Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

A total of 553 Y‐chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub‐populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum‐Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub‐clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre‐Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub‐Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex‐related gene flow, most likely mediated by the Atlantic slave trade.     

Diversity of γδ T-cell antigens

In the last two decades, it has become clear that γδ T cells recognize a diverse array of antigens including self and foreign, large and small, and peptidic and non-peptidic molecules. In this respect, γδ antigens as a whole resemble more the antigens recognized by antibodies than those recognized by αβ T cells. Because of this antigenic diversity, no single mechanism—such as the major histocompatibility complex (MHC) restriction of αβ T cells—is likely to provide a basis for all observed T-cell antigen receptor (TCR)-dependent γδ T-cell responses. Furthermore, available evidence suggests that many individual γδ T cells are poly-specific, probably using different modes of ligand recognition in their responses to unrelated antigens. While posing a unique challenge in the maintenance of self-tolerance, this broad reactivity pattern might enable multiple overlapping uses of γδ T-cell populations, and thus generate a more efficient immune response.     

Sephardic signature in haplogroup T mitochondrial DNA

A rare combination of mutations within mitochondrial DNA subhaplogroup T2e is identified as affiliated with Sephardic Jews, a group that has received relatively little attention. Four investigations were pursued: Search of the motif in 250 000 control region records across 8 databases, comparison of frequencies of T subhaplogroups (T1, T2b, T2c, T2e, T4, T^*) across 11 diverse populations, creation of a phylogenic median-joining network from public T2e control region entries, and analysis of one Sephardic mitochondrial full genomic sequence with the motif. It was found that the rare motif belonged only to Sephardic descendents (Turkey, Bulgaria), to inhabitants of North American regions known for secret Spanish–Jewish colonization, or were consistent with Sephardic ancestry. The incidence of subhaplogroup T2e decreased from the Western Arabian Peninsula to Italy to Spain and into Western Europe. The ratio of sister subhaplogroups T2e to T2b was found to vary 40-fold across populations from a low in the British Isles to a high in Saudi Arabia with the ratio in Sephardim more similar to Saudi Arabia, Egypt, and Italy than to hosts Spain and Portugal. Coding region mutations of 2308G and 14499T may locate the Sephardic signature within T2e, but additional samples and reworking of current T2e phylogenetic branch structure is needed. The Sephardic Turkish community has a less pronounced founder effect than some Ashkenazi groups considered singly (eg, Polish), but other comparisons of interest await comparable averaging. Registries of signatures will benefit the study of populations with a large number of smaller-size founders.     

Genetic characterization of uniparental lineages in populations from Southwest Iberia with past malaria endemicity

Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD—Coruche, Pias, and Alcacer do Sal—to evaluate if their present‐day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty‐five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y‐chromosome markers. Results were then compared with data from other Portuguese and non‐Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub‐Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub‐Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia. Am. J. Hum. Biol. 22:588–595, 2010. © 2010 Wiley‐Liss, Inc.     

Mitochondrial super-haplogroup U diversity in Serbians

Abstract

Background: Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balkans, a region having a turbulent demographic history.

Aim: The aim was to thoroughly study complete mitogenomes of Serbians, a population linking westward and eastward South Slavs.

Subjects and methods: Forty-six predominantly Serbian super-haplogroup U complete mitogenomes were analysed phylogenetically against ～4000 available complete mtDNAs of modern and ancient Western Eurasians.

Results: Serbians share a number of U mtDNA lineages with Southern, Eastern-Central and North-Western Europeans. Putative Balkan-specific lineages (e.g. U1a1c2, U4c1b1, U5b3j, K1a4l and K1a13a1) and lineages shared among Serbians (South Slavs) and West and East Slavs were detected (e.g. U2e1b1, U2e2a1d, U4a2a, U4a2c, U4a2g1, U4d2b and U5b1a1).

Conclusion: The exceptional diversity of maternal lineages found in Serbians may be associated with the genetic impact of both autochthonous pre-Slavic Balkan populations whose mtDNA gene pool was affected by migrations of various populations over time (e.g. Bronze Age pastoralists) and Slavic and Germanic newcomers in the early Middle Ages.     

"Mid-G" region sequences of the glycoprotein gene of Austrian infectious hematopoietic necrosis virus isolates form two lineages within European isolates and are distinct from American and Asian lineages

Infectious hematopoietic necrosis virus (IHNV) is one of the most important pathogens of salmonid fish. In this study a comprehensive phylogenetic analysis of the genetic evolution and variety of Austrian IHNV strains, as well as selected strains ensuring worldwide coverage, is presented. The phylogenetic investigation is based on sequences comprising the “mid-G” region of the G gene, and it includes all currently available IHNV sequences of the G gene with a length of at least 615 bp. Austrian IHNVs are located—together with other European IHNV isolates—in two clusters of genogroup M (M-Eur1 and M-Eur2) and are clearly separated from American and Asian lineages. The genetic clustering, however, could not be linked to certain clinical symptoms or significant differences in the mortality rates.     

Understanding the development and function of T follicular helper cells

A fundamental function of T helper (Th) cells is to regulate B-cell proliferation and immunoglobulin class switching, especially in the germinal centers. Th1 and Th2 lineages of CD4⁺ T cells have long been considered to play an essential role in helping B cells by promoting the production immunoglobulin G2a (IgG2a) and IgG1/IgE, respectively. Recently, it has become clear that a subset CD4⁺ T cells, named T follicular helper (Tfh) cells, is critical to B-cell response induction. In this review, we summarize the latest advances in our understanding of the regulation of Tfh cell differentiation, the relationship of Tfh cells to other CD4⁺ T-cell lineages, and the role of Tfh cells in health and disease.     

β-Thalassemia mutations and hemoglobinopathies in Adana,Turkey: results from a single center study

Introduction

β-Thalassemia and hemoglobinopathies are common genetic disorders in Turkey and in this retrospective study our aim was to determine the frequency of β-thalassemia and hemoglobinopathies in Adana, which is one of the biggest cities located in the southern part of Turkey.

Material and methods

Data from 3000 individuals admitted to Seyhan Hereditary Blood Disorders Center in Adana were evaluated. The blood samples were collected into EDTA-containing tubes and hematological parameters were analyzed using an automatic cell counter. High performance liquid chromatography technique was used to determine the type of hemoglobin. Molecular screening of the β-globin gene was performed with β-Globin StripAssay.

Results

Of 3000 cases, 609 were diagnosed as β-thalassemia or hemoglobinopathy. We have found that the rates of occurrence of β-thalassemia and hemoglobinopathies are 13.46% and 6.83% respectively in this area. We have identified 18 different β-thalassemia mutations and three separate abnormal hemoglobins: HbS, HbD Los Angeles, and HbE. In molecular analyses, β-thalassemia gene mutations of IVSI.110 (G > A), codon 8 (–AA), IVSI.1 (G > A), IVSI.6 (T > C), –30 (T > A), IVSII.1 (G > A), codon 39 (C > T), codon 44 (–C), IVSI.5 (G > C), codon 5 (–CT), codon 8/9 (+G), IVSII.745 (C > G), codon 22 (7bp del), –101(C > T), codon 36/37 (–T), IVSI.15 (T > G), codon 6 (–A), –88 (G > A) were detected.

Conclusions

Considering the high incidence of mutations that we have found, β-thalassemia and hemoglobinopathies still seem to be a public health problem in Adana.     

Antigen-non-specific regulation centered on CD25+Foxp3+ Treg cells

CD4⁺CD25⁺Foxp3⁺ regulatory T cells (Tregs) are of special interest in immunology because of their potent inhibitory function. Many fundamental aspects of Tregs, including their antigenic profile, development and peripheral homeostasis, remain highly controversial. Here, we propose a Treg-centered antigen-non-specific immunoregulation model focused on the T-cell system, particularly on CD4⁺ T cells. The T-cell pool consists of naive T cells (Tnais), Tregs and effector T cells (Teffs). Regardless of antigen specificity, the ratio of the activated T-cell subsets (Treg/Teff/Tnai) and their temporal and spatial uniformity dictate the differentiation of Tnais. Activated Tregs inhibit the activation, proliferation, induction and activity of Teffs; in contrast, activated Teffs inhibit the induction of Tregs from Tnais but cooperate with Treg-specific antigens to promote the proliferation and activity of Tregs. In many cases, these interactions are antigen-non-specific, whereas the activation of both Tregs and Teffs is antigen-specific. Memory T-cell subsets are essential for the maintenance of adaptive immune responses, but the antigen-non-specific interactions among T-cell subsets may be more important during the establishment of the adaptive immune system to a newly encountered antigen. This is especially important when new and memory antigens are presented closely—both temporally and spatially—to T cells, because there are always baseline levels of activated Tregs, which are usually higher than levels of memory T cells for new antigens. Based on this hypothesis, we further infer that, under physiological conditions, Tregs in lymph nodes mainly recognize antigens frequently released from draining tissues, and that these self-reactive Tregs are commonly involved in the establishment of adaptive immunity to new antigens and in the feedback control of excessive responses to pathogens.     

What people really change after genetic testing (GT) performed in private labs: results from an Italian study

Despite the widespread diffusion of direct-to-consumer genetic testing (GT), it is still unclear whether people who learn about their genetic susceptibility to a clinical condition change their behaviors, and the psychological factors involved. The aim of the present study is to investigate long-term changes in health-related choices, individual tendencies and risk attitudes in an Italian sample of GT users. In the context of the Mind the Risk study, which investigated a sample of Italian adults who underwent GT in a private laboratory, 99 clients participated in the follow up assessment. They completed a self-administered questionnaire investigating: (a) clinical history and motivation for testing, (b) lifestyle and risk behaviors, (c) individual tendencies toward health, and (d) risk-taking attitude and risk tolerance. Such variables were measured at three different time-points: T0—before GT, T1—at 6 months after genetic results, and T2—at 1 year from results. Results showed that, at baseline, participants who stated they intended to modify their behavior after GT results, effectively did so over time. This result held both for participants who received a positive or negative test result. In general, a healthier diet was the most frequently observed long-term behavioral change. As regards psychological variables, a risk-taking attitude and risk tolerance did not seem to affect the decision to change the lifestyle. Finally, we found an overall reduction in anxiety and worry over health over time, but also a reduction in the motivation for health promotion and prevention, health esteem, and positive expectations for their health in the future.Subject terms: Genetic testing, Human behaviour     

Differences in interaction between immune complexes and complement receptors in serum and cerebrospinal fluid

Antigen—antibody complexes (Ag—Ab), prepared from ¹²⁵I-radiolabelled bovine serum albumin (BSA) and guinea-pig antibody, were (1) pre-incubated at 37°C for 30 min with serum or cerebrospinal fluid (CSF) in different proportions and then reacted with cells, (2) incubated at 37°C directly with cells suspended in serum or CSF for different time periods, or (3) bound to cells (following incubation with serum in optimal proportions) and the cell-bound immune complexes (IC) incubated with serum or CSF at 37°C for different time periods. When Ag—Ab were pre-incubated with serum or CSF and reacted with unfractionated blood cells or mononuclear cells, binding decreased as serum to Ag—Ab proportion was increased above 1:16, but increased as CSF to Ag—Ab proportion was increased. When serum diluted 200-fold (to approximate the protein concentration of CSF) was used in place of undiluted serum, serum-mediated binding paralleled CSF-mediated binding. Inactivation of serum, CSF, and 1:200 serum in different ways and substitution of human red blood cells (RBC) (known to possess C3b receptors) or sheep RBC (known not to possess C3b receptors) demonstrated that binding was to C3b receptors. Addition of CSF to serum did not alter serum-mediated binding. When Ag—Ab were incubated directly with unfractionated blood cells suspended in serum or CSF, binding increased rapidly in serum, reaching a maximum within 2—4 min, and IC then rapidly dissociated, whereas binding increased gradually in CSF and IC remained associated with cells. When serum diluted approximately 100-fold was used in place of undiluted serum, kinetics of serum-mediated interaction approached that of CSF-mediated interaction. When IC were bound to Raji cells or human RBC and the cell-bound IC incubated in serum or CSF, > 85% of IC dissociated in serum after 30 min, but no dissociation occurred in CSF. Dilution of serum > 1:16 and > 1:64 abolished dissociation from the two cell types, respectively. These results indicate that CSF mediates binding of IC to complement receptors on cells but lacks the activities of serum which convert IC into a non-binding state.     

Changes in Immune Parameters Seen in Gulf War Veterans but Not in Civilians with Chronic Fatigue Syndrome

The purpose of this study was to evaluate immune function through the assessment of lymphocyte subpopulations (total T cells, major histocompatibility complex [MHC] I- and II-restricted T cells, B cells, NK cells, MHC II-restricted T-cell-derived naive and memory cells, and several MHC I-restricted T-cell activation markers) and the measurement of cytokine gene expression (interleukin 2 [IL-2], IL-4, IL-6, IL-10, IL-12, gamma interferon [IFN-γ], and tumor necrosis factor alpha [TNF-α]) from peripheral blood lymphocytes. Subjects included two groups of patients meeting published case definitions for chronic fatigue syndrome (CFS)—a group of veterans who developed their illness following their return home from participating in the Gulf War and a group of nonveterans who developed the illness sporadically. Case control comparison groups were comprised of healthy Gulf War veterans and nonveterans, respectively. We found no significant difference for any of the immune variables in the nonveteran population. In contrast, veterans with CFS had significantly more total T cells and MHC II⁺ T cells and a significantly higher percentage of these lymphocyte subpopulations, as well as a significantly lower percentage of NK cells, than the respective controls. In addition, veterans with CFS had significantly higher levels of IL-2, IL-10, IFN-γ, and TNF-α than the controls. These data do not support the hypothesis of immune dysfunction in the genesis of CFS for sporadic cases of CFS but do suggest that service in the Persian Gulf is associated with an altered immune status in veterans who returned with severe fatiguing illness.     

Diversity and evolution of MHII β genes in a non-model percid species—The Eurasian perch (Perca fluviatilis L.)

This study provides the first investigation of the diversity, structure, and molecular evolution of MHII β genes in a non-model percid species – the Eurasian perch (Perca fluviatilis L.). PCR primers developed here were highly specific, and documented a high diversity of the MHII β1 domain in perch. Our results suggest a minimum of eight MHII β loci in this species – a finding congruent with several studies suggesting that many Euteleostei posses multiple MHII β loci. As for other vertebrates, both positive selection and gene-conversion contribute to the reported high allelic diversity. Similarly, the MHII β1 domain in perch exhibits a characteristic MHC fold known from other vertebrates. In addition, our results suggest some teleost specific differences of the MHII β1 domain, including: differences in chemical properties of specific amino acids in the β1 domain, the absence of the tetrapod specific glycolisation signal, and differences in the positions of some of the positively selected codons in the MHII β1 domain, which are presumably involved in antigen binding. Future studies should investigate the teleost MHII β genes in more details in order to confirm the suggested differences, and to determine the extent to which these differences prevail in different teleost lineages.     

Anti-thyroid drugs and lymphocyte function: II. The in vivo effect on blastogenesis and suppressor cell activity in graves' disease

The proliferative response (PR) of T lymphocytes in PHA stimulated cultures (5 μg/ml and 0·5 μg/ml; 72 hr) was used to assess the suppressive capabilities of peripheral blood mononuclear cells (PBMC) in the thyrotoxic phase of Graves' disease and their possible modification by propylthiouracil (PTU) and methimazole (MMI) treatment. Graves' patients had 50% higher PR than controls. Treatment with PTU (n=6) for 9·5 weeks (mean) or MMI (n=6) for 18 weeks (mean) resulted in continuous decrease in PR, starting after 3 weeks and down to control values and plateau at 7-10 weeks. This decrease correlated with the decline in plasma thyroxine (T4) levels which had already dropped by 3 weeks. Grouped according to thyroid functional state PR was significantly decreased only in the euthyroid state. Suppressor cell function, expressed as suppressor removal index (PR of PBMC pre-incubated for 24 hr/PR of fresh PBMC), was significantly lower in Graves' patients compared to controls and reached above normal values under PTU treatment: 0·98±0·16, 1·39±0·09 and 1·94±0·19 (mean±s.e.m.) respectively. A direct suppressive effect of PTU in culture, observed in normal subjects, did not exist in untreated patients and evolved under MMI treatment to above normal levels. The cell-mediated PTU effect, exercised by PBMC pre-incubated with PTU on autologous cells pre-incubated in medium alone, increased under PTU treatment to above normal levels. Both this cell-mediated suppressive effect and augmented PR of pre-incubated cells were already significantly increased after 3 weeks of PTU treatment, when all patients were still thyrotoxic. We conclude therefore that PBMC of patients in the untreated, thyrotoxic phase of Graves' disease are deficient in an active cell-mediated suppressive function, a deficiency corrected—with compensatory overshoot—during anti-thyroid drug treatment.     

Induction of immunological tolerance to human gamma-globulin in rabbits using the maternal route of inoculation

A method of producing tolerance in rabbits to human γ-globulin is described. This method differs from those in common use in that the antigen is administered to the mother, rather than direct to the foetus, and allowed to pass across the foetal—maternal barrier. Attention is drawn to the importance of the timing of administration of antigen in relation to the duration of pregnancy in order to avoid interference by maternal antibody.     

Maternal antibodies in human foetal sera at different stages of gestation

Complement-fixing antibodies to ten viral antigens and/or mercaptoethanol treated anti-streptolysin-O and anti-staphylolysin-α were determined in thirty human sera from foetuses at different stages of gestation, in fifty-seven full-term cord sera, and in the corresponding maternal sera. In the smallest foetuses (crown—heel length of 125–150 mm), no antibody was found. In those of length 155–215 mm, antibody was detectable if the corresponding maternal value was high. In foetuses of 230–380 mm, antibody was detected occasionally even when the maternal value was low. Sera of foetuses of 390 mm or more contained the same antibodies as the maternal sample, and foetal titres sometimes exceeded those of the mother. Titres in the full-term cord sera were significantly higher than the maternal titres for seven of the twelve antibodies studied.     

IFN-γ +874 A>T (rs2430561) gene polymorphism and risk of pulmonary tuberculosis: a meta-analysis

IntroductionThe role of interferon gamma (IFN-γ) +874 A>T (rs2430561) gene polymorphism has been evaluated in different ethnicities with pulmonary tuberculosis (PTB) infection, and inconsistent results have been reported. In this study, a meta-analysis was performed to determine the precise association between IFN-γ +874 A>T gene polymorphism and PTB susceptibility.Material and methodsA total of 21 studies comprising 4281 confirmed PTB cases and 5186 healthy controls were included in this meta-analysis by searching the PubMed (Medline), EMBASE, and Google Scholar web-databases.ResultsWe observed reduced risk of PTB in allelic contrast (T vs. A: p = 0.001; OR = 0.818, 95% CI: 0.723–0.926), homozygous (TT vs. AA: p = 0.017; OR = 0.715, 95% CI: 0.543–0.941), heterozygous (AT vs. AA: p = 0.002; OR = 0.782, 95% CI: 0.667–0.917), dominant (TT+AT vs. AA: p = 0.002; OR = 0.768, 95% CI: 0.652–0.906), and recessive (TT vs. AA+AT: p = 0.042; OR = 0.802, 95% CI: 0.649–0.992) genetic models. In ethnicity-wise subgroup analysis, reduced risk of PTB was found in the Caucasian population. However, we did not find an association with any of the genetic models in the Asian population.ConclusionsIn conclusion, the IFN-γ +874 A>T gene polymorphism is significantly associated with reduced risk of PTB, showing a protective effect in the overall and in the Caucasian population. However, this polymorphism is not associated with PTB risk in the Asian population.     

Origin and development of the γδ T-cell system in sheep: a critical role for the thymus in the generation of TcR diversity and tissue tropism

Ruminant γδ T cells are concentrated at epithelial surfaces and share many features in common with species such as mice and humans which contain relatively fewer γδ T cells than ruminants. To date no γδ T cells with invariant TcR have been found in sheep and the generation of γδ TcR diversity which is thymic dependent follows a developmentally regulated sequence. Analysis of thymic export of γδ T cells shows that emigration of γδ T-cell subsets increases markedly during fetal life and after birth suggesting intrathymic processes leading to mature γδ T cells may change during development. Skin homing γδ T cells acquire their tissue tropism inside the thymus and pathways of recirculation of γδ T cells to skin are laid down during fetal development independent of antigen and remain stable through into adult life.