QuickGO: a web-based tool for Gene Ontology searching

Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation

Student Knowledge of Signs, Risk Factors, and Resources for Depression, Anxiety, Sleep Disorders, and Other Mental Health Problems on Campus

A mixed methods study sought to assess student knowledge of signs, risk factors, and campus services available for mental health disorders. A survey was completed by 831 students and three focus groups were conducted. Respondents felt more knowledgeable about depression than about anxiety and sleep disorders. Graduate students and seniors had a keener awareness of risk factors for anxiety and sophomores were in the greatest danger of failing to recognize these risks. Males often failed to recognize signs and risk factors for mental health problems. Support groups, courses, and workshops on managing relationships, transition to college, and specific mental health disorders are advocated

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

from A critical assessment of text mining methods in molecular biolog

Student Knowledge of Signs, Risk Factors, and Resources for Depression, Anxiety, Sleep Disorders, and Other Mental Health Problems on Campus

A mixed methods study sought to assess knowledge of the signs, risk factors, and campus services available for mental health disorders. A survey was completed by 831 participants at a college of approximately 9,000 students in the northeastern region of the United States. Students evidenced a need for more education about mental health problems on the college campus. Respondents felt more knowledgeable about depression than about anxiety and sleep disorders. Over half of the respondents were unable to identify specific mental health problems that they were aware of. Upperclassmen had a keener awareness of risk factors for anxiety and sophomores were in the greatest danger of failing to recognize risk factors for anxiety. Females consistently recognized signs and risk factors for anxiety, sleep disorders, and depression more frequently than males. Support groups, courses, and workshops on managing relationships, transition to college, and other mental health issues are recommended to increase awareness of mental health needs and services. Convenient access to counseling and fitness activities are encouraged

Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes

Several major invasive bacterial pathogens are encapsulated. Expression of a polysaccharide capsule is essential for survival in the blood, and thus for virulence, but also is a target for host antibodies and the basis for effective vaccines. Encapsulated species typically exhibit antigenic variation and express one of a number of immunochemically distinct capsular polysaccharides that define serotypes. We provide the sequences of the capsular biosynthetic genes of all 90 serotypes of Streptococcus pneumoniae and relate these to the known polysaccharide structures and patterns of immunological reactivity of typing sera, thereby providing the most complete understanding of the genetics and origins of bacterial polysaccharide diversity, laying the foundations for molecular serotyping. This is the first time, to our knowledge, that a complete repertoire of capsular biosynthetic genes has been available, enabling a holistic analysis of a bacterial polysaccharide biosynthesis system. Remarkably, the total size of alternative coding DNA at this one locus exceeds 1.8 Mbp, almost equivalent to the entire S. pneumoniae chromosomal complement

Evaluation of Lateglacial temperatures in the Southern Alps of New Zealand based on glacier modelling at Irishman Stream, Ben Ohau Range

Climate proxy records from the middle to high latitude Southern Hemisphere indicate that a Lateglacial (15,000-11,500 years ago) climate reversal, approximately coeval with the Antarctic Cold Reversal (ACR), interrupted a warming trend during deglaciation. In New Zealand, some palaeoclimate proxy records indicate a cool episode during the ACR (ca 14,500-12,500 years ago), while others do not express a significant change in climate. Recently published moraine maps and ages present an opportunity to improve the palaeoclimate interpretation through numerical modelling of glaciers. We use a coupled energy-balance and ice-flow model to quantify palaeoclimate from past glacier extent constrained by mapped and dated moraines in the headwaters of Irishman Stream, a high-elevation catchment in the Southern Alps. First, a suite of steady-state model runs is used to identify the temperature and precipitation forcing required to fit the modelled glacier to well-dated Lateglacial moraine crests. Second, time dependent glacier simulations forced by a nearby proxy temperature record derived from chironomids are used to assess the fit with the glacial geomorphic record. Steady-state experiments using an optimal parameter set demonstrate that the conditions under which the 13,000 year old moraine formed were 2.3-3.2 *C colder than present with the range in temperature corresponding to a +/- 20% variance in precipitation relative to the present-day. This reconstructed climate change relative to the present-day corresponds to an equilibrium-line altitude of ca 2000 +/- 40 m above sea level (asl), which is ca 400 m lower than present. Time-dependent simulations of glacier length produce ice advance to within 100 m of the 13,000 year old terminal moraine, indicating that the chironomid-based temperature forcing and moraine record provide consistent information about past climate. Our results, together with other climate proxy reconstructions from pollen records and marine sediment cores, support the notion that temperatures during the ACR in New Zealand were ~2-3 *C cooler than today

AgBase: a functional genomics resource for agriculture

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms

GOing Bayesian: model-based gene set analysis of genome-scale data

The interpretation of data-driven experiments in genomics often involves a search for biological categories that are enriched for the responder genes identified by the experiments. However, knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categories. Thus, enrichment analysis performed on one category at a time frequently returns large numbers of correlated categories, leaving the choice of the most relevant ones to the user's; interpretation

QuickGO: a user tutorial for the web-based Gene Ontology browser

The Gene Ontology (GO) has proven to be a valuable resource for functional annotation of gene products. At well over 27 000 terms, the descriptiveness of GO has increased rapidly in line with the biological data it represents. Therefore, it is vital to be able to easily and quickly mine the functional information that has been made available through these GO terms being associated with gene products. QuickGO is a fast, web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. After undergoing a redevelopment, QuickGO is now able to offer many more features beyond simple browsing. Users have responded well to the new tool and given very positive feedback about its usefulness. This tutorial will demonstrate how some of these features could be useful to the researcher wanting to discover more about their dataset, particular areas of biology or to find new ways of directing their research