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12,799 results for “Immunization”
Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function
GEO Series GSE36890. Mus musculus. 68 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Plant_Innate_Immunity_ATAC-seq
<p><strong>Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors</strong></p> <p>Ding et al 2020</p> <p>This repository stored all input dataset & output dataset except bam files.</p> <p>To make bam files, raw read data are stored in accession number PRJEB38923.</p> <ul> <li>ACR_annotation.zip, Correlation_replicates.zip, Integrate_ATAC-seq_and_RNA-seq.zip, Motif_binding_analysis.zip ... input/output files for each analysis.</li> <li>other zip files ... output files of MACS (call ACRs, call DARs)</li> <li>These outputs are generated by scripts stored in github. (<a href="https://github.com/slt666666/Plant_Innate_Immunity_ATAC-seq">https://github.com/slt666666/Plant_Innate_Immunity_ATAC-seq</a>)</li> </ul>
The effects of intestinal dendritic cells on the imbalance of mucosal Th1/Th2 immune response pathway and visceral hypersensitivity in IBS-D rats
<p class="15"><span><span><span>To study the role of intestinal dendritic cells in the imbalance of local mucosal Th1/Th2 immune response pathway and its effect on visceral hypersensitivity in IBS-D rats through the synergy effects by CD4</span></span></span><span><span><span>+</span></span></span><span><span><span>Th cells and mast cells. Methods: 45 adult SD rats were randomly divided into a blank control group, model control group, and model group,each group (n = 15). Rats in the model group were subjected to IBS visceral hypersensitive modeling by acetic acid enema combined with restraint stress. AWR test and fecal characteristics were used to evaluate the visceral sensitivity of rats. The expression of CD103, a surface molecule specific to dendritic cells in the colon tissue of the ileocecal region, was detected by immunohistochemistry. Flow separation technique was employed to isolate dendritic cells from mesenteric lymph nodes and CD4+T lymphocytes from spleen, and the dendritic cells were co-cultured with T lymphocytes in vitro. MTT assay was employed to detect the ability of dendritic cells to promote the proliferation of initial T lymphocytes. The cytokine levels of IL-12 and INF-γ secreted through Th1-pathway, and IL-4 and IL-9 secreted through Th2-pathway were determined by ELISA.Results: Compared with the blank control group and model control group, the number of CD103-labeled dendritic cells in the model group were significantly increased. Dendritic cells from intestinal lymph nodes developed enhanced ability to promote the proliferation of spleen CD4+Tcell, and secreted more IL-4 and IL-9 than that in the control group while the secretion of IL-12 was significantly reduced (P < 0.05).</span></span></span></p>
Conservation of cell communication systems in invertebrate host–defence mechanisms: possible role in immunity and disease
<p>Video S1. TNT-like structures (white arrow) in live hemocytes from Mytilus galloprovincialis.</p>
Data from: The identification of loci for immune traitsin chickens using a genome-wide association study
The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.
Data from: Quantifying the coevolutionary potential of multistep immune defenses
Coevolutionary models often assume host infection by parasites depends on a single bout of molecular recognition. As detailed immunological studies accumulate, however, it becomes increasingly apparent that the outcome of host-parasite interactions more generally depends on complex multiple step infection processes. For example, in plant and animal innate immunity, recognition steps are followed by downstream effector steps that kill recognized parasites, with the outcome depending on an escalatory molecular arms race. Here, we explore the consequences of such multi-step infection processes for coevolution using a genetically explicit model. Model analyses reveal that polymorphism is much greater at recognition loci than effector loci, that host-genotype by parasite-genotype (Gh x Gp) interactions are larger for the recognition step, and that the recognition step contributes more to local adaptation than the effector step. These results suggest that (1) local adaptation is more likely when fitness measures are related to recognition versus downstream effectors, (2) effector loci, while mechanistically important, are less likely to harbor the Gh x Gp variation that fuels coevolution, and (3) recognition loci are better candidates for genomic hotspots of coevolution.
Data from: The effect of a transient immune activation on subjective health perception in two placebo controlled randomised experiments
Background Patient-reported outcomes predict mortality and play increasingly important roles in care, but factors that modify central measures such as health ratings have been little investigated. Building on designated immune-to-brain pathways, we aimed to determine how a short-term induced inflammation response impacts self-reported health status. Methods Lipopolysaccharide injections were used to provoke acute systemic inflammatory responses in healthy men and women and were compared to placebo in two double-blind randomized experiments. In Experiment 1, 8 individuals (mean 24 years; SD=3.7) received lipopolysaccharide 0.8 ng/kg once and placebo once in a cross-over design, and in Experiment 2, 52 individuals received either lipopolysaccharide 0.6 ng/kg or placebo once in a non-cross-over design (28.6 years; SD=7.1). Main outcomes were perceived health (general and current), sickness behaviour (like fatigue, pain and negative affect), and plasma interleukin (IL)-6, IL-8 and TNF-α, before and after injection. Results Compared to placebo, lipopolysaccharide lead to a deterioration in both self-rated general (Experiment 1, b=1.88 for 0.8 ng/kg) and current health (Experiment 1 b=-3.00; and Experiment 2 b=-1.79) 1.5h after injection (p's<0.01), effects that remained after 4.5 to 5 hours (p's<0.05). The effect on current health in Experiment 2 was mediated by increased inflammation and sickness behaviour in response to lipopolysaccharide injection (β=-0.28, p=0.01). Conclusion Health is drastically re-evaluated during inflammatory activation. The findings are consistent with notions that inflammation forms part of health-relevant interoceptive computations of bodily state, and hint at one mechanism as to why subjective health predicts longevity.
Data from: Indices of immune function used by ecologists are mostly unaffected by repeated freeze-thaw cycles and methodological deviations
Background: Over the past couple of decades, measuring immunological parameters has become widespread in studies of ecology and evolution. A combination of different immunological indices is useful for quantifying different parts of the immune system and comprehensively assessing immune function. Running multiple immune assays usually requires samples to be repeatedly thawed and re-frozen. There is some evidence that repeated freezing and thawing can affect assay results, but this has never been comprehensively studied in some common ecological immunology assays. We tested the effect of multiple (1, 2, 3, 4, 5, 10) freeze-thaw cycles on the results of four commonly used immunological assays: haemolysis-haemagglutination titres, haptoglobin concentration, bacterial killing capacity and total immunoglobulins (IgY). We tested five different bird species from four different bird orders (Passeriformes, Columbiformes, Charadriiformes and Galliformes), and we included both captive and free-living individuals. In addition, we tested for haptoglobin concentrations and the haemolysis-haemagglutination assay if re-analysing samples 1 year apart led to different results. For the haemolysis-haemagglutination assay we also tested two different sources of rabbit blood, and we compared untreated microtitre plates with plates that were "blocked" to prevent nonspecific interactions between the plate and assay reagents. Results: Repeated freezing and thawing of plasma had no effect on lysis titres, haptoglobin concentrations, bacterial killing capacity, or total immunoglobulin levels. Agglutination titres were unaffected by up to five cycles but were lower after ten freeze-thaw cycles. For the haemolysis-haemagglutination assay and haptoglobin concentrations, re-analysing samples 1 year apart yielded highly correlated data. For the haemolysis haemagglutination assay,thesourceofrabbit blood did not influence the results, and the untreated vs. blocked plates differed slightly overall, but at the individual level assay results were highly correlated. Using different rabbit blood sources or different types of microtitre plates yielded highly correlated data.Conclusions: Our data suggest that repeated freeze-thaw cycles do not impair assay results to the point of influencing ecological or evolutionary conclusions. Plasma samples can be safely stored in one tube and thawed repeatedly for different assays. Nevertheless, we recommend consistent treatment of samples in terms of freeze-thaw cycles or other laboratory treatments to minimize the potential for introducing a systematic bias.
Data from: Selection for brain size impairs innate, but not adaptive immune responses
The brain and the immune system are both energetically demanding organs, and when natural selection favors increased investment into one, then the size or performance of the other should be reduced. While comparative analyses have attempted to test this potential evolutionary trade-off, the results remain inconclusive. To test this hypothesis, we compared the tissue graft rejection (an assay for measuring innate and acquired immune responses) in guppies (Poecilia reticulata) artificially selected for large and small relative brain size. Individual scales were transplanted between pairs of fish, creating reciprocal allografts, and the rejection reaction was scored over eight days (before acquired immunity develops). Acquired immune responses were tested two weeks later, when the same pairs of fish received a second set of allografts and were scored again. Compared to large-brained animals, small-brained animals of both sexes mounted a significantly stronger rejection response to the first allograft. The rejection response to the second set of allografts did not differ between large- and small-brained fish. Our results show that selection for large brain size reduced innate immune responses to an allograft, which supports the hypothesis that there is a selective trade-off between investing into brain size and innate immunity.
Data from: Evaluation of the innate immunostimulatory potential of originator and non-originator copies of insulin glargine in an in vitro human immune model
Background: The manufacture of insulin analogs requires sophisticated production procedures which can lead to differences in the structure, purity, and/or other physiochemical properties of resultant products that can affect their biologic activity. Here, we sought to compare originator and non-originator copies of insulin glargine for innate immune activity and mechanisms leading to differences in these response profiles in an in vitro model of human immunity. Methods: An endothelial/dendritic cell-based innate immune model was used to study antigen-presenting cell activation, cytokine secretion, and insulin receptor signalling pathways induced by originator and non-originator insulin glargine products. Mechanistic studies included signalling pathway blockade with specific inhibitors, analysis of the products in a Toll-like receptor reporter cell line assay, and insulin removal from the products by immunopurification. Findings: All insulin glargine products elicited at least a minor innate immune response comparable to human insulin, but some lots of a non-originator copy product induced the elevated secretion of the cytokines, IL-8 and IL-6. In studies aimed at addressing the mechanisms leading to differential cytokine production by these products, we found (1) the inflammatory response was not mediated by bacterial contaminants, (2) the innate response was driven by the insulin receptor through the MAPK pathway, and (3) the removal of insulin significantly reduced their capacity to induce innate activity. No evidence of product aggregates was detected, though the presence of some high molecular weight proteins argues for the presence of insulin dimers or others contaminants in these products. Conclusion: The data presented here suggests some non-originator insulin glargine product lots drive heightened in vitro human innate activity and provides preliminary evidence that changes in their biochemical composition (dimers, impurities) might be responsible for their greater immunostimulatory potential.
Dynamic Prediction of HIV-Related Incomplete Immune Reconstitution: A Multi-Center, Large Cohort Study Using Advanced Joint Modeling
Open the record for dataset details and reuse information.
Subclonal immune evasion in non-small lung cancer
<p>Datasets and associated code accompanying manuscript "Subclonal immune evasion in non-small cell lung cancer". <br><br></p> <p>This dataset is available through Zenodo for academic non-commercial use only. If you are a commercial entity wishing to access the dataset please email <a title="mailto:ctc.tracerx@ucl.ac.uk" href="mailto:ctc.tracerx@ucl.ac.uk">ctc.tracerx@ucl.ac.uk</a> and include in the subject heading ‘Zenodo Data Access Request – [Subclonal immune evasion in non-small cell lung cancer].</p>
Prolonged immune alteration following resolution of acute inflammation in humans
<p>Nine files are added</p> <p>Lipid analysis. This is a portion of original data provided by collaborator Dalli that was independently re-analysed and published in https://www.biorxiv.org/content/10.1101/2023.03.06.530669v1.</p> <p>Methodology</p> <p>Sts Curve</p> <p>Dara Analysis-raw values</p> <p>LM identification</p> <p>MS data files</p> <p> </p> <p>In addition, there are flow and cytokine data files </p> <p> </p> <p> </p>
Data for "Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint"
<p>Data associated with the manuscript:</p> <p>"Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint"</p> <p>Please see code/documentation associated with these data at the links below: </p> <p>Analysis code + documentation: <a href="https://niaid.github.io/fsc/">https://niaid.github.io/fsc/</a></p> <p>Analysis code Github repository: <a href="https://github.com/niaid/fsc">https://github.com/niaid/fsc</a></p> <p>In the downloaded directory the subdirectory 'data' contains data files including: </p> <p><strong>flu_vacc_CITEseq_Seurat4.rds </strong>is CITE-seq data as a Seurat version 4 object for R. </p> <p><strong>flu_vacc_CITEseq_combinedassay.h5ad</strong> is CITE-seq data as a .h5ad object for python. </p>
SARS-CoV-2-specific cellular and humoral immunity after bivalent BA.4/5 COVID-19-vaccination in previously infected and non-infected individuals
<p>Data accompanying manuscript by Urschel et al. </p>
Benchmarking the Performance of Healthcare Systems in the Provision of Childhood Immunization Services
<p>This dataset was used to conduct data analysis of a research paper with a title "Bechmarking the Performance of Healthcare Systems in the Provision of Childhood Services".</p>
Association of copy number alterations with the immune transcriptomic landscape in cancer
<p>This repository contains supplementary materials for the research paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:</p> <ul> <li>00_code: code to reproduce the analysis</li> <li>01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets</li> <li>02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs</li> <li>03_ica_immune_tc: identified immune-TCs, list of immune gene sets</li> <li>04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets</li> <li>05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs</li> <li>06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset</li> <li>07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample</li> <li>08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs</li> <li>09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology </li> <li>10_projection_spatial_transcriptomics: activity of CNA-TC and immune-TC for each spot in spatial transcriptomic datasets from 10xGenomics</li> <li>11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune-TCs for 13 immunotherapy response datasets with predictive performance</li> </ul>
Heterologous immunization with inactivated vaccine followed by mRNA booster elicits strong humoral and cellular immune responses against the SARS-CoV-2 Omicron variant
<p>The recent emergence of the Omicron variant has raised concerns on vaccine efficacy and the urgent need to study more efficient vaccination strategies. Here we evaluated the effect of an mRNA vaccine booster on immunogenicity in individuals vaccinated with two doses of inactivated vaccine. We observed that an mRNA vaccine booster significantly increased the plasma level of specific antibodies that bind to the receptor-binding domain (RBD) or the spike (S) ectodomain (S1+S2) of both the G614 and the Omicron variants, compared to two doses of homologous inactivated vaccine. The level of RBD- and S-specific IgG antibodies and virus neutralization titers against variants of concern in the heterologous vaccination group were similar to that in individuals receiving three doses of homologous mRNA vaccine or a boost of mRNA vaccine after infection, but markedly higher than that in individuals receiving three doses of a homologous inactivated vaccine. Moreover, this heterologous vaccination regime significantly enhanced the RBD-specific memory B cell response and S1-specific T cell response compared to two or three doses of homologous inactivated vaccine. Our study demonstrates that an mRNA vaccine booster in individuals vaccinated with inactivated vaccines can be highly beneficial, as it markedly increases the humoral and cellular immune responses against the virus, including the Omicron variant</p>
Structural basis of Omicron immune evasion: A comparative computational study of Spike protein-Antibody interaction
<p>The COVID-19 pandemic has caused more than 424 million infections and 5.9 million deaths so far. The vaccines used against SARS-COV-2 by now have been able to develop some neutralising antibodies in the vaccinated human population and slow down the infection rate. The effectiveness of the vaccines has been challenged by the emergence of the new strains with numerous mutations in the spike (S) protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus and also contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern (VOC) of the virus have emerged so far. Among them, the most critical are Delta (B.1.617.2), and recently reported Omicron (B. 1.1.529) which have acquired a lot of mutations in the spike protein. We have mapped those mutations on the modelled RBD and evaluated the binding affinities of various human antibodies with it. Docking and molecular dynamics simulation studies have been used to explore the effect of the mutations on the structure of the RBD and the RBD-antibody interaction. The analysis shows that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty per cent, with a downfall in the number of interactions formed as a whole and therefore, it implies the generation of immune escape variants. Notable mutations and their effect was characterised by performing various analyses that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Our results pave the way for robust vaccine design that can be effective for many variants.</p>
Potent anti-tumor immunity and reversal of CD8 T cell exhaustion by spatially and functionally targeting Treg cells in the tumor microenvironment
<p>1×10<sup>6</sup> of splenic GFP<sup>+</sup> Tregs were purified from WT (n=4) and KO mice (n=4) via FACS isolation. RNA was extracted using RNeasy Micro Kit (Qiagen) following its standard protocol and RNA degradation and contamination was monitored on 1% agarose gels. For RNA sequencing, libraries were prepared using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. All samples were prepared at the same time and sequenced on the same lane. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data in FASTQ format were processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. All the downstream analyses were based on the clean data with high quality. Reference mouse genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were mapped against the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene. The FPKM gene expression matrix, R code, DEG list, and targeted gene list are uploaded in this project.</p>
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