Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

Autor: John R Houser, Craig Barnhart, Daniel R Boutz, Sean M Carroll, Aurko Dasgupta, Joshua K Michener, Brittany D Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K Sydykova, Christopher J Marx, M Stephen Trent, Jeffrey E Barrick, Edward M Marcotte, Claus O Wilke

Publikováno v: PLoS Computational Biology, Vol 11, Iss 8, p e1004400 (2015)

How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components,

Externí odkaz: https://doaj.org/article/9de889c5ee104d68a308ff43690012fc

Rates of gene conversions betweenEscherichia coliribosomal operons

Autor: Jeffrey E. Barrick, Aurko Dasgupta, Isaac Gifford

Due to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::06488258b5edf442eedccedf4d42bcf2
https://doi.org/10.1101/2020.08.03.235192

Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx

Autor: Brian A. Renda, Gabriel A. Suárez, Jeffrey E. Barrick, Aurko Dasgupta

Publikováno v: Applied and Environmental Microbiology. 83

The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a de

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::def197530b76d0a061a388a4395581c0
https://doi.org/10.1128/aem.01025-17

Tempo and mode of genome evolution in a 50,000-generation experiment

Autor: Aurko Dasgupta, Richard E. Lenski, Jeffrey E. Barrick, Sébastien Wielgoss, Noah Ribeck, Claudine Médigue, Jeffrey L. Blanchard, Gabriel C. Wu, Stéphane Cruveiller, Daniel E. Deatherage, Dominique Schneider, Olivier Tenaillon

Publikováno v: Nature
Nature, Nature Publishing Group, 2016, 536 (7615), pp.165-170. ⟨10.1038/nature18959⟩
Nature, 2016, 536 (7615), pp.165-170. ⟨10.1038/nature18959⟩

Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Esche

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::44f1d4fdefb165159116692dad406134
https://hal.archives-ouvertes.fr/hal-01653393

Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5

Autor: Peter B. Otoupal, Jeffrey E. Barrick, James L. Bachman, Mani Subramanian, Ryan M. Summers, Erik M. Quandt, Ben Slater, Aurko Dasgupta, Razan N. Alnahhas, Michael J. Hammerling

Publikováno v: ACS synthetic biology. 2(6)

The widespread use of caffeine (1,3,7-trimethylxanthine) and other methylxanthines in beverages and pharmaceuticals has led to significant environmental pollution. We have developed a portable caffeine degradation operon by refactoring the alkylxanth

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe0257495bdbf6d0587638b5183a7857
https://pubmed.ncbi.nlm.nih.gov/23654268