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232 results for “Retrovirus”
A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats
<p>Additional file - A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats </p>
Data from: The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)
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In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
<p>Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these events <i>in vivo</i>. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous and oral routes. BLI permitted temporal tracking of orally administered retroviruses along the gastrointestinal tract as they traversed the lumen through Peyer's Patches to reach the draining mesenteric sac. Importantly, capture and acquisition of lymph-, blood- and milk-borne retroviruses spanning three routes, was promoted by a common host factor, the I-type lectin CD169, expressed on sentinel macrophages. These results highlight how retroviruses co-opt the immune surveillance function of tissue resident sentinel macrophages for establishing infection.</p>
In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
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Horizontal transmission of a murine retrovirus is driven by males within semi-natural enclosures
<p>1. Transmission is a key component of a pathogen's life history, but it is often difficult to obtain reliable ecological estimates of the dominant mode(s) of transmission and how host traits, such as sex, influence transmission dynamics.<br> 2. Here, we have developed a robust system pairing the use of semi-natural populations of house mice (Mus musculus) with modern molecular viral titering approaches to evaluate the transmission dynamics of Friend Virus Complex (FVC). <br> 3. Semi-natural populations were founded with female and male mice that were either 'index' (initially infected via intraperitoneal injection) or 'contact' (uninfected at the start of experiment). Three experimental population designs were implemented: female index only, male index only, and both female and male index.<br> 4. Utilizing these enclosures, we found male-male transmission to be the predominant mode of transmission, with low rates of horizontal female transmission and no evidence of vertical transmission. Additionally, contact males that became infected harbor higher titers than females, while suffering a similar amount of spleen enlargement; this, paired with a strong correlation between titer and spleen size in males, and no correlation in females, indicates FVC viral dynamics differ between the sexes.<br> 5. Lastly, natural transmission may be an impediment to FVC replication as infected contact animals have a lower viral titer than index animals. These results illuminate the complex life history of murine leukemia viruses and demonstrate the important role of host sex on pathogen transmission dynamics.</p>
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
<p>The Chinese hamster ovary (CHO) cells used to produce biopharmaceutical proteins are known to contain type‐C endogenous retrovirus (ERV) sequences in their genome and to release retroviral‐like particles. Although evidence for their infectivity is missing, this has raised safety concerns. As the genomic origin of these particles remained unclear, we characterized type‐C ERV elements at the genome, transcriptome, and viral particle RNA levels. We identified 173 type‐C ERV sequences clustering into three functionally conserved groups. Transcripts from one type‐C ERV group were full‐ length, with intact open reading frames, and cognate viral genome RNA was loaded into retroviral‐like particles, suggesting that this ERV group may produce functional viruses. CRISPR‐Cas9 genome editing was used to disrupt the gag gene of the expressed type‐C ERV group. Comparison of CRISPR‐derived mutations at the DNA and RNA level led to the identification of a single ERV as the main source of the release of RNA‐loaded viral particles. Clones bearing a Gag loss‐of‐function mutation in this ERV showed a reduction of RNA‐containing viral particle release down to detection limits, without compromising cell growth or therapeutic protein production. Overall, our study provides a strategy to mitigate potential viral particle contaminations resulting from ERVs during biopharmaceutical manufacturing.</p>
Hijacking of transcriptional condensates by endogenous retroviruses
<p>This dataset provides companion data to the paper "Hijacking of transcriptional condensates by endogenous retroviruses", Nature Genetics, 2022 (NG-A58214). It includes raw data, images and computational code to generate the figures in the study.</p>
RNA-Seq data of Raji cells transduced with retrovirus expressing WT or mutant IRF4
<p>Total RNA was extracted using RNAiso Plus (TaKaRa) from Raji cells transduced with retrovirus expressing WT or mutant IRF4. RNA-seq was performed by BGI (Beijing Genomic Institute, ShenZhen, China) using the BGISEQ-500 platform, pair end 100 bases read lengths. The sequencing data were filtered with SOAPnuke (v1.5.2). The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to identify genes and differentially spliced genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI with known and novel coding transcripts included, then the expression level of gene was calculated by RSEM (v1.2.12).</p>
A bovine GWAS reveals determinants of mobilization rate and dynamics of endogenous retroviruses
<p>We develop a novel method to measure the rate of ERVK[2-1-LTR] mobilization in the male germline, and show that this rate averages 1 per 150 sperm cells, yet varies more than ten-fold between animals. We perform a genome wide association study with 430 bulls and identify eight loci that affect ERVK[2-1-LTR] mobilization rate. We provide strong evidence that ERVK[2-1-LTR] elements in four of these, cause the association. We generate an exhaustive catalogue of ERVK[2-1-LTR] elements for the bovine, and show that is composed for 15% of 10 Kb <em>C</em>-type autonomous elements encoding GAG, PRO, POL and ENV genes, and 85% of 6.8 Kb <em>D</em>-type non-autonomous elements devoid of functional genes. We show that >25% of the variance of ERVK[2-1-LTR] mobilization rate is determined by the number of <em>C</em>-type elements in the genome, yet that <em>de novo</em> ERVK[2-1-LTR] insertions are dominated by <em>D</em>-type elements. </p>
Simplified Treatment of Anti-retrovirus in China (C-STAR)
ClinicalTrials.gov study NCT03603977. IPD Sharing: NO. Countries: 1. Publications: 3.
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
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Horizontal transmission of a murine retrovirus is driven by males within semi-natural enclosures
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GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle
<p>The VCF file contains imputed genotypes of ~10 million SNP, INDEL and polymorphic ERVK for 430 Belgian blue bulls used for a genome wide association study on ERVK mobilisation rate. </p>
Comparison Between Clinical and MRI Multiple Sclerosis Activity and Expression of Human Endogenous Retrovirus Type W and Herpesvirus
ClinicalTrials.gov study NCT02489877. IPD Sharing: Not stated. Countries: 0. Publications: 26.
The KRAB zinc finger protein SNERV represses proviral endogenous retroviruses and underlies the Sgp3 and Gv1 loci
GEO Series GSE121640. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Activation of endogenous retroviruses during brain development causes neuroinflammation
GEO Series GSE154196. Mus musculus. 38 samples. Type: Other; Expression profiling by high throughput sequencing.
TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells
GEO Series GSE84259. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment
GEO Series GSE102187. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [RNA-seq]
GEO Series GSE243546. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1
GEO Series GSE150584. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.