A single multiplex SNaPshot reaction of 42 SNPs to classify admixture populations into mitochondrial DNA haplogroups

SNaPshot minisequencing reaction is in increasing use because of its fast detection of many polymorphisms in a single assay. In this work we described a highly sensitive single nucleotide polymorphisms (SNPs) typing method with detection of 42 mitochondrial DNA (mtDNA) SNPs in a single PCR and SNaPshot multiplex reaction in order to allow haplogroup classification in Latin American admixture population. We validated the panel typing 160 Brazilian individuals. DNA was extracted from blood spotted on filter paper using Chelex protocol. Forty SNPs were selected targeting haplogroup-specific mutations in Europeans, Africans and Asians (only precursors of Native Americans haplogroups A2, B2, C1, and D1) and two non-coding SNPs were chosen to increase the power of discrimination between individuals (SNPs positions 16,519 and 16,362). It was done using a modified version of a previously published multiplex SNaPshot minisequencing reaction established to resolve European haplogroups, adding SNPs targeting Africans (L0, L1, L2, L3, and L*) and Asians (A, B, C, and D) haplogroups based on SNPs described at PhyloTree.org build 2. PCR primers were designed using PerlPrimer software and checked with the Autodimer program. Thirty-three primer-pairs were used to amplify 42 SNPs. Using this panel, we were able to successfully classify 160 individuals into their correct haplogroups. Complete SNP profiles were obtained from 10. pg of total DNA. We conclude that it is possible to build and genotype more than 40 mtDNA SNPs in a single multiplex PCR and SNaPshot reaction, with sensitivity and reliability, resolving haplogroup classification in admixture populations. © 2011.

Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis

This study describes the comparison of three methods for genotyping of Mycobacterium tuberculosis, namely MIRU-VNTR (mycobacterial interspersed repetitive units-variable number of tandem repeats), spoligotyping and, for the first time, MLST (Multilocus Sequence Typing). In order to evaluate the discriminatory power of these methods, a total of 44 M. tuberculosis isolates obtained from sputum specimens of patients from Brazil were genotyped. Among the three methods, MLST showed the lowest discriminatory power compared to the other two techniques. MIRU-VNTR showed better discriminatory power when compared to spoligotyping, however, the combination of both methods provides the greatest level of discrimination and therefore this combination is the most useful genotyping tool to be applied to M. tuberculosis isolates. © 2013 Elsevier B.V.

Occurrence of mycobacteria in bovine milk samples from both individual and collective bulk tanks at farms and informal markets in the southeast region of Sao Paulo, Brazil

Background: Mycobacterium spp. is one of the most important species of zoonotic pathogens that can be transmitted from cattle to humans. The presence of these opportunistic, pathogenic bacteria in bovine milk has emerged as a public-health concern, especially among individuals who consume raw milk and related dairy products. To address this concern, the Brazilian control and eradication program focusing on bovine tuberculosis, was established in 2001. However, bovine tuberculosis continues to afflict approximately 1,3 percent of the cattle in Brazil. In the present study, 300 samples of milk from bovine herds, obtained from both individual and collective bulk tanks and informal points of sale, were cultured on Löwenstein-Jensen and Stonebrink media. Polymerase chain reaction (PCR)-based tests and restriction-enzyme pattern analysis were then performed on the colonies exhibiting phenotypes suggestive of Mycobacterium spp., which were characterized as acid-fast bacilli.Results: Of the 300 bovine milk samples that were processed, 24 were positively identified as Mycobacterium spp.Molecular identification detected 15 unique mycobacterial species: Mycobacterium bovis, M. gordonae, M. fortuitum, M. intracellulare, M. flavescens, M. duvalii, M. haemophilum, M. immunogenum, M. lentiflavum, M. mucogenicum, M. novocastrense, M. parafortuitum, M. smegmatis, M. terrae and M. vaccae. The isolation of bacteria from the various locations occurred in the following proportions: 9 percent of the individual bulk-tank samples, 7 percent of the collective bulk-tank samples and 8 percent of the informal-trade samples. No statistically significant difference was observed between the presence of Mycobacterium spp. in the three types of samples collected, the milk production profiles, the presence of veterinary assistance and the reported concerns about bovine tuberculosis prevention in the herds.Conclusion: The microbiological cultures associated with PCR-based identification tests are possible tools for the investigation of the presence of Mycobacterium spp. in milk samples. Using these methods, we found that the Brazilian population may be regularly exposed to mycobacteria by consuming raw bovine milk and related dairy products. These evidences reinforces the need to optimize quality programs of dairy products, to intensify the sanitary inspection of these products and the necessity of further studies on the presence of Mycobacterium spp. in milk and milk-based products. © 2013 Franco et al.; licensee BioMed Central Ltd.

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Scaling invariance of the diffusion coefficient in a family of two-dimensional Hamiltonian mappings

We consider a family of two-dimensional nonlinear area-preserving mappings that generalize the Chirikov standard map and model a variety of periodically forced systems. The action variable diffuses in increments whose phase is controlled by a negative power of the action and hence effectively uncorrelated for small actions, leading to a chaotic sea in phase space. For larger values of the action the phase space is mixed and contains a family of elliptic islands centered on periodic orbits and invariant Kolmogorov-Arnold-Moser (KAM) curves. The transport of particles along the phase space is considered by starting an ensemble of particles with a very low action and letting them evolve in the phase until they reach a certain height h. For chaotic orbits below the periodic islands, the survival probability for the particles to reach h is characterized by an exponential function, well modeled by the solution of the diffusion equation. On the other hand, when h reaches the position of periodic islands, the diffusion slows markedly. We show that the diffusion coefficient is scaling invariant with respect to the control parameter of the mapping when h reaches the position of the lowest KAM island. © 2013 American Physical Society.

Mean surface temperature prediction models for broiler chickens-a study of sensible heat flow

Body surface temperature can be used to evaluate thermal equilibrium in animals. The bodies of broiler chickens, like those of all birds, are partially covered by feathers. Thus, the heat flow at the boundary layer between broilers' bodies and the environment differs between feathered and featherless areas. The aim of this investigation was to use linear regression models incorporating environmental parameters and age to predict the surface temperatures of the feathered and featherless areas of broiler chickens. The trial was conducted in a climate chamber, and 576 broilers were distributed in two groups. In the first trial, 288 broilers were monitored after exposure to comfortable or stressful conditions during a 6-week rearing period. Another 288 broilers were measured under the same conditions to test the predictive power of the models. Sensible heat flow was calculated, and for the regions covered by feathers, sensible heat flow was predicted based on the estimated surface temperatures. The surface temperatures of the feathered and featherless areas can be predicted based on air, black globe or operative temperatures. According to the sensible heat flow model, the broilers' ability to maintain thermal equilibrium by convection and radiation decreased during the rearing period. Sensible heat flow estimated based on estimated surface temperatures can be used to predict animal responses to comfortable and stressful conditions. © 2013 ISB.

Experimental study of bottom feed updraft gasifier

The updraft biomass gasifiers currently available produce a gas with high tar content. For almost all downstream applications a substantial reduction of the tar concentration is required. The gravimetric tar concentration behavior in producer gas, obtained at a modified updraft fixed bed gasifier, was studied. The feedstock feeding system was modified respect to the traditional updraft gasification design in order to decrease the tar concentration in the producer gas; the material is feeding continuously through a conduit in the base of the reactor over the grate. The caloric power of the syngas obtained was slightly lower than the typical value for this type of reactor and the highest efficiency obtained for the woodchip gasification was 77%. The highest tar concentration obtained during the experiments was 1652.7 mg N m-3 during the first our of experiments, comparable with the smaller value reported for the updraft reactors, this value is reduced significantly after the stabilization of the gasification process in the reactor. The smaller value obtained was 21 mg N m-3. © 2013 Elsevier Ltd.

A comunicação das campanhas sociais na televisão: a leitura do jovem sobre o referendo da comercialização de armas de fogo e munição do Brasil

Pós-graduação em Comunicação - FAAC

Entre o porão e sótão: espaços de formação em The wives of Bath, de Susan Swan

Pós-graduação em Letras - FCLAS

Results of the International Comparison Program (ICP) 2011 for Latin America and the Caribbean

The International Comparison Programme (ICP) is a worldwide statistical project whose purpose is to collect comparative price data from a broad list or basket of products and to compile detailed values for spending-side gross domestic product (GDP) in order to calculate purchasing power parities (PPPs). Using PPPs, rather than market exchange rates, to convert macroeconomic aggregates aids comparison of production across economies and of the well-being of populations in real terms, insofar as they are compared on the basis of the purchasing power of each of the participant countries.

An assessment of the economic impact of climate change on the Agriculture, Health and Tourism sectors in Saint Lucia

This report analyses the agriculture, health and tourism sectors in Saint Lucia to assess the potential economic impacts of climate change on the sectors. The fundamental aim of this report is to assist with the development of strategies to deal with the potential impact of climate change in Saint Lucia. It also has the potential to provide essential input for identifying and preparing policies and strategies to help advance the Caribbean subregion closer to solving problems associated with climate change and attaining individual and regional sustainable development goals. Some of the key anticipated impacts of climate change for the Caribbean include elevated air and sea-surface temperatures, sea-level rise, possible changes in extreme events and a reduction in freshwater resources. The economic impact of climate change on the three sectors was estimated for the A2 and B2 IPCC scenarios until 2050. An evaluation of various adaptation strategies for each sector was also undertaken using standard evaluation techniques. The key subsectors in agriculture are expected to have mixed impacts under the A2 and B2 scenarios. Banana, fisheries and root crop outputs are expected to fall with climate change, but tree crop and vegetable production are expected to rise. In aggregate, in every decade up to 2050, these sub-sectors combined are expected to experience a gain under climate change with the highest gains under A2. By 2050, the cumulative gain under A2 is calculated as approximately US$389.35 million and approximately US$310.58 million under B2, which represents 17.93% and 14.30% of the 2008 GDP respectively. This result was unexpected and may well be attributed to the unavailability of annual data that would have informed a more robust assessment. Additionally, costs to the agriculture sector due to tropical cyclones were estimated to be $6.9 million and $6.2 million under the A2 and B2 scenarios, respectively. There are a number of possible adaptation strategies that can be employed by the agriculture sector. The most attractive adaptation options, based on the benefit-cost ratio are: (1) Designing and implementation of holistic water management plans (2) Establishment of systems of food storage and (3) Establishment of early warning systems. Government policy should focus on the development of these adaption options where they are not currently being pursued and strengthen those that have already been initiated, such as the mainstreaming of climate change issues in agricultural policy. The analysis of the health sector placed focus on gastroenteritis, schistosomiasis, ciguatera poisoning, meningococal meningitis, cardiovascular diseases, respiratory diseases and malnutrition. The results obtained for the A2 and B2 scenarios demonstrate the potential for climate change to add a substantial burden to the health system in the future, a factor that will further compound the country’s vulnerability to other anticipated impacts of climate change. Specifically, it was determined that the overall Value of Statistical Lives impacts were higher under the A2 scenario than the B2 scenario. A number of adaptation cost assumptions were employed to determine the damage cost estimates using benefit-cost analysis. The benefit-cost analysis suggests that expenditure on monitoring and information provision would be a highly efficient step in managing climate change and subsequent increases in disease incidence. Various locations in the world have developed forecasting systems for dengue fever and other vector-borne diseases that could be mirrored and implemented. Combining such macro-level policies with inexpensive micro-level behavioural changes may have the potential for pre-empting the re-establishment of dengue fever and other vector-borne epidemic cycles in Saint Lucia. Although temperature has the probability of generating significant excess mortality for cardiovascular and respiratory diseases, the power of temperature to increase mortality largely depends on the education of the population about the harmful effects of increasing temperatures and on the existing incidence of these two diseases. For these diseases it is also suggested that a mix of macro-level efforts and micro-level behavioural changes can be employed to relieve at least part of the threat that climate change poses to human health. The same principle applies for water and food-borne diseases, with the improvement of sanitation infrastructure complementing the strengthening of individual hygiene habits. The results regarding the tourism sector imply that the tourism climatic index was likely to experience a significant downward shift in Saint Lucia under the A2 as well as the B2 scenario, indicative of deterioration in the suitability of the island for tourism. It is estimated that this shift in tourism features could cost Saint Lucia about 5 times the 2009 GDP over a 40-year horizon. In addition to changes in climatic suitability for tourism, climate change is also likely to have important supply-side effects on species, ecosystems and landscapes. Two broad areas are: (1) coral reefs, due to their intimate link to tourism, and, (2) land loss, as most hotels tend to lie along the coastline. The damage related to coral reefs was estimated at US$3.4 billion (3.6 times GDP in 2009) under the A2 scenario and US$1.7 billion (1.6 times GDP in 2009) under the B2 scenario. The damage due to land loss arising from sea level rise was estimated at US$3.5 billion (3.7 times GDP) under the A2 scenario and US$3.2 billion (3.4 times GDP) under the B2 scenario. Given the potential for significant damage to the industry a large number of potential adaptation measures were considered. Out of these a short-list of 9 potential options were selected by applying 10 evaluation criteria. Using benefit-cost analyses 3 options with positive ratios were put forward: (1) increased recommended design speeds for new tourism-related structures; (2) enhanced reef monitoring systems to provide early warning alerts of bleaching events, and, (3) deployment of artificial reefs or other fish-aggregating devices. While these options had positive benefit-cost ratios, other options were also recommended based on their non-tangible benefits. These include the employment of an irrigation network that allows for the recycling of waste water, development of national evacuation and rescue plans, providing retraining for displaced tourism workers and the revision of policies related to financing national tourism offices to accommodate the new climate realities.

Genetic characterization of the population of São Luís, MA, Brazil

Five loci (vWA1, F13A1, D12S67, Apo-B and D1S80) were investigated by polyacrylamide gel electrophoresis followed by silver staining in a sample of 177 individuals from the population of São Luís, State of Maranhão, Brazil. A total of 70 different alleles were identified. A statistically significant deviation from the Hardy-Weinberg equilibrium was observed in a single locus (F13A1, p = 0.0075). The average heterozygosity (H) was estimated at 77.7%, the mean number of alleles per locus as 14. The PD (capacity of genotype differentiation at each locus) ranged from 88.9% (vWA1) to 96.7% (F13A1). The combined PE (power of exclusion) of these five loci was 99.8%. In terms of racial admixture (42% European, 39% Indian, and 19% African Black ancestry), São Luís presented an estimate similar to Belém, another trihybrid Amazonian population.

Vida material: entre casas e objetos, Belém 1920-1945

A vida material na cidade de Belém é o palco da análise deste trabalho ao buscar compreender as relações sociais, econômicas e culturais através do universo das casas e objetos das famílias abastadas entre 1920-1945. As mudanças e permanências na forma de morar se fazia presente no discurso do poder público que paulatinamente com o discurso pautado na higiene buscou inserir práticas no cotidiano que interferiram nos interiores das residências e nas ações dos seus moradores. Pretendemos acompanhar os moradores no interior de suas residências, observando a chegada de objetos e hábitos que estavam pautados no conceito de civilização divulgada pelo Estado republicano. Assim nos propomos a observar as notícias da economia paraense e seu crescimento no setor da produção de móveis e os sujeitos que estavam atrelados ao consumo destes objetos, conhecendo os lugares de venda e compra de utensílios domésticos e suas formas de divulgação. Tentamos analisar a uso social dos objetos nos cômodos das residências e as transformações que estes provocaram entre seus usuários ao apresentarem vínculos entre vida material e práticas culturais.

Comparative neurophysiology of spatial luminance contrast sensitivity

The luminance contrast sensitivity function has been investigated using behavioral and electrophysiological methods in many vertebrate species. Some features are conserved across species as a shape of the function, but other features, such as the contrast sensitivity peak value, spatial frequency contrast sensitivity peak, and visual acuity have changed. Here, we review contrast sensitivity across different classes of vertebrates, with an emphasis on the frequency contrast sensitivity peak and visual acuity. We also correlate the data obtained from the literature to test the power of the association between visual acuity and the spatial frequency of the contrast sensitivity function peak.

Põe tapioca, põe farinha d’água?: gastronomia do açaí e identidade socioespacial e cultural na Grande Belém

O presente trabalho teve como objetivo principal analisar as mudanças nas formas de venda e consumo do açaí na Região Metropolitana de Belém (RMB), e sua relação com a identidade de lugar de seus consumidores. O interesse pelo tema teve origem na observação da ocorrência da globalização do açaí, alimento base da dieta das populações amazônicas de origem ribeirinha que hoje é largamente consumido fora da Região Amazônica, em padrões muito diferentes daqueles nela estabelecidos. A escolha da RMB como lócus de pesquisa se justifica pelo fato de que nela se concentra alto consumo de açaí, nos padrões tradicionais e nos modernos, suscitando questionamentos sobre os efeitos dessa convivência na vida cotidiana dos que a habitam. Teoricamente, a pesquisa articula a definição de identidade de lugar de Abe-Lima (2012) com as elaborações de Henri Lefèbvre (1991) sobre a vida cotidiana no mundo moderno e com teoria dos circuitos econômicos de Milton Santos (2008). Metodologicamente, foi adotada uma estratégia multimétodos, envolvendo pesquisa documental, um painel de especialistas com 5 entidades de acompanhamento da produção de açaí, observações pautadas na etnografia urbana em 9 locais de venda e entrevistas semiabertas com 40 consumidores de açaí, maiores de 18 anos e residentes na RMB, recrutados por meio de cadeia tipo bola de neve. Além dos roteiros de entrevistas, foram utilizados como estratégias de coleta de dados diários de campo e fotografias. O conjunto dos dados foi submetido à técnica da análise de conteúdo temática, com eventual apoio do software QDA Miner Lite. Os resultados situaram a globalização do açaí em meados da década de 1990, momento de intensificação dos efeitos da metropolização em Belém, como o aumento populacional, a segregação espacial e a imposição de um ritmo de vida mais acelerado. As análises apontaram que tal processo significou a entrada do açaí no circuito superior da economia, com um processo produtivo mais organizado, utilizando mais tecnologia e envolvendo maiores volumes financeiros, atingindo escala industrial. No entanto, prevalece na RMB o processamento artesanal, em estruturas de pequeno porte, construídas em alvenaria, de organização simples e controle financeiro ausente. O consumo público aumentou, com grande número de locais especializados na oferta de açaí, em caráter de entretenimento, sendo incipiente a adesão a novos acompanhamentos, como granola e aveia. A preferência pelos acompanhamentos tradicionais, como farinha d’água ou de tapioca, açúcar e peixe, permanece, assim como pelo consumo privado, no âmbito da casa, que tem sido favorecido pela disponibilidade do serviço de entrega, recurso recente. A frequência geral de consumo diminuiu, em função do aumento de preço e de mudanças na rotina, como aumento da distância entre local de trabalho e residência. A pesquisa permitiu reafirmar a importância do açaí na vida cotidiana dos belenenses que o consomem, para os quais ele funciona como elemento de distintividade, continuidade, autoestima e autoeficácia, em estreita relação com aspectos próprios da metrópole. Por esse motivo, torna-se preocupante que o acesso a açaí de qualidade, nos padrões desejados pelos indivíduos, esteja tornando-SE privilégio inacessível aos consumidores de menor poder aquisitivo. Assim, espera-se que o conjunto de dados contribua para a compreensão da importância de políticas públicas voltadas ao açaí que considerem melhor as demandas daqueles que o consomem.