Tephritis conura host shift gene expression
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ABSTRACT:
PROVIDER: PRJEB73529 | ENA |
REPOSITORIES: ENA
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Project description:The mechanism of evolution in different conditions can be examined from various molecular aspects that constitute a cell, namely, transcript, protein or metabolite abundance. We have analyzed transcript and metabolite abundance changes in evolved and ancestor strains in three different evolutionary conditions, namely, excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift, in two different strains of Escherichia coli K-12 (MG1655 and DH10B).
2007-10-02 | E-MEXP-1166 | biostudies-arrayexpress
Project description:In response to changing environmental conditions, organisms can acclimate through phenotypic plasticity or adapt by evolving mechanisms to cope with novel stressors. Changes in gene expression, whether dynamic or evolved, are an important way in which environmental responses are mediated; however, much is still unknown about how the molecular networks underlying plastic phenotypes evolve. Here, we compare transcriptional responses to acute heat stress among four populations of the nematode Caenorhabditis remanei-one selected to withstand heat stress, one selected under oxidative stress, an unselected control, and the ancestral population. We used a weighted gene coexpression network analysis within these lines to identify transcriptional modules, which are sets of genes that respond similarly to stress via plastic responses, evolutionary responses, or both. The transcriptional response to acute heat stress is dominated by a plastic response that is shared in the ancestor and all evolved populations. However, we also identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings reveal that while it is possible to perturb the nature of the transcriptional response network with short bouts of intense selection, the overall structure of transcriptional plasticity is dominated by inherent, ancestral regulatory systems.
2019-02-04 | GSE115496 | GEO
Project description:During the over 300 million years of co-evolution between herbivorous insects and their host plants, a dynamic equilibrium of evolutionary arms race has been established. However, the co-adaptation between insects and their host plants is a complex process, often driven by multiple evolutionary mechanisms. We found that various lepidopteran pests that use maize as a host exhibit differential adaptation to the plant secondary metabolites, benzoxazinoids (BXs). Notably, the Spodoptera genus, including Spodoptera frugiperda (fall armyworm) and Spodoptera litura (cotton leafworm), demonstrate greater tolerance to BXs compared to other insects. Through comparative transcriptomic analysis of the midgut, we identified four candidate genes potentially involved in BXs detoxification in S. frugiperda. Subsequently, we confirmed two UGT genes, Sfru33T10 and Sfru33F32, as key players in BXs detoxification using CRISPR/Cas9 gene-editing technology. Phylogenetic analysis revealed that Sfru33T10 evolved independently within the Noctuidae family and is involved in the glycosylation of HDMBOA, while Sfru33F32 evolved independently within the Spodoptera genus and functions as a key detoxification enzyme responsible for the glycosylation of both DIMBOA and HMBOA. Our study demonstrates that the UGT gene family plays a crucial role in the adaptation of noctuid insects to maize, with multiple independent evolutionary events within the Noctuidae family and the Spodoptera genus contributing significantly to host adaptation.
2024-09-18 | GSE276946 | GEO
Project description:MYC is an oncoprotein transcription factor that is overexpressed in the majority cancers. Although MYC itself is considered undruggable, it may be possible to inhibit MYC by targeting the co-factors it uses to drive oncogenic gene expression patterns. Here, we use loss- and gain- of function approaches to interrogate how one MYC co-factor—Host Cell Factor (HCF)-1—contributes to MYC activity in a Burkitt lymphoma setting. We identify high-confidence direct targets of the MYC–HCF-1 interaction that are regulated through a recruitment-independent mechanism, including genes that control mitochondrial function and rate-limiting steps for ribosome biogenesis and translation. We describe how these gene expression events impact cell growth and metabolism, and demonstrate that the MYC–HCF-1 interaction is essential for tumor maintenance in vivo. This work highlights the MYC–HCF-1 interaction as a focal point for development of novel anti-cancer therapies.
2020-07-15 | ST001429 | MetabolomicsWorkbench
Project description:Marseilleviruses comprise a family of large double-stranded DNA viruses belonging to the proposed order "Megavirales." These viruses have a circular genome of ∼370 kbp, coding hundreds of genes. Over a half of their genes are associated with AT-rich putative promoter motifs, which have been demonstrated to be important for gene regulation. However, the transcriptional profile of Marseilleviruses is currently unknown. Here we used RNA sequencing technology to get a general transcriptional profile of Marseilleviruses. Eight million 75-bp-long nucleotide sequences were robustly mapped to all 457 genes initially predicted for Marseillevirus isolate T19, the prototype strain of the family, and we were able to assemble 359 viral contigs using a genome-guided approach with stringent parameters. These reads were differentially mapped to the genes according to the replicative cycle time point from which they were obtained. Cluster analysis indicated the existence of three main temporal categories of gene expression, early, intermediate and late, which were validated by quantitative reverse transcription polymerase chain reaction assays targeting several genes. Genes belonging to different functional groups exhibited distinct expression levels throughout the infection cycle. We observed that the previously predicted promoter motif, AAATATTT, as well as new predicted motifs, were not specifically related to any of the temporal or functional classes of genes, suggesting that other components are involved in temporally regulating virus transcription. Moreover, the host transcription machinery is heavily altered, and many genes are down regulated, including those related to translation process. This study provides an overview of the transcriptional landscape of Marseilleviruses.
| S-EPMC7192143 | biostudies-literature
Project description:We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after beetles’ exposure to new environments that differed from ancestral control conditions in temperature, humidity or both. Using experimental evolution with ten replicated lines per condition, we were able to demonstrate adaptation (higher offspring number compared to control lines) after 20 generations. We measured whole-transcriptome gene expression with RNA-seq to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.
2020-08-15 | GSE156256 | GEO
Project description:Saccharomyces cerevisiae colonies were grown on synthetic minimal media containing 1% glucose. The top layer of cells was scraped off using a custom plastic guide and a cell scraper. The remaining bottom layer of cells was then washed off with water and proteomics samples were prepared from both layers separately. Label-free quantification by DIA-SWATH was used to assess differences in gene expression between top and bottom layers.
2023-02-13 | PXD033395 | Pride
Project description:In this study, we aimed to investigate the influence of the local mechanical cell niche on mechano-responsive signaling activities and germ layer specification by engineering a unique 3D semispherical colony of human-induced pluripotent stem cells (iPSCs). To achieve this, we utilized a combination of an electrospun nanofibrous substrate and PDMS microwells. Specifically, we compared the gene expression profiles of iPSCs cultured on a plastic plate with those cultured on a PCL nanofibrous substrate (19 kPa).
2023-06-13 | GSE234529 | GEO
Project description:Primary outcome(s): Gene expression of targeted genes
| 2625389 | ecrin-mdr-crc
Project description:Gene expression in BM niche populations
| PRJNA429030 | ENA