KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds
AbstractKIR2DL4 is an important immune modulator expressed in natural killer cells; HLA-G is its main ligand. We have characterized theKIR2DL4 genetic diversity by considering the promoter, all exons, and all introns in a highly admixed Brazilian population sample and by using massively parallel sequencing. We introduce a molecular method to amplify and to sequence the completeKIR2DL4 gene. To avoid the mapping bias and genotype errors commonly observed in gene families, we have developed and validated a bioinformatic pipeline designed to minimize these errors and applied it to survey the variability of 220 individuals fro...
Source: Immunogenetics - February 17, 2021 Category: Genetics & Stem Cells Source Type: research
Annotation of immune genes in the extinct thylacine ( Thylacinus cynocephalus )
AbstractAdvances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylac...
Source: Immunogenetics - February 5, 2021 Category: Genetics & Stem Cells Source Type: research
Major histocompatibility complex (MHC) associations with diseases in ethnic groups of the Arabian Peninsula
AbstractSince the discovery of human leukocyte antigens (HLAs), the function of major histocompatibility complex (MHC) gene families in a wide range of diseases have been the subject of research for decades. In particular, the associations of autoimmune disorders to allelic variants and candidate genes encoding the MHC are well documented. However, despite decades of research, the knowledge of MHC associations with human disease susceptibility have been predominantly studied in European origin, with limited understanding in different populations and ethnic groups. This is particularly evident in countries and ethnic popula...
Source: Immunogenetics - February 2, 2021 Category: Genetics & Stem Cells Source Type: research
A method for making alignments of related protein sequences that share very little similarity; shark interleukin 2 as an example
AbstractAn optimized alignment of related protein sequences helps to see their important shared features and to deduce their phylogenetic relationships. At low levels of sequence similarity, there are no suitable computer programs for making the best possible alignment. This review summarizes some guidelines for how in such instances, nevertheless, insightful alignments can be made. The method involves, basically, the understanding of molecular family features at both the protein and intron-exon level, and the collection of many related sequences so that gradual differences may be observed. The method is exemplified by ide...
Source: Immunogenetics - January 29, 2021 Category: Genetics & Stem Cells Source Type: research
Characterization of the domestic goat γδ T cell receptor gene loci and gene usage
AbstractGoats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCR γ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied sl...
Source: Immunogenetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research
CDR3 and V genes show distinct reconstitution patterns in T cell repertoire post-allogeneic bone marrow transplantation
AbstractRestoration of T cell repertoire diversity after allogeneic bone marrow transplantation (allo-BMT) is crucial for immune recovery. T cell diversity is produced by rearrangements of germline gene segments (V (D) and J) of the T cell receptor (TCR) α and β chains, and selection induced by binding of TCRs to MHC-peptide complexes. Multiple measures were proposed for this diversity. We here focus on the V-gene usage and the CDR3 sequences of the beta chain. We compared multiple T cell repertoires to follow T cell repertoire changes post-allo-B MT in HLA-matched related donor and recipient pairs. Our analyses of the d...
Source: Immunogenetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research
Differences in pyroptosis of recent thymic emigrants CD4+ T Lymphocytes in ART-treated HIV-positive patients are influenced by sex
AbstractPyroptosis cell death in recent thymus emigrants (RTE) CD4+ T lymphocytes plays an important role on HIV-1 infection as a cause of CD4+ T cell depletion, being influenced by several factors, among them, the sex. Thus, the aim of this study was evaluated pyroptosis levels in RTE CD4+ T lymphocytes of individuals under antiretroviral therapy (ART) strat ified by sex. Thirty-seven ART-treated HIV-positive patients (22 females and 15 males) and 12 (seven females and five males) clinically health subjects were recruited. Analysis by flow-cytometry of RTE CD4+ cells (CD4+ CD31+ /fluorescent-labeled inhibitor...
Source: Immunogenetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research
Lost structural and functional inter-relationships between Ig and TCR loci in mammals revealed in sharks
AbstractImmunoglobulins and T cell receptors (TCR) have obvious structural similarities as well as similar immunogenetic diversification and selection mechanisms. Nevertheless, the two receptor systems and the loci that encode them are distinct in humans and classical murine models, and the gene segments comprising each repertoire are mutually exclusive. Additionally, while both B and T cells employ recombination-activating genes (RAG) for primary diversification, immunoglobulins are afforded a supplementary set of activation-induced cytidine deaminase (AID)-mediated diversification tools. As the oldest-emerging vertebrate...
Source: Immunogenetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research
Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer
In this study, we developed a new high-throughput NGS-based genotyping method for MHC class I alleles in rhesus macaques and cynomolgus macaques. By using our method, 95% and 100% of alleles identified by PCR cloning-based method were detected in rhesus macaques and cynomolgus macaques, respectively, which were highly correlated with their expression levels. It was noted that the simulation of new-allele detection step using artificial alleles differing by a few nucleotide sequences from a known allele could be identified with high accuracy and that we could detect a real novel allele from a rhesus macaque sample. These fi...
Source: Immunogenetics - January 14, 2021 Category: Genetics & Stem Cells Source Type: research
Immunoglobulins in teleosts
AbstractImmunoglobulins are glycoproteins which are produced as membrane-bound receptors on B-cells or in a secreted form, known as antibodies. In teleosts, three immunoglobulin isotypes, IgM, IgT, and IgD, are present, each comprising two identical heavy and two identical light polypeptide chains. The basic mechanisms for generation of immunoglobulin diversity are similar in teleosts and higher vertebrates. The B-cell pre-immune repertoire is diversified by VDJ recombination, junctional flexibility, addition of nucleotides, and combinatorial association of light and heavy chains, while the post-immune repertoire undergoes...
Source: Immunogenetics - January 13, 2021 Category: Genetics & Stem Cells Source Type: research
Anatomy of teleost fish immune structures and organs
AbstractThe function of a tissue is determined by its construction and cellular composition. The action of different genes can thus only be understood properly when seen in the context of the environment in which they are expressed and function. We now experience a renaissance in morphological research in fish, not only because, surprisingly enough, large structures have remained un-described until recently, but also because improved methods for studying morphological characteristics in combination with expression analysis are at hand. In this review, we address anatomical features of teleost immune tissues. There are appr...
Source: Immunogenetics - January 11, 2021 Category: Genetics & Stem Cells Source Type: research
The intersection of stress, sex and immunity in fishes
AbstractWhile sexual dimorphism in immune responses has been documented in other vertebrates, evidence for a similar phenomenon in fish is lacking. Here, we review the relationship between immunity, stress, spawning, and sex hormones in fish to gain a better understanding of sex-based differences in fish immune responses and its consequences for aquaculture. It is well known that there is a strong link between the stress response and immune function in fish. In addition, research to date has demonstrated that sexual dimorphism in the stress response exists in many species; yet, the relationship between the sexual dimorphic...
Source: Immunogenetics - January 11, 2021 Category: Genetics & Stem Cells Source Type: research
Identification of distinct LRC- and Fc receptor complex-like chromosomal regions in fish supports that teleost leukocyte immune-type receptors are distant relatives of mammalian Fc receptor-like molecules
AbstractLeukocyte immune-type receptors (LITRs) are a large family of immunoregulatory receptor-types originally identified in the channel catfish (Ictalurus punctatus (Ip)LITRs). Phylogenetic analyses of LITRs show that they share distant evolutionary relationships with important mammalian immunoregulatory receptors belonging to the Fc receptors family and the leukocyte receptor complex (LRC), but their syntenic relationships with these immunoglobulin superfamily members have not been investigated. To further examine the possible evolutionary connections between teleost LITRs and various mammalian immunoregulatory recepto...
Source: Immunogenetics - January 7, 2021 Category: Genetics & Stem Cells Source Type: research
A systematic review of microRNAs as potential biomarkers for diagnosis and prognosis of gastric cancer
AbstractGastric cancer (GC) is the third leading cause of global cancer morbidity and mortality. One of the significant challenges in GC treatment is that most GC patients are diagnosed with advanced-stage disease due to the lack of suitable biomarkers. Recent studies have shown that microRNAs (miRNAs) can acts as a potential biomarker in GC diagnosis and prognosis. I performed a systematic review of published miRNA studies in GC, which includes the miRNA expression profiles between GC tissues and normal tissues and also miRNA studies to evaluate their potential value in the diagnosis and prognosis of GC. Among the studies...
Source: Immunogenetics - January 5, 2021 Category: Genetics & Stem Cells Source Type: research
Immunogenetics special issue 2021: fish immunology
(Source: Immunogenetics)
Source: Immunogenetics - January 4, 2021 Category: Genetics & Stem Cells Source Type: research
