Ontology highlight
ABSTRACT:
PROVIDER: PRJNA826324 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18740601_1.fastq.gz | Fastqsanger.gz | |||
| SRR18740601_2.fastq.gz | Fastqsanger.gz | |||
| SRR18740602_1.fastq.gz | Fastqsanger.gz | |||
| SRR18740602_2.fastq.gz | Fastqsanger.gz | |||
| SRR18740603_1.fastq.gz | Fastqsanger.gz |
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Project description:The velvetbean caterpillar Anticarsia gemmatalis is one of the main soybean defoliators in Brazil. Currently, the main biopesticide used to control not only A. gemmatalis but also other insect pests worldwide is the bacteria Bacillus thuringiensis (Bt), which produces entomopathogenic Crystal toxins (Cry) that act in the midgut of susceptible insects, leading them to death. The mode of action of Cry toxins in the midgut involves binding to specific receptors present on the brush border of epithelial cells such as aminopeptidase N (APN), alkaline phosphatase (ALP), cadherin, and others. Mutations in these receptors, among other factors, may be involved in the development of resistance; identification of functional Cry receptors in the midgut of A. gemmatalis is crucial to develop effective strategies to overcome this possible scenario. This study’s goal is to characterize APNs of A. gemmatalis and identify a receptor for Cry1Ac in the midgut. The interaction of Bt spores with the midgut epithelium was observed in situ by immunohistochemistry and total aminopeptidase activity was estimated in brush border membrane vesicle (BBMV) samples, presenting higher activity in challenged individuals than in control ones. Ten APN sequences were found in a A. gemmatalis’ transcriptome and subjected to different in silico analysis, such as phylogenetic tree, multiple sequence alignment and identification of signal peptide, activity domains and GPI-anchor signal. BBMV proteins from 5th instar larvae were submitted to a ligand blotting using activated Cry toxin and a commercial anti-Cry polyclonal antibody; corresponding bands of proteins that showed binding to Cry toxin were excised from the SDS-PAGE gel and subjected to mass spectrometry analysis, which resulted in the identification of seven of those APNs. Quantitative PCR was realized to compare expression levels between individuals subjected to sublethal infection with Bt spores and control ones, presenting up- and downregulations upon Bt infection. From these results, we can infer that aminopeptidases N in A. gemmatalis could be involved in the mode of action of Cry toxins in its larval stage.
2025-05-07 | PXD055041 | Pride
Project description:Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC). However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed mouse and microbiota RNA-sequencing on colon tissue from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. The bacteria in BT mice differentially expressed >2,900 genes related to bacterial secretion, virulence and biofilms, but only affected 62 host genes. Importantly, the bacterial communities from BT mice were transmissible and carcinogenic when administered to a new GF ApcMin/+;Il10-/- cohort, maintaining a set of 13 bacterial genera. Our findings suggest complex interactions within bacterial communities affecting bacterial composition and CRC development.
2019-12-30 | GSE108156 | GEO
Project description:Host-pathogen interactions result in complex relationship, many aspects of which are not completely understood. Vip proteins, which are Bacillus thuringensis (Bt) insecticidal toxins produced during the vegetative stage, are selectively effective against specific insect pests. This new group of Bt proteins represents an interesting alternative to the classical Bt Cry toxins because current data suggests that they do not share the same mode of action. We have designed and developed a genome-wide microarray for the beet armyworm Spodoptera exigua, a serious lepidopteran pest of many agricultural crops, and used it to better understand how Lepidopteran larvae respond to the treatment with the insecticidal protein Vip3Aa. With this approach, the goal of our study was to evaluate the changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa at 8 and 24 h after treatment. Results indicated that the toxin provoked a wide transcriptional response, with 19% of unigenes in the microarray responding significantly to treatment. The number of up- and down-regulated unigenes was very similar.. The number of genes whose expression was regulated at 8 h was similar to the number of genes whose expression was regulated after 24 h of treatment. The up-regulated sequences were enriched for genes involved in innate immune response and in pathogen response such as antimicrobial peptides (AMPs) and repat genes. The down-regulated sequences were mainly unigenes with homology to genes involved in metabolism. Genes related to the mode of action of Bt Cry proteins were found, in general, to be slightly overexpressed. The present study is the first genome-wide analysis of the response of lepidopteran insects to Vip3Aa intoxication. An insight into the molecular mechanisms and components related to Vip intoxication will allow designing of more effective management strategies for pest control.
2013-09-27 | GSE51195 | GEO
Project description:Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC). However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed small RNA sequencing on the stool of from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. revealed a group of significant differentially expressed miRNAs specific to BT compared to BX associated ApcMin/+;Il10-/- mice and several miRNAs that correlated with bacterial genera abundances. Our findings suggest complex interactions within bacterial communities affecting host-derived miRNA and CRC development.
2019-12-30 | GSE108164 | GEO
Project description:Human activity is altering the environment at a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity are particularly suited to offer solutions. To explore the paths leading to bacteria-assisted rapid adaptation, we used Caenorhabditis elegans harboring a defined microbiome, and the antibiotic neomycin as a model toxin, harmful for the worm host and neutralized to different extents by microbiome members. Worms exposed to neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Through a combination of 16S gene sequencing, counting of live bacteria and behavioral assays we identified two distinct mechanisms that facilitated adaptation: gut enrichment for a neomycin-modifying strain driven by altered bacterial competition; and host avoidance behavior, which depended on the stress-activated KGB-1/JNK and enabled preference of neomycin-protective bacteria. The straightforwardness of these mechanisms suggests that bacteria-assisted host adaptation may be more common than currently appreciated, protecting animals from novel stressors. However, gut remodeling may also cause dysbiosis, and additional experiments identified fitness trade-offs including increased susceptibility to infection as well as metabolic remodeling. Extending these results to other toxins suggests yet unaccounted-for microbiome-dependent long-term consequences of toxin exposure.
2023-11-09 | GSE246966 | GEO
Project description:Host-pathogen interactions result in complex relationship, many aspects of which are not completely understood. Vip proteins, which are Bacillus thuringensis (Bt) insecticidal toxins produced during the vegetative stage, are selectively effective against specific insect pests. This new group of Bt proteins represents an interesting alternative to the classical Bt Cry toxins because current data suggests that they do not share the same mode of action. We have designed and developed a genome-wide microarray for the beet armyworm Spodoptera exigua, a serious lepidopteran pest of many agricultural crops, and used it to better understand how Lepidopteran larvae respond to the treatment with the insecticidal protein Vip3Aa. With this approach, the goal of our study was to evaluate the changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa at 8 and 24 h after treatment. Results indicated that the toxin provoked a wide transcriptional response, with 19% of unigenes in the microarray responding significantly to treatment. The number of up- and down-regulated unigenes was very similar.. The number of genes whose expression was regulated at 8 h was similar to the number of genes whose expression was regulated after 24 h of treatment. The up-regulated sequences were enriched for genes involved in innate immune response and in pathogen response such as antimicrobial peptides (AMPs) and repat genes. The down-regulated sequences were mainly unigenes with homology to genes involved in metabolism. Genes related to the mode of action of Bt Cry proteins were found, in general, to be slightly overexpressed. The present study is the first genome-wide analysis of the response of lepidopteran insects to Vip3Aa intoxication. An insight into the molecular mechanisms and components related to Vip intoxication will allow designing of more effective management strategies for pest control. Changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa were measured at 8 and 24 h after treatment by means of custom Spodoptera exigua microarray. Six to seven larvae were used for each time point and three independent experiments were performed at each time point.
2013-09-27 | E-GEOD-51195 | biostudies-arrayexpress
Project description:Virulence of many bacterial pathogens, including the important human pathogen Staphylococcus aureus, depends on the secretion of frequently high amounts of toxins. Toxin production involves the need for the bacteria to make physiological adjustments for energy conservation. While toxins are primarily known to be targets of gene regulation, such changes may be accomplished by regulatory functions of the toxins themselves. However, mechanisms by which toxins regulate gene expression have remained poorly understood. We show here that the phenol-soluble modulin toxins have gene regulatory functions, which in particular include regulation of their own export by direct interference with a GntR-type repressor protein. This capacity was most pronounced in PSMs with low cytolytic capacity, demonstrating functional specification among closely related members of that toxin family. Our study presents a paradigmatic example of how bacterial toxins may regulate gene expression to adapt to the physiological needs in situations of enhanced toxin production.
2016-12-19 | GSE72878 | GEO
Project description:WGS sequence data from cell lines BT-54/BT-88/BT-92/BT-142
| EGAD00001003920 | EGA
Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses. RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis. Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH). Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.
2016-04-01 | E-GEOD-77505 | biostudies-arrayexpress