Complete genomic sequence of the Australian south-west genotype of Sindbis virus: Comparisons with other Sindbis strains and identification of a unique deletion in the 3 '-untranslated region

Our previous studies have shown that two distinct genotypes of Sindbis (SIN) virus occur in Australia. One of these, the Oriental/Australian type, circulates throughout most of the Australian continent, whereas the recently identified south-west (SW) genetic type appears to be restricted to a distinct geographic region located in the temperate south-west of Australia. We have now determined the complete nucleotide and translated amino acid sequences of a SW isolate of SIN virus (SW6562) and performed comparative analyses with other SIN viruses at the genomic level. The genome of SW6562 is 11,569 nucleotides in length, excluding the cap nucleotide and poly (A) tail. Overall this virus differs from the prototype SIN virus (strain AR339) by 23% in nucleotide sequence and 12.5% in amino acid sequence. Partial sequences of four regions of the genome of four SW isolates were determined and compared with the corresponding sequences from a number of SIN isolates from different regions of the World. These regions are the non-structural protein (nsP3), the E2 gene, the capsid gene, and the repeated sequence elements (RSE) of the 3'UTR. These comparisons revealed that the SW SIN viruses were more closely related to South African and European strains than to other Australian isolates of SIN virus. Thus the SW genotype of SIN virus may have been introduced into this region of Australia by viremic humans or migratory birds and subsequently evolved independently in the region. The sequence data also revealed that the SW genotype contains a unique deletion in the RSE of the 3'UTR region of the genome. Previous studies have shown that deletions in this region of the SIN genome can have significant effects on virus replication in mosquito and avian cells, which may explain the restricted distribution of this genotype of SIN virus.

Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects

A number of studies indicated that lineages of animals with high rates of mitochondrial (mt) gene rearrangement might have high rates of mt nucleotide substitution. We chose the hemipteroid assemblage and the Insecta to test the idea that rates of mt gene rearrangement and mt nucleotide substitution are correlated. For this purpose, we sequenced the mt genome of a lepidopsocid from the Psocoptera, the only order of hemipteroid insects for which an entire mtDNA sequence is not available. The mt genome of this lepidopsocid is circular, 16,924 bp long, and contains 37 genes and a putative control region; seven tRNA genes and a protein-coding gene in this genome have changed positions relative to the ancestral arrangement of mt genes of insects. We then compared the relative rates of nucleotide substitution among species from each of the four orders of hemipteroid insects and among the 20 insects whose mt genomes have been sequenced entirely. All comparisons among the hernipteroid insects showed that species with higher rates of gene rearrangement also had significantly higher rates of nucleotide substitution statistically than did species with lower rates of gene rearrangement. In comparisons among the 20 insects, where the mt genomes of the two species differed by more than five breakpoints, the more rearranged species always had a significantly higher rate of nucleotide substitution than the less rearranged species. However, in comparisons where the mt genomes of two species differed by five or less breakpoints, the more rearranged species did not always have a significantly higher rate of nucleotide substitution than the less rearranged species. We tested the statistical significance of the correlation between the rates of mt gene rearrangement and mt nucleotide substitution with nine pairs of insects that were phylogenetically independent from one 2 another. We found that the correlation was positive and statistically significant (R-2 = 0.73, P = 0.01; R-s = 0.67, P < 0.05). We propose that increased rates of nucleotide substitution may lead to increased rates of gene rearrangement in the mt genomes of insects.

A molecular phylogeny of the Australian skink genera Eulamprus, Gnypetoscincus and Nangura

Skinks from the genera Eulamprus, Gnypetoscincus and Nangura are a prominent component of the reptile fauna of the mesic forests of the east coast of Australia and have been the subject of numerous ecological studies. Highly conserved morphology and the retention of ancestral traits have limited our understanding of the relationships within and among these genera beyond an initial identification of species groups within Eulamprus. To address this deficit and to explore the relationships between Eulamprus and the monotypic genera Nangura and Gnypetoscincus, sections of two mitochondrial genes (ND4 and 16S rRNA) were sequenced and subjected to Bayesian phylogenetic analysis. This phylogenetic analysis supports recognition of the three species groups proposed for Eulamprus (murrayi, quoyii and tenuis) and indicates that this genus is paraphyletic, with Gnypetoscincus and Nangura being proximal to basal lineages of the tenuis group. To resolve these and broader problems of paraphyly, we suggest that each of the species groups from 'Eulamprus' should be recognised as a distinct genus. The phylogenetically and ecologically distinct water skinks of the quoyii group would be retained within Eulamprus and the diverse species of the tenuis group allocated to Concinnia. We suggest placing the monophyletic murrayi group, endemic to the rainforests of central eastern Australia, in a new genus ( yet to be formally described). The sequencing data also revealed the existence of a genetically divergent but morphologically cryptic lineage within E. murrayi and substantial diversity within E. quoyii. There is evidence for two major habitat shifts from rainforest towards drier habitats, one leading to the quoyii group and the second defining a clade of three species within the tenuis complex. These ecological transitions may represent adaptations to general drying across eastern Australia during the late Miocene - Pliocene. Each of the major areas of east coast tropical or subtropical rainforest contains multiple phylogenetically diverse endemic species, reflecting the long-term persistence and high conservation value of wet forest habitats in each area.

Hyperinsulinism and overgrowth without obesity

We report a 5 year old girl with postnatal overgrowth (height velocity >97th centile), hyperinsulinaemia, and increased insulin-like growth factor 1 for age, without evidence of bioactive or immunoreactive growth hormone excess or pituitary abnormality. Although her overgrowth may be a result of hyperinsulinism, her serum contains a factor (neither insulin nor IGF-1) which is able to stimulate the proliferation of lymphocyte precursors, and this could also account for the overgrowth. Over the course of two years observation she has developed acanthosis nigricans and diabetes mellitus.

Tool support for testing concurrent Java components

Concurrent programs are hard to test due to the inherent nondeterminism. This paper presents a method and tool support for testing concurrent Java components. Too[ support is offered through ConAn (Concurrency Analyser), a too] for generating drivers for unit testing Java classes that are used in a multithreaded context. To obtain adequate controllability over the interactions between Java threads, the generated driver contains threads that are synchronized by a clock. The driver automatically executes the calls in the test sequence in the prescribed order and compares the outputs against the expected outputs specified in the test sequence. The method and tool are illustrated in detail on an asymmetric producer-consumer monitor. Their application to testing over 20 concurrent components, a number of which are sourced from industry and were found to contain faults, is presented and discussed.

Effects of herbicides diuron and atrazine on corals of the Great Barrier Reef, Australia

In response to recent reports of contamination of the nearshore marine environment along the Queensland coast by herbicides (including areas inside the Great Barrier Reef Marine Park), an ecotoxicological assessment was conducted of the impact of the herbicides diuron and atrazine on scleractinian corals. Pulse-amplitude modulated (PAM) chlorophyll fluorescence techniques were used to assess the herbicide effects on the symbiotic dinoflagellates within the tissues (in hospite) of 4 species of coral (Acropora formosa, Montipora digitata, Porites cylindrica, Seriatopora hystrix) in static toxicity tests, and in freshly isolated symbiotic dinoflagellates from Stylophora pistillata. Using change in the effective quantum yield (DeltaF/F-m') as an effect criterion, diuron (no observable effect concentration, NOEC = 0.3 mug 1(-1); lowest observable effect concentration, LOEC = 1 mug 1(-1); median effective concentration, EC50 4 to 6 mug 1(-1)) was found to be more toxic than atrazine (NOEC = 1 mug 1(-1), LOEC = 3 mug 1(-1), EC50 40 to 90 mug 1(-1)) in short-term (10 h) toxicity tests. In the tests with isolated algae, significant reductions in DeltaF/F-m' were recorded as low as 0.25 mug 1(-1) diuron (LOEC, EC50 = 5 mug 1(-1)). Time-course experiments indicated that the effects of diuron were rapid and reversible. At 10 mug 1(-1) diuron, DeltaF/F-m' was reduced by 25% in 20 to 30 min, and by 50% in 60 to 90 min. Recovery of DeltaF/F-m' in corals exposed to 10 mug 1(-1) diuron and then transferred to running seawater was slower, returning to within 10% of control values inside 1 to 7 h. The effect of a reduction in salinity (35 to 27%) on diuron toxicity (at 1 and 3 mug 1(-1) diuron) was tested to examine the potential consequences of contaminated coastal flood plumes inundating inshore reefs. DeltaF/F-m' was reduced in the diuron-exposed corals, but there was no significant interaction between diuron and reduced salinity seawater within the 10 h duration of the test. Exposure to higher (100 and 1000 mug 1(-1)) diuron concentrations for 96 h caused a reduction in DeltaF/F-m' the ratio variable to maximal fluorescence (F,1F.), significant loss of symbiotic dinoflagellates and pronounced tissue retraction, causing the corals to pale or bleach. The significance of the results in relation to diuron contamination of the coastal marine environment from terrestrial sources (mainly agricultural) and marine sources (antifouling paints) are discussed.

The genetics of glycosylation in Gram-negative bacteria

In recent years there has been a dramatic increase in reports of glycosylation of proteins in various Gram-negative systems including Neisseria meningitidis, Neisseria gonorrhoeae, Campylobacter jejuni, Pseudomonas aeruginosa, Escherichia coli, Caulobacter crescentus, Aeromonas caviae and Helicobacter pylori. Although this growing list contains many important pathogens (reviewed by Benz and Schmidt [Mol. Microbiol. 45 (2002) 267-276]) and the glycosylations are found on proteins important in pathogenesis such as pili, adhesins and flagella the precise role(s) of the glycosylation of these proteins remains to be determined. Furthermore, the details of the glycosylation biosynthetic process have not been determined in any of these systems. The definition of the precise role of glycosylation and the mechanism of biosynthesis will be facilitated by a detailed understanding of the genes involved. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Genetic characterization of pilin glycosylation and phase variation in Neisseria meningitidis

Pili of Neisseria meningitidis are a key virulence factor, being the major adhesin of this capsulate organism and contributing to specificity for the human host. Pili are post-translationally modified by addition of either an O-linked trisaccharide, Gal (beta1-4) Gal (alpha1-3) 2,4-diacetamido-2,4,6-trideoxyhexose or an O-linked disaccharide Gal (alpha1,3) GlcNAc. The role of these structures in meningococcal pathogenesis has not been resolved. In previous studies we identified two separate genetic loci, pglA and pglBCD, involved in pilin glycosylation. Putative functions have been allocated to these genes; however, there are not enough genes to account for the complete biosynthesis of the described structures, suggesting additional genes remain to be identified. In addition, it is not known why some strains express the trisaccharide structure and some the disaccharide structure. In order to find additional genes involved in the biosynthesis. of these structures, we used the recently published group A strain Z2491 and group B strain MC58 Neisseria meningitidis genomes and the unfinished Neisseria meningitidis group C strain FAM18 and Neisseria gonorrhoeae strain FA1090 genomes to identify novel genes involved in pilin glycosylation, based on homology to known oligosaccharide biosynthetic genes. We identified a new gene involved in pilin glycosylation designated pglE and examined four additional genes pgIB/B2, pglF, pglG and pglH. A strain survey revealed that pglE and pglF were present in each strain examined. The pglG, pglH and pgIB2 polymorphisms were not found in strain C311#3 but were present in a large number of clinical isolates. Insertional mutations were constructed in pglE and pglF in N. meningitidis strain C311#3, a strain with well-defined lipopolysaccharide (LPS) and pilin-linked glycan structures. Increased gel migration of the pilin subunit molecules of pglE and pglF mutants was observed by Western analysis, indicating truncation of the trisaccharide structure. Antisera specific for the C311#3 trisaccharide failed to react with pilin from these pglE and pglF mutants. GC-MS analysis of the sugar composition of the pglE mutant showed a reduction in galactose compared with C311#3 wild type. Analysis of amino acid sequence homologies has suggested specific roles for pglE and pglF in the biosynthesis of the trisaccharide structure. Further, we present evidence that pglE, which contains heptanucleotide repeats, is responsible for the phase variation between trisaccharide and disaccharide structures in strain C311#3 and other strains. We also present evidence that pglG, pglH and pgIB2 are potentially phase variable.

A crise do transporte a??reo no Brasil: 2006-2007

Este estudo de caso aborda a crise vivida pelo setor de transporte a??reo brasileiro nos anos de 2006 e 2007. Deflagrada por um acidente de vulto, a crise teve como protagonistas os controladores de tr??fego a??reo, que, sob suspeita de falha funcional e comunica????o dif??cil com as autoridades do setor, reagiram por meio de uma estrat??gia de opera????o-padr??o (greve branca). Essa situa????o, somada ?? escassez de pessoal, provocou, de novembro de 2006 at?? meados de 2007, o descontrole operacional dos principais aeroportos do pa??s, com grandes preju??zos aos usu??rios. Um novo acidente a??reo, no decorrer da crise, agravou ainda mais a situa????o do setor, expondo defici??ncias estruturais e profissionais ?? opini??o p??blica brasileira, em uma ??rea at?? ent??o considerada segura. O caso relata as tentativas de equacionamento da crise por parte das autoridades respons??veis pela pol??tica de transporte a??reo, frente ao descontentamento e ??s reivindica????es dos controladores de tr??fego a??reo e ?? indigna????o da sociedade. O objetivo do estudo de caso ?? ilustrar uma situa????o de crise e de processo de negocia????o, tendo sido originalmente utilizado em uma oficina sobre negocia????es no setor p??blico. O caso pode ser utilizado como material de apoio em cursos que abordem, entre outros, os seguintes t??picos: negocia????o, gest??o de crises, comunica????o e planejamento estrat??gico

Simula????o de reuni??o com dirigente: prepara????o de informa????es e an??lise sobre programa governamental

A simula????o visa preparar gerentes e assessores para organizarem informa????es e diagn??sticos para tomada de decis??o. Apresenta diversos pontos de vista sobre um programa em andamento e estimula debates entre gestores e atores das ??reas envolvidas. A partir da aprecia????o dos pontos de vista desses atores, os participantes dever??o se preparar, em curto espa??o de tempo, para uma reuni??o com o dirigente rec??m-empossado respons??vel pelo programa em quest??o

Coopera????o Horizontal em Terra Linda: mito ou aposta?

Nas ??ltimas d??cadas o protagonismo do Brasil na arena pol??tica internacional tem se tornado mais evidente. O Pa??s tem atuado no sentido de promover a coopera????o para o desenvolvimento de v??rios pa??ses com problemas bastante complexos, buscando por meio de a????es de longo prazo alterar estruturas sociais e econ??micas. O estudo de caso apresenta o sum??rio de um diagn??stico realizado por um consultor contratado pelo governo fict??cio de Terra Linda, a fim de auxiliar a elabora????o de projeto de coopera????o horizontal a ser desenvolvido com Brasil. Embora se trate de um pa??s imagin??rio, o Estudo de Caso ?? baseado em dados reais e visa estimular o debate sobre qual o melhor modo de gerir uma parceria entre Estados-na????es, quais as ??reas priorit??rias a serem atendidas, qual a melhor forma de utilizar os recursos, bem como qual o papel de cada ator envolvido

O combate ?? viol??ncia contra a mulher: a luta entre antigos valores e novos padr??es de pol??ticas p??blicas

O caso relata uma situa????o de viol??ncia dom??stica vivenciada por uma mulher negra e os obst??culos por ela enfrentados para denunciar o agressor e fazer valer seus direitos. Mostra a contradi????o entre normas e sua efetiva aplica????o, quando o comportamento de agentes p??blicos ainda conserva padr??es e valores de um Estado autorit??rio, patriarcal e escravocrata. O caso ?? fict??cio, mas espelha situa????es reais coletadas em documentos e relat??rios da Ouvidoria da Secretaria de Pol??ticas para as Mulheres- SPM/PR. O estudo suscita discuss??es sobre a dimens??o ??tica da atividade de agentes p??blicos de um Estado democr??tico, englobando quest??es referentes aos direitos humanos, direitos e deveres do Estado e da sociedade, o papel da transpar??ncia, do controle social e da responsabiliza????o por resultados (accountability) etc. Pode ser aplicado em cursos sobre ??tica e servi??o p??blico, pol??ticas p??blicas de g??nero e ra??a e atendimento ao cidad??o

Estrutura e propriedades da difenil-4-amina sulfonato de sódio : um dopante de filmes condutores

This work contains the theoretical simulation of the conformation of diphenyl-4-amine sodium sulphonate (DASNa) and correlates its geometry with conductivity, showing that the conductivity increases as the molecule becomes more planar. The solvent effect was also evaluated, using water and dimethylsulfoxide. Some properties, such as bond distance, vibration al frequency and effective charge were calculated. The utilization of diphenyl-4-amine sodium sulphonate (DASNa) as dopant of aniline was investigated in view of the HOMO-LUMO energy gap.

Uma avaliação das metodologias de desagregação da exergia física para a modelagem termoeconômica de sistemas

Talvez não seja nenhum exagero afirmar que há quase um consenso entre os praticantes da Termoeconomia de que a exergia, ao invés de só entalpia, seja a magnitude Termodinâmica mais adequada para ser combinada com o conceito de custo na modelagem termoeconômica, pois esta leva em conta aspectos da Segunda Lei da Termodinâmica e permite identificar as irreversibilidades. Porém, muitas vezes durante a modelagem termoeconômica se usa a exergia desagregada em suas parcelas (química, térmica e mecânica), ou ainda, se inclui a neguentropia que é um fluxo fictício, permitindo assim a desagregação do sistema em seus componentes (ou subsistemas) visando melhorar e detalhar a modelagem para a otimização local, diagnóstico e alocação dos resíduos e equipamentos dissipativos. Alguns autores também afirmam que a desagregação da exergia física em suas parcelas (térmica e mecânica) permite aumentar a precisão dos resultados na alocação de custos, apesar de fazer aumentar a complexidade do modelo termoeconômico e consequentemente os custos computacionais envolvidos. Recentemente alguns autores apontaram restrições e possíveis inconsistências do uso da neguentropia e deste tipo de desagregação da exergia física, propondo assim alternativas para o tratamento de resíduos e equipamentos dissipativos que permitem a desagregação dos sistemas em seus componentes. Estas alternativas consistem, basicamente, de novas propostas de desagregação da exergia física na modelagem termoeconômica. Sendo assim, este trabalho tem como objetivo avaliar as diferentes metodologias de desagregação da exergia física para a modelagem termoeconômica, tendo em conta alguns aspectos como vantagens, restrições, inconsistências, melhoria na precisão dos resultados, aumento da complexidade e do esforço computacional e o tratamento dos resíduos e equipamentos dissipativos para a total desagregação do sistema térmico. Para isso, as diferentes metodologias e níveis de desagregação da exergia física são aplicados na alocação de custos para os produtos finais (potência líquida e calor útil) em diferentes plantas de cogeração considerando como fluido de trabalho tanto o gás ideal bem como o fluido real. Plantas essas com equipamentos dissipativos (condensador ou válvula) ou resíduos (gases de exaustão da caldeira de recuperação). Porém, foi necessário que uma das plantas de cogeração não incorporasse equipamentos dissipativos e nem caldeira de recuperação com o intuito de avaliar isoladamente o efeito da desagregação da exergia física na melhoria da precisão dos resultados da alocação de custos para os produtos finais.

Honorários, serviços fora da área de auditoria e independência do auditor : evidências nas companhias abertas listadas na BM&FBovespa

O presente trabalho possui o objetivo de identificar os determinantes dos honorários e serviços fora da área de auditoria, bem como avaliar se a prestação destes serviços conjuntamente com a auditoria das demonstrações financeiras afeta a independência dos auditores externos das companhias abertas brasileiras negociadas na BM&FBovespa. A amostra contempla um total de 180 empresas não financeiras observadas no período de 2010 a 2012. Os resultados indicam que as proxies para esforço e risco elevam os honorários de auditoria, enquanto a governança corporativa apresentou tanto o efeito demanda (elevam os honorários) quanto o efeito risco (reduzem os honorários) dependendo da proxy observada. No que tange a contratação de serviços fora da área de auditoria foi constatado que empresas com maior necessidade de monitoramento e com comitês de auditoria demandam esses serviços, embora o conselho fiscal iniba a contratação dos mesmos. Por fim, as evidências indicam que a prestação de serviços fora da área de auditoria não afeta a independência do auditor. Estes resultados são mantidos mesmo quando observada a probabilidade de ocorrência da modificação no parecer da auditoria relacionada à violação da premissa de continuidade da firma (Going Concern Opinion). Os testes adicionais realizados confirmam a manutenção da independência do auditor, inclusive quando observado o tipo de auditor (não Big4), expectativa de ganhos futuros relacionados a serviços fora da área de auditoria adicionais, empresas consideradas ressalváveis, bem como o efeito de melhores práticas de governança corporativa.