Cab45 is required for Ca(2+)-dependent secretory cargo sorting at the trans-Golgi network

Ca(2+) import into the lumen of the trans-Golgi network (TGN) by the secretory pathway calcium ATPase1 (SPCA1) is required for the sorting of secretory cargo. How is Ca(2+) retained in the lumen of the Golgi, and what is its role in cargo sorting? We show here that a soluble, lumenal Golgi resident protein, Cab45, is required for SPCA1-dependent Ca(2+) import into the TGN; it binds secretory cargo in a Ca(2+)-dependent reaction and is required for its sorting at the TGN.

TRPM5-mediated calcium uptake regulates mucin secretion from human colon goblet cells

Mucin 5AC (MUC5AC) is secreted by goblet cells of the respiratory tract and, surprisingly, also expressed de novo in mucus secreting cancer lines. siRNA-mediated knockdown of 7343 human gene products in a human colonic cancer goblet cell line (HT29-18N2) revealed new proteins, including a Ca(2+)-activated channel TRPM5, for MUC5AC secretion. TRPM5 was required for PMA and ATP-induced secretion of MUC5AC from the post-Golgi secretory granules. Stable knockdown of TRPM5 reduced a TRPM5-like current and ATP-mediated Ca(2+) signal. ATP-induced MUC5AC secretion depended strongly on Ca(2+) influx, which was markedly reduced in TRPM5 knockdown cells. The difference in ATP-induced Ca(2+) entry between control and TRPM5 knockdown cells was abrogated in the absence of extracellular Ca(2+) and by inhibition of the Na(+)/Ca(2+) exchanger (NCX). Accordingly, MUC5AC secretion was reduced by inhibition of NCX. Thus TRPM5 activation by ATP couples TRPM5-mediated Na(+) entry to promote Ca(2+) uptake via an NCX to trigger MUC5AC secretion

Kinesin-5/Eg5 is important for transport of CARTS from the trans-Golgi network to the cell surface

Here we report that the kinesin-5 motor Klp61F, which is known for its role in bipolar spindle formation in mitosis, is required for protein transport from the Golgi complex to the cell surface in Drosophila S2 cells. Disrupting the function of its mammalian orthologue, Eg5, in HeLa cells inhibited secretion of a protein called pancreatic adenocarcinoma up-regulated factor (PAUF) but, surprisingly, not the trafficking of vesicular stomatitis virus G protein (VSV-G) to the cell surface. We have previously reported that PAUF is transported from the trans-Golgi network (TGN) to the cell surface in specific carriers called CARTS that exclude VSV-G. Inhibition of Eg5 function did not affect the biogenesis of CARTS; however, their migration was delayed and they accumulated near the Golgi complex. Altogether, our findings reveal a surprising new role of Eg5 in nonmitotic cells in the facilitation of the transport of specific carriers, CARTS, from the TGN to the cell surface.

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

BACKGROUND: Understanding how alternative phenotypes arise from the same genome is a major challenge in modern biology. Eusociality in insects requires the evolution of two alternative phenotypes - workers, who sacrifice personal reproduction, and queens, who realize that reproduction. Extensive work on honeybees and ants has revealed the molecular basis of derived queen and worker phenotypes in highly eusocial lineages, but we lack equivalent deep-level analyses of wasps and of primitively eusocial species, the latter of which can reveal how phenotypic decoupling first occurs in the early stages of eusocial evolution. RESULTS: We sequenced 20 Gbp of transcriptomes derived from brains of different behavioral castes of the primitively eusocial tropical paper wasp Polistes canadensis. Surprisingly, 75% of the 2,442 genes differentially expressed between phenotypes were novel, having no significant homology with described sequences. Moreover, 90% of these novel genes were significantly upregulated in workers relative to queens. Differential expression of novel genes in the early stages of sociality may be important in facilitating the evolution of worker behavioral complexity in eusocial evolution. We also found surprisingly low correlation in the identity and direction of expression of differentially expressed genes across similar phenotypes in different social lineages, supporting the idea that social evolution in different lineages requires substantial de novo rewiring of molecular pathways. CONCLUSIONS: These genomic resources for aculeate wasps and first transcriptome-wide insights into the origin of castes bring us closer to a more general understanding of eusocial evolution and how phenotypic diversity arises from the same genome.

Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis

Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains the main cause, the incidence of emerging Candida species, such as C. parapsilosis is increasing. It has been postulated that C. parapsilosis clinical isolates result from a recent global expansion of a virulent clone. However, the availability of a single genome for this species has so far prevented testing this hypothesis at genomic scales. We present here the sequence of three additional strains from clinical and environmental samples. Our analyses reveal unexpected patterns of genomic variation, shared among distant strains, that argue against the clonal expansion hypothesis. All strains carry independent expansions involving an arsenite transporter homolog, pointing to the existence of directional selection in the environment, and independent origins of the two clinical isolates. Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis.

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

Strategies and tools for preventing neurotoxicity: to test, to predict and how to do it

A change in paradigm is needed in the prevention of toxic effects on the nervous system, moving from its present reliance solely on data from animal testing to a prediction model mostly based on in vitro toxicity testing and in silico modeling. According to the report published by the National Research Council (NRC) of the US National Academies of Science, high-throughput in vitro tests will provide evidence for alterations in"toxicity pathways" as the best possible method of large scale toxicity prediction. The challenges to implement this proposal are enormous, and provide much room for debate. While many efforts address the technical aspects of implementing the vision, many questions around it need also to be addressed. Is the overall strategy the only one to be pursued? How can we move from current to future paradigms? Will we ever be able to reliably model for chronic and developmental neurotoxicity in vitro? This paper summarizes four presentations from a symposium held at the International Neurotoxicology Conference held in Xi"an, China, in June 2011. A. Li reviewed the current guidelines for neurotoxicity and developmental neurotoxicity testing, and discussed the major challenges existing to realize the NCR vision for toxicity testing. J. Llorens reviewed the biology of mammalian toxic avoidance in view of present knowledge on the physiology and molecular biology of the chemical senses, taste and smell. This background information supports the hypothesis that relating in vivo toxicity to chemical epitope descriptors that mimic the chemical encoding performed by the olfactory system may provide a way to the long term future of complete in silico toxicity prediction. S. Ceccatelli reviewed the implementation of rodent and human neural stem cells (NSCs) as models for in vitro toxicity testing that measures parameters such as cell proliferation, differentiation and migration. These appear to be sensitive endpoints that can identify substances with developmental neurotoxic potential. C. Sun ol reviewed the use of primary neuronal cultures in testing for neurotoxicity of environmental pollutants, including the study of the effects of persistent exposures and/or in differentiating cells, which allow recording of effects that can be extrapolated to human developmental neurotoxicity.

Endometrial cancer and oral contraceptives : an individual participant meta-analysis of 27 276 women with endometrial cancer from 36 epidemiological studies.

BACKGROUND: Oral contraceptives are known to reduce the incidence rate of endometrial cancer, but it is uncertain how long this effect lasts after use ceases, or whether it is modified by other factors. METHODS: Individual participant datasets were sought from principal investigators and provided centrally for 27 276 women with endometrial cancer (cases) and 115 743 without endometrial cancer (controls) from 36 epidemiological studies. The relative risks (RRs) of endometrial cancer associated with oral contraceptive use were estimated using logistic regression, stratified by study, age, parity, body-mass index, smoking, and use of menopausal hormone therapy. FINDINGS: The median age of cases was 63 years (IQR 57-68) and the median year of cancer diagnosis was 2001 (IQR 1994-2005). 9459 (35%) of 27 276 cases and 45 625 (39%) of 115 743 controls had ever used oral contraceptives, for median durations of 3·0 years (IQR 1-7) and 4·4 years (IQR 2-9), respectively. The longer that women had used oral contraceptives, the greater the reduction in risk of endometrial cancer; every 5 years of use was associated with a risk ratio of 0·76 (95% CI 0·73-0·78; p<0·0001). This reduction in risk persisted for more than 30 years after oral contraceptive use had ceased, with no apparent decrease between the RRs for use during the 1960s, 1970s, and 1980s, despite higher oestrogen doses in pills used in the early years. However, the reduction in risk associated with ever having used oral contraceptives differed by tumour type, being stronger for carcinomas (RR 0·69, 95% CI 0·66-0·71) than sarcomas (0·83, 0·67-1·04; case-case comparison: p=0·02). In high-income countries, 10 years use of oral contraceptives was estimated to reduce the absolute risk of endometrial cancer arising before age 75 years from 2·3 to 1·3 per 100 women. INTERPRETATION: Use of oral contraceptives confers long-term protection against endometrial cancer. These results suggest that, in developed countries, about 400 000 cases of endometrial cancer before the age of 75 years have been prevented over the past 50 years (1965-2014) by oral contraceptives, including 200 000 in the past decade (2005-14). FUNDING: Medical Research Council, Cancer Research UK.

Eficàcia de la imitació, teràpia que activa les neurones mirall, en la rehabilitació de persones que han patit un ACV.

L’objectiu d’aquest projecte és avaluar l’eficàcia de la teràpia d’imitació, basada en l’activació de les neurones mirall, per augmentar la funcionalitat de l’extremitat superior parètica i millorar la qualitat de vida dels pacients que presenten un accident cerebrovascular a través d’un assaig clínic controlat aleatoritzat. Es crea un grup experimental ( teràpia imitació més teràpia fisioteràpia convencional) i un grup control ( teràpia fisioteràpia convencional) que duran a terme un tractament de 13 setmanes. Per a comprovar els resultats es realitzaran sis avaluacions ( primer dia, sis setmanes, tretze setmanes, sis mesos i al cap d’un any) a través de les següents escales: Medical Research Council (MRC) per la força, Action Research Arm test (ARAT) per la motricitat de la mà, l’índex de Barthel per al grau d’independència de les activitats bàsiques de la vida diària, l’índex de Lawton i Brody pel grau d’independència de les activitats instrumentals de la vida diària i el SF-36 per la qualitat de vida.

Com ha de ser l'economia del coneixement?

Catalunya ha apostat per una política de recerca que cada dia aconsegueix bons resultats. Aquesta setmana s'ha fet públic que 14 investigadors que treballen en centres i universitats catalanes han rebut les prestigioses 'Starting Grants de l'European Research Council'. El resultat és destacable si es considera que tot l'Estat espanyol, amb Catalunya, n'ha rebut 29. Catalunya està per sobre de Dinamarca, Àustria, Finlàndia, Noruega, Portugal, Irlanda, Grècia, Hongria, Turquia, Polònia i Eslovàquia

Desempenho reprodutivo entre receptoras bovinas não contaminadas e naturalmente infectadas por Neospora caninum, após a transferência de embriões

O uso do conhecimento de biotécnicas para a melhoria da produção de bens e serviços tem avançado significativamente. O controle de doenças infecciosas continua a representar o maior obstáculo para a saúde dos animais. A perda embrionária pode ser responsável pelo aumento de prejuízos econômicos isolados para os produtores de bovinos. A infecção por Neospora caninum tem emergido como uma importante doença reprodutiva e, em vários países, tem sido diagnosticada como principal causa de aborto. O objetivo desse trabalho foi comparar o desempenho reprodutivo em receptoras bovinas não contaminadas e naturalmente infectadas por Neospora caninum após a transferência de embriões (TE). A escolha dos animais (n=395) para o experimento foi realizada através de avaliação ginecológica, via palpação transretal. As vacinações seguiram protocolo sanitário recomendado para a TE. O manejo nutricional foi baseado no National Research Council (NRC, 1999). A TE de embriões descongelados foi feita após a sincronização do ciclo estral das receptoras. Para a avaliação do desempenho reprodutivo se utilizou de ultrassonografia transretal. A identificação das receptoras positivas para Neospora caninum realizou-se através do teste de ELISA e, para as amostras reagentes, confirmação através de imunofluorescência indireta (IFI). Os dados foram analisados utilizando Past® e foram considerados estatisticamente significantes (P<0,01). Os resultados mostram uma taxa de prenhes (n=191) de 48,35%, seguida de uma taxa de abortos aos 60 dias de gestação (n=14) de 3,5% e abortos ao sexto mês de gestação (n=12) de 3,04%. Esses resultados tornam-se relevantes quando se leva em consideração que, receptoras infectadas pelo protozoário não apresentaram uma taxa elevada de perdas gestacionais. A insignificância estatística dos dados obtidos nesse estudo confere a segurança em sugerir que não há necessidade em implantar o diagnóstico ou controle prévios para Neosporose em rebanhos aptos a TE.

Seletividade de herbicidas para a cultura de milho (Zea mays) aplicados em diferentes estádios fenológicos da cultura

O objetivo deste trabalho foi avaliar a seletividade de herbicidas aplicados em condições de pré e pós-emergência da cultura de milho, conduzida sob sistema de semeadura direta, sem a presença de plantas daninhas durante todo o ciclo da cultura. O híbrido utilizado foi o Pioneer 3027, e o delineamento experimental adotado foi em blocos casualizados, com 22 tratamentos e três repetições. Os tratamentos herbicidas utilizados (em g i.a. ha-1), com os respectivos estádios fenológicos (número de folhas definitivas = NF) no momento da aplicação dos respectivos tratamentos herbicidas, foram: atrazine + metolachlor (1.400 + 2.100) em condições de pré-emergência da cultura; (atrazine + metolachlor) + nicosulfuron [(1.000 + 1.500 + 20)] com a cultura apresentando NF = 2; atrazine + óleo vegetal (2.400 + 1.800), NF = 2, 4 e 8; atrazine + simazine (1.250 + 1.250), NF = 2, 4 e 8; nicosulfuron (40 - NF = 2, 4 e 8; 20 - NF = 4 e 8 e 52 - NF = 4 e 8); e (atrazine + óleo vegetal) + nicosulfuron [(800 + 600) + 20; (800 + 600) + 40 e (800 + 600) + 52), NF = 4 e 8]. Foram feitas avaliações visuais de sintomas de fitotoxicidade provocados pelos herbicidas aos 7, 14 e 21 dias após aplicação, usando a escala proposta pela European Weed Research Council, além dos parâmetros relativos aos componentes de produção da cultura e produtividade final. Os resultados obtidos indicaram que a duração dos estádios fenológicos da cultura não foi afetada pelos herbicidas utilizados e que alguns tratamentos herbicidas, quando aplicados no estádio fenológico 2 (NF = 8 ), reduzem o rendimento da cultura, devido à alteração do número de fileiras por espiga, do número de grãos por fileira e da massa de 1.000 grãos de milho, sendo recomendável a aplicação de herbicidas na cultura de milho até o estádio fenológico 1 (NF = 4), para evitar danos à cultura por fitotoxicidade.

Visual Arts Data Skills for Researchers (VADS4R)

Workshop at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Relationship between disease severity and quality of life in patients with chronic obstructive pulmonary disease

Few studies have evaluated the relationship between Airways Questionnaire 20 (AQ20), a measure of the quality of life, scores and physiological outcomes or with systemic markers of disease in patients with chronic obstructive pulmonary disease (COPD). The aim of the present study was to investigate the relationship of forced expiratory volume in 1 s (FEV1), body mass index, fat-free mass index, 6-min walk test (6MWT) results, dyspnea sensation and peripheral oxygen saturation (SpO2) with the quality of life of COPD patients. Ninety-nine patients with COPD (mean age: 64.2 ± 9.2 years; mean FEV1: 60.4 ± 25.2% of predicted) were evaluated using spirometry, body composition measurement and the 6MWT. The baseline dyspnea index (BDI) and the Modified Medical Research Council (MMRC) scale were used to quantify dyspnea. Quality of life was assessed using the AQ20 and the St. George's Respiratory Questionnaire (SGRQ). The Charlson index was used to determine comorbidity. The body mass index/airflow obstruction/dyspnea/exercise capacity (BODE) index was also calculated. AQ20 and SGRQ scores correlated significantly with FEV1, SpO2, 6MWT, MMRC and BDI values as did with BODE index. In the multivariate analyses, MMRC or BDI were identified as predictors of AQ20 and SGRQ scores (P < 0.001 in all cases). Thus, the relationship between AQ20 and disease severity is similar to that described for SGRQ. Therefore, the AQ20, a simple and brief instrument, can be very useful to evaluate the general impact of disease when the time allotted for measurement of the quality of life is limited.