  60. Andi, B., Cook, P. F., & West, A. H. (2006). Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-Å resolution. Cell Biochemistry and Biophysics, 46(1), 17–26. https://doi.org/10.1385/cbb:46:1:17
  61. Smela, M. E., Hamm, M. L., Henderson, P. T., Harris, C. M., Harris, T. M., & Essigmann, J. M. (2002). The aflatoxin B1 formamidopyrimidine adduct plays a major role in causing the types of mutations observed in human hepatocellular carcinoma. Proceedings of the National Academy of Sciences, 99(10), 6655–6660. https://doi.org/10.1073/pnas.102167699
  62. Chou, C. K., Liang, K. H., Tzeng, C. C., Huang, G. C., Chuang, J. I., Chang, T. Y., & Liu, H. S. (2006). Dominant-negative Rac1 suppresses Ras-induced apoptosis possibly through activation of NFκB in Ha-ras oncogene-transformed NIH/3T3 cells. Life Sciences, 78(16), 1823–1829. https://doi.org/10.1016/j.lfs.2005.08.039
  63. Kim, S., Miska, K. B., McElroy, A. P., Jenkins, M. C., Fetterer, R. H., Cox, C. M., … & Dalloul, R. A. (2009). Molecular cloning and functional characterization of avian interleukin-19. Molecular Immunology, 47(2-3), 476-484. https://doi.org/10.1016/j.molimm.2009.08.027
  64. Dall’Acqua, W., Goldman, E. R., Eisenstein, E., & Mariuzza, R. A. (1996). A mutational analysis of the binding of two different proteins to the same antibody. Biochemistry, 35(30), 9667. https://doi.org/10.1021/bi960819i
  65. Veglia, G., Ha, K. N., Shi, L., Verardi, R., & Traaseth, N. J. (2010). What can we learn from a small regulatory membrane protein?. In: Lacapère JJ. (eds) Membrane Protein Structure Determination. Methods in Molecular Biology (Methods and Protocols), vol 654. (pp. 303-319) https://doi.org/10.1007/978-1-60761-762-4_16
  66. Chocklett, S. W., & Sobrado, P. (2010). Aspergillus fumigatus SidA is a highly specific ornithine hydroxylase with bound flavin cofactor. Biochemistry, 49(31), 6777-6783.https://doi.org/10.1021/bi100291n
  67. Kumar, A., Chua, K. L., & Schweizer, H. P. (2006). Method for regulated expression of single-copy efflux pump genes in a surrogate Pseudomonas aeruginosa strain: identification of the BpeEF-OprC chloramphenicol and trimethoprim efflux pump of Burkholderia pseudomallei 1026b. Antimicrobial Agents and Chemotherapy, 50(10), 3460-3463. https://doi.org/10.1128/AAC.00440-06
  68. Angov, E., & Camerini-Otero, R. D. (1994). The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization. Journal of Bacteriology, 176(5), 1405-1412. https://doi.org/10.1128/jb.176.5.1405-1412.1994
  69. Habben, J. E., Moro, G. L., Hunter, B. G., Hamaker, B. R., & Larkins, B. A. (1995). Elongation factor 1 alpha concentration is highly correlated with the lysine content of maize endosperm. Proceedings of the National Academy of Sciences, 92(19), 8640-8644. https://doi.org/10.1073/pnas.92.19.8640
  70. Coyne, C. J., McClendon, M. T., Walling, J. G., Timmerman-Vaughan, G. M., Murray, S., Meksem, K., … & Inglis, D. A. (2007). Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome, 50(9), 871-875. https://doi.org/10.1139/G07-063
  71. Ota, I. M., & Mapes, J. (2007). Targeting of PP2C in budding yeast. In Protein Phosphatase Protocols (pp. 309-322). Humana Press https://doi.org/10.1385/1-59745-267-x:309
  72. Richard‐Fogal, C. L., Frawley, E. R., Bonner, E. R., Zhu, H., San Francisco, B., & Kranz, R. G. (2009). A conserved haem redox and trafficking pathway for cofactor attachment. The EMBO Journal, 28(16), 2349-2359. https://doi.org/10.1038/emboj.2009.189
  73. Guo, L. W., Assadi-Porter, F. M., Grant, J. E., Wu, H., Markley, J. L., & Ruoho, A. E. (2007). One-step purification of bacterially expressed recombinant transducin α-subunit and isotopically labeled PDE6 γ-subunit for NMR analysis. Protein Expression and Purification, 51(2), 187-197. https://doi.org/10.1016/j.pep.2006.07.012
  74. Norais, C. A., Chitteni-Pattu, S., Wood, E. A., Inman, R. B., & Cox, M. M. (2009). DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. Journal of Biological Chemistry, 284(32), 21402-21411. https://doi.org/10.1074/jbc.M109.010454
  75. Sandoval, C. M., Baker, S. L., Jansen, K., Metzner, S. I., & Sousa, M. C. (2011). Crystal structure of BamD: an essential component of the β-barrel assembly machinery of gram-negative bacteria. Journal of Molecular Biology, 409(3), 348-357. https://doi.org/10.1016/j.jmb.2011.03.035
  76. Larabee, J. L., Maldonado-Arocho, F. J., Pacheco, S., France, B., DeGiusti, K., Shakir, S. M., … & Ballard, J. D. (2011). Gsk-3 activation is important for anthrax edema toxin induced dendritic cell maturation and antxr2 expression in macrophages. Infection and Immunity 79(8) 3302-3308 https://doi.org/10.1128/IAI.05070-11
  77. Matthews, M. L., Krest, C. M., Barr, E. W., Vaillancourt, F. H., Walsh, C. T., Green, M. T., … & Bollinger Jr, J. M. (2009). Substrate-triggered formation and remarkable stability of the C− H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2. Biochemistry, 48(20), 4331-4343.https://doi.org/10.1021/bi900109z
  78. Wang, Y., Fu, T. J., Howard, A., Kothary, M. H., McHugh, T. H., & Zhang, Y. (2013). Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5. Journal of Agricultural and Food Chemistry, 61(7), 1573-1578. https://doi.org/10.1021/jf303861p
  79. Song, L., Huang, Z., Chen, Y., Li, H., Jiang, C., & Li, X. (2014). High-efficiency production of bioactive recombinant human fibroblast growth factor 18 in Escherichia coli and its effects on hair follicle growth. Applied Microbiology and Biotechnology, 98(2), 695-704. https://doi.org/10.1007/s00253-013-4929-3
  80. Schaefer-Ramadan, S., Gannon, S. A., & Thorpe, C. (2013). Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase. Biochemistry, 52(46), 8323–8332. https://doi.org/10.1021/bi401305w
  81. Dempsey, D. R., Bond, J. D., Carpenter, A. M., Ospina, S. R., & Merkler, D. J. (2014). Expression, purification, and characterization of mouse glycine N-acyltransferase in Escherichia coli. Protein Expression and Purification, 97, 23-28. https://doi.org/10.1016/j.pep.2014.02.007
  82. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  83. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  84. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  85. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  86. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  87. Guerra, D., Ballard, K., Truebridge, I., & Vierling, E. (2016). S-nitrosation of conserved cysteines modulates activity and stability of S-nitrosoglutathione reductase (GSNOR). Biochemistry, 55(17), 2452-2464.https://doi.org/10.1021/acs.biochem.5b01373
  88. Sutherland, M. C., Rankin, J. A., & Kranz, R. G. (2016). Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry, 55(22), 3150-3156.https://doi.org/10.1021/acs.biochem.6b00427
  89. Robbins, T., Kapilivsky, J., Cane, D. E., & Khosla, C. (2016). Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry, 55(32), 4476-4484. https://doi.org/10.1021/acs.biochem.6b00639
  90. Inan, K., Sal, F. A., Rahman, A., Putman, R. J., Agblevor, F. A., & Miller, C. D. (2016). Microbubble assisted polyhydroxybutyrate production in Escherichia coli. BMC Research Notes, 9(1), 338. https://doi.org/10.1186/s13104-016-2145-9
  91. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  92. Tanner, J. J., Frey, B. B., Pemberton, T., & Henzl, M. T. (2016). EF5 is the high-affinity Mg2+ site in ALG-2. Biochemistry, 55(36), 5128-5141. https://doi.org/10.1021/acs.biochem.6b00596
  93. Kennedy, E. N., Menon, S. K., & West, A. H. (2016). Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions. FEMS Yeast Research, 16(6) fow068. https://doi.org/10.1093/femsyr/fow068
  94. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  95. Sigala, P. A., Morante, K., Tsumoto, K., Caaveiro, J. M., & Goldberg, D. E. (2016). In-Cell Enzymology To Probe His–Heme Ligation in Heme Oxygenase Catalysis. Biochemistry, 55(34), 4836-4849. https://doi.org/10.1021/acs.biochem.6b00562
  96. Fancher, A. T., Hua, Y., Camarco, D. P., Close, D. A., Strock, C. J., & Johnston, P. A. (2016). Reconfiguring the AR-TIF2 protein–protein interaction HCS assay in prostate cancer cells and characterizing the hits from a LOPAC screen. Assay and Drug Development Technologies, 14(8), 453-477. https://doi.org/10.1089/adt.2016.741
  97. Wang, X., Zhang, Z. T., Wang, Y., & Wang, Y. (2016). Production of polyhydroxybuyrate (PHB) from switchgrass pretreated with a radio frequency-assisted heating process. Biomass and Bioenergy, 94, 220-227. https://doi.org/10.1016/j.biombioe.2016.09.006
  98. Devendran, S., Abdel-Hamid, A. M., Evans, A. F., Iakiviak, M., Kwon, I. H., Mackie, R. I., & Cann, I. (2016). Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Scientific Reports, 6, 35342. https://doi.org/10.1038/srep35342
  99. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  100. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114

View all references

IPTG EZ Pak™ for 1 M Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., … & Das, A. (2015). Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2–lipid bilayer interactions. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(10), 2460-2470.https://doi.org/10.1016/j.bbamem.2015.07.015
  3. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  4. Blaszczyk, A. J., Silakov, A., Zhang, B., Maiocco, S. J., Lanz, N. D., Kelly, W. L., … & Booker, S. J. (2016). Spectroscopic and electrochemical characterization of the iron–sulfur and cobalamin cofactors of TsrM, an unusual radical S-adenosylmethionine methylase. Journal of the American Chemical Society, 138(10), 3416-3426.https://doi.org/10.1021/jacs.5b12592
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Guerra, D., Ballard, K., Truebridge, I., & Vierling, E. (2016). S-nitrosation of conserved cysteines modulates activity and stability of S-nitrosoglutathione reductase (GSNOR). Biochemistry, 55(17), 2452-2464.https://doi.org/10.1021/acs.biochem.5b01373
  7. Sutherland, M. C., Rankin, J. A., & Kranz, R. G. (2016). Heme trafficking and modifications during system I cytochrome c biogenesis: insights from heme redox potentials of Ccm proteins. Biochemistry, 55(22), 3150-3156.https://doi.org/10.1021/acs.biochem.6b00427
  8. Robbins, T., Kapilivsky, J., Cane, D. E., & Khosla, C. (2016). Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry, 55(32), 4476-4484. https://doi.org/10.1021/acs.biochem.6b00639
  9. Inan, K., Sal, F. A., Rahman, A., Putman, R. J., Agblevor, F. A., & Miller, C. D. (2016). Microbubble assisted polyhydroxybutyrate production in Escherichia coli. BMC Research Notes, 9(1), 338. https://doi.org/10.1186/s13104-016-2145-9
  10. Wei, Y., Kuzmič, P., Yu, R., Modi, G., & Hedstrom, L. (2016). Inhibition of inosine-5′-monophosphate dehydrogenase from Bacillus anthracis: mechanism revealed by pre-steady-state kinetics. Biochemistry, 55(37), 5279-5288.https://doi.org/10.1021/acs.biochem.6b00265
  11. Tanner, J. J., Frey, B. B., Pemberton, T., & Henzl, M. T. (2016). EF5 is the high-affinity Mg2+ site in ALG-2. Biochemistry, 55(36), 5128-5141. https://doi.org/10.1021/acs.biochem.6b00596
  12. Kennedy, E. N., Menon, S. K., & West, A. H. (2016). Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions. FEMS Yeast Research, 16(6) fow068. https://doi.org/10.1093/femsyr/fow068
  13. Roy, J., Adili, R., Kulmacz, R., Holinstat, M., & Das, A. (2016). Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet function. Journal of Pharmacology and Experimental Therapeutics, 359(1), 134-141. https://doi.org/10.1124/jpet.116.234781
  14. Sigala, P. A., Morante, K., Tsumoto, K., Caaveiro, J. M., & Goldberg, D. E. (2016). In-Cell Enzymology To Probe His–Heme Ligation in Heme Oxygenase Catalysis. Biochemistry, 55(34), 4836-4849. https://doi.org/10.1021/acs.biochem.6b00562
  15. Fancher, A. T., Hua, Y., Camarco, D. P., Close, D. A., Strock, C. J., & Johnston, P. A. (2016). Reconfiguring the AR-TIF2 protein–protein interaction HCS assay in prostate cancer cells and characterizing the hits from a LOPAC screen. Assay and Drug Development Technologies, 14(8), 453-477. https://doi.org/10.1089/adt.2016.741
  16. Wang, X., Zhang, Z. T., Wang, Y., & Wang, Y. (2016). Production of polyhydroxybuyrate (PHB) from switchgrass pretreated with a radio frequency-assisted heating process. Biomass and Bioenergy, 94, 220-227. https://doi.org/10.1016/j.biombioe.2016.09.006
  17. Devendran, S., Abdel-Hamid, A. M., Evans, A. F., Iakiviak, M., Kwon, I. H., Mackie, R. I., & Cann, I. (2016). Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides. Scientific Reports, 6, 35342. https://doi.org/10.1038/srep35342
  18. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  19. Arnold, W. R., Baylon, J. L., Tajkhorshid, E., & Das, A. (2016). Asymmetric binding and metabolism of polyunsaturated fatty acids (PUFAs) by CYP2J2 epoxygenase. Biochemistry, 55(50), 6969-6980. https://doi.org/10.1021/acs.biochem.6b01037
  20. Fiers, W. D., Dodge, G. J., Sherman, D. H., Smith, J. L., & Aldrich, C. C. (2016). Vinylogous dehydration by a polyketide dehydratase domain in curacin biosynthesis. Journal of the American Chemical Society, 138(49), 16024-16036. https://doi.org/10.1021/jacs.6b09748
  21. Le, C. Q., Oyugi, M., Joseph, E., Nguyen, T., Ullah, M. H., Aubert, J., … & Johnson-Winters, K. (2017). Effects of isoleucine 135 side chain length on the cofactor donor-acceptor distance within F420H2: NADP+ oxidoreductase: a kinetic analysis. Biochemistry and Biophysics Reports, 9, 114-120. https://doi.org/10.1016/j.bbrep.2016.11.012
  22. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate 50 mg/mL Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  3. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  4. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  7. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  8. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  9. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  10. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate EZ Pak™ for 50 mg/mL Solution
  1. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  2. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  3. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  4. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  5. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  6. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  7. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  8. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  9. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  10. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
Kanamycin Monosulfate, USP Grade
  1. Wang, Y., Fu, T. J., Howard, A., Kothary, M. H., McHugh, T. H., & Zhang, Y. (2013). Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5. Journal of Agricultural and Food Chemistry, 61(7), 1573-1578. https://doi.org/10.1021/jf303861p
  2. Rabara, R. C., Tripathi, P., Lin, J., & Rushton, P. J. (2013). Dehydration-induced WRKY genes from tobacco and soybean respond to jasmonic acid treatments in BY-2 cell culture. Biochemical and Biophysical Research Communications, 431(3), 409–414. https://doi.org/10.1016/j.bbrc.2012.12.156
  3. Zhang, J., Suflita, M., Fiaschetti, C. M., Li, G., Li, L., Zhang, F., … & Linhardt, R. J. (2015). High cell density cultivation of a recombinant Escherichia coli strain expressing a 6‐O‐sulfotransferase for the production of bioengineered heparin. Journal of Applied Microbiology, 118(1), 92-98. https://doi.org/10.1111/jam.12684
  4. Caliando, B. J., & Voigt, C. A. (2015). Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nature Communications, 6, 6989. https://doi.org/10.1038/ncomms7989
  5. Lowell, A. N., Santoro, N., Swaney, S. M., McQuade, T. J., Schultz, P. J., Larsen, M. J., & Sherman, D. H. (2015). Microscale adaptation of in vitro transcription/translation for high throughput screening of natural product extract libraries. Chemical Biology & Drug Design, 86(6), 1331-1338. https://doi.org/10.1111/cbdd.12614
  6. Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L. B., Giannoukos, G., … & Gordon, D. B. (2014). Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology, 32(12), 1241.https://doi.org/10.1038/nbt.3063
  7. Lanz, N. D., Lee, K. H., Horstmann, A. K., Pandelia, M. E., Cicchillo, R. M., Krebs, C., & Booker, S. J. (2016). Characterization of lipoyl synthase from Mycobacterium tuberculosis. Biochemistry, 55(9), 1372-1383. https://doi.org/10.1021/acs.biochem.5b01216
  8. Dooley, K., Devalliere, J., Uygun, B. E., & Yarmush, M. L. (2016). Functionalized biopolymer particles enhance performance of a tissue-protective peptide under proteolytic and thermal stress. Biomacromolecules, 17(6), 2073-2079. https://doi.org/10.1021/acs.biomac.6b00280
  9. Si, M., Zhao, C., Zhang, B., Wei, D., Chen, K., Yang, X., … & Shen, X. (2016). Overexpression of mycothiol disulfide reductase enhances Corynebacterium glutamicum robustness by modulating cellular redox homeostasis and antioxidant proteins under oxidative stress. Scientific Reports, 6, 29491.https://doi.org/10.1038/srep29491
  10. Zhang, Y., Du, W. X., Fan, Y., Yi, J., Lyu, S. C., Nadeau, K. C., & McHugh, T. H. (2016). Identification, characterization, and initial epitope mapping of pine nut allergen Pin k 2. Food Research International, 90, 268-274. https://doi.org/10.1016/j.foodres.2016.10.043
  11. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
  12. Plumley, B. A., Martin, K. H., Borlee, G. I., Marlenee, N. L., Burtnick, M. N., Brett, P. J., … & Borlee, B. R. (2017). Thermoregulation of biofilm formation in Burkholderia pseudomallei is disrupted by mutation of a putative diguanylate cyclase. Journal of Bacteriology, 199(5), e00780-16.https://doi.org/10.1128/JB.00780-16
  13. Zhang, K., Xie, Y., Muñoz-Moreno, R., Wang, J., Zhang, L., Esparza, M., … & Ren, Y. (2019). Structural basis for influenza virus NS1 protein block of mRNA nuclear export. Nature Microbiology, 1. https://doi.org/10.1038/s41564-019-0482-x
  14. Heater, B. S., Lee, M. M., & Chan, M. K. (2018). Direct production of a genetically-encoded immobilized biodiesel catalyst. Scientific Reports, 8(1), 12783.https://doi.org/10.1038/s41598-018-31213-y
  15. Howell, M., Daniel, J. J., & Brown, P. J. (2017). Live cell fluorescence microscopy to observe essential processes during microbial cell growth. JoVE (Journal of Visualized Experiments), (129), e56497. https://doi.org/10.3791/56497
  16. Arias, R. S., Dang, P. M., & Sobolev, V. S. (2015). RNAi-mediated control of aflatoxins in peanut: method to analyze mycotoxin production and transgene expression in the peanut/Aspergillus pathosystem. JoVE (Journal of Visualized Experiments), (106), e53398. https://doi.org/10.3791/53398
  17. Liu, Z., Sivasankar, P., & Sharma, H. (2019). An improved bioassay to study arabidopsis induced systemic resistance (ISR) against bacterial pathogens and insect pests. Bio-protocol 9 (10): e3236. https://doi.org/10.21769/BioProtoc.3236
  18. Hu, Q., & Shokat, K. M. (2018). Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell, 173(5), 1254–1264.e11. https://doi.org/10.1016/j.cell.2018.03.018
  19. Ding, B., Patterson, E. L., Holalu, S. V., Li, J., Johnson, G. A., Stanley, L. E., … & Blackman, B. K. (2020). Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns. Current Biology. 30(5), 802–814.e8. https://doi.org/10.1016/j.cub.2019.12.067
  20. Karunadasa, S. S., Kurepa, J., Shull, T. E., & Smalle, J. A. (2020). Cytokinin‐induced protein synthesis suppresses growth and osmotic stress tolerance. New Phytologist. https://doi.org/10.1111/nph.16519
  21. Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., … & Liu, D. R. (2020). Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nature Biotechnology, 1-11. https://doi.org/10.1038/s41587-020-0412-8
  22. Shin, J., Zhang, S., Der, B. S., Nielsen, A. A., & Voigt, C. A. (2020). Programming Escherichia coli to function as a digital display. Molecular Systems Biology, 16(3). https://doi.org/10.15252/msb.20199401
  23. Joseph, A. M., Pohl, A. E., Ball, T. J., Abram, T. G., Johnson, D. K., Geisbrecht, B. V., & Shames, S. R. (2020). The Legionella pneumophila metaeffector Lpg2505 (MesI) regulates SidI-mediated translation Inhibition and novel glycosyl hydrolase activity. Infection and Immunity, 88(5). https://doi.org/10.1128/iai.00853-19
  24. Parks, T., & Yordanov, Y. S. (2020). Composite plants for a composite plant: an efficient protocol for root studies in the sunflower using composite plants approach. Plant Cell, Tissue and Organ Culture (PCTOC), 140(3), 647–659. https://doi.org/10.1007/s11240-019-01760-x
  25. González, L. M., Mukhitov, N., & Voigt, C. A. (2019). Resilient living materials built by printing bacterial spores. Nature Chemical Biology, 16(2), 126–133. https://doi.org/10.1038/s41589-019-0412-5
  26. Zhou, D., Tanzawa, T., Lin, J., & Gagnon, M. G. (2019). Structural basis for ribosome recycling by RRF and tRNA. Nature Structural & Molecular Biology, 27(1), 25–32. https://doi.org/10.1038/s41594-019-0350-7
  27. Moroz, N., & Tanaka, K. (2020). FlgII-28 is a major flagellin-derived defense elicitor in potato. Molecular Plant-Microbe Interactions, 33(2), 247–255. https://doi.org/10.1094/mpmi-06-19-0164-r
  28. Reighard, S. D., Cranert, S. A., Rangel, K. M., Ali, A., Gyurova, I. E., de la Cruz-Lynch, A. T., … Waggoner, S. N. (2020). Therapeutic targeting of follicular T cells with chimeric antigen receptor-expressing natural killer cells. Cell Reports Medicine, 100003. https://doi.org/10.1016/j.xcrm.2020.100003
  29. Smith, M. D., Robinson, S. L., Molomjamts, M., & Wackett, L. P. (2020). In vivo assay reveals microbial OleA thiolases initiating hydrocarbon and β-lactone biosynthesis. mBio, 11(2). https://doi.org/10.1128/mbio.00111-20
  30. Wang, T., Badran, A. H., Huang, T. P., & Liu, D. R. (2018). Continuous directed evolution of proteins with improved soluble expression. Nature Chemical Biology, 14(10), 972-980. https://doi.org/10.1038/s41589-018-0121-5
  31. Song, M., Sukovich, D. J., Ciccarelli, L., Mayr, J., Fernandez-Rodriguez, J., Mirsky, E. A., Tucker, A. C., Gordon, D. B., Marlovits, T. C., & Voigt, C. A. (2017). Control of type III protein secretion using a minimal genetic system. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14737
  32. Silpe, J. E., Bridges, A. A., Huang, X., Coronado, D. R., Duddy, O. P., & Bassler, B. L. (2020). Separating functions of the phage-encoded quorum-sensing-activated antirepressor Qtip. Cell Host & Microbe, 27(4), 629–641.e4. https://doi.org/10.1016/j.chom.2020.01.024
  33. Fukuda, S., Yan, S., Komi, Y., Sun, M., Gabizon, R., & Bustamante, C. (2020). The biogenesis of SRP RNA is modulated by an RNA folding intermediate attained during transcription. Molecular Cell, 77(2), 241–250.e8. https://doi.org/10.1016/j.molcel.2019.10.006
  34. Kim, W. J., Higashi, D., Goytia, M., Rendón, M. A., Pilligua-Lucas, M., Bronnimann, M., … & So, M. (2019). Commensal Neisseria kill Neisseria gonorrhoeae through a DNA-dependent mechanism. Cell Host & Microbe, 26(2), 228–239.e8. https://doi.org/10.1016/j.chom.2019.07.003
  35. Moss, S. M., Taylor, I. R., Ruggero, D., Gestwicki, J. E., Shokat, K. M., & Mukherjee, S. (2019). A Legionella pneumophila kinase phosphorylates the Hsp70 chaperone family to inhibit eukaryotic protein synthesis. Cell Host & Microbe, 25(3), 454–462.e6. https://doi.org/10.1016/j.chom.2019.01.006
  36. Silpe, J. E., & Bassler, B. L. (2019). A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell, 176(1-2), 268-280.e13. https://doi.org/10.1016/j.cell.2018.10.059
  37. Barton, B., Grinnell, A., & Morgenstein, R. M. (2021). Disruption of the MreB elongasome Is overcome by mutations in the tricarboxylic acid cycle. Frontiers in Microbiology, 12 https://doi.org/10.3389/fmicb.2021.664281
D-Luciferin Firefly, free acid (Proven and Published®)
  1. Thines, B., & Harmon, F. G. (2010). Ambient temperature response establishes ELF3 as a required component of the core Arabidopsis circadian clock. Proceedings of the National Academy of Sciences, 107(7), 3257–3262. https://doi.org/10.1073/pnas.0911006107
  2. Vallera, D. A., Oh, S., Chen, H., Shu, Y., & Frankel, A. E. (2010). Bioengineering a unique deimmunized bispecific targeted toxin that simultaneously recognizes human CD22 and CD19 receptors in a mouse model of B-cell metastases. Molecular Cancer Therapeutics, 9(6), 1872–1883. https://doi.org/10.1158/1535-7163.mct-10-0203
  3. Stish, B. J., Oh, S., & Vallera, D. A. (2008). Anti-glioblastoma effect of a recombinant bispecific cytotoxin cotargeting human IL-13 and EGF receptors in a mouse xenograft model. Journal of Neuro-Oncology, 87(1), 51-61. https://doi.org/10.1007/s11060-007-9499-8
  4. Andreu, N., Zelmer, A., Fletcher, T., Elkington, P. T., Ward, T. H., Ripoll, J., … & Wiles, S. (2010). Optimisation of bioluminescent reporters for use with mycobacteria. PLoS ONE, 5(5), e10777. https://doi.org/10.1371/journal.pone.0010777
  5. Aird, K. M., Ghanayem, R. B., Peplinski, S., Lyerly, H. K., & Devi, G. R. (2010). X-linked inhibitor of apoptosis protein inhibits apoptosis in inflammatory breast cancer cells with acquired resistance to an ErbB1/2 tyrosine kinase inhibitor. Molecular Cancer Therapeutics, 9(5), 1432-1442 https://doi.org/10.1158/1535-7163.MCT-10-0160
  6. Martin, M. D., Carter, K. J., Jean-Philippe, S. R., Chang, M., Mobashery, S., Thiolloy, S., … & Fingleton, B. (2008). Effect of ablation or inhibition of stromal matrix metalloproteinase-9 on lung metastasis in a breast cancer model is dependent on genetic background. Cancer Research, 68(15), 6251-6259 https://doi.org/10.1158/0008-5472.CAN-08-0537
  7. Li, J., Jiang, J., Qian, Q., Xu, Y., Zhang, C., Xiao, J., … & Huang, Y. (2011). Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation. The Plant Cell, 23(2), 628-640. https://doi.org/10.1105/tpc.110.081901
  8. Vallera, D. A., Chen, H., Sicheneder, A. R., Panoskaltsis-Mortari, A., & Taras, E. P. (2009). Genetic alteration of a bispecific ligand-directed toxin targeting human CD19 and CD22 receptors resulting in improved efficacy against systemic B cell malignancy. Leukemia Research, 33(9), 1233-1242. https://doi.org/10.1016/j.leukres.2009.02.006
  9. Bai, X., Yan, Y., Song, Y. H., Seidensticker, M., Rabinovich, B., Metzele, R., … & Alt, E. (2009). Both cultured and freshly isolated adipose tissue-derived stem cells enhance cardiac function after acute myocardial infarction. European Heart Journal, 31(4), 489-501. https://doi.org/10.1093/eurheartj/ehp568
  10. Lam, W., Bussom, S., & Cheng, Y. C. (2009). Effect of hypoxia on the expression of phosphoglycerate kinase and antitumor activity of troxacitabine and gemcitabine in non-small cell lung carcinoma. Molecular Cancer Therapeutics, 8(2), 415-423. https://doi.org/10.1158/1535-7163.MCT-08-0692
  11. Buckley, S. M., Howe, S. J., Rahim, A. A., Buning, H., McIntosh, J., Wong, S. P., … & McKay, T. R. (2008). Luciferin detection after intranasal vector delivery is improved by intranasal rather than intraperitoneal luciferin administration. Human gene therapy, 19(10), 1050-1056. https://doi.org/10.1089/hum.2008.023
  12. Marques, C. P., Cheeran, M. C., Palmquist, J. M., Hu, S., Urban, S. L., & Lokensgard, J. R. (2008). Prolonged microglial cell activation and lymphocyte infiltration following experimental herpes encephalitis. The Journal of Immunology, 181(9), 6417–6426. https://doi.org/10.4049/jimmunol.181.9.6417
  13. Coffey, R. T., Shi, Y., Long, M. J., Marr, M. T., & Hedstrom, L. (2016). Ubiquilin-mediated small molecule inhibition of mammalian target of rapamycin complex 1 (mTORC1) signaling. Journal of Biological Chemistry, 291(10), 5221-5233. https://doi.org/10.1074/jbc.M115.691584
  14. Parvez, S., Long, M. J., Lin, H. Y., Zhao, Y., Haegele, J. A., Pham, V. N., … & Aye, Y. (2016). T-REX on-demand redox targeting in live cells. Nature Protocols, 11(12), 2328. https://doi.org/10.1038/nprot.2016.114
D-Luciferin, Potassium Salt (Proven and Published®)