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High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

ABSTRACT: High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

PROVIDER: PRJNA565219 | ENA |

REPOSITORIES: ENA

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High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

Project description:Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.

2020-10-12 | GSE137348 | GEO

High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli.

Project description: Not available

| S-EPMC7686311 | biostudies-literature

Developmental constraints shape the evolution of the nematode mid-developmental transition

Project description:Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same ‘hourglass’ pattern of variation may result from increased positive selection at the earlier and later stages of development. To distinguish between these scenarios, we examined gene expression variation in a population of the nematode C. elegans using an experimental design that eliminated the influence of positive selection. By measuring gene expression for all genes throughout development in twenty strains, we found that variations were dramatically uneven throughout development, with a significant depletion during mid-embryogenesis. In particular, the family of homeodomain transcription factors, whose expression generally coincides with mid-embryogenesis, evolved under high constraint. Our data further shows that genes responsible for the integration of germ layers during morphogenesis are the most constrained class of genes. Together, these results provide the first evidence for developmental constraints as the mechanism underlying the hourglass model of animal evolution. Understanding the pattern and mechanism of developmental constraints provides a framework to understand how evolutionary processes have interacted with embryogenesis and led to the diversity of animal life on earth.

2017-04-04 | GSE87528 | GEO

Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Project description:Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

| PRJNA137505 | ENA

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

| PRJNA704835 | ENA

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

| PRJNA704830 | ENA

Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

Project description:Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

| PRJNA704832 | ENA

Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints

2011-10-22 | GSE33147 | GEO

Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

2011-10-21 | E-GEOD-33147 | biostudies-arrayexpress

Adaptive laboratory evolution with heterologous pgi

Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.

2023-02-09 | GSE224989 | GEO

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