Biology subjects

Meyer, E.

Publications and source records attributed to Meyer, E..

5 recordsLinked to original sources

bioRxiv2018

New inhibitors of Mycobacterium tuberculosis identified using systems chemical biology

New antibiotics are needed to combat rising resistance, with new Mycobacterium tuberculosis (Mtb) drugs of highest priority. Conventional whole-cell and biochemical antibiotic screens have failed. We developed a novel strategy termed PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets) in which we screen compounds against pools of strains depleted for essential bacterial targets. We engineered strains targeting 474 Mtb essential genes and screened pools of 100-150 strains against activity-enriched and unbiased compounds libraries, measuring > 8.5-million chemical-genetic interactions. Primary screens identified >10-fold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insight. We identified > 40 novel compounds targeting DNA gyrase, cell wall, tryptophan, folate biosynthesis, and RNA polymerase, as well as inhibitors of a novel target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating PROSPECTs ability to yield inhibitors against novel targets which would have eluded conventional drug discovery.

microbiology↗

bioRxiv2017

Heritable variation in bleaching responses and its functional genomic basis in reef-building corals (Orbicella faveolata)

Reef-building corals are highly sensitive to rising ocean temperatures, and substantial adaptation will be required for animals and the ecosystems they support to persist in changing ocean conditions. Genetic variation that might support adaptive responses has been measured in larval stages of some corals, but these estimates remain unavailable for adult corals and the functional basis of this variation remains unclear. In this study, we focused on the potential for adaptation in Orbicella faveolata, a dominant reef-builder in the Caribbean. We conducted thermal stress experiments using corals collected from natural populations in Bocas del Toro, Panama, and used multilocus SNP genotypes to estimate genetic relatedness among samples. This allowed us to estimate narrow-sense heritability of variation in bleaching responses, revealing that this variation was highly heritable (h2=0.91). This estimate suggests substantial potential for adaptive responses to warming by natural populations of O. faveolata in this region. To investigate the functional basis for this variation, we applied genomic and transcriptomic approaches enabled by expanding sequence resources for this species. We used a genetic linkage map we have recently developed to map associations between SNP genotypes and bleaching responses, and identified four genetic markers associated with bleaching. We also profiled gene expression in corals with contrasting bleaching phenotypes, uncovering substantial variation in responses to thermal stress between heat-tolerant and heat-susceptible corals. Integrating these genomic and transcriptomic data with quantitative genetic analysis provides a new perspective on the mechanistic basis for thermal tolerance phenotypes and the potential for adaptation to rising ocean temperatures.

evolutionary biology↗

bioRxiv2017

Genomic and transcriptomic signals of thermal tolerance in heat-tolerant corals (Platygyra daedalea) of the Arabian/Persian Gulf

Scleractinian corals occur in tropical regions near their upper thermal limits, and are severely threatened by rising ocean temperatures. Ocean warming leads to loss of symbiotic algae (Symbiodinium), reduced fitness for the coral host, and degradation of the reef. However, several recent studies have shown that natural populations of corals harbor genetic variation in thermal tolerance that may support adaptive responses to warming. Here weve extended these approaches to study heat tolerance of corals in the Persian/Arabian Gulf, where heat-tolerant local populations have adapted to warm summer temperatures (>36{degrees}C). To evaluate whether selection has depleted genetic variation in thermal tolerance, estimate the potential for future adaptive responses, and understand the functional basis for these corals unusual heat tolerance, we measured thermal tolerance using controlled crosses in the Gulf coral Platygyra daedalea. We found that heat tolerance is highly heritable in this population (0.487-0.748), suggesting substantial potential for adaptive responses to selection for thermal tolerance. To identify genetic markers associated with this variation, we conducted genomewide SNP genotyping in parental corals and tested for relationships between paternal genotype and thermal tolerance of the offspring. We found that multilocus SNP genotypes explained a large fraction of variation in thermal tolerance in these crosses (69%). To investigate the functional basis of these differences in thermal tolerance, we profiled transcriptional responses in tolerant and susceptible families, revealing substantial sire effects on transcriptional responses to thermal stress. We also studied sequence variation in these expressed sequences, identifying alleles and functional groups associated with thermal tolerance. Our findings demonstrate that corals in these populations harbor extensive genetic variation in thermal tolerance, and these heat-tolerant phenotypes differ in both gene sequences and transcriptional stress responses from their susceptible counterparts.

evolutionary biology↗

bioRxiv2017

Integrating genomic resources for a threatened Caribbean coral (Orbicella faveolata) using a genetic linkage map developed from individual larval genotypes

Genomic methods are powerful tools for studying evolutionary responses to selection, but the application of these tools in non-model systems threatened by climate change has been limited by the availability of genomic resources in those systems. High-throughput DNA sequencing has enabled development of genome and transcriptome assemblies in non-model systems including reef-building corals, but the fragmented nature of early draft assemblies often obscures the relative positions of genes and genetic markers, and limits the functional interpretation of genomic studies in these systems. To address this limitation and improve genomic resources for the study of adaptation to ocean warming in corals, weve developed a genetic linkage map for the mountainous star coral, Orbicella faveolata. We analyzed genetic linkage among multilocus SNP genotypes to infer the relative positions of markers, transcripts, and genomic scaffolds in an integrated genomic map. To illustrate the utility of this resource, we tested for genetic associations with bleaching responses and fluorescence phenotypes, and estimated genome-wide patterns of population differentiation. Mapping the significant markers identified from these analyses in the integrated genomic resource identified hundreds of genes linked to significant markers, highlighting the utility of this resource for genomic studies of corals. The functional interpretations drawn from genomic studies are often limited by the availability of genomic resources linking genes to genetic markers. The resource developed in this study provides a framework for comparing genetic studies of O. faveolata across genotyping methods or references, and illustrates an approach for integrating genomic resources that may be broadly useful in other non-model systems.

genomics↗

bioRxiv2017

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of functional protein variants or to the regulation of gene expression, notably via nonsense-mediated mRNA decay (NMD). However, a fraction of splice variants might correspond to spurious transcripts, and the question of the relative proportion of splicing errors vs. functional splice variants remains highly debated. We propose here a test to quantify the fraction of AS events corresponding to errors. This test is based on the fact that the fitness cost of splicing errors increases with the number of introns in a gene and with expression level. We first analyzed the transcriptome of the intron-rich unicellular eukaryote Paramecium tetraurelia. We show that both in normal and in NMD-deficient cells, AS rates (intron retention, alternative splice site usage or cryptic intron splicing) strongly decrease with increasing expression level and with increasing number of introns. This relationship is observed both for AS events that are detectable by NMD or not, which invalidates the hypothesis of a possible link with the regulation of gene expression. Our results indicate that in genes with a median expression level, 92%-98% of observed splice variants correspond to errors. Interestingly, we observed the same patterns in human transcriptomes. These results are consistent with the mutation-selection-drift theory, which predicts that genes under weaker selective pressure should accumulate more maladaptive substitutions, and therefore should be more prone to errors of gene expression.

genomics↗