Phylogeographic Analysis of HIV-1 Subtype C Dissemination in Southern Brazil

The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Parana). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianopolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Parana state). This analysis further suggested that Florianopolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r(2) = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades.

Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (1000 km) or restricted distributions. Most (80 ) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 ) and self-incompatible species (71 ) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 ). Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely distributed. This is, to a certain extent, similar to the geographical parthenogenesis pattern of temperate apomictics.

Possible Host Adaptation as an Evolution Factor of Cowpea aphid-borne mosaic virus Deduced by Coat Protein Gene Analysis

Cowpea aphid-borne mosaic virus (CABMV) causes major diseases in cowpea and passion flower plants in Brazil and also in other countries. CABMV has also been isolated from leguminous species including, Cassia hoffmannseggii, Canavalia rosea, Crotalaria juncea and Arachis hypogaea in Brazil. The virus seems to be adapted to two distinct families, the Passifloraceae and Fabaceae. Aiming to identify CABMV and elucidate a possible host adaptation of this virus species, isolates from cowpea, passion flower and C.hoffmannseggii collected in the states of Pernambuco and Rio Grande do Norte were analysed by sequencing the complete coat protein genes. A phylogenetic tree was constructed based on the obtained sequences and those available in public databases. Major Brazilian isolates from passion flower, independently of the geographical distances among them, were grouped in three different clusters. The possible host adaptation was also observed in fabaceous-infecting CABMV Brazilian isolates. These host adaptations possibly occurred independently within Brazil, so all these clusters belong to a bigger Brazilian cluster. Nevertheless, African passion flower or cowpea-infecting isolates formed totally different clusters. These results showed that host adaptation could be one factor for CABMV evolution, although geographical isolation is a stronger factor.

Physical-chemical, thermal, and functional properties of achira (Canna indica L.) flour and starch from different geographical origin

Achira (Canna indica L.) is a plant native to the Andes in South America, a starchy source, and its cultivation has expanded to different tropical countries, like Brazil. In order to evaluate the potential of this species, starch and flours with different particle size were obtained from Brazilian achira rhizomes. Proximal analyses, size distribution, SEM, swelling power, solubility, DSC, XRD analysis, and FTIR were performed for characterization of these materials. Flours showed high dietary fiber content (16.532.2% db) and high concentration of starch in the case of the smaller particle size fraction. Significant differences in protein and starch content, swelling power, solubility, and thermal properties were observed between the Brazilian and the Colombian starch. All the studied materials displayed the B-type XRD pattern with relative crystallinity of 20.1% for the flour and between 27.0 and 28.0% for the starches. Results showed that the starch and flour produced from achira rhizomes have great technological potential for use as functional ingredient in the food industry.

Suicide rates and income in São Paulo and Brazil: a temporal and spatial epidemiologic analysis from 1996 to 2008

Abstract Background In a classical study, Durkheim noted a direct relation between suicide rates and wealth in the XIX century France. Since that time, several studies have verified this relationship. It is known that suicide rates are associated with income, although the direction of this association varies worldwide. Brazil presents a heterogeneous distribution of income and suicide across its territory; however, evaluation for an association between these variables has shown mixed results. We aimed to evaluate the relationship between suicide rates and income in Brazil, State of São Paulo (SP), and City of SP, considering geographical area and temporal trends. Methods Data were extracted from the National and State official statistics departments. Three socioeconomic areas were considered according to income, from the wealthiest (area 1) to the poorest (area 3). We also considered three regions: country-wide (27 Brazilian States and 558 Brazilian micro-regions), state-wide (645 counties of SP State), and city-wide (96 districts of SP city). Relative risks (RR) were calculated among areas 1, 2, and 3 for all regions, in a cross-sectional approach. Then, we used Joinpoint analysis to explore the temporal trends of suicide rates and SaTScan to investigate geographical clusters of high/low suicide rates across the territory. Results Suicide rates in Brazil, the State of SP, and the city of SP were 6.2, 6.6, and 5.4 per 100,000, respectively. Taking suicide rates of the poorest area (3) as reference, the RR for the wealthiest area was 1.64, 0.88, and 1.65 for Brazil, State of SP, and city of SP, respectively (p for trend <0.05 for all analyses). Spatial cluster of high suicide rates were identified at Brazilian southern (RR = 2.37), state of SP western (RR = 1.32), and city of SP central (RR = 1.65) regions. A direct association between income and suicide were found for Brazil (OR = 2.59) and the city of SP (OR = 1.07), and an inverse association for the state of SP (OR = 0.49). Conclusions Temporospatial analyses revealed higher suicide rates in wealthier areas in Brazil and the city of SP and in poorer areas in the State of SP. We further discuss the role of socioeconomic characteristics for explaining these discrepancies and the importance of our findings in public health policies. Similar studies in other Brazilian States and developing countries are warranted.

A three-pronged approach to social business: a Brazilian multi-case analysis

Social businesses present a new paradigm to capitalism, in which private companies, non-profit organizations and civil society create a new type of business with the main objective of solving social problems with financial sustainability and efficiency through market mechanisms. As any new phenomenon, different authors conceptualize social businesses with distinct views. This article aims to present and characterize three different perspectives of social business definitions: the European, the American and that of the emerging countries. Each one of these views was illustrated by a different Brazilian case. We conclude with the idea that all the cases have similar characteristics, but also relevant differences that are more than merely geographical. The perspectives analyzed in this paper provide an analytical framework for understanding the field of social businesses. Moreover, the cases demonstrate that in the Brazilian context the field of social business is under construction and that as such it draws on different conceptual influences to deal with a complex and challenging reality.

Comparative analysis of the corps en cerise in several species of Laurencia (Ceramiales, Rhodophyta) from the Atlantic Ocean

Different species of Laurencia have proven to be a rich source of natural products yielding interesting bioactive halogenated secondary metabolites, such as terpenoids and acetogenins. It is shown that such compounds are accumulated in the spherical, reniform to claviform refractive inclusions called corps en cerise (CC), which are intensively osmiophilic and located mainly in the cortical cells of the thalli and also in trichoblast cells. Up to now, it was believed that CC were present only in these two kinds of cells. Recently, however, a species of Laurencia, L. marilzae, with CC in all cells of the thallus, i.e., cortical, medullary, including the pericentral and axial cells, as well as in the trichoblasts, was described from the Canary Islands, and subsequently also reported to Brazil and Mexico. Within the Laurencia complex, only Laurencia species produce CC. Since the species of Laurencia are targets of interest for the prospection of bioactive substances due to their potential antibacterial, antifungal, anticholinesterasic, antileishmanial, cytotoxic, and antioxidant activities, the present paper carries out a comparative analysis of the corps en cerise in several species of Laurencia from the Atlantic Ocean to obtain basic information that can support natural product bioprospection projects. Our results show that the number and size of the CC are constant within a species, independent of the geographical distribution, corroborating their use for taxonomical purposes to differentiate groups of species that present a lower number from those that have a higher number. In this regard, there was a tendency for the number of CC to be higher in some species of Laurencia from the Canary Islands. The presence of CC can also be used to distinguish species in which these organelles are present in all cells of the thallus from those in which CC are restricted to the cortical cells. Among the species analyzed, L. viridis displayed the most varied secondary metabolites composition, such as sesquiterpenes, diterpenes, triterpenes, all of which showed potent antiviral, cytotoxic, and antitumoral activities, including protein phosphatase type 2A (PP2A) inhibitory effects.

Isolation of Microsporum gypseum in soil samples from different geographical regions of Brazil, evaluation of the extracellular proteolytic enzymes activities (keratinase and elastase) and molecular sequencing of selected strains

A survey of Microsporum gypseum was conducted in soil samples in different geographical regions of Brazil. The isolation of dermatophyte from soil samples was performed by hair baiting technique and the species were identified by morphology studies. We analyzed 692 soil samples and the recuperating rate was 19.2%. The activities of keratinase and elastase were quantitatively performed in 138 samples. The sequencing of the ITS region of rDNA was performed in representatives samples. M. gypseum isolates showed significant quantitative differences in the expression of both keratinase and elastase, but no significant correlation was observed between these enzymes. The sequencing of the representative samples revealed the presence of two teleomorphic species of M. gypseum (Arthroderma gypseum and A. incurvatum). The enzymatic activities may play an important role in the pathogenicity and a probable adaptation of this fungus to the animal parasitism. Using the phenotypical and molecular analysis, the Microsporum identification and their teleomorphic states will provide a useful and reliable identification system.

Studies on the interaction of surfactants and neutral cyclodextrins by capillary electrophoresis. Application to chiral analysis

In the present study, mixed systems composed of SDS in the presence of neutral cyclodextrins were considered. Firstly, the effect of the CDs on the CMC of the surfactant was evaluated by CE experiments. Furthermore, a new CE approach based on electric current measurement was developed for the estimation of the stoichiometry as well as of the binding constants of SDS-CDs complexes. The results of these investigations were compared to those obtained with a different technique, electronic paramagnetic resonance (EPR). The obtained results suggested that methylated CDs, in particular (2,6-di-O-methyl)-beta-cyclodextrin (DM-beta-CD), strongly affect the micellization of SDS in comparison to the other studied CDs. This effect also paralleled the chiral CD-MEKC performance, as indicated by the enantioresolution of (+/-)-Catechin, which was firstly selected as a model compound representative of important chiral phytomarkers. Then a CD-MEKC system, composed of sodium dodecyl sulfate as surfactant (90 mM) and hydroxypropyl-beta-cyclodextrin (25 mM) as chiral selector, under acidic conditions (25 mM borate – phosphate buffer, pH 2.5) was applied to study the thermal epimerisation of epi-structured catechins, (-)-Epicatechin and (-)-Epigallocatechin, to non epi-structured (-)-Catechin and (-)-Gallocatechin. The latter compounds, being non-native molecules, were for the first time regarded as useful phytomarkers of tea sample degradation. The proposed method was applied to the analysis of more than twenty tea samples of different geographical origins (China, Japan, Ceylon), having undergone different storage conditions and manufacturing processes.

Business Clusters in Eastern Europe: Policy Analysis and Cluster Performance

Clusters have increasingly become an essential part of policy discourses at all levels, EU, national, regional, dealing with regional development, competitiveness, innovation, entrepreneurship, SMEs. These impressive efforts in promoting the concept of clusters on the policy-making arena have been accompanied by much less academic and scientific research work investigating the actual economic performance of firms in clusters, the design and execution of cluster policies and going beyond singular case studies to a more methodologically integrated and comparative approach to the study of clusters and their real-world impact. The theoretical background is far from being consolidated and there is a variety of methodologies and approaches for studying and interpreting this phenomenon while at the same time little comparability among studies on actual cluster performances. The conceptual framework of clustering suggests that they affect performance but theory makes little prediction as to the ultimate distribution of the value being created by clusters. This thesis takes the case of Eastern European countries for two reasons. One is that clusters, as coopetitive environments, are a new phenomenon as the previous centrally-based system did not allow for such types of firm organizations. The other is that, as new EU member states, they have been subject to the increased popularization of the cluster policy approach by the European Commission, especially in the framework of the National Reform Programmes related to the Lisbon objectives. The originality of the work lays in the fact that starting from an overview of theoretical contributions on clustering, it offers a comparative empirical study of clusters in transition countries. There have been very few examples in the literature that attempt to examine cluster performance in a comparative cross-country perspective. It adds to this an analysis of cluster policies and their implementation or lack of such as a way to analyse the way the cluster concept has been introduced to transition economies. Our findings show that the implementation of cluster policies does vary across countries with some countries which have embraced it more than others. The specific modes of implementation, however, are very similar, based mostly on soft measures such as funding for cluster initiatives, usually directed towards the creation of cluster management structures or cluster facilitators. They are essentially founded on a common assumption that the added values of clusters is in the creation of linkages among firms, human capital, skills and knowledge at the local level, most often perceived as the regional level. Often times geographical proximity is not a necessary element in the application process and cluster application are very similar to network membership. Cluster mapping is rarely a factor in the selection of cluster initiatives for funding and the relative question about critical mass and expected outcomes is not considered. In fact, monitoring and evaluation are not elements of the cluster policy cycle which have received a lot of attention. Bulgaria and the Czech Republic are the countries which have implemented cluster policies most decisively, Hungary and Poland have made significant efforts, while Slovakia and Romania have only sporadically and not systematically used cluster initiatives. When examining whether, in fact, firms located within regional clusters perform better and are more efficient than similar firms outside clusters, we do find positive results across countries and across sectors. The only country with negative impact from being located in a cluster is the Czech Republic.

Evolution of South African Bruniaceae: evidence from ecological and geographical investigations

The central aim of the present study was to analyse ecological and geographical mechanisms that led to the species diversity and distribution pattern of the South African (sub-) endemic Bruniaceae shown today. To answer the question if the endangerment of some species and the sometimes restricted distribution area is due to an incongruence of pollination and breeding system, pollinator observations and the breeding system were analysed. rnThe effectiveness of the plant-pollinator interactions should be reflected in the reproductive success wherefore fruit set analyses were carried out. The genetic constitution of distant and close-by populations along a spatial gradient should illuminate gene-flow or habitat isolation that could have led to the species diversity. Since niche-inhabitation could be shown in the present study, an overall biogeographical analysis illuminated the distribution pattern on family level and the geographical as well as ecological factors that led to species persistence. rnThe study illuminated that the plant-pollinator interactions and the breeding system are adaptations to the fynbos biome but can not be defined as factors that drove speciation or have tremendous influence on distribution of Bruniaceae. In fact the geography of South Africa with its fragmented landscape as well as close niche-inhabitation of co-occuring species is the reason for species diversity and the recent distribution.rn

Conservation genetics of European wildcat (Felis silvestris silvestris): a wide and integrating analysis protocol for admixture inferences and population structure

Introgression of domestic cat genes into European wildcat (Felis silvestris silvestris) populations and reduction of wildcats’ range in Europe, leaded by habitat loss and fragmentation, are considered two of the main conservation problems for this endangered feline. This thesis addressed the questions related with the artificial hybridization and populations’ fragmentation, using a conservation genetics perspective. We combined the use of highly polymorphic loci, Bayesian statistical inferences and landscape analyses tools to investigate the origin of the geographic-genetic substructure of European wildcats (Felis silvestris silvestris) in Italy and Europe. The genetic variability of microsatellites evidenced that European wildcat populations currently distributed in Italy differentiated in, and expanded from two distinct glacial refuges during the Last Glacial Maximum. The genetic and geographic substructure detected between the eastern and western sides of the Apennine ridge, resulted by adaptation to specific ecological conditions of the Mediterranean habitats. European wildcat populations in Europe are strongly structured into 5 geographic-genetic macro clusters corresponding to: the Italian peninsular & Sicily; Balkans & north-eastern Italy; Germany eastern; central Europe; and Iberian Peninsula. Central European population might have differentiated in the extra-Mediterranean Würm ice age refuge areas (Northern Alps, Carpathians, and the Bulgarian mountain systems), while the divergence among and within the southern European populations might have resulted by the Pleistocene bio geographical framework of Europe, with three southern refugia localized in the Balkans, Italian Peninsula and Iberia Peninsula. We further combined the use of most informative autosomal SNPs with uniparental markers (mtDNA and Y-linked) for accurately detecting parental genotypes and levels of introgressive hybridization between European wild and domestic cats. A total of 11 hybrids were identified. The presence of domestic mitochondrial haplotypes shared with some wild individuals led us to hypnotize the possibility that ancient introgressive events might have occurred and that further investigation should be recommended.

Stock boundaries of Parapenaeus longirostris (Lucas, 1846) populations in the Italian seas: Development of genomic 2b-RAD markers and biological variation analysis.

This thesis is developed in the contest of Ritmare project WP1, which main objective is the development of a sustainable fishery through the identification of populations boundaries in commercially important species in Italian Seas. Three main objectives are discussed in order to help reach the main purpose of identification of stock boundaries in Parapenaeus longirostris: 1 -Development of a representative sampling design for Italian seas; 2 -Evaluation of 2b-RAD protocol; 3 -Investigation of populations through biological data analysis. First of all we defined and accomplished a sampling design which properly represents all Italian seas. Then we used information and data about nursery areas distribution, abundance of populations and importance of P. longirostris in local fishery, to develop an experimental design that prioritize the most important areas to maximize the results with actual project funds. We introduced for the first time the use of 2b-RAD on this species, a genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Thanks to this method we were able to move from genetics to the more complex genomics. In order to proceed with 2b-RAD we performed several tests to identify the best DNA extraction kit and protocol and finally we were able to extract 192 high quality DNA extracts ready to be processed. We tested 2b-RAD with five samples and after high-throughput sequencing of libraries we used the software “Stacks” to analyze the sequences. We obtained positive results identifying a great number of SNP markers among the five samples. To guarantee a multidisciplinary approach we used the biological data associated to the collected samples to investigate differences between geographical samples. Such approach assures continuity with other project, for instance STOCKMED, which utilize a combination of molecular and biological analysis as well.

Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.

Does published orthodontic research account for clustering effects during statistical data analysis?

In orthodontics, multiple site observations within patients or multiple observations collected at consecutive time points are often encountered. Clustered designs require larger sample sizes compared to individual randomized trials and special statistical analyses that account for the fact that observations within clusters are correlated. It is the purpose of this study to assess to what degree clustering effects are considered during design and data analysis in the three major orthodontic journals. The contents of the most recent 24 issues of the American Journal of Orthodontics and Dentofacial Orthopedics (AJODO), Angle Orthodontist (AO), and European Journal of Orthodontics (EJO) from December 2010 backwards were hand searched. Articles with clustering effects and whether the authors accounted for clustering effects were identified. Additionally, information was collected on: involvement of a statistician, single or multicenter study, number of authors in the publication, geographical area, and statistical significance. From the 1584 articles, after exclusions, 1062 were assessed for clustering effects from which 250 (23.5 per cent) were considered to have clustering effects in the design (kappa = 0.92, 95 per cent CI: 0.67-0.99 for inter rater agreement). From the studies with clustering effects only, 63 (25.20 per cent) had indicated accounting for clustering effects. There was evidence that the studies published in the AO have higher odds of accounting for clustering effects [AO versus AJODO: odds ratio (OR) = 2.17, 95 per cent confidence interval (CI): 1.06-4.43, P = 0.03; EJO versus AJODO: OR = 1.90, 95 per cent CI: 0.84-4.24, non-significant; and EJO versus AO: OR = 1.15, 95 per cent CI: 0.57-2.33, non-significant). The results of this study indicate that only about a quarter of the studies with clustering effects account for this in statistical data analysis.