EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)

BACKGROUND: Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. RESULTS: The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site through the quick link 'Browse Records by 3D Structure.' CONCLUSION: The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required

Predicting impacts of an invading copepod by ecological assessment in the animal's native range

We assembled data from 11 years of observational research on zooplankton in subtropical Florida, USA, lakes to determine potential impacts of the copepod Arctodiaptomus dorsalis on biodiversity and biomass of co-occurring crustacean zooplankton. This synthesis provided insight into how the species might impact plankton in limnologically similar lakes that it invades outside of its native range. A. dorsalis recently was found in the Philippines, and it was suggested that it could invade lakes in Asia and reduce biodiversity. In 7 shallow eutrophic lakes in Florida, we found no relationship between relative biomass of A. dorsalis and number of species of crustacean zooplankton, and we were equally likely to find a similar-sized copepod Diaptomus floridanus in lakes with or without A. dorsalis. In Lake Okeechobee, where a 7-year dataset existed for crustacean zooplankton, we found no evidence that A. dorsalis impacts the biomass of cladocerans or other dominant copepods. Gut analysis and grazing experiments documented that A. dorsalis is capable of eating bacteria and nearly all phytoplankton taxa, including cyanobacteria. This ability to exploit a broad range of resources and to execute rapid escape maneuvers to avoid fish predation may explain why A. dorsalis often is dominant in shallow eutrophic lakes with high densities of omnivorous fish. We conclude that A. dorsalis will not negatively affect the biodiversity of plankton in similar lakes of Asia; instead, it may fill a vacant niche in lakes with high fish predation where other copepods cannot survive. Further research is needed to determine how A. dorsalis will influence the plankton in less enriched lakes where food ersources may be limiting

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

The body of human genomic and proteomic evidence continues to grow at ever-increasing rates, while annotation efforts struggle to keep pace. A surprisingly small fraction of human genes have clear, documented associations with specific functions, and new functions continue to be found for characterized genes. Here we assembled an integrated collection of diverse genomic and proteomic data for 21,341 human genes and make quantitative associations of each to 4333 Gene Ontology terms. We combined guilt-by-profiling and guilt-by-association approaches to exploit features unique to the data types. Performance was evaluated by cross-validation, prospective validation, and by manual evaluation with the biological literature. Functional-linkage networks were also constructed, and their utility was demonstrated by identifying candidate genes related to a glioma FLN using a seed network from genome-wide association studies. Our annotations are presented—alongside existing validated annotations—in a publicly accessible and searchable web interface

An analysis of fast photochemistry over high northern latitudes during spring and summer using in-situ observations from ARCTAS and TOPSE

Observations of chemical constituents and meteorological quantities obtained during the two Arctic phases of the airborne campaign ARCTAS (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites) are analyzed using an observationally constrained steady state box model. Measurements of OH and HO2 from the Penn State ATHOS instrument are compared to model predictions. Forty percent of OH measurements below 2 km are at the limit of detection during the spring phase (ARCTAS-A). While the median observed-to-calculated ratio is near one, both the scatter of observations and the model uncertainty for OH are at the magnitude of ambient values. During the summer phase (ARCTAS-B), model predictions of OH are biased low relative to observations and demonstrate a high sensitivity to the level of uncertainty in NO observations. Predictions of HO2 using observed CH2O and H2O2 as model constraints are up to a factor of two larger than observed. A temperature-dependent terminal loss rate of HO2 to aerosol recently proposed in the literature is shown to be insufficient to reconcile these differences. A comparison of ARCTAS-A to the high latitude springtime portion of the 2000 TOPSE campaign (Tropospheric Ozone Production about the Spring Equinox) shows similar meteorological and chemical environments with the exception of peroxides; observations of H2O2 during ARCTAS-A were 2.5 to 3 times larger than those during TOPSE. The cause of this difference in peroxides remains unresolved and has important implications for the Arctic HOx budget. Unconstrained model predictions for both phases indicate photochemistry alone is unable to simultaneously sustain observed levels of CH2O and H2O2; however when the model is constrained with observed CH2O, H2O2 predictions from a range of rainout parameterizations bracket its observations. A mechanism suitable to explain observed concentrations of CH2O is uncertain. Free tropospheric observations of acetaldehyde (CH3CHO) are 2–3 times larger than its predictions, though constraint of the model to those observations is sufficient to account for less than half of the deficit in predicted CH2O. The box model calculates gross O3 formation during spring to maximize from 1–4 km at 0.8 ppbv d−1, in agreement with estimates from TOPSE, and a gross production of 2–4 ppbv d−1 in the boundary layer and upper troposphere during summer. Use of the lower observed levels of HO2 in place of model predictions decreases the gross production by 25–50%. Net O3 production is near zero throughout the ARCTAS-A troposphere, and is 1–2 ppbv in the boundary layer and upper altitudes during ARCTAS-B

Prevalence and Correlates of Fire-Setting in the United States: Results from the National Epidemiologic Survey on Alcohol and Related Conditions

Fire-setting is a serious and costly form of antisocial behavior. Our objective in this study was to examine the prevalence and correlates of intentional fire-setting behavior in the U. S. Data were derived from a nationally representative sample of U.S. residents 18 years and older. Structured psychiatric interviews (N = 43,093) were completed by trained lay interviewers between 2001-2002. Fire-setting and DSM-IV mood, anxiety, substance use and personality disorders were assessed with the Alcohol Use Disorder and Associated Disabilities Interview Schedule (DSM-IV) version. The prevalence of lifetime fire-setting in the U.S. population was 1.0%. Respondents who were men, Caucasian, 18 to 35, born in the U.S., and living in the western region of the U.S. had significantly higher rates of fire-setting than their counterparts. Fire-setting was significantly associated a wide range of antisocial behaviors. Multivariate logistic regression analyses identified strong associations between lifetime alcohol and marijuana use disorders, conduct disorder, antisocial and obsessive-compulsive personality disorders, and family history of antisocial behavior. Intentional illicit fire-setting behavior is associated with a broad array of antisocial behaviors and psychiatric comorbidities. Given the substantial personal and social costs related to arson, prevention and treatment interventions targeting fire-setters potentially could save lives and property

Aerobic capacity, activity levels and daily energy expenditure in male and female adolescents of the kenyan nandi sub-group

The relative importance of genetic and socio-cultural influences contributing to the success of east Africans in endurance athletics remains unknown in part because the pre-training phenotype of this population remains incompletely assessed. Here cardiopulmonary fitness, physical activity levels, distance travelled to school and daily energy expenditure in 15 habitually active male (13.9±1.6 years) and 15 habitually active female (13.9±1.2) adolescents from a rural Nandi primary school are assessed. Aerobic capacity ([Formula: see text]) was evaluated during two maximal discontinuous incremental exercise tests; physical activity using accelerometry combined with a global positioning system; and energy expenditure using the doubly labelled water method. The [Formula: see text] of the male and female adolescents were 73.9±5.7 ml(.) kg(-1.) min(-1) and 61.5±6.3 ml(.) kg(-1.) min(-1), respectively. Total time spent in sedentary, light, moderate and vigorous physical activities per day was 406±63 min (50% of total monitored time), 244±56 min (30%), 75±18 min (9%) and 82±30 min (10%). Average total daily distance travelled to and from school was 7.5±3.0 km (0.8-13.4 km). Mean daily energy expenditure, activity-induced energy expenditure and physical activity level was 12.2±3.4 MJ(.) day(-1), 5.4±3.0 MJ(.) day(-1) and 2.2±0.6. 70.6% of the variation in [Formula: see text] was explained by sex (partial R(2) = 54.7%) and body mass index (partial R(2) = 15.9%). Energy expenditure and physical activity variables did not predict variation in [Formula: see text] once sex had been accounted for. The highly active and energy-demanding lifestyle of rural Kenyan adolescents may account for their exceptional aerobic fitness and collectively prime them for later training and athletic success

Insect assemblages attacking seeds and fruits in a rainforest in Thailand

Insect seed predators are important agents of mortality for tropical trees, but little is known about the impact of these herbivores in rainforests. During three years at Khao Chong (KHC) in southern Thailand we reared 17,555 insects from 343.2 kg or 39,252 seeds/fruits representing 357 liana and tree species. A commented list of the 243 insect species identified is provided, with details about their host plants. We observed that: (1) about 43% of identified species can be considered pests. Most were seed eaters, particularly on dry fruits. (2) About 19% of parasitoid species (all Opiinae) for which we could determine whether their primary insect host was a pest or not (all Bactrocera spp. breeding in fruits) can be considered beneficials. (3) The seeds/fruits of about 28% of the plant species in this forest were free of attack. Phyllanthaceae, Rubiaceae, and Meliaceae were attacked relatively infrequently; in contrast, Annonaceae, Fabaceae, Sapindaceae, and Myristicaceae were more heavily attacked. There was no apparent effect of plant phylogeny on rates of attack but heavily attacked tree species had larger basal area in the KHC plot than rarely attacked tree species. (4) Insects reared from fleshy fruits were more likely to exhibit relatively stable populations compared to insects reared from dry fruits, but this was not true of insects reared from dipterocarps, which appeared to have relatively stable populations throughout the study period. We tentatively conclude that insects feeding on seeds and fruits have little effect on observed levels of host abundance in this forest

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.

Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic targets. As multiple large-scale screens become available, a formal assessment of the reproducibility of these experiments becomes necessary. We analyze data from recently published pan-cancer CRISPR-Cas9 screens performed at the Broad and Sanger Institutes. Despite significant differences in experimental protocols and reagents, we find that the screen results are highly concordant across multiple metrics with both common and specific dependencies jointly identified across the two studies. Furthermore, robust biomarkers of gene dependency found in one data set are recovered in the other. Through further analysis and replication experiments at each institute, we show that batch effects are driven principally by two key experimental parameters: the reagent library and the assay length. These results indicate that the Broad and Sanger CRISPR-Cas9 viability screens yield robust and reproducible findings