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A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

Jonathan M. Stokes, Arnaud Gutierrez, Allison J. Lopatkin, Ian W. Andrews, Shawn French, Ivan Matic, Eric D. Brown & James J. Collins Nature Methods (2019) Antibiotic screens typically rely on growth inhibition to characterize compound bioactivity—an approach that cannot be used to assess the bactericidal activity of antibiotics against bacteria in drug-tolerant states. To address … Continue reading A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria



PIXL EFFICIENCY REPORT: AGAR-AGAR

Precision and accuracy are values we’ve held as the core of our business since starting in 1934. Delivering robotic solutions to the academic and industrial markets, our accuracy is relied upon to support the research and work that our customers do! The newest addition to our portfolio is PIXL, built to be the most accurate … Continue reading PIXL EFFICIENCY REPORT: AGAR-AGAR



The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

Côté, J. P., French, S., Gehrke, S. S., MacNair, C. R., Mangat, C. S., Bharat, A., & Brown, E. D. mBio. 2016 Nov-Dec; 7(6): e01714-16. Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under … Continue reading The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli



Construction and Analysis of Two Genome-scale Deletion Libraries for Bacillus subtilis

Koo, B. M., Kritikos, G., Farelli, J. D., Todor, H., Tong, K., Kimsey, H., Wapinski, I., Galardini, M., Cabal, A., Peters, J. M., Hachmann, A. B., Rudner, D. Z., Allen, K. N., Typas, A., … Gross, C. A. Cell Syst. 2017 Mar 22; 4(3): 291–305.e7. A systems level understanding of Gram-positive bacteria is important from … Continue reading Construction and Analysis of Two Genome-scale Deletion Libraries for Bacillus subtilis



Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli

Takeuchi, R., Tamura, T., Nakayashiki, T., Tanaka, Y., Muto, A., Wanner, B. L., & Mori, H. BMC Microbiol. 2014; 14: 171. Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement … Continue reading Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli



Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12

Hirotada Mori and Barry L. Wanner Methods Mol Biol. 2015;1279:45-65. doi: 10.1007/978-1-4939-2398-4_4. Here we describe the systematic identification of single genes and gene pairs, whose knockout causes lethality in Escherichia coli K-12. During construction of precise single-gene knockout library of E. coli K-12, we identified 328 essential gene candidates for growth in complex (LB) medium. … Continue reading Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12



Toward Network Biology in E. coli Cells

Hirotada Mori and Barry L. Wanner Adv Exp Med Biol. 2015;883:155-68. doi: 10.1007/978-3-319-23603-2_9. E. coli has been a critically important model research organism for more than 50 years, particularly in molecular biology. In 1997, the E. coli draft genome sequence was published. Post-genomic techniques and resources were then developed that allowed E. coli to become … Continue reading Toward Network Biology in E. coli Cells



Phenotypic Landscape of a Bacterial Cell

Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA Cell. Elsevier; 2011 Jul 1;144(1):143–56 Bacteria/SGA The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes … Continue reading Phenotypic Landscape of a Bacterial Cell



Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways

Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe’er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A PLoS Genet. 2011 Nov;7(11):e1002377 Bacteria/SGA As the interface between … Continue reading Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways