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Bacteria

ABSTRACT: Resequencing whole-genome PCR products of insect symbionts

PROVIDER: PRJDB18473 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR591237_1.fastq.gz	Fastqsanger.gz
	DRR591237_2.fastq.gz	Fastqsanger.gz
	DRR591238_1.fastq.gz	Fastqsanger.gz
	DRR591238_2.fastq.gz	Fastqsanger.gz

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The Drosophila immune response towards entomopathogenic nematodes and their associated bacteria.

Project description:Entomopathogenic nematodes (EPNs) of the genera Heterorhabditis are obligate and lethal insect parasites. In recent years they have been used increasingly as biological control agents. These EPNs are symbiotically associated with bacteria of the genera Photorhabdus. The bacterial symbionts are essential to kill the host (within 24-48 hours) and digest its tissues to provide nutrients for themselves as well for expanding nematodes. Drosophila larvae are suitable insect hosts and part of the tripartite model system we used before to show the importance of haemolymph clotting and eicosanoids during the infection. We used the well-established tripartite model (Drosophila, nematodes, bacteria), DNA chips and bioinformatic tools to compare gene expression in non-infected and infected fly larvae. We focused on the early time point of nematode infection and therefore infected Drosophila larvae using H. bacteriophora harbouring GFP-labelled P. luminescens bacteria. Infected (GFP positive) larvae were collected 6 hours after infection.

2014-03-07 | E-MTAB-1542 | biostudies-arrayexpress

Bacteria

Project description:F. occidentalis bacterial symbionts genome sequencing

| PRJNA234511 | ENA

Laboratory evolution of Jen1p-independent lactate transport in Saccharomyces cerevisiae: identification of ADY2 alleles by whole genome resequencing and mRNA expression analysis

Project description:Background: Evolutionary engineering is a powerful approach to isolate suppressor mutants and industrially relevant genotypes. Until recently, DNA microarray analysis was the only affordable genome-wide approach to identify the responsible mutations. This situation has changed due to the rapidly decreasing costs of whole genome (re)sequencing. DNA microarray-based mRNA expression analysis and whole genome resequencing were combined in a study on lactate transport in Saccharomyces cerevisiae. Jen1p is the only S. cerevisiae lactate transporter reported in literature. To identify alternative lactate transporters, a jen1Δ strain was evolved for growth on lactate. Results: Two independent evolution experiments yielded Jen1p-independent growth on lactate (μmax 0.14 and 0.18 h-1 for single-cell lines IMW004 and IMW005, respectively). Whereas mRNA expression analysis did not provide leads, whole-genome resequencing showed different single nucleotide changes (C755G/Leu219Val and C655G/Ala252Gly) in the acetate transporter gene ADY2. Analysis of mRNA levels and depth of coverage of DNA sequencing combined with karyotyping, gene deletions and diagnostic PCR showed that in IMW004 an isochromosome III (~475 kb), which contains two additional copies of ADY2C755G, was formed via crossover between YCLWΔ15 and YCRCΔ6. Introduction of the ADY2 alleles in a jen1 ady2 strain resulted in growth on lactate (μmax 0.14 h-1 for Ady2pLeu219Val and 0.12 h-1 for Ady2pAla252Gly). Conclusions: Whole-genome resequencing of yeast strains obtained from independent evolution experiments enabled rapid identification of a key gene that was not identified by mRNA expression analysis of the same strains. Reverse metabolic engineering showed that mutated alleles of ADY2 (C655G and C755G) encode efficient lactate transporters.

2011-12-21 | GSE31634 | GEO

Time course differential profiles of proteins expressed in Holotrichia serrata during tritrophic interaction among EPN and associated bacteria. LC-MSMS

Project description:Entomopathogenic nematodes, the beneficial soil-dwelling nematodes identified with noteworthy ecological services of insect pest management naturally, harbor and vector obligate bacterial symbionts which together cause rapid insect mortality. The tritrophism among the bacterium-nematode-insect host is a treasure box of biological, molecular and biochemical information that was examined to a limited extent. In this project, we intend to explore the time-course expression of proteins of test insect, Holotrichia serrata larvae, during the progression of larval mortality due to nematode-bacterium infection, more specifically, Heterorhabditis indica- Photorhabdus luminescens, Steinernema spp. vs Xenorhabdus spp., respectively. The data submitted relates to the insect protein profiles (LC-MSMS) in healthy, infected and morbid, and dead larvae of Holotrichia serrata.

2025-01-10 | PXD048306 | JPOST Repository

Whole-genome resequencing of T-DNA insertion lines

Project description:Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.

2017-08-15 | GSE102126 | GEO

Hidden players in plant-insect interactions: effects of third-trophic level symbionts on responses of plants to herbivory

Project description:Mutualistic symbionts are increasingly recognized as hidden players in plant-insect interactions. Understanding how symbionts affect plant responses to herbivory provides important insight into the fascinating complexity of terrestrial ecological networks and how we could specifically target symbionts to achieve sustainable pest management. Although the role of herbivore-associated symbionts is gaining increased attention in ecology of plant-insect interactions, how symbionts of members of higher trophic levels affect these interactions is poorly understood. The natural enemies of insect herbivores such as parasitic wasps that are used in biological pest control are associated with mutualistic symbionts (polydnaviruses) that they inject into the herbivore along with eggs in an event of parasitisation. We showed previously that polydnavirus-genes are expressed in the salivary glands of parasitized caterpillars suggesting that third-trophic level symbionts may alter the herbivore’s salivary composition and consequently, affect the way the herbivore interacts with the plant. By using a novel multidisciplinary approach that integrates molecular, chemical, behavioral and field ecology, the proposed project aims to manipulate the phenotype of caterpillars to study the effect of symbiotic viruses of third-trophic-level insects at the plant-herbivore interface. We will address this issue at different levels of biological organization, from plant gene expression to plant-mediated ecological consequences. The project will thereby provide novel fundamental insights into the hidden role played by parasitic wasp symbionts in plant responses to herbivory and these insights will generate important knowledge for pest management programs that focus on polydnaviruses as biological control agents.

2025-08-25 | PXD060225 | Pride

Bacteria

Project description:Genome sequencing and assembly of Vavilovia formosa symbionts

| PRJNA316801 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Hypertrophic Cardiomyopathy/Healthy control Left Ventricular Transcriptomes

Project description:In the present study, we performed the whole transcriptome resequencing in left ventricular samples from HCM patients and healthy controls. Quantitative real-time PCR (qRT-PCR) was used to validate circRNA expression. By analysing the differentially expressed circRNAs and mRNAs, we constructed the ceRNA networks based on ceRNA theory. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed of target mRNAs of differentially expressed circRNA.

2025-07-02 | GSE191120 | GEO

Zoysia

Project description:PCR products from monocots

| PRJDB37752 | ENA

Human ependymoma samples, Subgrouping [aCGH - German Cancer Research Center human 33K BAC array]

Project description:Whole-genome array comparative genomic hybridization (aCGH) of human ependymoma tumors. DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system,BioRad, Munich, Germany) at 20C and 40% humidity. After spotting, slides were cross-linked,baked for 1 hr at 80C, and cross-linked again.

2011-08-15 | GSE27286 | GEO

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