Project description:Swine influenza virus (SIV) is a prevalent respiratory pathogen in pigs that has deleterious consequences to animal health, production, and public health. Pigs represent an important reservoir for influenza as well as a potential mixing vessel for novel gene reassortments. Despite the central role of the pig in the 2009 pandemic and 2012 variant H3N2 outbreak, much remains unknown about the impact of swine immunity on SIV transmission, pathogenesis, and evolution. An incomplete understanding of interactions between the porcine immune system and SIV has hindered the development of new diagnostic tools and CD8+ T cell influenza epitope based vaccines. In order to address this gap in knowledge, we identified swine leukocyte antigen (SLA) restricted influenza virus peptides presented by swine respiratory epithelial cells using an immunoproteomics approach. The majority of MHC associated peptides belonged to matrix 1, nucleocapsid, and nonstructural 1 proteins. Specific epitopes, such as M1229-242, NS177-89, and NP417-426, may have value in epitope based vaccines. Future investigations examining the potential cross-reactive nature of these peptides are needed to confirm antigen recognition by cytotoxic T lymphocytes and utility as vaccine candidates.
Project description:Triple negative breast cancer is an aggressive phenotypic breast cancer characterized by ER negative, PR negative and Her2 negative immunohistochemistry status. We embarked on a study to explore the transcriptome of Kenyan TNBC patients and identify potential biomarkers specific to Kenyan population. The transcriptome sequencing of tumors from Kenyan TNBC patients and comparisons with African American and Caucasian TNBC transcriptomes revealed several interesting targets and dysregulated pathways.
Project description:Gene expression data from whole-blood collected from Kenyan children with Plasmodium falciparum malaria infection at acute hospital admission (n=15) and at convalescence (n=9). A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Disease State: with Plasmodium falciparum malaria infection at acute hospital admission and at convalescence clinical_history_design
Project description:Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (CTRL).
Project description:Gene expression data from whole-blood collected from Kenyan children with Plasmodium falciparum malaria infection at acute hospital admission (n=15) and at convalescence (n=9). A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Disease State: with Plasmodium falciparum malaria infection at acute hospital admission and at convalescence
Project description:Transcriptional profiling of macrophages derived from immune-selected (phagocytosis, complement activity in the alternative pathway, and antibody response after vaccination with swine erysipelas) in comparison with those from normal pigs
Project description:African swine fever virus (ASFV) is a highly contagious pathogen that primarily affects domestic and wild pigs with specific tropism to porcine alveolar macrophages (PAMs). However, the host receptors involved in ASFV infection remain unknow. Here, we present a multi-omic epigenetic atlas of ASFV-exposed PAMs and profile 3D chromatin architecture and single-nucleus chromatin accessibility landscapes (sn-ATAC)
Project description:Understanding the pulmonary adaptive immune system of pigs is of importance as respiratory pathogens present a major challenge for swine producers and pigs are increasingly used to model human pulmonary diseases. Single-cell RNA sequencing (scRNAseq) has accelerated the characterization of cellular phenotypes in the pig respiratory tract under both healthy and diseased conditions. However, combining scRNAseq with recovery of paired VJ and VDJ T cell receptor (TCR) as well as heavy (IGH) and light (IGL) chains of B cell receptors (BCR) to interrogate receptor repertoires has not to our knowledge been demonstrated for pigs. Here, we developed primers to enrich porcine TCR and BCR chains that are compatible with the 10x Genomics VDJ sequencing protocol. Using these pig-specific assays, we sequenced the T and B cell receptors of cryopreserved lung cells from CD1D-expressing and -deficient pigs after one or two infections with influenza A virus (IAV), a major swine and human respiratory pathogen, to examine whether natural killer T (NKT) cells alter pulmonary TCR and BCR repertoire selection. We also performed paired single-cell RNA and TCR sequencing of FACS-sorted T cells longitudinally sampled from the lungs of IAV-vaccinated and -infected pigs to track clonal expansion in response to IAV exposure. All pigs presented highly diverse repertoires. Pigs re-exposed to influenza antigens from either vaccination or infection exhibited higher numbers of expanded CD4 and CD8 T cell clonotypes with activated phenotypes, suggesting potential IAV reactive T cell populations. Our results demonstrate the utility of high throughput single-cell TCR and BCR sequencing in pigs.
Project description:The aim of this study was to acquire a better understanding of porcine reproductive and respiratory syndrome (PRRS) disease through a deeper knowledge of gene expression changes that occur in pulmonary lymph nodes by comparing PRRS virus (PRRSV), porcine circovirus type 2 (PCV-2), and swine influenza virus (IAV-S) infections. The PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in these domestic pigs typical of experimental infection of young pigs with these viruses. PRRSV isolate SDSU-73 was pathogenic in this study inducing fever, anorexia, listlessness, and dyspnea.