Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the similar to 12-Mb genome of CAT-1, when compared with the reference S228c genome, contains similar to 36,000 homozygous and similar to 30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC

We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.

Intestinal Lymph-Borne Factors Induce Lung Release of Inflammatory Mediators and Expression of Adhesion Molecules After an Intestinal Ischemic Insult

Background. Intestinal ischemia and reperfusion (I/R) is a documented cause of acute lung injury (ALI) and systemic inflammation. We previously reported that obstruction of thoracic lymphatic flow during intestinal I/R blunts pulmonary neutrophil recruitment and microvascular injury and decreases the systemic levels of tumor necrosis factor. Here, we consider the existence of a gut-lung axis promoting the induction of systemic inflammation, whereby drained intestinal lymph stimulates lung expression of adhesion molecules and matrix components and generation of inflammatory mediators. Material and Methods. Upon administration of anesthesia, male Wistar rats were subjected to occlusion of the superior mesenteric artery for 45 min, followed by 2 h of intestinal reperfusion (I/R); groups of rats were subjected to I/R with or without thoracic lymphatic duct ligation immediately before the procedure. The non-manipulated rats were used to investigate basal parameters. Results. Obstruction of thoracic lymphatic flow before intestinal I/R decreased the ability of cultured lung tissue explants to release IL-1 beta, IL-10, and VEGF. In contrast, lymphatic obstruction normalized the elevated lung expression of PECAM-1 caused by intestinal I/R. On the other hand, lung E-selectin expression was significantly reduced, whereas fibronectin expression and collagen synthesis were not affected. Lymph levels of LTB4 and TXB2 were found to be significantly increased. Conclusions. These data suggest that lymph factors drained from the intestine during ischemic trauma stimulate the lung to generate inflammatory mediators and alter the expression of adhesion molecules. Disturbances in lung homeostasis mediated by lymph might contribute to the spread of inflammatory processes, thereby accounting for the systemic inflammation induced by intestinal I/R. (C) 2012 Elsevier Inc. All rights reserved.

Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV

The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.

A emergência dos conselhos setoriais na agroindústria brasileira: gênese de uma governança mais ampla?

O artigo apresenta uma avaliação dos novos mecanismos de regulação setorial rural implementados na década passada no Brasil. O trabalho é baseado na abordagem estabelecida pelos autores da Sociologia Econômica e da Nova Economia Institucional e são analisadas as diferentes fases pelas quais passou a constituição dos complexos agroindustriais. Com isso, torna-se possível demonstrar que estamos diante de um novo período no qual os diversos setores, como o sucroalcooleiro e o citrícola, vêm se organizado de forma a pactuar os preços e as margens a serem praticadas em cada elo da cadeia. No caso do complexo canavieiro, o sistema Consecana vem obtendo relativo sucesso apesar de descontentamentos pontuais por parte dos fornecedores. Com o funcionamento do Consecana, o setor logrou progredir em outros temas como a questão da disseminação de um padrão tecnológico agrícola e industrial mais avançado, a remuneração dos trabalhadores rurais e até mesmo o preço da terra. No caso do complexo citrícola, o sistema proposto, denominado Consecitrus, ainda está em negociação, mas, devido à baixa legitimidade de representação e o histórico de conflitos entre as partes, dificuldades para a sua implementação podem ser registradas.

Landscape and soil regionalization in southern Brazilian Amazon and contiguous areas: methodology and relevance for ecological studies

Soils of a large tropical area with differentiated landscapes cannot be treated uniformly for ecological applications. We intend to develop a framework based on physiography that can be used in regional applications. The study region occupies more than 1.1 million km² and is located at the junction of the savanna region of Central Brazil and the Amazon forest. It includes a portion of the high sedimentary Central Brazil plateau and large areas of mostly peneplained crystalline shield on the border of the wide inner-Amazon low sedimentary plain. A first broad subdivision was made into landscape regions followed by a more detailed subdivision into soil regions. Mapping information was extracted from soil survey maps at scales of 1:250000-1:500000. Soil units were integrated within a homogenized legend using a set of selected attributes such as taxonomic term, the texture of the B horizon and the associated vegetation. For each region, a detailed inventory of the soil units with their area distribution was elaborated. Ten landscape regions and twenty-four soil regions were recognized and delineated. Soil cover of a region is normally characterized by a cluster composed of many soil units. Soil diversity is comparable in the landscape and the soil regions. Composition of the soil cover is quantitatively expressed in terms of area extension of the soil units. Such geographic divisions characterized by grouping soil units and their spatial estimates must be used for regional ecological applications.

Consenso 2012 da Sociedade Brasileira de Reumatologia para o tratamento da artrite reumatoide

OBJETIVO: Elaborar recomendações para o tratamento da artrite reumatoide no Brasil. MÉTODO: Revisão da literatura com seleção de artigos baseados em evidência e opinião de especialistas da Comissão de Artrite Reumatoide da Sociedade Brasileira de Reumatologia. RESULTADOS E CONCLUSÕES: 1) A decisão terapêutica deve ser compartilhada com o paciente; 2) imediatamente após o diagnóstico, uma droga modificadora do curso da doença (DMCD) deve ser prescrita e o tratamento ajustado para atingir remissão; 3) o tratamento deverá ser conduzido por reumatologista; 4) o tratamento inicial inclui DMCD sintéticas; 5) o metotrexato é a droga de escolha; 6) pacientes que não alcançaram resposta após a utilização de dois esquemas de DMCD sintéticas devem ser avaliados para DMCD biológicas; 7) excepcionalmente, DMCD biológicas poderão ser consideradas mais precocemente; 8) recomenda-se preferencialmente o uso de agentes anti-TNF como terapia biológica inicial; 9) após falha terapêutica a uma primeira DMCD biológica, outros biológicos poderão ser utilizados; 10) ciclofosfamida e azatioprina podem ser consideradas em manifestações extra-articulares graves; 11) recomenda-se a utilização de corticoide oral em baixas doses e por curtos períodos; 12) os anti-inflamatórios não hormonais devem sempre ser prescritos em associação à DMCD; 13) avaliações clínicas devem ser mensais no início do tratamento; 14) terapia física, reabilitação e terapia ocupacional são indicadas; 15) deve-se recomendar tratamento cirúrgico para correção de sequelas; 16) métodos de terapia alternativa não substituem a terapia tradicional; 17) deve-se orientar planejamento familiar; 18) orienta-se a busca ativa e o manejo de comorbidades; 19) atualizar e documentar a vacinação do paciente; 20) doenças transmissíveis endêmico-epidêmicas devem ser investigadas e tratadas.

Consenso 2012 da Sociedade Brasileira de Reumatologia sobre o manejo de comorbidades em pacientes com artrite reumatoide

OBJETIVO: Elaborar recomendações da Comissão de Artrite Reumatoide da Sociedade Brasileira de Reumatologia (SBR) para o manuseio das comorbidades em artrite reumatoide (AR). MÉTODOS: Revisão da literatura e opinião de especialistas da Comissão de AR da SBR. RESULTADOS E CONCLUSÕES: Recomendações: 1) Diagnosticar e tratar precoce e adequadamente as comorbidades; 2) O tratamento específico da AR deve ser adaptado às comorbidades; 3) Inibidores da enzima conversora da angiotensina (IECA) ou bloqueadores dos receptores de angiotensina II (BRA) são preferidos no tratamento da hipertensão arterial sistêmica; 4) Em pacientes com AR e diabetes mellitus, deve-se evitar o uso contínuo de dose cumulativa alta de corticoides; 5) Sugere-se o uso de estatinas para manter níveis de LDL menor que 100 mg/dL e índice aterosclerótico menor que 3,5 em pacientes com AR e comorbidades; 6) A síndrome metabólica deve ser tratada; 7) Recomenda-se a realização de exames para a investigação de aterosclerose subclínica; 8) Maior vigilância para um diagnóstico precoce de neoplasia oculta; 9) Medidas de prevenção para trombose venosa são sugeridas; 10) Recomenda-se a realização de densitometria óssea em pacientes com AR acima de 50 anos, e naqueles com idade menor com corticoide maior que 7,5 mg por mais de três meses; 11) Pacientes com AR e osteoporose devem evitar quedas, e devem ser aconselhados a aumentarem a ingestão de cálcio, aumentarem a exposição solar e fazerem atividade física; 12) Suplementação de cálcio e vitamina D é sugerida.Autilização de bisfosfonatos é sugerida para pacientes com escore T menor que -2,5 na densidade mineral óssea; 13) Recomenda-se equipe multidisciplinar, com participação ativa do médico reumatologista no tratamento das comorbidades.

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Molecular phylogeography of tick-borne encephalitis virus in central Europe

In order to obtain a better understanding of tick-borne encephalitis virus (TBEV) strain movements in central Europe the E gene sequences of 102 TBEV strains collected from 1953 to 2011 at 38 sites in the Czech Republic, Slovakia, Austria and Germany were determined. Bayesian analysis suggests a 350-year history of evolution and spread in central Europe of two main lineages, A and B. In contrast to the east to west spread at the Eurasian continent level, local central European spreading patterns suggest historic west to east spread followed by more recent east to west spread. The phylogenetic and network analyses indicate TBEV ingressions from the Czech Republic and Slovakia into Germany via landscape features (Danube river system), biogenic factors (birds, red deer) and anthropogenic factors. The identification of endemic foci showing local genetic diversity is of paramount importance to the field as these will be a prerequisite for in-depth analysis of focal TBEV maintenance and long-distance TBEV spread.

Cirrus clouds observation in Santa Maria, Rio Grande do Sul during the experiment Chuva - Sul.

Cirrus clouds are an interesting point in the research of the atmosphere due their behavior and the effect on the earth radiation budget. They can affect the atmospheric radiation budget by reflecting the incoming solar radiation and absorbing the outgoing terrestrial radiation. Also, this cloud type is involved in the dehydration of the upper troposphere and lower stratosphere. So, it is interesting to increment the measurements of this type of clouds from the ground. During November and December 2012, through the CHUVA-SUL campaign, measurements with lidar in Santa Maria, Rio Grande do Sul were conducted. The system installed in Santa Maria site (29.8 °S; 53.7 °W, 100 m asl) was a single elastic-backscatter lidar using the wavelength of 532 nm. Some days with cirrus clouds lidar measurements were detected. Four days with presence of cirrus cloud are showed in the present study. These days, 7, 8, 19 and 28 November 2012, was selected due the persistence of cirrus clouds over many hours. The raw retrieval lidar signals and inverted backscatter coefficient profiles were analyzed for the selected days. Base and top height was obtained by analysis of raw signal and backscatter coefficient. Extinction coefficient profiles were obtained by the assumption of the lidar ratio. Cirrus cloud optical depth (COD) values were calculated, from the integration of the extinction coefficient between the base and top altitudes of the cirrus clouds.