PSICQUIC and PSISCORE: accessing and scoring molecular interactions

To the Editor.-- Author Manuscript.-- et al.This study was supported by the European Commission under the Serving Life-science Information for the Next Generation contract 226073; Proteomics Standards Initiative and International Molecular Exchange contract FP7-HEALTH-2007-223411; Apoptosis Systems Biology Applied to Cancer and AIDS contract FP7-HEALTH-2007-200767; Experimental Network for Functional Integration contract LSHG-CT-2005-518254; German National Genome Research Network; German Research Foundation contract KFO 129/1-2; US National Institutes of Health grant R01GM071909; the Italian Association for Cancer Research; a Wellcome Trust Strategic Award to the European Molecular Biology Laboratory–European Bioinformatics Institute for Chemogenomics Databases; Grand Challenges in Global Health Research, the Canadian Institutes of Health Research, Foundation for the National Institutes of Health and Genome British Columbia; and a German Research Foundation–funded Cluster of Excellence for Multimodal Computing and Interaction.Peer Reviewe

Natural variation in FLOWERING LOCUS T, HvFT1

1 .pdf copy (A3) of the original poster presented by the Authors.The barley ortholog of FLOWERING LOCUS T, HvFT1, also called VrnH3, is the main integrator of the photoperiod and vernalization signals leading to the transition from the vegetative to the reproductive stage. Results gathered by us and other groups for the last years have repeatedly identified variation in this gene related with flowering time QTL in mapping populations and also in genome wide association studies. Differences in the promoter, SNPs in the first intron and also copy number variation have all being associated with phenotypic and expression differences, resulting in earlier or later heading. The first reports found that mutations in the HvFT1 first intron differentiated plants with dominant and recessive alleles, with large phenotypic effect on time to flowering. The catalog of polymorphisms at this gene with potential phenotypic effect has been enlarged with copy number variation and sequence variation at the promoter. There is variation in the number of copies of the HvFT1 gene, apparently related to growth habit. A large set of winter genotypes, with a functional VrnH2 allele, has one copy of VrnH3, whereas variable number (1-5), was found in also a large set of spring or facultative barleys (without VrnH2). The dominant VrnH3 allele, which overrides the vernalization requirement of winter VrnH1 and VrnH2 alleles, is found only in Nordic barleys and carries a particular structure of the gene, with one promoter and variable number of transcribed regions. Using two indels from the promoter region and allele-specific markers for two SNPs in the first intron, we were able to classify four VrnH3 haplotypes, which showed differences in heading time among Spanish landraces. We will present results from several mapping populations and association analyses to contribute to describe the different polymorphisms that should be taken into consideration when analyzing this gene and its phenotypic effects.Peer reviewe

Effect of social instigation and aggressive behavior on hormone levels of lactating dams and adult male Wistar rats

Among rodents, maternal aggression in the postpartum period represents a species-typical adaptation, but when aggressive behavior increases beyond this adaptive level, it can represent a model of excessive aggression. This study assessed the neuroendocrine response of lactating rats and socially instigated male rats. The aim of the present study was to assess neuroendocrine responses and the behavioral pattern of lactating rats and males that were subjected to an emotional stressor using the social instigation protocol. We measured plasma corticosterone levels as the key hormonal parameter of the hypothalamic-pituitary-adrenal (HPA) axis and oxytocin, prolactin, and progesterone, which are released in response to several types of stressors. Our results showed that lactating rats that were subjected to only social instigation or aggressive confrontation in the presence of their pups had lower plasma corticosterone levels, and this response was similar to oxytocin, prolactin, and progesterone levels. By contrast, male rats showed increased corticosterone levels after being subjected only to social instigation. Male rats also engaged in aggressive behavior compared with the control group. In conclusion, this study demonstrated that lactating rats subjected to social instigation exhibited an attenuation of the HPA axis response, which is considered to be crucial to the dam's welfare so that it can care for its offspring. Thus, we can infer that lactation is a relevant factor in neuroendocrine responses to stress because of the increased levels of corticosterone in males.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES

Effect of social instigation and aggressive behavior on hormone levels of lactating dams and adult male Wistar rats

Among rodents, maternal aggression in the postpartum period represents a species-typical adaptation, but when aggressive behavior increases beyond this adaptive level, it can represent a model of excessive aggression. This study assessed the neuroendocrine response of lactating rats and socially instigated male rats. The aim of the present study was to assess neuroendocrine responses and the behavioral pattern of lactating rats and males that were subjected to an emotional stressor using the social instigation protocol. We measured plasma corticosterone levels as the key hormonal parameter of the hypothalamic-pituitary-adrenal (HPA) axis and oxytocin, prolactin, and progesterone, which are released in response to several types of stressors. Our results showed that lactating rats that were subjected to only social instigation or aggressive confrontation in the presence of their pups had lower plasma corticosterone levels, and this response was similar to oxytocin, prolactin, and progesterone levels. By contrast, male rats showed increased corticosterone levels after being subjected only to social instigation. Male rats also engaged in aggressive behavior compared with the control group. In conclusion, this study demonstrated that lactating rats subjected to social instigation exhibited an attenuation of the HPA axis response, which is considered to be crucial to the dam's welfare so that it can care for its offspring. Thus, we can infer that lactation is a relevant factor in neuroendocrine responses to stress because of the increased levels of corticosterone in males.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES

The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions.

The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.This study was supported by the King Abdullah University of Science and Technology under baseline funds to C.R.V. and the Center Competitive Fund Program FCC/1/1973-22-01. Further funding was contributed by the Natural Environment Research Council (NE/K00641X/1 to J.W.) and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/European Research Council (grant agreement no. 311179 to J.W.)

PROPOSIÇÃO DE DIRETRIZES PARA CERTIFICAÇÃO PÚBLICA DE ARBORIZAÇÃO URBANA - ESTUDO DE CASO

A boa gestão da arborização urbana municipal pode contribuir para a sustentabilidade das cidades, resultando em benefícios para o meio ambiente, as pessoas e a aplicação eficiente de recursos. Assim, foram propostas quatro diretrizes que poderão auxiliar nas discussões para a elaboração de um modelo de certificação pública de arborização urbana, como forma de incentivar os municípios a endossarem o planejamento do manejo arbóreo e melhorar sua realidade ambiental. Essas diretrizes dizem respeito à elaboração participativa do Plano Municipal de Arborização Urbana, configuração mínima do conteúdo, aplicação das ações e, por fim, a revisão e avaliação contínua. Para tal desenvolvimento, foram selecionados por amostragem trinta e nove Planos Municipais de Arborização Urbana do Estado de São Paulo a fim de identificar seu conteúdo e propor diretrizes de uma certificação para respaldar o planejamento desses planos. Os documentos verificados tinham informações básicas em comum, mas não aprofundavam seu conteúdo e raramente definiam ações e recursos para sua implementação, indicando uma provável má aplicação desses planos

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A. R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. The data used in this project were funded by the Great Barrier Reef Foundation’s Resilient Coral Reefs Successfully Adapting to Climate Change research and development program in collaboration with the Australian Government, Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy (NCRIS), Rio Tinto and a family foundation. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consuming and the coverage of published interaction data is therefore far from complete. The use of text-mining tools to identify relevant publications and to assist in the initial information extraction could help to improve the efficiency of the curation process and, as a consequence, the database coverage of data available in the literature. The 2006 BioCreative competition was aimed at evaluating text-mining procedures in comparison with manual annotation of protein-protein interactions

Validity of Virtual Reality Body Exposure to Elicit Fear of Gaining Weight, Body Anxiety and Body-Related Attentional Bias in Patients with Anorexia Nervosa

Fear of gaining weight (FGW), body image disturbances, associated anxiety and body-related attentional bias are the core symptoms of anorexia nervosa (AN) and play critical roles in its development and maintenance. The aim of the current study is to evaluate the usefulness of virtual reality-based body exposure software for the assessment of important body-related cognitive and emotional responses in AN. Thirty female patients with AN, one of them subclinical, and 43 healthy college women, 25 with low body dissatisfaction (BD) and 18 with high BD, owned a virtual body that had their silhouette and body mass index. Full-body illusion (FBI) over the virtual body was induced using both visuo-motor and visuo-tactile stimulation. Once the FBI was induced, the FBI itself, FGW, body anxiety and body-related attentional bias toward weight-related and non-weight-related body areas were assessed. One-way analyses of covariance (ANCOVA), controlling for age, showed that AN patients reported higher FGW, body anxiety and body-related attentional bias than healthy controls. Unexpectedly, patients with AN reported significantly lower FBI levels than healthy participants. Finally, Pearson correlations showed significant relationships between visual analog scales and body-related attentional bias measures, compared to other eating disorder measures. These results provide evidence about the usefulness of virtual reality-based body exposure to elicit FGW and other body-related disturbances in AN patients. Thus, it may be a suitable intervention for reducing these emotional responses and for easing weight recovery