A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

Background: Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity. Results: The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data. Conclusion: After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.

HIV/AIDS: use of the ICF in Brazil and South Africa - comparative data from four cross-sectional studies

Introduction Human immunodeficiency virus (HIV) is a serious disease which can be associated with various activity limitations and participation restrictions. The aim of this paper was to describe how HIV affects the functioning and health of people within different environmental contexts, particularly with regard to access to medication. Method Four cross-sectional studies, three in South Africa and one in Brazil, had applied the International Classification of Functioning, Disability and Health (ICF) as a classification instrument to participants living with HIV. Each group was at a different stage of the disease. Only two groups had had continuing access to antiretroviral therapy. The existence of these descriptive sets enabled comparison of the disability experienced by people living with HIV at different stages of the disease and with differing access to antiretroviral therapy. Results Common problems experienced in all groups related to weight maintenance, with two-thirds of the sample reporting problems in this area. Mental functions presented the most problems in all groups, with sleep (50%, 92/185), energy and drive (45%, 83/185), and emotional functions (49%, 90/185) being the most affected. In those on long-term therapy, body image affected 93% (39/42) and was a major problem. The other groups reported pain as a problem, and those with limited access to treatment also reported mobility problems. Cardiopulmonary functions were affected in all groups. Conclusion Functional problems occurred in the areas of impairment and activity limitation in people at advanced stages of HIV, and more limitations occurred in the area of participation for those on antiretroviral treatment. The ICF provided a useful framework within which to describe the functioning of those with HIV and the impact of the environment. Given the wide spectrum of problems found, consideration could be given to a number of ICF core sets that are relevant to the different stages of HIV disease. (C) 2010 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.

The eager fight for supremacy in the online service industry: a comparative study of M&A activities: case studies of Apple, Google and Microsoft

A indústria de serviços online é caracterizada por um volume alto de Fusões e Aquisições no período de 2005 a 2015. As líderes de mercado, Apple, Google e Microsoft, incorporaram essa forma de crescimento inorgânico em suas estratégias corporativas. Essa tese examina as atividades de Fusões e Aquisições dessas três empresas. Consequentemente, ela tem foco em dois aspectos principais. Primeiro, existe o objetivo de saciar uma escassez na literatura acadêmica, no que se diz respeito ao estabelecimento de uma conexão entre a estratégia corporativa dessas empresas e as decisões tomadas de Fusões e Aquisições. Segundo, há também o objetivo de estimar possíveis futuros desenvolvimentos no setor. Através de uma análise de conteúdo qualitativa das publicações das empresas, relatórios de análise de mercado, e outros conteúdos de terceiros, estudos de caso foram desenvolvidos. Os resultados mostram o processo de posicionamento estratégico por parte da Apple, Google e Microsoft, dentro do mercado de serviços online, entre os anos de 2005 e 2015. As recorrentes fusões e aquisições são analisadas, no que se diz respeito as estratégias corporativas dessas empresas e a responsividade perante as atividades de seus competidores. Os resultados evidenciam atividades agressivas de Fusões e Aquisições em grupos estratégicos em comum entre as três empresas, especialmente no mercado de aparelhos de comunicação móvel e serviços de comunicação.

Comparative structural studies on Lys49-phospholipases A(2) from Bothrops genus reveal their myotoxic site

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparative biochemical studies of myotoxic phospholipase A(2) from Bothrops venom

Venoms from Bothrops jararacussu, Bothrops asper, Bothrops atrox, Bothrops pirajai, Bothrops moojeni, Bothrops alternatus and Bothrops (Bothriopsis) bilineata were fractionated using a simplified procedure based on ion-exchange chromatography on CM-Sepharose at pH 8.0 or reverse phase HPLC. The resulting elution profiles showed important differences in the myotoxin content of these venoms. The venoms from B. alternatus, B. atrox and Bothriopsis bilineata did not contain the major myotoxin found in the other venoms. The amino acid sequence of the first 50 residues of the N-terminal region of the PLA(2)-like myotoxins showed a homology of 90-96% with other bothropic myotoxins. All of the myotoxins isolated induced rat paw edema, increased the level of plasma creatine kinase and produced myonecrosis together with polymorphonuclear cell infiltration.

Comparative cytogenetic studies of Bufo ictericus, B. paracnemis (Amphibia, Anura) and an intermediate form in sympatry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparative cytogenetic studies of eleven species of the Tropidurus torquatus group (Sauria, Tropiduridae), with banding patterns

The chromosomes of 173 specimens representing eleven species of the Tropidurus torquatus group, from 33 localities in Brazil, were analysed after Giemsa staining, C-banding, NORs, and replication banding techniques. A karyotype with 2n = 36, including 12 macrochromosomes and 24 microchromosomes (12 M + 24 m), and sex determination of the XY:XX type were found in Tropidurus cocorobensis, T. erythrocephalus, T. etheridgei, T. hispidus, T. hygomi, T. montanus, T. mucujensis, T. oreadicus, and T. torquatus. The two other species, T. itambere and T. psammonastes, presented 2n = 36 (12 M + 23 m) karyotype only in females while males had 2n = 35 (12 M + 23 m), due to the sex determination of the X(1)X(2)Y:X(1)X(1)X(2)X(2) type. Other interspecific differences as well as some intraspecific variation regarding the NORs and C-banding patterns have been observed, mainly in the microchromosome set. on the contrary, the macrochromosomes were highly conservative. Although consistent karyotypic diversity occurred in the torquatus group, the cytogenetic data obtained up to now did not allow us to clarify the phylogenetic relationships of the species. Nevertheless, the geographical distribution of the distinct cytotypes in T. hispidus and T. torquatus suggested that more than one species might be involved in each case.

Comparative cytogenetic studies in species of the subfamily Callichthyinae (Teleostei: Siluriformes: Callichthyidae)

In the present study, the karyotype of three species (nine populations) of the Callichthyinae subfamily were investigated with the objective of better understanding the pattern of relationship among the genera that compose the subfamily. Among the four populations of Callichthys callichthys studied, two showed 2n=56 chromosomes and two 2n=58 chromosomes. Up to eight additional microchromosomes were observed in the sample from Marilia. The three populations of Hoplosternum littorale displayed the same number of chromosomes, 2n=60, and karyotypic constitution, 6M+2SM+52A. The two populations of Megalechis personata showed 2n=62 chromosomes and similar karyotypic formulae, 8M+54A and 6M+2SM+54A. Terminal Ag-NORs were found in one chromosome pair of C. callichthys, H. littorale, and M. personata from Itiquira, and in two pairs in M. personata from Rio Branco. The populations of C. callichthys showed C-band positive segments in centromeric and pericentromeric position and the populations of H. littorale and M. personata exhibited C-band positive segments in centromeric and/or interstitial position. Contrarily to the extensive chromosome rearrangements verified in the Corydoradinae subfamily, in the Callichthyinae subfamily a small number of changes seems to have occurred in its karyotypic evolution.

A comparative evaluation of the CF:CS and CRS models in Pb-210 chronological studies applied to hydrographic basins in Brazil

The Constant Flux: Constant Sedimentation (CF:CS) and Constant Rate of Supply (CRS) of unsupported/excess Pb-210 models have been applied to a Pb-210 data set providing of eighteen sediments profiles sampled at four riverine systems occurring in Brazil, South America: Corumbatai River basin (S1=Site 1, Sao Paulo State), Atibaia River basin (S2=Site 2, Sao Paulo State), Ribeirao dos Bagres basin (S3=Site 3, Sao Paulo State) and Amazon River mouth. (S4=Site 4, Amapa State). These sites were chosen for a comparative evaluation of the performance of the CF:CS and CRS models due to their pronounced differences on the geographical location, geological context, soil composition, biodiversity, climate, rainfall, and water flow regime, among other variable aspects. However, all sediments cores exhibited a common denominator consisting on a database built from the use of the same techniques for acquiring the sediments major chemical composition (SiO2, Al2O3, Na2O, K2O, CaO, MgO, Fe2O3, MnO, P2O5, TiO2 and LOI-Loss on Ignition) and unsupported/excess 210Pb activity data. In terms of sedimentation rates, the performance of the CRS model was better than that of the CF:CS model as it yielded values more compatible with those expected from field evidences. Under the chronological point of view, the CRS model always provided ages within the permitted range of the Pb-210-method in the studied sites, whereas the CF:CS model predicted some values above 150 years. The SiO2 content decreased in accordance with the LOI increase in all cores analyzed and such inverse relationship was also tracked in the SiO2-LOI curves of historical trends. The SiO2-LOI concentration fluctuations in sites S1 and S3 also coincided with some Cu and Cr inputs in the drainage systems. (C) 2014 Elsevier Ltd. All rights reserved.

Rural governance and livelihoods systems diversification in the Western Balkans: comparative case studies of Bosnia and Herzegovina, Montenegro and Serbia

Agriculture is still important for socio-economic development in rural areas of Bosnia, Montenegro and Serbia (BMS). However, for sustainable rural development rural economies should be diversified so attention should be paid also to off-farm and non-farm income-generating activities. Agricultural and rural development (ARD) processes and farm activity diversification initiatives should be well governed. The ultimate objective of this work is to explore linkages between ARD governance and rural livelihoods diversification in BMS. The thesis is based on an extended secondary data analysis and surveys. Questionnaires for ARD governance and coordination were sent via email to public, civil society and international organizations. Concerning rural livelihood diversification, the field questionnaire surveys were carried out in three rural regions of BMS. Results show that local rural livelihoods are increasingly diversified but a significant share of households are still engaged in agriculture. Diversification strategies have a chance to succeed taking into consideration the three rural regions’ assets. However, rural households have to tackle many problems for developing new income-generating activities such as the lack of financial resources. Weak business skills are also a limiting factor. Fully exploiting rural economy diversification potential in BMS requires many interventions including improving rural governance, enhancing service delivery in rural areas, upgrading rural people’s human capital, strengthening rural social capital and improving physical capital, access of the rural population to finance as well as creating a favourable and enabling legal and legislative environment fostering diversification. Governance and coordination of ARD policy design, implementation and evaluation is still challenging in the three Balkan countries and this has repercussions also on the pace of rural livelihoods diversification. Therefore, there is a strong and urgent need for mobilization of all rural stakeholders and actors through appropriate governance arrangements in order to foster rural livelihoods diversification and quality of life improvement.

Linking rural tourism to agriculture. Evidences from comparative case studies in Kosovo, Italy and Spain

Rural tourism has been widely promoted in the European Union as an effective measure counteracting economic and social challenges facing rural areas especially those with declining agriculture economies. Particularly its role is seen in provision and maintenance of public goods which are more and more demanded by the public and considered in the policymaking. In Kosovo, rural tourism has been developed through the support of the international organizations and private sector initiatives, with primary aim to generate additional income for rural households and sustainable management of natural and cultural resources. Anyhow, it could be stated that the use of territorial capital to enhance the quality of the tourist offer and undertake promotion at wider circles of people has not been well explored so far, particularly possible links with agriculture that would satisfy visitors demand. In this regard this research study analyzes involvement of local stakeholders and use of territorial capital to develop tourist offer in rural areas of Kosovo. Beside, study applies comparative approach with other two areas of the European Union, Appennino Bolognese in Italy and Alpujara in Spain, to understand and compare the process of rural tourism development and demand characteristics between Kosovo and these areas. A survey has been conducted in all three study areas with rural tourism visitors to understand their preferences for public and private goods and services when visiting rural areas and the role of agriculture in sustaining rural tourism. Results show that there is a potential to link rural tourism with agriculture in Kosovo, which would help in sustaining agriculture and add additional value to local food products, which in return would enhance the tourist offer and make it more attractive for the visitors but also for the farmers as an additional revenue generating sector.