Genetic and environmental factors associated with cardiovascular diseases and acute myocardial infarction

Acute myocardial infarction (AMI) is a multifactorial disease with a complex pathogenesis where lifestyle, individual genetic background and environmental risk factors are involved. Altered inflammatory responses seems to be implicated in the pathogenesis of atherosclerosis. To understand which genes may predispose to increased risk of cardiovascular disease gene polymorphism of immune regulatory genes, and clinical events from the Offs of parents with an early AMI were investigated. Genetics data from Offs were compared with those obtained from healthy subjects and an independent cohort of patients with clinical sporadic AMI. Rates of clinical events during a 24 years follow up from Offs and from an independent Italian population survey were also evaluated. This study showed that a genetic signature consisting of the concomitant presence of the CC genotype of VEGF, the A allele of IL-10 and the A allele of IFN-γ was indeed present in the Offs population. During the 24-year follow-up, Offs with a positive familiarity in spite of a relatively young age showed an increased prevalence of diabetes, ischemic heart disease and stroke. In these patients with the genetic signature the EBV and HHV-6 herpes virus were also investigated and founded. These findings reinforce the notion that subjects with a familial history of AMI are at risk of an accelerated aging of cardiovascular system resulting in cardiovascular events. These data suggest that selected genes with immune regulatory functions and envoronmental factors are part of the complex genetic background contributing to familiarity for cardiovascular diseases.N

Genetic and morphological variation and differentiation of Raja clavata populations in the European seas: marker development and preliminary data

In this study the population structure and connectivity of the Mediterranean and Atlantic Raja clavata (L., 1758) were investigated by analyzing the genetic variation of six population samples (N = 144) at seven nuclear microsatellite loci. The genetic dataset was generated by selecting population samples available in the tissue databases of the GenoDREAM laboratory (University of Bologna) and of the Department of Life Sciences and Environment (University of Cagliari), all collected during past scientific surveys (MEDITS, GRUND) from different geographical locations in the Mediterranean basin and North-east Atlantic sea, as North Sea, Sardinian coasts, Tuscany coasts and Cyprus Island. This thesis deals with to estimate the genetic diversity and differentiation among 6 geographical samples, in particular, to assess the presence of any barrier (geographic, hydrogeological or biological) to gene flow evaluating both the genetic diversity (nucleotide diversity, observed and expected heterozygosity, Hardy- Weinberg equilibrium analysis) and population differentiation (Fst estimates, population structure analysis). In addition to molecular analysis, quantitative representation and statistical analysis of morphological individuals shape are performed using geometric morphometrics methods and statistical tests. Geometric coordinates call landmarks are fixed in 158 individuals belonging to two population samples of Raja clavata and in population samples of closely related species, Raja straeleni (cryptic sibling) and Raja asterias, to assess significant morphological differences at multiple taxonomic levels. The results obtained from the analysis of the microsatellite dataset suggested a geographic and genetic separation between populations from Central-Western and Eastern Mediterranean basins. Furthermore, the analysis also showed that there was no separation between geographic samples from North Atlantic Ocean and central-Western Mediterranean, grouping them to a panmictic population. The Landmark-based geometric morphometry method results showed significant differences of body shape able to discriminate taxa at tested levels (from species to populations).

Software tools and efficient algorithms for the feature detection, feature tracking, event localization, and visualization of large sets of atmospheric data

Data sets describing the state of the earth's atmosphere are of great importance in the atmospheric sciences. Over the last decades, the quality and sheer amount of the available data increased significantly, resulting in a rising demand for new tools capable of handling and analysing these large, multidimensional sets of atmospheric data. The interdisciplinary work presented in this thesis covers the development and the application of practical software tools and efficient algorithms from the field of computer science, aiming at the goal of enabling atmospheric scientists to analyse and to gain new insights from these large data sets. For this purpose, our tools combine novel techniques with well-established methods from different areas such as scientific visualization and data segmentation. In this thesis, three practical tools are presented. Two of these tools are software systems (Insight and IWAL) for different types of processing and interactive visualization of data, the third tool is an efficient algorithm for data segmentation implemented as part of Insight.Insight is a toolkit for the interactive, three-dimensional visualization and processing of large sets of atmospheric data, originally developed as a testing environment for the novel segmentation algorithm. It provides a dynamic system for combining at runtime data from different sources, a variety of different data processing algorithms, and several visualization techniques. Its modular architecture and flexible scripting support led to additional applications of the software, from which two examples are presented: the usage of Insight as a WMS (web map service) server, and the automatic production of a sequence of images for the visualization of cyclone simulations. The core application of Insight is the provision of the novel segmentation algorithm for the efficient detection and tracking of 3D features in large sets of atmospheric data, as well as for the precise localization of the occurring genesis, lysis, merging and splitting events. Data segmentation usually leads to a significant reduction of the size of the considered data. This enables a practical visualization of the data, statistical analyses of the features and their events, and the manual or automatic detection of interesting situations for subsequent detailed investigation. The concepts of the novel algorithm, its technical realization, and several extensions for avoiding under- and over-segmentation are discussed. As example applications, this thesis covers the setup and the results of the segmentation of upper-tropospheric jet streams and cyclones as full 3D objects. Finally, IWAL is presented, which is a web application for providing an easy interactive access to meteorological data visualizations, primarily aimed at students. As a web application, the needs to retrieve all input data sets and to install and handle complex visualization tools on a local machine are avoided. The main challenge in the provision of customizable visualizations to large numbers of simultaneous users was to find an acceptable trade-off between the available visualization options and the performance of the application. Besides the implementational details, benchmarks and the results of a user survey are presented.

Weighted geometric mean of large-scale matrices: numerical analysis and algorithms

Computing the weighted geometric mean of large sparse matrices is an operation that tends to become rapidly intractable, when the size of the matrices involved grows. However, if we are not interested in the computation of the matrix function itself, but just in that of its product times a vector, the problem turns simpler and there is a chance to solve it even when the matrix mean would actually be impossible to compute. Our interest is motivated by the fact that this calculation has some practical applications, related to the preconditioning of some operators arising in domain decomposition of elliptic problems. In this thesis, we explore how such a computation can be efficiently performed. First, we exploit the properties of the weighted geometric mean and find several equivalent ways to express it through real powers of a matrix. Hence, we focus our attention on matrix powers and examine how well-known techniques can be adapted to the solution of the problem at hand. In particular, we consider two broad families of approaches for the computation of f(A) v, namely quadrature formulae and Krylov subspace methods, and generalize them to the pencil case f(A\B) v. Finally, we provide an extensive experimental evaluation of the proposed algorithms and also try to assess how convergence speed and execution time are influenced by some characteristics of the input matrices. Our results suggest that a few elements have some bearing on the performance and that, although there is no best choice in general, knowing the conditioning and the sparsity of the arguments beforehand can considerably help in choosing the best strategy to tackle the problem.

Are there genetic breaks between Atlantic and Pacific Yellowfin tuna (Thunnus albacares) populations? A preliminary study based on microsatellites gene variation

Yellowfin tuna (Thunnus albacares, YFT, Bonnaterre 1788) is one of the most important market tuna species in the world. The high mortality of juveniles is in part caused by their bycatch. Indeed, if unregulated, it could permanently destabilize stocks health. For this reason investigating and better knowing the stock boundaries represent a crucial concern. Aim of this thesis was to preliminary investigate the YFT population structure within and between Atlantic and Pacific Oceans through the analysis of genetic variation at eight microsatellite loci and assess the occurrence of barriers to the gene flow between Oceans. For this propouse we collected 4 geographical samples coming from Atlantic and Pacific Ocean and selected a panel of 8 microsatellites loci developped by Antoni et al., (2014). Samples 71-2-Y and 77-2-Y, came from rispectively west central pacific ocean (WCPO) and east central pacific ocean (ECPO), instead samples 41-1-Y and 34-2-Y derive from west central atlantic ocean (WCAO) and east central atlantic ocean (ECAO). Total 160 specimens were analyzed (40 per sample) and were carried out several genetic information as allele frequencies, allele number, allelic richness, HWE (using He and Ho) and pairwise Fst genetic distance. Results obtained, may support the panmictic theory of this species, only one of pairwise Fst obtained is statistically significant (Fst= 0.00927; pV= 0.00218) between 41-1-Y and 71-2-Y samples. Results suggest low genetic differentiation and consequent high level of gene flow between Atlantic and Pacific populations. Furthermore, we performed an analysis of molecular taxonomy through the use of ATCO (the flaking region between ATPse6 and cytochrome oxidase subunit III genes mt DNA, to discriminate within the gener Thunnus two of the related species (Yellofin and bigeye tuna) according with their difficult recognition at certain size (<40 cm). ATCO analysis in this thesis, has provided strong discriminate evidence between the target species proving to be one of the most reliable genetic tools capable to indagate within the genus Thunnus. Thus, our study has provided useful information for possible use of this protocol for conservation plans and management of this fish stocks.

Neocartilage formation in 1 g, simulated, and microgravity environments: implications for tissue engineering

The aim of this study was to analyze and compare the deposition of cartilage-specific extracellular matrix components and cellular organization in scaffold-free neocartilage produced in microgravity and simulated microgravity.

The genetic basis of craniofacial and dental abnormalities

The embryonic head development, including the formation of dental structures, is a complex and delicate process guided by specific genetic programs. Genetic changes and environmental factors can disturb the execution of these programs and result in abnormalities in orofacial and dental structures. Orofacial clefts and hypodontia/ oligodontia are examples of such abnormalities frequently seen in dental clinics. An insight into the mechanisms and genes involved in the formation of orofacial and dental structures has been gradually gained by genetic analysis of families and by the use of experimental vertebrate models such as the mouse and chick models. The development of novel clinical therapies for orofacial and dental pathological conditions depends very much on a detailed knowledge of the molecular and cellular processes that are involved in head formation.

Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys

Hatchery fish stocking for stock enhancement has been operated at a massive and global scale. However, the use of hatchery fish as a means of stock enhancement is highly controversial, and little is known about its effects on wild stock and consequences for stock enhancement. Here we review the scientific literature on this subject in order to address a fundamental - question is hatchery stocking a help or harm for wild stock and stock enhancement? We summarized 266 peer-reviewed papers that were published in the last 50 years, which describe empirical case studies on ecology and genetics of hatchery stocks and their effects on stock enhancement. Specifically, we asked whether hatchery stock and wild stock differed in fitness and the level of genetic variation, and whether stocking affected population abundance. Seventy studies contained comparisons between hatchery and wild stocks, out of which 23 studies showed significantly negative effects of hatchery rearing on the fitness of stocked fish, and 28 studies showed reduced genetic variation in hatchery populations. None of these studies suggested a positive genetic effect on the fitness of hatchery-reared individuals after release. These results suggest that negative effects of hatchery rearing are not just a concern but undeniably present in many aquaculture species. In a few cases, however, no obvious effect of hatchery rearing was observed, and a positive contribution of hatchery stock to the abundance of fish populations was indicated. These examples suggest that there is a chance to improve hatchery practices and mitigate the negative effects on wild stocks, although scientific data supporting the positive effect on stock enhancement are largely missing at this moment. Technically, microsatellite-based parentage assignments have been proven as a useful tool for the evaluation of reproductive fitness in natural settings, which is a key for stock enhancement by hatchery-based stocking. We discuss implications of these results, as well as their limitations and future directions. (C) 2010 Elsevier B.V. All rights reserved.

A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and UST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (5 Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements UST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Developmental Brain Dysfunction: Revival and Expansion of Old Concepts Based on New Genetic Evidence

Neurodevelopmental disorders can be caused by many different genetic abnormalities that are individually rare but collectively common. Specific genetic causes, including certain copy number variants and single-gene mutations, are shared among disorders that are thought to be clinically distinct. This evidence of variability in the clinical manifestations of individual genetic variants and sharing of genetic causes among clinically distinct brain disorders is consistent with the concept of developmental brain dysfunction, a term we use to describe the abnormal brain function underlying a group of neurodevelopmental and neuropsychiatric disorders and to encompass a subset of various clinical diagnoses. Although many pathogenic genetic variants are currently thought to be variably penetrant, we hypothesise that when disorders encompassed by developmental brain dysfunction are considered as a group, the penetrance will approach 100%. The penetrance is also predicted to approach 100% when the phenotype being considered is a specific trait, such as intelligence or autistic-like social impairment, and the trait could be assessed using a continuous, quantitative measure to compare probands with non-carrier family members rather than a qualitative, dichotomous trait and comparing probands with the healthy population. Copyright 2013 Elsevier Ltd. All rights reserved.

High specificity of line-immunoassay based algorithms for recent HIV-1 infection independent of viral subtype and stage of disease

Background Serologic testing algorithms for recent HIV seroconversion (STARHS) provide important information for HIV surveillance. We have shown that a patient's antibody reaction in a confirmatory line immunoassay (INNO-LIATM HIV I/II Score, Innogenetics) provides information on the duration of infection. Here, we sought to further investigate the diagnostic specificity of various Inno-Lia algorithms and to identify factors affecting it. Methods Plasma samples of 714 selected patients of the Swiss HIV Cohort Study infected for longer than 12 months and representing all viral clades and stages of chronic HIV-1 infection were tested blindly by Inno-Lia and classified as either incident (up to 12 m) or older infection by 24 different algorithms. Of the total, 524 patients received HAART, 308 had HIV-1 RNA below 50 copies/mL, and 620 were infected by a HIV-1 non-B clade. Using logistic regression analysis we evaluated factors that might affect the specificity of these algorithms. Results HIV-1 RNA <50 copies/mL was associated with significantly lower reactivity to all five HIV-1 antigens of the Inno-Lia and impaired specificity of most algorithms. Among 412 patients either untreated or with HIV-1 RNA ≥50 copies/mL despite HAART, the median specificity of the algorithms was 96.5% (range 92.0-100%). The only factor that significantly promoted false-incident results in this group was age, with false-incident results increasing by a few percent per additional year. HIV-1 clade, HIV-1 RNA, CD4 percentage, sex, disease stage, and testing modalities exhibited no significance. Results were similar among 190 untreated patients. Conclusions The specificity of most Inno-Lia algorithms was high and not affected by HIV-1 variability, advanced disease and other factors promoting false-recent results in other STARHS. Specificity should be good in any group of untreated HIV-1 patients.

Detecting and resolving position-dependent temperature effects in real-time quantitative polymerase chain reaction

Real-time quantitative polymerase chain reaction (qPCR) depends on precise temperature control of the sample during cycling. In the current study, we investigated how temperature variation in plate-based qPCR instruments influences qPCR results. Temperature variation was measured by amplicon melting analysis as a convenient means to assess well-to-well differences. Multiple technical replicates of several SYBR Green I-based qPCR assays allowed correlation of relative well temperature to quantification cycle. We found that inadequate template denaturation results in an inverse correlation and requires increasing the denaturation temperature, adding a DNA destabilizing agent, or pretreating with a restriction enzyme. In contrast, inadequate primer annealing results in a direct correlation and requires lowering the annealing temperature. Significant correlations were found in 18 of 25 assays. The critical nature of temperature-dependent effects was shown in a blinded study of 29 patients for the diagnosis of Prader-Willy and Angelman syndromes, where eight diagnoses were incorrect unless temperature-dependent effects were controlled. A method to detect temperature-dependent effects by pairwise comparisons of replicates in routine experiments is presented and applied. Systematic temperature errors in qPCR instruments can be recognized and their effects eliminated when high precision is required in quantitative genetic diagnostics and critical complementary DNA analyses.

Genetic diversity of EBV-encoded LMP1 in the Swiss HIV Cohort Study and implication for NF-Κb activation

Epstein-Barr virus (EBV) is associated with several types of cancers including Hodgkin's lymphoma (HL) and nasopharyngeal carcinoma (NPC). EBV-encoded latent membrane protein 1 (LMP1), a multifunctional oncoprotein, is a powerful activator of the transcription factor NF-κB, a property that is essential for EBV-transformed lymphoblastoid cell survival. Previous studies reported LMP1 sequence variations and induction of higher NF-κB activation levels compared to the prototype B95-8 LMP1 by some variants. Here we used biopsies of EBV-associated cancers and blood of individuals included in the Swiss HIV Cohort Study (SHCS) to analyze LMP1 genetic diversity and impact of sequence variations on LMP1-mediated NF-κB activation potential. We found that a number of variants mediate higher NF-κB activation levels when compared to B95-8 LMP1 and mapped three single polymorphisms responsible for this phenotype: F106Y, I124V and F144I. F106Y was present in all LMP1 isolated in this study and its effect was variant dependent, suggesting that it was modulated by other polymorphisms. The two polymorphisms I124V and F144I were present in distinct phylogenetic groups and were linked with other specific polymorphisms nearby, I152L and D150A/L151I, respectively. The two sets of polymorphisms, I124V/I152L and F144I/D150A/L151I, which were markers of increased NF-κB activation in vitro, were not associated with EBV-associated HL in the SHCS. Taken together these results highlighted the importance of single polymorphisms for the modulation of LMP1 signaling activity and demonstrated that several groups of LMP1 variants, through distinct mutational paths, mediated enhanced NF-κB activation levels compared to B95-8 LMP1.

Genetic variations in IL28B and allergic disease in children

Environmental changes affecting the relationship between the developing immune system and microbial exposure have been implicated in the epidemic rise of allergic disease in developed countries. While early developmental differences in T cell function are well-recognised, there is now emerging evidence that this is related to developmental differences in innate immune function. In this study we sought to examine if differences associated with innate immunity contribute to the altered immune programming recognised in allergic children. Here, we describe for the first time, the association of carriage of the T allele of the tagging single nucleotide polymorphism rs12979860 3 kb upstream of IL28B, encoding the potent innate immune modulator type III interferon lambda (IFN-λ3), and allergy in children (p = 0.004; OR 4.56). Strikingly, the association between rs12979860 genotype and allergic disease is enhanced in girls. Furthermore, carriage of the T allele at rs12979860 correlates with differences in the pro-inflammatory profile during the first five years of life suggesting this contributes to the key differences in subsequent innate immune development in children who develop allergic disease. In the context of rising rates of disease, these immunologic differences already present at birth imply very early interaction between genetic predisposition and prenatal environmental influences.

The quantitative genetic basis of offspring solicitation and parental response in a passerine bird with biparental care

The coevolution of parental investment and offspring solicitation is driven by partly different evolutionary interests of genes expressed in parents and their offspring. In species with biparental care, the outcome of this conflict ma!: be influenced by the sexual conflict over parental investment, Models for the resolution of such family conflicts have made so far untested assumptions about genetic variation and covariation in the parental resource provisioning response and the level of offspring solicitation. Using a combination of cross-fostering and begging playback experiments, we show that, in the great tit (Parus major), (i) the begging call intensity of nestlings depends on their common origin, suggesting genetic variation for this begging display, (ii) only mothers respond to begging calls by increased food provisioning, and (iii! the size of the parental response is positively related to the begging call intensity of nestlings in the maternal but not paternal line. This study indicates that genetic covariation, its differential expression in the maternal and paternal lines and/or early environmental and parental effects need to be taken into account when predicting the phenotypic outcome of the conflict over investment between genes expressed in each parent and the offspring. [References: 36]