Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors

Autor: Rama P. Bhatia, Hande A. Kirit, Alexander V. Predeus, Jonathan P. Bollback

Publikováno v: Scientific Reports, Vol 12, Iss 1, Pp 1-14 (2022)

Abstract Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In thi

Externí odkaz: https://doaj.org/article/c300569dca9c4585b67b098436fef008

Predicting bacterial promoter function and evolution from random sequences

Autor: Mato Lagator, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, Gašper Tkačik

Publikováno v: eLife, Vol 11 (2022)

Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we devel

Externí odkaz: https://doaj.org/article/50f68b595e8143fc96311c7d7b58db73

Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella

Autor: Rama P Bhatia, Hande Acar Kirit, Cecil M Lewis, Krithivasan Sankaranarayanan, Jonathan P Bollback

Publikováno v: Evolution Letters.

Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::dbff3b88eb88669b741037f8f760aa23
https://doi.org/10.1093/evlett/qrad020

The Role of the Environment in Horizontal Gene Transfer

Autor: Hande Acar Kirit, Jonathan P Bollback, Mato Lagator

Publikováno v: Kirit, H A, Bollback, J P & Lagator, M 2022, ' The Role of the Environment in Horizontal Gene Transfer ', Molecular Biology and Evolution, vol. 39, no. 11, msac220 . https://doi.org/10.1093/molbev/msac220

Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematica

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b685947e93c422d32b6bc0d9daf21555
https://pubmed.ncbi.nlm.nih.gov/36227733

On the mechanistic nature of epistasis in a canonical cis-regulatory element

Autor: Mato Lagator, Tiago Paixão, Nicholas H Barton, Jonathan P Bollback, Călin C Guet

Publikováno v: eLife, Vol 6 (2017)

Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory tha

Externí odkaz: https://doaj.org/article/11bb70c8a0bf4635beec9630e54c7d42