GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments

BACKGROUND: The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. RESULTS: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. CONCLUSION: GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets

Climate change promotes parasitism in a coral symbiosis.

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change

Determination of urban volatile organic compound emission ratios and comparison with an emissions database

During the NEAQS-ITCT2k4 campaign in New England, anthropogenic VOCs and CO were measured downwind from New York City and Boston. The emission ratios of VOCs relative to CO and acetylene were calculated using a method in which the ratio of a VOC with acetylene is plotted versus the photochemical age. The intercept at the photochemical age of zero gives the emission ratio. The so determined emission ratios were compared to other measurement sets, including data from the same location in 2002, canister samples collected inside New York City and Boston, aircraft measurements from Los Angeles in 2002, and the average urban composition of 39 U.S. cities. All the measurements generally agree within a factor of two. The measured emission ratios also agree for most compounds within a factor of two with vehicle exhaust data indicating that a major source of VOCs in urban areas is automobiles. A comparison with an anthropogenic emission database shows less agreement. Especially large discrepancies were found for the C2-C4 alkanes and most oxygenated species. As an example, the database overestimated toluene by almost a factor of three, which caused an air quality forecast model (WRF-CHEM) using this database to overpredict the toluene mixing ratio by a factor of 2.5 as well. On the other hand, the overall reactivity of the measured species and the reactivity of the same compounds in the emission database were found to agree within 30%. Copyright 2007 by the American Geophysical Union

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency

In vitro and in vivo evaluation of human adenovirus type 49 as a vector for therapeutic applications

The human adenovirus phylogenetic tree is split across seven species (A–G). Species D adenoviruses offer potential advantages for gene therapy applications, with low rates of pre-exist-ing immunity detected across screened populations. However, many aspects of the basic virology of species D—such as their cellular tropism, receptor usage, and in vivo biodistribution profile— remain unknown. Here, we have characterized human adenovirus type 49 (HAdV-D49)—a rela-tively understudied species D member. We report that HAdV-D49 does not appear to use a single pathway to gain cell entry, but appears able to interact with various surface molecules for entry. As such, HAdV-D49 can transduce a broad range of cell types in vitro, with variable engagement of blood coagulation FX. Interestingly, when comparing in vivo biodistribution to adenovirus type 5, HAdV-D49 vectors show reduced liver targeting, whilst maintaining transduction of lung and spleen. Overall, this presents HAdV-D49 as a robust viral vector platform for ex vivo manipulation of human cells, and for in vivo applications where the therapeutic goal is to target the lung or gain access to immune cells in the spleen, whilst avoiding liver interactions, such as intravascular vaccine applications

Carbonyl sulfide (OCS): Large-scale distributions over North America during INTEX-NA and relationship to CO2

An extensive set of carbonyl sulfide (OCS) observations were made as part of the NASA Intercontinental Chemical Transport Experiment-North America (INTEX-NA) study, flown from 1 July to 14 August 2004 mostly over the eastern United States and Canada. These data show that summertime OCS mixing ratios at low altitude were dominated by surface drawdown and were highly correlated with CO2. Although local plumes were observed on some low-altitude flight legs, anthropogenic OCS sources were small compared to this sink. These INTEX-NA observations were in marked contrast to the early springtime 2001 Transport and Chemical Evolution over the Pacific experiment, which sampled Asian outflow dominated by anthropogenic OCS emissions. To test the gridded OCS fluxes used in past models, the INTEX-NA observations were combined with the sulfur transport Eulerian model (STEM) regional atmospheric chemistry model for a top-down assessment of bottom-up OCS surface fluxes for North America. Initial STEM results suggest that the modeled fluxes underestimate the OCS plant sink by more than 200%. Copyright 2008 by the American Geophysical Union

Photochemically re-bridging disulfide bonds and the discovery of a thiomaleimide mediated photodecarboxylation of C-terminal cysteines

Described in this work is a novel method for photochemically manipulating peptides and proteins via the installation of cysteine-selective photoactive tags. Thiomaleimides, generated simply by the addition of bromomaleimides to reduced disulfide bonds, undergo [2 + 2] photocycloadditions to reconnect the crosslink between the two cysteine residues. This methodology is demonstrated to enable photoactivation of a peptide by macrocyclisation, and reconnection of the heavy and light chains in an antibody fragment to form thiol stable conjugates. Finally we report on an intriguing thiomaleimide mediated photochemical decarboxylation of C-terminal cysteines, discovered during this study

Neural Responses to Novel and Existing Words in Children with Autism Spectrum and Developmental Language Disorder

\ua9 2021, the Authors.The formation of new phonological representations is key in establishing items in the mental lexicon. Phonological forms become stable with repetition, time and sleep. Atypicality in the establishment of new word forms is characteristic of children with developmental language disorder (DLD) and autism spectrum disorder (ASD), yet neural changes in response to novel word forms over time have not yet been directly compared in these groups. This study measured habituation of event-related-potentials (ERPs) to novel and known words within and between two sessions spaced 24 hours apart in typically developing (TD) children, and their peers with DLD or ASD. We hypothesised that modulation of the auditory N400 amplitude would mark real-time changes in lexical processing with habituation evident within and across sessions in the TD group, while the DLD group would show attenuated habituation within sessions, and the ASD group attenuated habituation between sessions. Twenty-one typically developing children, 19 children with ASD, and 16 children with DLD listened passively to known and novel words on two consecutive days, while ERPs were recorded using dry electrodes. Counter to our hypotheses, no habituation effect emerged within sessions. However, responses did habituate between sessions, with this effect being reduced in the DLD group, indicating less pre-activation of lexical representations in response to words encountered the previous day. No differences in change over time were observed between the TD and ASD groups. These data are in keeping with theories stressing the importance of sleep-related consolidation in word learning

Consenting to health record linkage: evidence from a multi-purpose longitudinal survey of a general population

Background: The British Household Panel Survey (BHPS) is the first long-running UK longitudinal survey with a non-medical focus and a sample covering the whole age range to have asked for permission to link to a range of administrative health records. This study determines whether informed consent led to selection bias and reflects on the value of the BHPS linked with health records for epidemiological research. Methods. Multivariate logistical regression is used, with whether the respondent gave consent to data linkage or not as the dependent variable. Independent variables were entered as four blocks; (i) a set of standard demographics likely to be found in most health registration data, (ii) a broader set of socio-economic characteristics, (iii) a set of indicators of health conditions and (iv) information about the use of health services. Results: Participants aged 16-24, males and those living in England were more likely to consent. Consent is not biased with respect to socio-economic characteristics or health. Recent users of GP services are underrepresented among consenters. Conclusions: Whilst data could only be linked for a minority of BHPS participants, the BHPS offers a great range of information on people's life histories, their attitudes and behaviours making it an invaluable source for epidemiological research. © 2012 Knies et al; licensee BioMed Central Ltd