Ontology highlight
ABSTRACT:
PROVIDER: PRJNA590324 | ENA |
REPOSITORIES: ENA
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Project description:Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. Here, we evaluated the physiological impact of the widespread parasite, the pike tapeworm (Triaenophorus nodulosus), on its second intermediate host, the Eurasian perch (Perca fluviatilis).
2024-07-04 | GSE237655 | GEO
Project description:High mitochondrial DNA (mtDNA) copy numbers are essential for oogenesis and embryogenesis and correlate with fertility of oocytes and viability of embryos. To understand the pathology and mechanisms associated with low mtDNA copy numbers, we knocked down mitochondrial transcription factor A (Tfam), a regulator of mtDNA replication, during early zebrafish development. Reduction of Tfam using a splice-modifying morpholino (MO) resulted in a 42%±4% decrease in mtDNA copy number in embryos at 4 days post fertilization (4 dpf). Morphant embryos displayed abnormal development of the eye, brain, heart and muscle, as well as a 50%±11% decrease in ATP production. Transcriptome analysis revealed a decrease in protein-encoding transcripts from the heavy strand of the mtDNA. In addition, various RNA translation pathways were increased, indicating an upregulation of nuclear and mitochondria-related translation. The developmental defects observed were supported by a decreased expression of pathways related to eye development and haematopoiesis. The increase in mRNA translation might serve as a compensation mechanism, but appears insufficient during prolonged periods of mtDNA depletion, highlighting the importance of high mtDNA copy numbers for early development in zebrafish.
2020-03-10 | GSE146696 | GEO
Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.
2018-04-18 | PXD003101 | Pride
Project description:The mucosa is an ideal route for vaccination against pathogen infection, but the effective adjuvant capable of overcoming the tolerogenic dendritic cell (DC) environment is unavailable. We characterized type 2 conventional DCs and lysozyme-expressing monocyte-derived DCs (LysoDCs) of Peyer’s patches to identify the vaccination target cells through single-cell RNA sequencing. Based on functional analysis of the data, we suggest that C5aR+ LysoDCs and Co1 peptide, a C5aR ligand, as a target cell and an adjuvant, respectively, for mucosal vaccination. Co1-mediated stimulation of C5aR+ LysoDCs increased the level of reactive oxygen species, leading to CCL3-mediated chemotaxis and exogenous antigen cross-presentation, which elicited an antigen-specific CD8+ T cell response. In a SARS-CoV-2 vaccine model, Co1 peptide increased the frequency of antigen-specific polyfunctional CD8+ T cells in systemic as well as mucosal compartments. Collectively, LysoDC activation by Co1 peptide potentiates vaccination efficiency by constructing an immunostimulatory environment in the mucosal immune inductive site.
2023-07-24 | GSE212701 | GEO
Project description:This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch (Perca flavescens) and zebrafish (Danio rerio) reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin, and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle, mimicking a realistic exposure scenario, and in adult yellow perch for twenty weeks, capturing early seasonal ovarian development. In zebrafish, several genes involved in reproductive processes were shown to be dysregulated by RNA-seq and QPCR, but no significant phenotypic or physiological changes were observed with ovarian staging, fecundity, or embryo mortality. Yellow perch did not appear to be affected by MeHg, either at a molecular level, as assessed by QPCR of eight genes in the pituitary, liver, and ovary tissue, or a physiological level, as seen with ovarian somatic index, circulating estradiol, and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish.
2018-01-01 | GSE73615 | GEO
Project description:In this study, we performed a comparative analysis of gut microbiota composition and gut microbiome-derived bacterial extracellular vesicles (bEVs) isolated from patients with solid tumours and healthy controls. After isolating bEVs from the faeces of solid tumour patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of faeces from patientsand controls using 16S rRNA sequencing. Machine learning was used to classify the samples into patients and controls based on their bEVs and faecal microbiomes.
2024-08-08 | PXD047510 | Pride
Project description:Maternal inheritance of mitochondrial DNA (mtDNA) is highly conserved in metazoans. While many species eliminate paternal mtDNA during late sperm development to foster maternal inheritance, the regulatory mechanisms governing this process remain elusive. Through a large-scale genetic screen in Drosophila, we identified 47 mutant lines exhibiting substantial retention of mtDNA in mature sperm. We mapped one line to Poldip2, a gene predominantly expressed in the testis. Disruption of Poldip2 led to pronounced mtDNA retention in mature sperm and subsequent paternal transmission to progeny. Further investigation via imaging, biochemical analyses and ChIP assays revealed that POLDIP2 is a mitochondrial matrix protein capable of binding to mtDNA. Moreover, we uncovered that CLPX, a key component of the major mitochondrial protease, binds to POLDIP2 to co-regulate mtDNA elimination in Drosophila spermatids. This study shed light on the mechanisms underlying mtDNA removal during spermatogenesis, underscoring the pivotal role of this process in safeguarding maternal inheritance.
2024-06-04 | E-MTAB-14100 | biostudies-arrayexpress
Project description:The Root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest causing severe fiber yield loss annual in China. The response mechanism of ramie to RLN-infection is poorly understood. Two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2) were individually used to sequence by Illumina pair-end sequencing. About 56.3, 51.7, 43.4 and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1 and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. Based on sequence similarity search with known proteins, a total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression level between CO and Inf ramie based on the normalized value of read counts per kilobase of exon model per million reads (RPKM) revealed that there were 777 differentially expressed genes (DEGs). Further, these functional category of DEGs were classified by assigning them to gene ontology (GO) and clusters of orthologous group (COG). Pathway enrichment analysis showed that three pathways (Phenylalanine metabolism, Carotenoid biosynthesis and Phenylpropanoid biosynthesis) were severely influenced by RLN-infection. The genome-wide expression profiling of ramie responding to RLN-infection was first characterized. A series of candidate genes and pathways that may contribute to defense response against RLN in ramie will be helpful for further improving the resistance to RLN-infection. A total of four samples, two replicates of control plant (CO1 and CO2) and two replicates of RLN-infected plants (Inf1 and Inf2) were used for RNA-seq.
2014-04-28 | E-GEOD-51900 | biostudies-arrayexpress