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247 results for “adaptive immunity”
Lower adaptive immunity in invasive Egyptian geese compared to sympatric native waterfowls
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Comparing raccoon MHC diversity in native and introduced ranges: evidence for the importance of functional immune diversity for adaptation and survival in novel environments.
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Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2
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Innate and adaptive immune genes associated with MERS-CoV infection in dromedaries
<p>The recent SARS-CoV-2 pandemic has refocused attention to the betacoronaviruses, only eight years after the emergence of another zoonotic betacoronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV). While the wild source of SARS-CoV-2 may be disputed, for MERS-CoV, dromedaries are considered as source of zoonotic human infections. Testing 100 immune- response genes in 121 dromedaries from United Arab Emirates (UAE) for potential association with present MERS-CoV infection, we identified candidate genes with important functions in the adaptive, MHC-class I (HLA-A-24-like) and II (HLA-DPB1-like), and innate immune response (PTPN4, MAGOHB), and in cilia coating the respiratory tract (DNAH7). </p>
Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats
<p>Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. Genomes were obtained from public repositories and one genome (<i>Phyllostomus hastatus</i>) was assembled de novo. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.</p>
IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)
<p>This repository contains the scRNA-Seq data (including TCR-Seq and BCR-Seq data) set used in the manuscript titled "IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)". This dataset is generated from 10x cell ranger software. In the study, we have 10 PBMC samples, from 5 MIS-C children at paired time points. T1 stands for admission time and T3 follow-up time, about 1 month post hospital discharge. </p>
Data from: Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull
<p>Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black headed gull <em>Chroicocephalus ridibundus</em>. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extra-cellular parasite communities (e.g. helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.</p>
Send-In Sample Collection for Comprehensive Analyses of Innate and Adaptive Immune Responses During Acute COVID-19 and Convalescence
ClinicalTrials.gov study NCT04582903. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Changes in Adaptive Immune Responses and Effector Cell Responses Upon Nasal Allergen Exposure - a Pilot Study
ClinicalTrials.gov study NCT03644680. IPD Sharing: NO. Countries: 1. Publications: 26.
Adapting Motivational Interviewing for Maternal Immunizations (MI4MI)
ClinicalTrials.gov study NCT04302675. IPD Sharing: NO. Countries: 1. Publications: 1.
Innate and Adaptive Immunity in Individuals Experiencing Chronic Obstructive Pulmonary Disease Exacerbations
ClinicalTrials.gov study NCT00281216. IPD Sharing: Not stated. Countries: 1. Publications: 6.
The Role of Adaptive Immunity in COVID-19 Associated Myocardial Injury
ClinicalTrials.gov study NCT04340921. IPD Sharing: NO. Countries: 1. Publications: 12.
Data from: Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull
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Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats
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Data from: Genes of the major histocompatibility complex highlight interactions of the innate and adaptive immune system
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Data from: Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences
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Adaptive immune response and resting metabolism are unaffected by manipulation of flight intensity, but negatively related to each other
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Innate and adaptive immune genes associated with MERS-CoV infection in dromedaries
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Data from: The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity
CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas–mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems.
Supplementary data for the manuscript, "Comprehensive Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Repertoires"
<p>This repository contains data and code used in the manuscript "Comparative Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Receptor Repertoires" by Girgis et al. For additional information regarding how these data were used, please refer to our manuscript.</p> <p>Code is organized per figure in the main text. Each figure folder contains a 'script-inputs' folder and 'script-outputs' folder. The outputs folder is empty and may be populated with graphs and results tables by executing code within the directory. The inputs folder contains some pre-formatted data which may be used in executing code. Most of these inputs may be generated from scratch using raw data (ie the results of Homolig clustering on simulated repertoires) but may require substantial time and/or computational resources. Raw patient data used in Figure 6 (Pancreatic cancer anti-mKRAS TCRB repertoire clustering) and Figure 7 (Rheumatoid arthritis TCRB and IGH repertoires) are not included here. However, several graphs may be reproduced stripped of sequence-specific data. Pancreatic cancer patient repertoire data will be made available on dbGaP,study accession number phs003425.v1.p1. Rheumatoid arthritis patient data will be made available on ImmuneAccess, accession pending.</p> <p>To browse repo, first unzip all subdirectories: </p> <blockquote> <p><code>for f in *.zip; do</code><br><code> unzip "$f"</code><br><code>done</code></p> </blockquote> <p>All non-code files have been compressed to .gz format. To decompress, use: <code>gzip -dr *</code>, or <code>pigz -dr ./raw-data/* </code>for parallel decompression (recommended). </p> <p>Alexander Girgis <br>agirgis3@jhmi.edu <br>July 2025 </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.