Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills

Spatiotemporal variation of the epifaunal assemblages associated to Sargassum muticum on the NW Atlantic coast of Morocco

Epifaunal assemblages inhabiting the non-indigenous macroalga Sargassum muticum (Yendo) Fensholt were investigated on two physically distinct intertidal rocky (S1) and sandy (S2) sites along the Atlantic coast of Morocco. The objective of this study was to test whether the habitat-forming marine alga S. muticum invasive in these sites supported different epifaunal assemblages under different environmental conditions and through time. The gastropods Steromphala umbilicalis, S. pennanti, and Rissoa parva and the isopod Dynamene bidentata were the most contributive species to the dissimilarity of epifaunal assemblage structure between both sites throughout seasons. SIMPER analysis showed a dissimilarity of 58.3-78.5% in the associated species composition of S. muticum between study sites with respect to sampling season. Species diversity and total abundance were significantly higher at the rocky site compared to the sandy site. PERMANOVA analyses showed significant differences of associated epifaunal assemblage structure for the season and site interaction. Accordingly, site and season were determinant factors conditioning the role of habitat in structuring epifaunal assemblages.info:eu-repo/semantics/publishedVersio

Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors

The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5) mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors

A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r(2) of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r(2) of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62863/1/nature06258.pd

Global Diversity of Ascidiacea

The class Ascidiacea presents fundamental opportunities for research in the fields of development, evolution, ecology, natural products and more. This review provides a comprehensive overview of the current knowledge regarding the global biodiversity of the class Ascidiacea, focusing in their taxonomy, main regions of biodiversity, and distribution patterns. Based on analysis of the literature and the species registered in the online World Register of Marine Species, we assembled a list of 2815 described species. The highest number of species and families is found in the order Aplousobranchia. Didemnidae and Styelidae families have the highest number of species with more than 500 within each group. Sixty percent of described species are colonial. Species richness is highest in tropical regions, where colonial species predominate. In higher latitudes solitary species gradually contribute more to the total species richness. We emphasize the strong association between species richness and sampling efforts, and discuss the risks of invasive species. Our inventory is certainly incomplete as the ascidian fauna in many areas around the world is relatively poorly known, and many new species continue to be discovered and described each year

Dose reduzida de clethodim no controle de papua na cultura da soja, em função da época de aplicação Reduced rate of clethodim for alexandergrass: control in soybeans as a function of application time

Foi realizado um experimento a campo em Eldorado do Sul, RS, no ano agrícola de 19 94 /9 5, para avaliar o controle de papuã (Brachiaria plantaginea (Linck) Hitchc.), que ocorreu numa população média de 95 plantas/m2. Foi avaliado o herbicida clethodim à dose-plena (120g/ ha) e à meia-dose (60g/ha). A cultivar de soja utilizada foi RS-7 Jacuí e usado o delineamento experimental em blocos casualizados com quatro repetições. Os tratamentos foram aplicados aos 14, 21, 28 e 35 dias após a emergência da soja (DAE). Foram mantidas testemunhas capinadas, com operações iniciadas nas mesmas épocas de aplicação do herbicida, e uma testemunha infestada durante todo o ciclo da cultura. O controle foi avaliado visualmente, em três ocasiões, através de escala percentual. Os graus de controle de papua obtidos à dose-plena foram equivalentes entre si quando aplicado nas três primeiras épocas, com eficiência entre 95 e 98% na última avaliação. A meia-dose mostrou, para as três primeiras épocas de aplicação, resultados semelhantes aos de doseplena, porém em níveis um pouco inferiores, situando-se entre 85 e 95% o controle obtido na última avaliação. O controle do papuã foi mediano quando clethodim foi aplicado aos 35 DAE, tanto par a dose-plena quanto para meiadose. Quanto ao rendimento de grãos, não houve diferença estatística significativa entre os tratamentos em suas várias modalidades, embora todos tenham superado a testemunha infestada, com incrementos na produtividade de grãos entre 73 e 10 5% . O experimento permite concluir pela viabilidade da utilização de meiadose de clethodim para o controle de papua em soja, realizando as aplicações preferencialmente até a quarta semana após a emergência da cultura.<br>A field trial was carried out in Eldorado do Sul, RS, during the 1994/95 growing season to evaluate Alexandergrass (Brachiaria plantaginea (Linck ) Hitchc ) control, that occurred with na average population of 95 plants/m2. The herbicide used was clethodim at full-rate (120g/ha) and at half-rate (60g/ha). The tested cultivar was RS-7 Jacuí and it was use d a complete randomized blocks design with four replicates. The treatments were applied at 14, 21, 28, and 35 days after soybean emergence (DAE) . Hand hoeing treatments were included, and started at the same date of herbicide applications. A weeded check was kept during all crop cycle. Control evaluations were visualy performed in three opportunities using percentual scale. The levels of Alexandergrass control got with full herbicide rate were equival ents when clethodim was applied at the three first times. Its efficiency ranged from 95 to 98% at the last evaluation. Half herbicide rate showed si mil ar trends at the la st eval uation, although at lower levels, ranging from 85 to 95% control for the three first application times. Alexandergrass control was only fair when clethodim was applied at 35 DAE at either rate. Grain yield did not show differences between treatments except for weedy check; nevertheless, all of them supplanted the weeded treatment with increments ranging from 73 to 105%. This trial allows to conclude that it is possible to use half-rate of clethodim to control Alexandergrass in soybean, being the application done preferably until the fourth week after soybean emergence