Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency characterized by low immunoglobulin (Ig)G and IgA, and/or IgM. In addition to bacterial infections, a ...large subgroup has noninfectious inflammatory and autoimmune complications. We performed 16S ribosomal RNA-based profiling of stool samples in 44 CVID patients, 45 patients with inflammatory bowel disease (disease controls), and 263 healthy controls. We measured plasma lipopolysaccharide (LPS) and markers of immune cell activation (i.e., soluble (s) CD14 and sCD25) in an expanded cohort of 104 patients with CVID and in 30 healthy controls. We found a large shift in the microbiota of CVID patients characterized by a reduced within-individual bacterial diversity (alpha diversity, P<0.001) without obvious associations to antibiotics use. Plasma levels of both LPS (P=0.001) and sCD25 (P<0.0001) were elevated in CVID, correlating negatively with alpha diversity and positively with a dysbiosis index calculated from the taxonomic profile. Low alpha diversity and high dysbiosis index, LPS, and immune markers were most pronounced in the subgroup with inflammatory and autoimmune complications. Low level of IgA was associated with decreased alpha diversity, but not independently from sCD25 and LPS. Our findings suggest a link between immunodeficiency, systemic immune activation, LPS, and altered gut microbiota.
The genes of the major histocompatibility complex (MHC) are important model genes for understanding selective forces in evolution. Here, we document, using a cloning and sequencing approach, high ...polymorphism at the exon 2 of the MHC class II B (MHCIIB) genes in the bluethroat (Luscinia svecica); a minimum of 61 unique alleles were detected in 20 individuals, and at least 11 functional loci. In addition, several pseudogenes were revealed. The specimens originated from three different bluethroat subspecies (azuricollis, cyanecula and svecica), and we also analysed four specimens of the closely related thrush nightingale (L. luscinia) for comparison. Phylogenetic analyses of the functional alleles revealed 258 equally parsimonious trees with poor statistical support for the majority of nodes. The distribution of the sequences in the trees point to an ancestral origin of the polymorphism in MHC class II B genes, a portion of which predated the phylogenetic split between the bluethroat and the thrush nightingale. Strong signatures of balancing selection were uncovered for the codons coding for the peptide‐binding residues of the functional MHCIIB exon 2 alleles. Our results highlight the importance of duplication and recombination events for shaping passerine MHC and give insights in the evolutionary dynamics of MHC variation among closely related taxa.
The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic ...variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.
Background & Aims
Small duct primary sclerosing cholangitis (PSC) is phenotypically a mild version of large duct PSC, but it is unknown whether these phenotypes share aetiology. We aimed to ...characterize their relationship by investigating genetic associations in the human leucocyte antigen (HLA) complex, which represent the strongest genetic risk factors in large duct PSC.
Methods
Four classical HLA loci (HLA‐A, HLA‐B, HLA‐C and HLA‐DRB1) were genotyped in 87 small duct PSC patients, 485 large duct PSC patients and 1117 controls across three geographical regions.
Results
HLA‐DRB1*13:01 (OR = 2.0, 95% CI 1.2–3.4, P = 0.01) and HLA‐B*08 (OR = 1.6, 95% CI 1.1–2.4, P = 0.02) were significantly associated with small duct PSC compared with healthy controls. Based on the observed frequency of HLA‐B*08 in small duct PSC, the strongest risk factor in large duct PSC, an estimated 32% (95% CI 4–65%) of this population can be hypothesized to represent early stages or mild variants of large duct PSC. This subgroup may be constituted by small duct PSC patients with inflammatory bowel disease (IBD), which greatly resembled large duct PSC in its HLA association. In contrast, small duct PSC without IBD was only associated with HLA‐DRB1*13:01(P = 0.03) and was otherwise distinctly dissimilar from large duct PSC.
Conclusions
Small duct PSC with IBD resembles large duct PSC in its HLA association and may represent early stages or mild variants of large duct disease. Different HLA associations in small duct PSC without IBD could indicate that this subgroup is a different entity. HLA‐DRB1*13:01 may represent a specific risk factor for inflammatory bile duct disease.
The genetic effects on Atlantic salmon, Salmo salar L., populations from potential bottleneck situations caused by human activities in two Norwegian rivers, Lærdalselva and Batnfjordelva, were ...studied by analysing DNA from fish scales collected before and after the populations had been exposed to human‐induced changes: river regulation, Gyrodactylus salaris infection and rotenone treatment. Using 15 microsatellites, no significant changes were found in the genetic structure and diversity of four population samples from Lærdalselva collected over 34 years. However, salmon from Lærdalselva were significantly differentiated from nearby (Årøyelva) and more distant (Batnfjordelva and Suldalslågen) populations, testifying to the power of the marker system to detect small genetic differences. Furthermore, two population samples from Batnfjordelva, collected 20 years apart, showed low but significant differentiation. The lack of effects on neutral genetic composition in Lærdalselva, despite several potentially severe bottleneck events, indicates that stocking and sea cohorts maintain the status quo of this population.
Ayurveda is one of the oldest systems of medicine in the world, but the growing commercial interest in Ayurveda based products has increased the incentive for adulteration and substitution within ...this herbal market. Fraudulent practices such as the use of undeclared fillers and use of other species of inferior quality is driven both by the increased as well as insufficient supply capacity of especially wild plant species. Developing novel strategies to exhaustively assess and monitor both the quality of raw materials and final marketed herbal products is a challenge in herbal pharmacovigilance. Seventy-nine Ayurvedic herbal products sold as tablets, capsules, powders, and extracts were randomly purchased via e-commerce and pharmacies across Europe, and DNA metabarcoding was used to assess the ability of this method to authenticate these products. Our analysis reveals that only two out of 12 single ingredient products contained only one species as labeled, eight out of 27 multiple ingredient products contained none of the species listed on the label, and the remaining 19 products contained 1 to 5 of the species listed on the label along with many other species not specified on the label. The fidelity for single ingredient products was 67%, the overall ingredient fidelity for multi ingredient products was 21%, and for all products 24%. The low level of fidelity raises concerns about the reliability of the products, and detection of threatened species raises further concerns about illegal plant trade. The study highlights the necessity for quality control of the marketed herbal products and shows that DNA metabarcoding is an effective analytical approach to authenticate complex multi ingredient herbal products. However, effort needs to be done to standardize the protocols for DNA metabarcoding before this approach can be implemented as routine analytical approaches for plant identification, and approved for use in regulated procedures.
Herbs and spices are some of the most vulnerable products in terms of fraud and adulteration in the food sector. Although standard analytical methods are accurate for quality control of specific lead ...or marker compounds, they cannot accurately assess the entire species composition of many marketed products. Complementary analytical approaches are thus often used for comprehensive screening of herbs and spices. In this study we evaluate DNA metabarcoding for the identification and authentication of 62 products, containing basil, oregano, and paprika collected from different retailers and importers in Norway. Our results show varying degrees of discrepancy between the constituent species and those listed on the product labels, despite high product authenticity. We suggest the false positives result from the sensitivity of DNA metabarcoding and filtering thresholds should be integrated into protocols to reduce false positives. Our results highlight how integrating DNA metabarcoding into the toolbox of analytical methods for quality control of fresh and/or processed plant-based food can improve product quality.
Abstract The genetic effects on A tlantic salmon, S almo salar L., populations from potential bottleneck situations caused by human activities in two Norwegian rivers, L ærdalselva and B ...atnfjordelva, were studied by analysing DNA from fish scales collected before and after the populations had been exposed to human‐induced changes: river regulation, G yrodactylus salaris infection and rotenone treatment. Using 15 microsatellites, no significant changes were found in the genetic structure and diversity of four population samples from L ærdalselva collected over 34 years. However, salmon from L ærdalselva were significantly differentiated from nearby ( Å røyelva) and more distant ( B atnfjordelva and S uldalslågen) populations, testifying to the power of the marker system to detect small genetic differences. Furthermore, two population samples from B atnfjordelva, collected 20 years apart, showed low but significant differentiation. The lack of effects on neutral genetic composition in L ærdalselva, despite several potentially severe bottleneck events, indicates that stocking and sea cohorts maintain the status quo of this population.
Background One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, ...reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. Results Here, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. Conclusion The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition.
Natural killer T (NKT) cells are activated by lipid antigens presented by CD1d molecules and represent a major lymphocyte subset of the liver. NOD.c3c4 mice spontaneously develop biliary inflammation ...in extra‐ and intrahepatic bile ducts. We demonstrated by flow cytometry that invariant NKT (iNKT) cells were more abundant in the thymus, spleen, and liver of NOD.c3c4 mice compared to NOD mice. iNKT cells in NOD.c3c4 mice displayed an activated phenotype. Further, NOD and NOD.Cd1d‐/‐ mice were irradiated and injected with NOD.c3c4 bone marrow, and injection of NOD.c3c4 bone marrow resulted in biliary infiltrates independently of CD1d expression in recipient mice. Activation or blocking of NKT cells with α‐galactosylceramide or anti‐CD1d antibody injections did not affect the biliary phenotype of NOD.c3c4 mice. NOD.c3c4.Cd1d‐/‐ mice were generated by crossing NOD.Cd1d‐/‐ mice onto a NOD.c3c4 background. NOD.c3c4.Cd1d‐/‐ and NOD.c3c4 mice developed the same extent of biliary disease. This study demonstrates that iNKT cells are more abundant and activated in the NOD.c3c4 model. The portal inflammation of NOD.c3c4 mice can be transferred to irradiated recipients, which suggests an immune‐driven disease. Our findings imply that NKT cells can potentially participate in the biliary inflammation, but are not the primary drivers of disease in NOD.c3c4 mice.
Natural killer T (NKT) cells are activated by lipid antigens presented by, for instance, the biliary epithelium, and these cells can potentially participate in the biliary inflammation. Invariant NKT cells are more abundant in mice with biliary disease (NOD.c3c4) compared to controls, but are not the primary drivers of disease in NOD.c3c4 mice.
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