Project description:Human astrovirus infection is known to disrupt intestinal barrier function by increasing barrier permeabilty. However, the exact cellular mechanism(s) involved is unknown. We used microarrays to detail the global gene expression changes occuring during astrovirus infection and identify necessary cellular pathways for astrovirus pathogenesis.
Project description:The cellular response to astrovirus infection is not well defined. We used single cell RNA sequencing (scRNA-seq) to determine cellular response to astrovirus early or late in infection.
Project description:In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed. This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed. Discovery of novel miRNAs involved in imbibed maize seed by deep sequencing 2 independent small RNA libraries
Project description:The proteome of two sperm sources, epididymal and ejaculated sperm, was compared and associated with sperm freezing capacity using samples collected from three wild small ruminants species. Protein identification was performed using two databases separately (Ovis aries and Capra hircus NCBI) and results were later combined.
2021-05-04 | PXD017462 | Pride
Project description:Listeriosis outbreaks in small ruminants
Project description:In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed. This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed.
Project description:Here, we analyzed ischemic stroke induced changes in microRNA levels in mouse brain using permanent cerebral ischemia model. We performed enrichment of small RNAs from peri-ischemic brain region for RNA sequencing and present data set containing several small RNA species to facilitate the discovery of ischemia induced changes in non-coding RNAs.
Project description:Human Umbelical Vein Endothelial Cells (HUVEC) were cultured in vitro and exposed to 1% oxygen or normoxia for 24 hours. Then, small RNA libraries were prepared and sequenced using sequencing-by-ligation technique (Solid3 Plus Sequencer platform). Alignment versus miRBase v14.0 identified >400 different microRNA/microRNA* species expressed in HUVEC. A complex repertoire of isomiR was also observed. For novel miRNA discovery, reads were mapped against the human genome. We identified 511 candidate new microRNAs and we validated 18 of them with independent techniques.
Project description:Mycobacterium avium subspecies paratuberculosis (MAP) is capable of causing a chronic enteritis known as Johne’s disease (JD) in ruminants, resulting in substantial economic loses. Sensitive and specific novel prognostic assays are required to help limit infection, and circulating microRNAs (miRNAs) have the potential to serve as biomarkers. Sequencing provides a thorough opportunity to characterise miRNAs but this technology is challenged by the low RNA concentrations in biofluids. The aim of this study was to determine whether small RNA-sequencing technology could be applied to bovine serum samples from an experimental JD infection model.
Project description:Infections of the central nervous system (CNS) in humans are on the rise due to changing environmental conditions and increase in vulnerable populations comprised of immunocompromised subjects with primary (genetic) or secondary (acquired) immunodeficiency. Many viruses take the opportunity to invade the CNS by capitalizing on impaired immunity of the host. Here we investigate neuropathogenesis of a rare CNS infection in immunocompromised patients caused by the astrovirus and show that it shares many features with another opportunistic infection of the CNS associated with human immunodeficiency virus. We show that astrovirus infects CNS neurons with a major impact on the brainstem. This leads to disrupted synaptic integrity loss of afferent innervation related to infected neurons and global impairment of both excitatory and inhibitory neurotransmission. In the settings of impaired peripheral adaptive immunity host responses to astrovirus infection are dominated by the microglia-macrophage-phagocytosis axis which may be a common compensatory defense mechanism employed by the CNS against opportunistic infections.
