Assessing strategies for improved superfamily recognition

There are more than 200 completed genomes and over 1 million nonredundant sequences in public repositories. Although the structural data are more sparse (approximately 13,000 nonredundant structures solved to date), several powerful sequence-based methodologies now allow these structures to be mapped onto related regions in a significant proportion of genome sequences. We review a number of publicly available strategies for providing structural annotations for genome sequences, and we describe the protocol adopted to provide CATH structural annotations for completed genomes. In particular, we assess the performance of several sequence-based protocols employing Hidden Markov model (HMM) technologies for superfamily recognition, including a new approach (SAMOSA [sequence augmented models of structure alignments]) that exploits multiple structural alignments from the CATH domain structure database when building the models. Using a data set of remote homologs detected by structure comparison and manually validated in CATH, a single-seed HMM library was able to recognize 76% of the data set. Including the SAMOSA models in the HMM library showed little gain in homolog recognition, although a slight improvement in alignment quality was observed for very remote homologs. However, using an expanded 1D-HMM library, CATH-ISL increased the coverage to 86%. The single-seed HMM library has been used to annotate the protein sequences of 120 genomes from all three major kingdoms, allowing up to 70% of the genes or partial genes to be assigned to CATH superfamilies. It has also been used to recruit sequences from Swiss-Prot and TrEMBL into CATH domain superfamilies, expanding the CATH database eightfold.     

EFFECTS OF DISTURBANCE ON EPIPHYTIC COMMUNITY ARCHITECTURE1

Microdistributional patterns of attached algal communities on Cladophora and glass slides were compared under varying disturbance regimes in the Upper Mississippi River, using light and scanning electron microscopy. Localized physical disturbance, induced by boat traffic and wind-generated wave action in the main channel, inhibited development of complex attached algal communities and maintained an adnate flora with two-dimensional architecture. In contrast, communities protected from disturbance developed a more complex, three-dimensional architecture. A high degree of architectural similarity was observed between communities on Cladophora and glass substrates exposed to similar levels of disturbance. Communities exposed to severe disturbance resembled ones in early stages of colonization and development, whereas less disturbed communities were similar to ones in advanced stages of development. These results demonstrated that turbulence strongly influences the community structure of periphyton on both micro and macro scale levels.     

Owlifier: Creating OWL-DL ontologies from simple spreadsheet-based knowledge descriptions

Discovery and integration of data is important in many ecological studies, especially those that concern broad-scale ecological questions. Data discovery and integration are often difficult and time consuming tasks for researchers, which is due in part to the use of informal, ambiguous, and sometimes inconsistent terms for describing data content. Ontologies offer a solution to this problem by providing consistent definitions of ecological concepts that in turn can be used to annotate, relate, and search for data sets. However, unlike in molecular biology or biomedicine, few ontology development efforts exist within ecology. Ontology development often requires considerable expertise in ontology languages and development tools, which is often a barrier for ontology creation in ecology. In this paper we describe an approach for ontology creation that allows ecologists to use common spreadsheet tools to describe different aspects of an ontology. We present conventions for creating, relating, and constraining concepts through spreadsheets, and provide software tools for converting these ontologies into equivalent OWL-DL representations. We also consider inverse translations, i.e., to convert ontologies represented using OWL-DL into our spreadsheet format. Our approach allows large lists of terms to be easily related and organized into concept hierarchies, and generally provides a more intuitive and natural interface for ontology development by ecologists.     

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.     

Capitalizing on multi-element interactions through balanced nutrition — A pathway to improve nitrogen use efficiency in China,India and North America

A viable option for increasing nitrogen (N) use efficiency and mitigation of negative impacts of N on the environment is to capitalize on multi-element interactions through implementation of nutrient management programs that provide balanced nutrition. Numerous studies have demonstrated the immediate efficacy of this approach in the developing regions like China and India as well as developed countries in North America. Based on 241 site-years of experiments in these countries, the first-year N recovery efficiency (RE) for the conventional or check treatments averaged 21% while the balanced treatments averaged 54% RE, for an average increase of 33% in RE due to balanced nutrition. Effective policies to promote adoption are most likely those that enable site-specific approaches to nutrient management decisions rather than sweeping, nation-wide incentives supporting one nutrient over another. Local farmers, advisers and officials need to be empowered with tools and information to help them define necessary changes in practices to create more balanced nutrient management.     

The evolution of Queensland spiny mountain crayfish of the genus Euastacus. I. Testing vicariance and dispersal with interspecific mitochondrial DNA

The upland mesic rainforests of eastern Australia have been described as a "mesothermal archipelago" where a chain of cool mountain "islands" arise from a warm "sea" of tropical and subtropical lowlands. An endemic freshwater crayfish belonging to the genus Euastacus is found on each of these mountain "islands." The Euastacus are particularly suitable for the study of evolution because each mountain harbors a unique species, there are many taxa present providing replication within the group and, most importantly, their distribution is linear, extending along a south-north axis. This group could have evolved by "simultaneous vicariance" where there was one vicariant separation event of a widespread ancestor, or by "south to north stepping stone dispersal" where there were long distance dispersal events from neighboring mountain islands, starting in the south and proceeding north in a dispersal-colonization wave. We used pairwise genetic distances between nearest geographic neighbors as a novel way to test the two hypotheses. If diversification was due to "south to north stepping stone dispersal," then pairwise genetic distances between nearest geographic neighbors should decrease progressively the farther north the taxon pairs are found, reflecting the decreasing periods of isolation. In this case there should be a negative correlation between the south to north rank order of nearest neighbors and pairwise genetic distances. A Spearman's correlation on 16S mtDNA pairwise genetic distances and geographic rank order was not significant, indicating there was no support for the south to north stepping stone dispersal hypothesis. If simultaneous vicariance was responsible for diversification then all nearest geographic neighbor taxon pairs should have similar genetic distances and, therefore, the variance in nearest neighbor distances should be zero, or close to it. To test if the observed variance was tending towards zero we developed a randomization test where nearest neighbor taxon pairs were assigned random genetic distances and the variances calculated. The observed variance lay in the < 0.05 range of the simulated variances, providing support for the simultaneous vicariance hypothesis. The data also suggest there was simultaneous vicariance of at least two ancestral Queensland lineages. The timing of this vicariant event was probably in the Pliocene, which is consistent with the divergence times reported for other Australian mesic rainforest restricted taxa.