TNFRSF13B Genetic variability an anthropological - evolutionary approach to Biomedical Research

In the recent years TNFRSF13B coding variants have been implicated by clinical genetics studies in Common Variable Immunodeficiency (CVID), the most common clinically relevant primary immunodeficiency in individuals of European ancestry, but their functional effects in relation to the development of the disease have not been entirely established. To examine the potential contribution of such variants to CVID, the more comprehensive perspective of an evolutionary approach was applied in this study, underling the belief that evolutionary genetics methods can play a role in dissecting the origin, causes and diffusion of human diseases, representing a powerful tool also in human health research. For this purpose, TNFRSF13B coding region was sequenced in 451 healthy individuals belonging to 26 worldwide populations, in addition to 96 control, 77 CVID and 38 Selective IgA Deficiency (IgAD) individuals from Italy, leading to the first achievement of a global picture of TNFRSF13B nucleotide diversity and haplotype structure and making suggestion of its evolutionary history possible. A slow rate of evolution, within our species and when compared to the chimpanzee, low levels of genetic diversity geographical structure and the absence of recent population specific selective pressures were observed for the examined genomic region, suggesting that geographical distribution of its variability is more plausibly related to its involvement also in innate immunity rather than in adaptive immunity only. This, together with the extremely subtle disease/healthy samples differences observed, suggests that CVID might be more likely related to still unknown environmental and genetic factors, rather than to the nature of TNFRSF13B variants only.

A candidate gene approach to identify DNA markers associated with meat quality and production traits: investigation of several cathepsin genes in Italian heavy pigs.

The cathepsin enzymes represent an important family of lysosomal proteinases with a broad spectrum of functions in many, if not in all, tissues and cell types. In addition to their primary role during the normal protein turnover, they possess highly specific proteolytic activities, including antigen processing in the immune response and a direct role in the development of obesity and tumours. In pigs, the involvement of cathepsin enzymes in proteolytic processes have important effects during the conversion of muscle to meat, due to their influence on meat texture and sensory characteristics, mainly in seasoned products. Their contribution is fundamental in flavour development of dry-curing hams. However, several authors have demonstrated that high cathepsin activity, in particular of cathepsin B, is correlated to defects of these products, such as an excessive meat softness together with abnormal free tyrosine content, astringent or metallic aftertastes and formation of a white film on the cut surface. Thus, investigation of their genetic variability could be useful to identify DNA markers associated with these dry cured hams parameters, but also with meat quality, production and carcass traits in Italian heavy pigs. Unfortunately, no association has been found between cathepsin markers and meat quality traits so far, in particular with cathepsin B activity, suggesting that other genes, besides these, affect meat quality parameters. Nevertheless, significant associations were observed with several carcass and production traits in pigs. A recent study has demonstrated that different single nucleotide polymorphisms (SNPs) localized in cathepsin D (CTSD), F (CTSF), H and Z genes were highly associated with growth, fat deposition and production traits in an Italian Large White pig population. The aim of this thesis was to confirm some of these results in other pig populations and identify new cathepsin markers in order to evaluate their effects on cathepsin activity and other production traits. Furthermore, starting from the data obtained in previous studies on CTSD gene, we also analyzed the known polymorphism located in the insulin-like growth factor 2 gene (IGF2 intron3-g.3072G>A). This marker is considered the causative mutation for the quantitative trait loci (QTL) affecting muscle mass and fat deposition in pigs. Since IGF2 maps very close to CTSD on porcine chromosome (SSC) 2, we wanted to clarify if the effects of the CTSD marker were due to linkage disequilibrium with the IGF2 intron3-g.3072G>A mutation or not. In the first chapter, we reported the results from these two SSC2 gene markers. First of all, we evaluated the effects of the IGF2 intron3-g.3072G>A polymorphism in the Italian Large White breed, for which no previous studies have analysed this marker. Highly significant associations were identified with all estimated breeding values for production and carcass traits (P<0.00001), while no effects were observed for meat quality traits. Instead, the IGF2 intron3-g.3072G>A mutation did not show any associations with the analyzed traits in the Italian Duroc pigs, probably due to the low level of variability at this polymorphic site for this breed. In the same Duroc pig population, significant associations were obtained for the CTSD marker for all production and carcass traits (P < 0.001), after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A polymorphism were also confirmed in a group of Italian Large White pigs homozygous for the IGF2 intron3-g.3072G allele G (IGF2 intron3-g.3072GG) and by haplotype analysis between the markers of the two considered genes. Taken together, all these data indicated that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition in pigs. In the second chapter, we reported the analysis of two new SNPs identified in cathepsin L (CTSL) and cathepsin S (CTSS) genes and the association results with meat quality parameters (including cathepsin B activity) and several production traits in an Italian Large White pig population. Allele frequencies of these two markers were evaluated in 7 different pig breeds. Furthermore, we mapped using a radiation hybrid panel the CTSS gene on SSC4. Association studies with several production traits, carried out in 268 Italian Large White pigs, indicated positive effects of the CTSL polymorphism on average daily gain, weight of lean cuts and backfat thickness (P<0.05). The results for these latter traits were also confirmed using a selective genotype approach in other Italian Large White pigs (P<0.01). In the 268 pig group, the CTSS polymorphism was associated with feed:gain ratio and average daily gain (P<0.05). Instead, no association was observed between the analysed markers and meat quality parameters. Finally, we wanted to verify if the positive results obtained for the cathepsin L and S markers and for other previous identified SNPs (cathepsin F, cathepsin Z and their inhibitor cystatin B) were confirmed in the Italian Duroc pig breed (third chapter). We analysed them in two groups of Duroc pigs: the first group was made of 218 performance-tested pigs not selected by any phenotypic criteria, the second group was made of 100 Italian Duroc pigs extreme and divergent for visible intermuscular fat trait. In the first group, the CTSL polymorphism was associated with weight of lean cuts (P<0.05), while suggestive associations were obtained for average daily gain and backfat thickness (P<0.10). Allele frequencies of the CTSL gene marker also differed positively among the visible intermuscular extreme tails. Instead, no positive effects were observed for the other DNA markers on the analysed traits. In conclusion, in agreement with the present data and for the biological role of these enzymes, the porcine CTSD and CTSL markers: a) may have a direct effect in the biological mechanisms involved in determining fat and lean meat content in pigs, or b) these markers could be very close to the putative functional mutation(s) present in other genes. These findings have important practical applications, in particular the CTSD and CTSL mutations could be applied in a marker assisted selection (MAS) both in the Italian Large White and Italian Duroc breeds. Marker assisted selection could also increase in efficiency by adding information from the cathepsin S genotype, but only in the Italian Large White breed.

Molecular phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Europe

Phylogeography is a recent field of biological research that links phylogenetics to biogeography through deciphering the imprint that evolutionary history has left on the genetic structure of extant populations. During the cold phases of the successive ice ages, which drastically shaped species’ distributions since the Pliocene, populations of numerous species were isolated in refugia where many of them evolved into different genetic lineages. My dissertation deals with the phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Central and Eastern Europe. This Palaearctic butterfly species is currently distributed from central France and south eastern Belgium over large parts of Central Europe and southern Siberia to the Pacific. It is absent from those parts of Europe with mediterranean, oceanic and boreal climates. It was supposed to be a Siberian faunal element with a rather homogeneous population structure in Central Europe due to its postglacial expansion out of a single eastern refugium. An already existing evolutionary scenario for the Woodland Ringlet in Central and Eastern Europe is based on nuclear data (allozymes). To know if this is corroborated by organelle evolutionary history, I sequenced two mitochondrial markers (part of the cytochrome oxydase subunit one and the control region) for populations sampled over the same area. Phylogeography largely relies on the construction of networks of uniparentally inherited haplotypes that are compared to geographic haplotype distribution thanks to recent developed methods such as nested clade phylogeographic analysis (NCPA). Several ring-shaped ambiguities (loops) emerged from both haplotype networks in E. medusa. They can be attributed to recombination and homoplasy. Such loops usually avert the straightforward extraction of the phylogeographic signal contained in a gene tree. I developed several new approaches to extract phylogeographic information in the presence of loops, considering either homoplasy or recombination. This allowed me to deduce a consistent evolutionary history for the species from the mitochondrial data and also adds plausibility for the occurrence of recombination in E. medusa mitochondria. Despite the fact that the control region is assumed to have a lack of resolving power in other species, I found a considerable genetic variation of this marker in E. medusa which makes it a useful tool for phylogeographic studies. In combination with the allozyme data, the mitochondrial genome supports the following phylogeographic scenario for E. medusa in Europe: (i) a first vicariance, due to the onset of the Würm glaciation, led to the formation of several major lineages, and is mirrored in the NCPA by restricted gene flow, (ii) later on further vicariances led to the formation of two sub-lineages in the Western lineage and two sub-lineages in the Eastern lineage during the Last Glacial Maximum or Older Dryas; additionally the NCPA supports a restriction of gene flow with isolation by distance, (iii) finally, vicariance resulted in two secondary sub-lineages in the area of Germany and, maybe, to two other secondary sub-lineages in the Czech Republic. The last postglacial warming was accompanied by strong range expansions in most of the genetic lineages. The scenario expected for a presumably Siberian faunal element such as E. medusa is a continuous loss of genetic diversity during postglacial westward expansion. Hence, the pattern found in this thesis contradicts a typical Siberian origin of E. medusa. In contrast, it corroboratess the importance of multiple extra-Mediterranean refugia for European fauna as it was recently assumed for other continental species.

Celiachia e difetti dello smalto in età evolutiva: correlazione tra periodo di esposizione al glutine, forme cliniche di celiachia e aplotipo HLA

The association between celiac disease (CD) and dental enamel defects (DED) is well known. AIM: This study was designed to investigate the prevalence of DED in CD children and to specifically find a possible correlation between DED and gluten exposure period, CD clinical forms, HLA class II haplotype. MATERIALS AND METHODS: This study was designed as a matched case-control study: 374 children were enrolled (187 celiac and 187 non celiac). Data about age at CD diagnosis, CD clinical form and HLA haplotype were recorded. RESULTS: DED were detected in 87 celiac subject while no dental lesions were found in the remaining 100 patients; in 187 healthy controls enamel lesion were significantly less frequent (5.3 % versus 46.5% ; p<0.005).We found a correlation between DED and gluten exposure period, since among CD patients the mean age at CD diagnosis was significantly (p= 0.0004) higher in the group with DED (3.41± 1.27) than without DED (1.26± 0.7). DED resulted more frequent in atypical and silent forms than in the typical one. The presence of HLA DR 52-53 and DQ7 antigens significantly increased the risk of DED (p=0.0017). CONCLUSIONS: Our results confirmed a possible correlation between CD clinical form, age at CD diagnosis, HLA antigens and DED. The origin of DED in CD children is due to multifactorial events and further studies are needed to investigate other determinants.

Metaheuristics for Search Problems in Genomics - New Algorithms and Applications

In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference by parsimony and the Founder Sequence Reconstruction Problem. We compare our algorithms with other effective techniques in the literature, we show strength and limitations of our approaches to various problem formulations and, finally, we propose further enhancements that could possibly improve the performance of our algorithms and widen their applicability. In the second part, we concentrate on Boolean network (BN) models of gene regulatory networks (GRNs). We detail our automatic design methodology and apply it to four use cases which correspond to different design criteria and address some limitations of GRN modeling by BNs. Finally, we tackle the Density Classification Problem with the aim of showing the learning capabilities of BNs. Experimental evaluation of this methodology shows its efficacy in producing network that meet our design criteria. Our results, coherently to what has been found in other works, also suggest that networks manipulated by a search process exhibit a mixture of characteristics typical of different dynamical regimes.

Mechanismen der Antigenpräsentation bei der Induktion der CD8-T-Zellantwort gegen das murine Cytomegalovirus

Die Kontrolle der Cytomegalovirus(CMV)-Infektion durch CD8 T-Zellen ist abhängig von der effizienten MHC-Klasse-I-Präsentation viraler Peptide auf der Zelloberfläche. Um die Erkennung infizierter Zellen zu unterdrücken, interferieren während der Early (E)-Phase der murinen CMV (mCMV)-Infektion virale Immunevasine mit dem intrazellulären Transport von Peptid-MHC-I (pMHC-I) Komplexen. Den Immunevasinen gelingt es allerdings nicht, ein Priming mCMV-spezifischer CD8 T-Zellen zu verhindern. Daher wurde angenommen, dass die Initiation der antiviralen CD8 T-Zellantwort primär auf der Cross-Präsentation viraler Peptide auf nicht-infizierten, professionellen Antigen-präsentierenden Zellen (profAPC) beruht und damit unabhängig von viralen Immunevasionsmechanismen ist.rnIm Rahmen der vorliegenden Arbeit wurde mittels BAC-Mutagenese eine mCMV-Rekombinante generiert, um die direkte Präsentation viraler Peptide durch die zusätzliche Expression des zentralen Immunevasins m152 bereits in der Immediate Early (IE)-Phase verstärkt zu unterdrücken. Wie erwartet reduzierte die verstärkte m152-Expression sowohl in der IE- als auch in der E-Phase die pMHC-I-Präsentation in vitro. Dies führte überraschenderweise nach Infektion immunkompetenter BALB/c-Mäuse (Haplotyp H-2d) zu einer verminderten CD8 T-Zellantwort und damit zur Verschlechterung der Kontrolle der Infektion im drainierenden Lymphknoten. Diese Beobachtungen weisen erstmals auf einen wichtigen Beitrag der direkten Antigenpräsentation bei der Initiation der mCMV-spezifischen CD8 T-Zellantwort im immunkompetenten Wirt hin. Zusätzlich konnte auch nach mCMV-Infektion von Cross-Präsentations-defizienten Mäusen (Haplotyp H-2b) eine antivirale CD8 T-Zellantwort initiiert werden. Diese Beobachtung bestätigt, dass durch direkte Antigenpräsentation auf infizierten profAPC trotz viraler Immunevasionsmechanismen eine CD8 T-Zellantwort induziert werden kann. Allerdings wurde weder die antivirale CD8 T-Zellantwort noch die Kontrolle der Infektion im Haplotyp H-2b durch die verstärkte m152-Expression moduliert.rnIn einem weiteren Teil der Arbeit konnte im klinisch relevanten Modellsystem der mCMV-Infektion von Knochenmarktransplantations (KMT)-Rezipienten (Haplotyp H-2d) gezeigt werden, dass die verstärkte m152-Expression die Rekrutierung IE1-spezifischer CD8 T-Zellen in die infizierte Lunge unterdrückt. Dies konnte sowohl früh nach Infektion, als auch während der viralen Latenz nachgewiesen werden. Zusätzlich war die Rekrutierung IE1-spezifischer CD8 T-Zellen in die Lunge deutlich vermindert in Ld--Rezipienten von Ld+-hämatopoetischen Zellen, die das IE1-präsentierende MHC-I-Molekül Ld nicht auf den nicht-hämatopoetischen Gewebszellen exprimieren. Diese Beobachtungen zeigen, dass die Rekrutierung antiviraler CD8 T-Zellen in ein peripheres Organ von der direkten Antigenpräsentation auf nicht-hämatopoetischen, infizierten Gewebszellen bestimmt wird.rnIn der vorliegenden Arbeit konnte somit erstmals gezeigt werden, dass trotz viraler Immunevasionsmechanismen nach mCMV-Infektion des immunkompetenten Wirtes und des KMT-Rezipienten die antivirale CD8 T-Zellantwort von der direkten Antigenpräsentation bestimmt wird.

Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin

Der Fokus dieser Dissertation ist die populationsgenetische Analyse der neolithischen Bevölkerungswechsel in den 6.-5. Jahrtausende vor Christus, die im westlichen Karpatenbecken stattfanden. Die Zielsetzung der Studie war, mittels der Analyse von mitochondrialer und Y-chromosomaler aDNA, den Genpool der sechs neolithischen und kupferzeitlichen Populationen zu untersuchen und die daraus resultierenden Ergebnisse mit anderen prähistorischen und modernen genetischen Daten zu vergleichen.rnInsgesamt wurden 323 Individuen aus 32 ungarischen, kroatischen und slowakischen Fundplätzen beprobt und bearbeitet in den archäogenetischen Laboren der Johannes Gutenberg-Universität in Mainz. Die DNA Ergebnisse wurden mit verschiedenen populationsgenetischen Methoden ausgewertet. Vergleichsdaten von prähistorischen und modernen eurasiatischen Populationen wurden dazu gesammelt.rnDie HVS-I Region der mitochondrialen DNA konnten bei 256 Individuen reproduziert und authentifiziert werden (mit einer Erfolgsrate von 85.9%). Die Typisierung der HVS-II Region war in 80 Fällen erfolgreich. Testend alle gut erhaltene Proben, die Y-chromosomale Haplogruppe konnte in 33 männlichen Individuen typisiert werden.rnDie neolithischen, mitochondrialen Haplogruppen deuten auf eine hohe Variabilität des maternalen Genpools hin. Sowohl die mitochondrialen als auch die Y-chromosomalen Daten lassen Rückschlüsse auf eine nah-östliche bzw. südwestasiatische Herkunft der frühen Bauern zu. Die Starčevo- und linearbandkermaischen-Populationen in westlichem Karpatenbecken (letztere abgekürzt als LBKT) und die linearbandkermaischen-Population in Mitteleuropa (LBK) haben so starke genetische Ähnlichkeit, dass die Verbreitung der LBK nach Mitteleuropa mit vorangegangenen Wanderungsereignissen zu erklären ist. Die Transdanubische aDNA Daten zeigen hohe Affinität zu den publizierten prähistorischen aDNA Datensätzen von Mitteleuropa aus den 6.-4. Jahrtausende vor Chr. Die maternal-genetische Variabilität der Starčevo-Population konnte auch innerhalb der nachfolgenden Populationen Transdanubiens festgestellt werden. Nur kleinere Infiltrationen und Immigrationsereignissen konnten während der Vinča-, LBKT-, Sopot- und Balaton-Lasinja-Kultur in Transdanubien identifiziert werden. Zwischen den transdanubischen Regionen konnten mögliche genetische Unterschiede nur in der LBKT und in der Lengyel-Periode beobachtet werden, als sich die nördlichen Gruppen von den südlichen Populationen trennten. rnDie festgestellte Heterogenität der mtDNA in Zusammenhang mit der Y-chromosomalen Homogenität in den Starčevo- und LBK-Populationen, weisen auf patrilokale Residenzregeln und patrilineare Abstammungsregeln in den ersten Bauergemeinschaften hin. rnObwohl die hier präsentierten Daten einen großen Fortschritt in der Forschung von aDNA und Neolithikum des Karpatenbeckens und Mitteleuropas bedeuten, werfen sie auch mehrere Fragen auf, deren Beantwortung durch zukünftige Genomforschungen erbracht werden könnte.

Phylogeny and phylogeography of the family Hyalidae (Crustacea: Amphipoda) along the northeast Atlantic coasts

The family Hyalidae comprises more than one hundred species, distributed worldwide. They are common and abundant in the littoral and shallow sublittoral habitats and they play an important role in the coastal food chain. Most studies about this family were dealing with taxonomy and ecology, while very little is known about phylogenetic relationship among genera and species. In the present study we aim to achieve the first approach of the phylogenetic patterns of this family in NE Atlantic Ocean and Mediterranean Sea, and to perform the first insight into the phylogeography Apohyale prevostii along both the North Atlantic coasts. In order to do that, eight species belonging to the genera Apohyale, Hyale, Serejohyale and Protohyale were investigated using the mitochondrial COI-5P barcode region. Specimens were collected along European and Moroccan Atlantic rocky shores, including Iceland, the British Isles, Macaronesia and in the Mediterranean Sea. Sequences of A. prevostii, from the NW Atlantic Ocean, available in BOLD and GenBank, were retrieved. As expected, phylogenetic analyses showed highly-divergent clades, clearly discriminating among different species clusters, confirming their morphology-based identifications. Although, within A. perieri, A. media, A. stebbingi, P. (Protohyale) schmidtii and S. spinidactylus, high genetic diversity was found, revealing putative cryptic species. The clade of A. prevostii and A. stebbingi appears well supported and divided from the other two congeneric species, and P. (Protohyale) schmidtii shows a basal divergence. The north-western Atlantic coasts were recently colonized by A. prevostii after the last glacial maximum from the European populations showing also a common haplotype in every population analysed. The use of the COI-5P as DNA barcode provided a good tool to underline the necessity of a revision of this emblematic family, as well as to discern taxonomically the possible new species flagged with this molecular device.

Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy

Narcolepsy is a rare sleep disorder with the strongest human leukocyte antigen (HLA) association ever reported. Since the associated HLA-DRB1*1501-DQB1*0602 haplotype is common in the general population (15-25%), it has been suggested that it is almost necessary but not sufficient for developing narcolepsy. To further define the genetic basis of narcolepsy risk, we performed a genome-wide association study (GWAS) in 562 European individuals with narcolepsy (cases) and 702 ethnically matched controls, with independent replication in 370 cases and 495 controls, all heterozygous for DRB1*1501-DQB1*0602. We found association with a protective variant near HLA-DQA2 (rs2858884; P < 3 x 10(-8)). Further analysis revealed that rs2858884 is strongly linked to DRB1*03-DQB1*02 (P < 4 x 10(-43)) and DRB1*1301-DQB1*0603 (P < 3 x 10(-7)). Cases almost never carried a trans DRB1*1301-DQB1*0603 haplotype (odds ratio = 0.02; P < 6 x 10(-14)). This unexpected protective HLA haplotype suggests a virtually causal involvement of the HLA region in narcolepsy susceptibility.

Hybridization between distant lineages increases adaptive variation during a biological invasion: stickleback in Switzerland

The three-spined stickleback is a widespread Holarctic species complex that radiated from the sea into freshwaters after the retreat of the Pleistocene ice sheets. In Switzerland, sticklebacks were absent with the exception of the far northwest, but different introduced populations have expanded to occupy a wide range of habitats since the late 19th century. A well-studied adaptive phenotypic trait in sticklebacks is the number of lateral plates. With few exceptions, freshwater and marine populations in Europe are fixed for either the low plated phenotype or the fully plated phenotype, respectively. Switzerland, in contrast, harbours in close proximity the full range of phenotypic variation known from across the continent. We addressed the phylogeographic origins of Swiss sticklebacks using mitochondrial partial cytochrome b and control region sequences. We found only five different haplotypes but these originated from three distinct European regions, fixed for different plate phenotypes. These lineages occur largely in isolation at opposite ends of Switzerland, but co-occur in a large central part. Across the country, we found a strong correlation between a microsatellite linked to the high plate ectodysplasin allele and the mitochondrial haplotype from a region where the fully plated phenotype is fixed. Phylogenomic and population genomic analysis of 481 polymorphic amplified fragment length polymorphism loci indicate genetic admixture in the central part of the country. The same part of the country also carries elevated within-population phenotypic variation. We conclude that during the recent invasive range expansion of sticklebacks in Switzerland, adaptive and neutral between-population genetic variation was converted into within-population variation, raising the possibility that hybridization between colonizing lineages contributed to the ecological success of sticklebacks in Switzerland.

Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance

The identification of associations between interleukin-28B (IL-28B) variants and the spontaneous clearance of hepatitis C virus (HCV) raises the issues of causality and the net contribution of host genetics to the trait. To estimate more precisely the net effect of IL-28B genetic variation on HCV clearance, we optimized genotyping and compared the host contributions in multiple- and single-source cohorts to control for viral and demographic effects. The analysis included individuals with chronic or spontaneously cleared HCV infections from a multiple-source cohort (n = 389) and a single-source cohort (n = 71). We performed detailed genotyping in the coding region of IL-28B and searched for copy number variations to identify the genetic variant or haplotype carrying the strongest association with viral clearance. This analysis was used to compare the effects of IL-28B variation in the two cohorts. Haplotypes characterized by carriage of the major alleles at IL-28B single-nucleotide polymorphisms (SNPs) were highly overrepresented in individuals with spontaneous clearance versus those with chronic HCV infections (66.1% versus 38.6%, P = 6 × 10(-9) ). The odds ratios for clearance were 2.1 [95% confidence interval (CI) = 1.6-3.0] and 3.9 (95% CI = 1.5-10.2) in the multiple- and single-source cohorts, respectively. Protective haplotypes were in perfect linkage (r(2) = 1.0) with a nonsynonymous coding variant (rs8103142). Copy number variants were not detected. CONCLUSION: We identified IL-28B haplotypes highly predictive of spontaneous HCV clearance. The high linkage disequilibrium between IL-28B SNPs indicates that association studies need to be complemented by functional experiments to identify single causal variants. The point estimate for the genetic effect was higher in the single-source cohort, which was used to effectively control for viral diversity, sex, and coinfections and, therefore, offered a precise estimate of the net host genetic contribution.

Common CFTR haplotypes and susceptibility to chronic pancreatitis and congenital bilateral absence of the vas deferens

CFTR mutations enhance susceptibility for idiopathic chronic pancreatitis (ICP) and congenital bilateral absence of the vas deferens (CBAVD); however, it is unknown why CFTR heterozygotes are at increased disease risk. We recently showed that common CFTR variants are associated with aberrantly spliced transcripts. Here, we genotyped for common CFTR variants and tested for associations in two ICP (ICP-A: 126 patients, 319 controls; ICP-B: 666 patients, 1,181 controls) and a CBAVD population (305 patients, 319 controls). Haplotype H10 (TG11-T7-470V) conferred protection (ICP-A: OR 0.19, P<0.0001; ICP-B: OR 0.78, P = 0.06; CBAVD OR 0.08, P<0.001), whereas haplotype H3 (TG10-T7-470M) increased disease risk (ICP-A: OR 8.34, P = 0.003; ICP-B: OR 1.88, P = 0.007; CBAVD: OR 5.67, P = 0.01). The risk of heterozygous CFTR mutations carriers for ICP (OR 2.44, P<0.001) and CBAVD (OR 14.73, P<0.001) was fully abrogated by the H10/H10 genotype. Similarly, ICP risk of heterozygous p.Asn34Ser SPINK1 mutation carriers (OR 10.34, P<0.001) was compensated by H10/H10. Thus, common CFTR haplotypes modulate ICP and CBAVD susceptibility alone and in heterozygous CFTR and p.Asn34Ser mutation carriers. Determination of these haplotypes helps to stratify carriers into high- and low-risk subjects, providing helpful information for genetic counseling.

An unusual splice defect in the mitofusin 2 gene (MFN2) is associated with degenerative axonopathy in Tyrolean Grey cattle

Tyrolean Grey cattle represent a local breed with a population size of approximately 5000 registered cows. In 2003, a previously unknown neurological disorder was recognized in Tyrolean Grey cattle. The clinical signs of the disorder are similar to those of bovine progressive degenerative myeloencephalopathy (weaver syndrome) in Brown Swiss cattle but occur much earlier in life. The neuropathological investigation of an affected calf showed axonal degeneration in the central nervous system (CNS) and femoral nerve. The pedigrees of the affected calves suggested a monogenic autosomal recessive inheritance. We localized the responsible mutation to a 1.9 Mb interval on chromosome 16 by genome-wide association and haplotype mapping. The MFN2 gene located in this interval encodes mitofusin 2, a mitochondrial membrane protein. A heritable human axonal neuropathy, Charcot-Marie-Tooth disease-2A2 (CMT2A2), is caused by MFN2 mutations. Therefore, we considered MFN2 a positional and functional candidate gene and performed mutation analysis in affected and control Tyrolean Grey cattle. We did not find any non-synonymous variants. However, we identified a perfectly associated silent SNP in the coding region of exon 20 of the MFN2 gene. This SNP is located within a putative exonic splice enhancer (ESE) and the variant allele leads to partial retention of the entire intron 19 and a premature stop codon in the aberrant MFN2 transcript. Thus we have identified a highly unusual splicing defect, where an exonic single base exchange leads to the retention of the preceding intron. This splicing defect represents a potential explanation for the observed degenerative axonopathy. Marker assisted selection can now be used to eliminate degenerative axonopathy from Tyrolean Grey cattle.

Dual origins of dairy cattle farming - evidence from a comprehensive survey of European Y-chromosomal variation

BACKGROUND: Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS: Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS: We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.

Molecular analysis of carbohydrate N-acetylgalactosamine 4-O sulfotransferase 8 (CHST8) as a candidate gene for bovine spongiform encephalopathy susceptibility

Endogenous prion proteins (PrP) play the central role in the pathogenesis of transmissible spongiform encephalopathies. The carbohydrate N-acetylgalactosamine 4-O sulfotransferase 8 (CHST8) promotes the conversion of the cellular PrP(C) into the pathogenic PrP(d). Six sequence variants within the CHST8 gene were identified by comparative sequencing and genotyped for a sample of 623 animals comprising bovine spongiform encephalopathy (BSE)-affected and healthy control cows representing German Fleckvieh (German Simmental), German Holstein (Holstein-Friesian) and Brown Swiss. Significant differences in the allele, genotype and haplotype frequencies between BSE-affected and healthy cows indicate an association of sequence variant g.37254017G>T with the development of the disease in Brown Swiss cattle.