National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.     

The United States, China, and invasive species: present status and future prospects

The exploding increase in trade between the United States and China, which share comparable ecosystem types, will result in unwanted establishment of alien invasive species that will inflict considerable ecological and economic damage. This undesirable result can be avoided by marshaling management tools and policy instruments that are readily available. High-level policy action is necessary to put the proper and available safeguards in place, and quickly.     

Interactive Effects of Fire, Elevated Carbon Dioxide, Nitrogen Deposition, and precipitation on a California Annual Grassland

Although it is widely accepted that elevated atmospheric carbon dioxide (CO₂), nitrogen (N) deposition, and climate change will alter ecosystem productivity and function in the coming decades, the combined effects of these environmental changes may be nonadditive, and their interactions may be altered by disturbances, such as fire. We examined the influence of a summer wildfire on the interactive effects of elevated CO₂, N deposition, and increased precipitation in a full-factorial experiment conducted in a California annual grassland. In unburned plots, primary production was suppressed under elevated CO₂. Burning alone did not significantly affect production, but it increased total production in combination with nitrate additions and removed the suppressive effect of elevated CO₂. Increased production in response to nitrate in burned plots occurred as a result of the enhanced aboveground production of annual grasses and forbs, whereas the removal of the suppressive effect of elevated CO₂ occurred as a result of increased aboveground forb production in burned, CO₂-treated plots and decreased root production in burned plots under ambient CO₂.The tissue nitrogen–phosphorus ratio, which was assessed for annual grass shoots, decreased with burning and increased with nitrate addition. Burning removed surface litter from plots, resulting in an increase in maximum daily soil temperatures and a decrease in soil moisture both early and late in the growing season. Measures of vegetation greenness, based on canopy spectral reflectance, showed that plants in burned plots grew rapidly early in the season but senesced early. Overall, these results indicate that fire can alter the effects of elevated CO₂ and N addition on productivity in the short term, possibly by promoting increased phosphorus availability.     

Why does a grasshopper have fewer,larger offspring at its range limits?

Analysis of size of offspring reared through three laboratory generations from populations of the field grasshopper Chorthippus brunneus from 27 sites around the British Isles showed that offspring were larger towards the cooler-wetter conditions in the western and northern limits of the range. This variation had a significant genetic component. There was a trade-off between clutch size and offspring size between and within populations. Under favourable thermal and feeding conditions maternal fitness was optimal when individuals produced the largest clutches of the smallest eggs, but under poor conditions maternal fitness was optimal when individuals produced small clutches of very large offspring. Calculation of geometric mean fitness over time indicated that having larger offspring near to the edge of the range could be advantageous as a conservative risk-spreading strategy. As well as geographic variation in egg size, significant environment-genotype interactions in egg size in relation to temperature were observed.     

Aerosol Evaluations of the De Vilbiss No. 40 and Vaponefrin Nebulizers

De Vilbiss no. 40 and Vaponefrin standard nebulizers produced aerosols of small particles suitable for deep pulmonary vaccination and therapy of respiratory infections in man and animals.     

A potential antioxidant resource: Endophytic fungi from medicinal plants

Medicinal plants and their endophytes are important resources for discovery of natural products. Several previous studies have found a positive correlation between total antioxidant capacity (TAC) and total phenolic content (TPC) of many medicinal plant extracts. However, no information is available on whether such a relationship also exists in their endophytic fungal metabolites. We investigated the relationship between TAC and TPC for 292 morphologically distinct endophytic fungi isolated from 29 traditional Chinese medicinal plants. The antioxidant capacities of the endophytic fungal cultures were significantly correlated with their total phenolic contents, suggesting that phenolics were also the major antioxidant constituents of the endophytes. Some of the endophytes were found to produce metabolites possessing strong antioxidant activities. Several bioactive constituents from the fungal cultures and host plant extracts were identified. This investigation reveals that the metabolites produced by a wide diversity of endophytic fungi in culture can be a potential source of novel natural antioxidants.     

Assembly dynamics of FtsZ rings in Bacillus subtilis and Escherichia coli and effects of FtsZ-regulating proteins

FtsZ is the major cytoskeletal component of the bacterial cell division machinery. It forms a ring-shaped structure (the Z ring) that constricts as the bacterium divides. Previous in vivo experiments with green fluorescent protein-labeled FtsZ and fluorescence recovery after photobleaching have shown that the Escherichia coli Z ring is extremely dynamic, continually remodeling itself with a half time of 30 s, similar to microtubules in the mitotic spindle. In the present work, under different experimental conditions, we have found that the half time for fluorescence recovery of E. coli Z rings is even shorter (approximately 9 s). As before, the turnover appears to be coupled to GTP hydrolysis, since the mutant FtsZ84 protein, with reduced GTPase in vitro, showed an approximately 3-fold longer half time. We have also extended the studies to Bacillus subtilis and found that this species exhibits equally rapid dynamics of the Z ring (half time, approximately 8 s). Interestingly, null mutations of the FtsZ-regulating proteins ZapA, EzrA, and MinCD had only modest effects on the assembly dynamics. This suggests that these proteins do not directly regulate FtsZ subunit exchange in and out of polymers. In B. subtilis, only 30 to 35% of the FtsZ protein was in the Z ring, from which we conclude that a Z ring only 2 or 3 protofilaments thick can function for cell division.