Similar Datasets
Project description:The major histocompatibility complex (SLA in pigs) encodes molecules for self-nonself discrimination, constitute a major transplantation barrier and is associated with a variety of diseases. Pigs with defined SLA genotypes are a resource for the study of immune response, disease resistance and production traits, as well as an important animal model for transplantation research. The aim of the present study was to explore the influence of defined SLA genotypes on gene expression patterns of immune-related genes in blood mononuclear cells (BMCs). Using a loop design, heterologous cDNA microarray hybridizations were performed to compare Yorkshire pigs representing three defined SLA-DRB1 genotypes (including a potentially new allele). Total RNA was treated with Dnase I treated and amplified. The amplified RNA was reverse transcribed using random primers and incorporating 5-(3-aminoallyl)-dUTP for post-synthesis labelling of the cDNA with the appropriate fluor dyes. Hybridization was performed on a bovine immune-endocrine in-house cDNA microarray printed on glass slides. Microarray fold-change analysis revealed that animals carrying confirmed SLA alleles (SLA-DRB1*070701 and SLA-DRB1*050502) showed consistent differences in gene expression when compared to the two other groups. On the other hand, the group carrying a potentially new allele showed differences that varied depending on the group it was being compared to. Genes that were identified as differentially expressed include macrophage inflammatory protein 1, interleukin 1, toll-like receptor 2 and caspase 1. A better understanding of SLA gene activity can facilitate the definition of new strategies to control animal health and optimize animal production. Keywords: SLA-defined genotype comparative genomic cDNA microarray hybridizations
2007-05-30 | GSE7908 | GEO
Project description:In this study the gene expression differences between three titanium surfaces produced by Straumann were investigated. These three surfaces were: flat pre-treated (Pt) titanium, sandblasted (S) titanium and sandblasted acid-etched (SLA) titanium. The SLA surface is known to boost the proliferation and osteogenic differentiation of MG-63 cells. SLA titanium is also widely used for dental implants.
2018-09-05 | E-MTAB-7217 | biostudies-arrayexpress
Project description:Background & Aims: In most autoimmune disorders, crosstalk of B cells and CD4 T cells results in the accumulation of autoantibodies targeting specific self-antigen like the Soluble Liver Antigen (SLA or SepSecs) in autoimmune hepatitis (AIH). But the associated autoreactive CD4 T cells have not been characterized yet. Here we isolated and deeply characterized SLA-specific CD4 T cells in AIH patients. Methods: We used brief ex vivo re-stimulation with overlapping SLA-derived peptides to isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterize their transcriptome and T cell receptor (TCR) repertoire. Identified auto-reactive TCRs were reconstituted cloned and expressed in T cell hybridoma to identify dominant SLA-derived CD4 T cell epitopes. SLA-specific CD4 T cells were tracked in peripheral blood through TCR sequencing, to identify their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content flow cytometry in an additional cohort of n=42 AIH patients and n=17 non-alcoholic steatohepatitis (NASH) controls. Results: Frequency of autoreactive SLA-specific CD4 T cells was associated with anti-SLA autoantibodies and had a memory CD45RA-CD27+PD-1+CXCR5-CCR6- phenotype. ScRNA-seq revealed their pro-inflammatory/B-Helper profile (IL21, IFNG, TIGIT, CTLA4, NR3C1, CD109, KLRB1 and CLEC2D). SLA81-100 and SLA177-204 contain dominant T cell epitopes. Autoreactive TCR clonotypes were restricted to the memory PD-1+CXCR5- CD4 T cells which was significantly increased in the blood of AIH patients and supported B cell differentiation through IL-21. Finally, we identified a specific phenotype (CD45RA-PD-1+CD38+CXCR5-CD127-CD27+) of T cells linked to disease activity and IgG response during AIH. Conclusions: This work provides for the first time a deep characterization of rare circulating autoreactive CD4 T cells and the identification of their peripheral reservoir in AIH. We also propose a generic phenotype of pathogenic T cells related to AIH disease activity which will be essential to track, delineate and potentially target those pathogenic cells.
2020-05-29 | GSE149298 | GEO
Project description:African swine fever virus (ASFV) is a lethal animal pathogen which enters its host cells through endocytosis. So far, host factors specifically required for ASFV replication have been barely identified. In this study a genome-wide CRISPR/Cas9 knockout screen in porcine cells indicated that the genes RFXANK, RFXAP, SLA-DMA, SLA-DMB, and CIITA are important for productive ASFV infection. The proteins encoded by these genes belong to the major-histocompatibility-complex II (MHC II), or swine-leucocyte-antigen-complex II (SLA II). RFXAP and CIITA are MHC II-specific transcription factors, whereas SLA-DMA/B are subunits of the non-classical MHC II molecule SLA-DM. Targeted knockout of either of these genes led to severe replication defects of different ASFV isolates, reflected by substantially reduced plating efficiency, cell-to-cell spread, and progeny virus titers. For the characterization of the knockouts on a proteome level the protein contents of the knockout cell lines were analyzed by mass spectrometry.
2023-08-21 | PXD034242 | Pride
Project description:Visceral leishmaniasis (VL; Leishmania donovani) cases produce interferon- (IFN) and tumour necrosis factor (TNF) in response to soluble leishmanial antigen (SLA) in whole blood assays. These pro-inflammatory cytokines are crucial for activation of macrophages to kill L. donovani parasites. Detailed immunological studies comparing active with cured patients suggest that a balance exists between the pro-inflammatory cytokines TNF and IFN, and anti-inflammatory interleukin-10 (IL10). Our interest was to obtain a global understanding of the response to SLA in whole blood from active VL cases, and to determine what effect neutralising anti-IL10 would have on this response. Transcriptional profiles following SLA stimulation of whole blood from VL patients showed very few differentially expressed genes (DEGs), the majority belonging to a single network with TNF at the hub. In contrast, when anti-IL10 was added with SLA, hundreds of DEGs were observed, 65% belonging to a single network with TNF, IFNG, NFKBIA, IL6 and IL1B as hub genes in concert with a remarkable chemokine/cytokine storm. Our data demonstrate the singular impact of IL10 as a potent immune modulator in VL.
2021-03-31 | GSE146908 | GEO
Project description:The project employs HDX-MS to study the conformational dynamics of DENV2 NS5 in its apo form and in complex with the viral promoter RNA, Stem Loop A (SLA). The conformational dynamics of the RdRp domain of DENV2 NS5 (NS5-RdRp) in its apo form and in complex with SLA was also studied.
2025-05-07 | PXD058297 | Pride
Project description:Comparisons of hippocampi of Syracuse High Avoidance (SHA) and Syracuse Low Avoidance (SLA) learning rats Keywords: other
2003-12-31 | GSE932 | GEO
Project description:Comparisons of hippocampi of Syracuse High Avoidance (SHA) and Syracuse Low Avoidance (SLA) learning rats
2007-10-12 | E-GEOD-932 | biostudies-arrayexpress
Project description:This study clarified how implant surfaces influence early osseointegration by coupling untargeted RNA sequencing with histomorphometry. Four rabbits each received three tibial implants: turned commercially pure titanium (Ti), sandblasted/large-grit/acid-etched titanium (SLA-Ti), and turned copper (Cu). Surface morphology was characterized by scanning electron microscopy, confocal microscopy, and energy dispersive spectroscopy. After 10 days, bone-to-implant contact (BIC), bone area (BA), and peri-implant transcriptomes were analyzed. Differentially expressed genes and Gene ontology (GO) enrichment were computed. SLA-Ti showed the greatest roughness. Both Ti groups yielded significantly higher BIC and BA than Cu (p < 0.001). GO terms on SLA-Ti were enriched for immune regulation and turned Cu was dominated by mitochondrial-stress pathways. Turned Ti showed minimal enrichment. SLA-Ti simultaneously up-regulated pro-inflammatory cytokines and immunoregulatory genes plus stress-adaptive markers, suggesting a balanced inflammatory milieu conducive to bone formation. Turned Cu markedly elevated mitochondrial genes and oxidative-stress markers, while suppressing antioxidant and innate-defense genes, reflecting immune-metabolic dysregulation. Turned Ti induced only modest transcript changes, consistent with passive biocompatibility. Early osseointegration hinges on a finely tuned immune-metabolic equilibrium rather than surface roughness alone. Optimal integration demands implant surfaces that trigger controlled immunomodulation while limiting oxidative stress, guiding the design of next-generation dental implants.
2025-06-10 | GSE299424 | GEO
Project description:Chlorella sp. strain:SLA-04 Genome sequencing
| PRJNA766673 | ENA