Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pair-wise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0-4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation. Copyright (C) 2012 S. Karger AG, Basel

Social anxiety and negative early life events in university students

INTRODUCTION: There is substantial evidence regarding the impact of negative life events during childhood on the aetiology of psychiatric disorders. We examined the association between negative early life events and social anxiety in a sample of 571 Spanish University students. METHODS: In a cross-sectional survey conducted in 2007, we collected data through a semistructured questionnaire of sociodemographic variables, personal and family psychiatric history, and substance abuse. We assessed the five early negative life events: (i) the loss of someone close, (ii) emotional abuse, (iii) physical abuse, (iv) family violence, and (v) sexual abuse. All participants completed the Liebowitz Social Anxiety Scale. RESULTS: Mean (SD) age was 21 (4.5), 75% female, LSAS score was 40 (DP = 22), 14.2% had a psychiatric family history and 50.6% had negative life events during childhood. Linear regression analyses, after controlling for age, gender, and family psychiatric history, showed a positive association between family violence and social score (p = 0.03). None of the remaining stressors produced a significant increase in LSAS score (p > 0.05). CONCLUSION: University students with high levels of social anxiety presented higher prevalence of negative early life events. Thus, childhood family violence could be a risk factor for social anxiety in such a population.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Genetic structure and connectivity between populations of two common Mediterranean sessile invertebrates

Population genetic and phylogeography of two common mediterranean species were studied in 10 localities located on the coasts of Toscana, Puglia and Calabria. The aim of the study was to verify the extent of genetic breaks, in areas recognized as boundaries between Mediterranean biogeographic sectors. From about 100 sequences obtained from the mitochondrial Cytochrome Oxidase subunit I (COI) gene of Halocynthia papillosa and Hexaplex trunculus genetic diversity, genetic structure at small and large distances and demographic history of both specieswere analyzed. No evidences of genetic breaks were found for the two species in Toscana and Puglia. The genetic structure of H. trunculus evidences the extent of a barrier to gene flow localized in Calabria, which could be represented by the Siculo-Tunisian Strait and the Strait of Messina. The observed patterns showed similar level of gene flow at small distances in both species, although the two species have different larval ecology. These results suggest that other factors, such as currents, local dynamics and seasonal temperatures, influence the connectivity along the Italian peninsula. The geographic distribution of the haplotypes shows that H. papillosacould represent a single genetic pool in expansion, whereas H. trunculus has two distinct genetic pools in expansion. The demographic pattern of the two species suggests that Pleistocene sea level oscillations, in particular of the LGM, may have played a key role in shaping genetic structure of the two species. This knowledge provides basic information, useful for the definition of management plans, or for the design of a network of marine protected areas along the Italian peninsula.

Novel investigation methods in Computational Social Dynamics and Complex Systems

In this thesis the evolution of the techno-social systems analysis methods will be reported, through the explanation of the various research experience directly faced. The first case presented is a research based on data mining of a dataset of words association named Human Brain Cloud: validation will be faced and, also through a non-trivial modeling, a better understanding of language properties will be presented. Then, a real complex system experiment will be introduced: the WideNoise experiment in the context of the EveryAware european project. The project and the experiment course will be illustrated and data analysis will be displayed. Then the Experimental Tribe platform for social computation will be introduced . It has been conceived to help researchers in the implementation of web experiments, and aims also to catalyze the cumulative growth of experimental methodologies and the standardization of tools cited above. In the last part, three other research experience which already took place on the Experimental Tribe platform will be discussed in detail, from the design of the experiment to the analysis of the results and, eventually, to the modeling of the systems involved. The experiments are: CityRace, about the measurement of human traffic-facing strategies; laPENSOcosì, aiming to unveil the political opinion structure; AirProbe, implemented again in the EveryAware project framework, which consisted in monitoring air quality opinion shift of a community informed about local air pollution. At the end, the evolution of the technosocial systems investigation methods shall emerge together with the opportunities and the threats offered by this new scientific path.

First assessment on genetic structure and phylogeography of Mediterranean blue shark (prionace glauca, L. 1758) population using mitochondrial gene variation: a comparison with the Atlantic.

The blue shark, Prionace glauca, is one of the most vagile shark species worldwide distributed. The particular body shape allows blue sharks make transoceanic movements, leading to a circumglobal distribution. Due to its reproductive cycle, an extraordinarily high number of specimens is globally registered but, even if it is still a major bycatch of longline fishery rather than a commercial target, it is characterized by a high vulnerability. In this perspective it is important to increase the amount of informations regarding its population extent in the different worldwide areas, evaluating the possible phylogeographic patterns between different locations. This study, included in the "MedBlueSGen" European project, aims exactly at filling a gap in knowledges regarding the genetic population structure of the Mediterranean blue sharks, which has never been investigated before, with a comparison with the North-Eastern Atlantic blue shark population. To reach this objective, we used a dataset of samples from different Mediterranean areas implementing it with some samples from North-Eastern Atlantic. Analyzing the variability of the two mitochondrial markers control region and cytochrome b, with the design of new species-specific primer pairs, we assessed the mitochondrial genetic structure of Mediterranean and North-Eastern Atlantic samples, focusing on the analysis of their possible connectivity, and we tried to reconstruct their demographic history and population size. Data analyses highlighted the absence of a genetic structuring within the Mediterranean and among it and North-Eastern Atlantic, suggesting that the Strait of Gibraltar doesn't represent a phylogeographic barrier. These results are coherent to what has been found in similar investigations on other worldwide blue shark populations. Analysis of the historical demographic trend revealed a general stable pattern for the cytochrome-b and a slightly population expansion for the control region marker.

Caregivers' Social Capital and Satisfaction with their Children's Service Providers

The authors examine children's access to and caregiver's satisfaction with organizations that provide leisure time activities for children on Saturdays. The authors argue that access and satisfaction are a function of familie's financial, cultural and social capital. Using data on 1,036 households in the Phoenix metropolitan area in 2003-04, the authors found that families' financial and cultural capital affected whether or not children participate din activities organized by organizations, but family ties to the organization directly (e.g., either worked there, volunteered, donated) resulted in caregivers being more satisfied with the services. The authors also found that the benefits of network closure (caregivers knowing the parents of other children on site) were greater the riskier the activities of the child (e.g., sports or cheerleading). Contrary to the authors expectations, having family or friends in the area did not affect caregiver's satisfaction with the child's provider.

Capitals and capabilities: linking structure and agency to reduce health inequalities

While empirical evidence continues to show that low socio-economic position is associated with less likely chances of being in good health, our understanding of why this is so remains less than clear. In this paper we examine the theoretical foundations for a structure-agency approach to the reduction of social inequalities in health. We use Max Weber's work on lifestyles to provide the explanation for the dualism between life chances (structure) and choice-based life conduct (agency). For explaining how the unequal distribution of material and non-material resources leads to the reproduction of unequal life chances and limitations of choice in contemporary societies, we apply Pierre Bourdieu's theory on capital interaction and habitus. We find, however, that Bourdieu's habitus concept is insufficient with regard to the role of agency for structural change and therefore does not readily provide for a theoretically supported move from sociological explanation to public health action. We therefore suggest Amartya Sen's capability approach as a useful link between capital interaction theory and action to reduce social inequalities in health. This link allows for the consideration of structural conditions as well as an active role for individuals as agents in reducing these inequalities. We suggest that people's capabilities to be active for their health be considered as a key concept in public health practice to reduce health inequalities. Examples provided from an ongoing health promotion project in Germany link our theoretical perspective to a practical experience.

The Modernity of la Mode: a History of the French Revolution Through the Lens of Fashion, Culture, and Identity

In my thesis, I explore the cultural history of the French Revolution and its relation to the modern era which ensued. Many historians have studied the French Revolution as it relates to culture, the rise of modernity, and fashion. I combine the unique histories of all three of these aspects to reach an understanding of the history of the French Revolution and fashion’s role in bringing about change. In the majority of literature of costume history, discussion of fashion surrounds its reflective properties. Many historians conclude fashion as a reflection of the broader cultural shifts that occurred during the Revolution. I, on the other hand, propose that fashion is an active force in bringing out cultural change during this time. In exploring fashion as a historical motivator, I examine the aesthetic world of fashion from 1740 to 1815, the modern system of cultural dissemination of fashion through particular historical heroes, and the rise of “taste” and its relation to modern identity. Through aesthetics, culture, and identity, I argue that fashion is a decisive force of culture in that it creates a visual world through which ideas form and communicate.

Imaging Tectonic Plates - Structure and Deformation of North America

The outermost layer of the Earth is broken into tectonic plates whose motions cause earthquakes and volcanism. Much of what we know about the structure of these plates comes from studying the Earth's surface. Seismic waves recorded by the EarthScope Transportable Array, however, show us the internal structure of plates down to 200 km deep and help us understand the relationship between deep structure and the Earth's surface. EarthScope images for the western United States hint at the presence of the mid-depth discontinuities. To better understand these features, Dr. Lekic relates them to the geologic history of the west.

The coevolution of cooperation and dispersal in social groups and its implications for the emergence of multicellularity

Background Recent work on the complexity of life highlights the roles played by evolutionary forces at different levels of individuality. One of the central puzzles in explaining transitions in individuality for entities ranging from complex cells, to multicellular organisms and societies, is how different autonomous units relinquish control over their functions to others in the group. In addition to the necessity of reducing conflict over effecting specialized tasks, differentiating groups must control the exploitation of the commons, or else be out-competed by more fit groups. Results We propose that two forms of conflict – access to resources within groups and representation in germ line – may be resolved in tandem through individual and group-level selective effects. Specifically, we employ an optimization model to show the conditions under which different within-group social behaviors (cooperators producing a public good or cheaters exploiting the public good) may be selected to disperse, thereby not affecting the commons and functioning as germ line. We find that partial or complete dispersal specialization of cheaters is a general outcome. The propensity for cheaters to disperse is highest with intermediate benefit:cost ratios of cooperative acts and with high relatedness. An examination of a range of real biological systems tends to support our theory, although additional study is required to provide robust tests. Conclusion We suggest that trait linkage between dispersal and cheating should be operative regardless of whether groups ever achieve higher levels of individuality, because individual selection will always tend to increase exploitation, and stronger group structure will tend to increase overall cooperation through kin selected benefits. Cheater specialization as dispersers offers simultaneous solutions to the evolution of cooperation in social groups and the origin of specialization of germ and soma in multicellular organisms.

Enabling Access to Welfare Services - the Place of Social Solidarity and Dialogue

The welfare state in the UK presents immigrant communities with a set of institutions, which are potentially new and unknown. What is the best way to ensure that the questions of access to the welfare institutions are best managed? Trusting, understanding and feeling solidarity with the welfare state will obviously help with this problem. In order to shed light on this phenomenon, this paper presents a qualitative exploratory study dealing with elements of solidarity as perceived by members of the South Asian Community in the UK. Six indepth interviews with South Asian first generation immigrants who had never experienced mental health problems were conducted. They were asked questions about who their support networks would be in the event of them experiencing mental health problems. The thematic analysis of the interviews suggests that the respondents believed that solidarity and support ties are found to be present in families, within the south Asian community and also with welfare institutions. It is concluded that there although things are far from perfect, assimilation and integration based on dialogue is an observable positive aspect of mental health service provision in the UK.

Differences in Internet Usage - Social Inequality and Informal Education

In the public debate the internet is regarded as a central resource for knowledge and information. Associated with this is the idea that everyone is able and even expected to serve himself or herself according to his or her own needs via this medium. Since more and more services are also delivered online the internet seems to allow its users to enjoy specific advantages in dealing with their everyday life. However, using the internet is based on a range of preconditions. New results of empirical and theoretical research indicate the rise of a social divide in this context. Within the internet, different ways of use can be identified alongside social inequalities. Boundaries of the "real life" are mirrored in the virtual space e.g. in terms of forms of communification and spaces for appropriation. These are not only shaped by invidual preferences but particularly by social structures and processes. In the context of the broader debate on education it is stated that formal educational structures are to be completed by arrangements which are structured in informal respectively nonformal ways. Particularly the internet is suggested to play an important role in this respect. However, the phenomenon of digital inequality points to limitations consolidated by effects of economic, social, and cultural ressources: Economical resources affect opportunities of access, priorities of everyday life shape respective intentions of internet use, social relationships have an impact on the support structures available and ways of appropriation reproduce a specific understanding of informal education ("informelle Bildung"). This produces an early stratification of opportunities especially for the subsequent generation and may lead to extensive inequalities regarding the distribution of advantages in terms of education. Thus the capacity of the virtual space in terms of participatory opportunities and democratic potentials raises concerns of major relevance with respect to social and educational policy. From the perspective of different disciplines involved in these issues it is essential to clarify this question in an empirical as well as in a theoretical way and to make it utilizable for a future-orientied practice. This article discusses central questions regarding young people's internet use and its implications for informal education and social service delivery on the basis of empirical findings. It introduces a methodological approach for this particular perspective and illustrates that the phenomena of digital divide and digital inequality are as much created by social processes as by technical issues.

Governing the Local: Sovereignty, Social Governance and Community Safety

There has been much commentary about the re-ordering of the relations between nation state government, geographical territory, and populations in the advanced liberal democracies. This is seen as a product of: increasing demographic and cultural diversity due to legal and illegal migration; economic, cultural, and political global interdependence; footloose mobility of capital and the outsourcing of jobs to poorer countries; the growing power of international corporations and financial markets; and the growth of supra-national bodies like the European Union and The North Atlantic Free Trade Association, the World Trade Organisation, and (debatably), the UN. These developments are held to be associated with the gradual demise of the model of the increasingly secular nation state first crystallised by the Treaty of Westphalia in 1648. This conception provided a mutual, guarantee of states’ jurisdiction over territory and populations through their legitimated attempts to monopolise the use of force. Though, the relations between these states have always been asymmetrical and often challenged (Hunter 1998).