SeqMaT: A sequence manipulation tool for phylogenetic analysis

Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset is large. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions: data format conversion,sequence name coding and decoding,redundant and highly similar sequence removal, anddata mining utilities. SeqMaT was developed using Java with two versions, web-based and standalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet. AVAILABILITY: The database is available for free at http://glee.ist.unomaha.edu/seqmat.     

Mining genomic patterns in Mycobacterium tuberculosis H37Rv using a web server Tuber-Gene

Mycobacterium tuberculosis (MTB), causative agent of tuberculosis, is one of the most dreaded diseases of the century. It has long been studied by researchers throughout the world using various wet-lab and dry-lab techniques. In this study, we focus on mining useful patterns at genomic level that can be applied for in silico functional characterization of genes from the MTB complex. The model developed on the basis of the patterns found in this study can correctly identify 99.77% of the input genes from the genome of MTB strain H37Rv. The model was tested against four other MTB strains and the homologue M. bovis to further evaluate its generalization capability. The mean prediction accuracy was 85.76%. It was also observed that the GC content remained fairly constant throughout the genome, implicating the absence of any pathogenicity island transferred from other organisms. This study reveals that dinucleotide composition is an efficient functional class discriminator for MTB complex. To facilitate the application of this model, a web server Tuber-Gene has been developed, which can be freely accessed at http://www.bifmanit.org/tb2/.     

Reduction in cricket (Orthoptera: Ensifera) populations along a gradient of sulphur dioxide from mining emissions in northern Australia

The impact of SO₂ dry deposition from mining emissions on cricket abundance, diversity and composition was investigated at Mount Isa in the semiarid tropics of northern Australia. Seventy-one sites were sampled, stratified at two levels: sulphur deposition zones (high, medium, low, and background zones) and habitat (rocky ridge, rocky plain and alluvial plain). The three habitats did not support distinctly different cricket assemblages. Crickets responded to SO₂ emissions, but impacts were largely restricted to the high-sulphur zone. Generalised linear modelling showed significant reductions in the probability of presence in the high-sulphur zone for the three genera Eurepella, Salmanites and Endacusta , and the subfamily Eneopterinae. In ordination space, the three high-sulphur zone by habitat combinations were clearly separated from all other combinations, and vector fitting of environmental variables showed soil SO₄ to be a primary correlative factor of this separation. Crickets are sensitive to SO₂ emissions and they appear to be a good indicator group in this context.     

The evolution of host use and unusual reproductive strategies in Achrysocharoides parasitoid wasps

We studied host selection and exploitation, two crucial aspects of parasite ecology, in Achrysocharoides parasitoid wasps, which show remarkable host specificity and unusual offspring sex allocation. We estimated a molecular phylogeny of 15 Achrysocharoides species and compared this with host (plant and insect) phylogenies. This tri-trophic phylogenetic comparison provides no evidence for cospeciation, but parasitoids do show phylogenetic conservation of the use of plant genera. Patterns of sequence divergence also suggest that the parasitoids radiated more recently (or evolved much faster) than their insect hosts. Three main categories of brood production occur in parasitoids: (1) solitary offspring, (2) mixed sex broods and (3) separate (split) sex broods. Split sex broods are very rare and virtually restricted to Achrysocharoides, while the other types occur very widely. Our phylogeny suggests that split sex broods have evolved twice and provides evidence for a transition from solitary to mixed sex broods, via split sex broods, as predicted by theory.     

Comparison of sequence and structure-based datasets for nonredundant structural data mining

Structural data mining studies attempt to deduce general principles of protein structure from solved structures deposited in the protein data bank (PDB). The entire database is unsuitable for such studies because it is not representative of the ensemble of protein folds. Given that novel folds continue to be unearthed, some folds are currently unrepresented in the PDB while other folds are overrepresented. Overrepresentation can easily be avoided by filtering the dataset. PDB_SELECT is a well-used representative subset of the PDB that has been deduced by sequence comparison. Specifically, structures with sequences that exhibit a pairwise sequence identity above a threshold value are weeded from the dataset. Although length criteria for pairwise alignments have a structural basis, this automated method of pruning is essentially sequence-based and runs into problems in the twilight zone, possibly resulting in some folds being overrepresented. The value-added structure databases SCOP and CATH are also a potential source of a nonredundant dataset. Here we compare the sequence-derived dataset PDB_SELECT with the structural databases SCOP (Structural Classification Of Proteins) and CATH (Class-Architecture-Topology-Homology). We show that some folds remain overrepresented in the PDB_SELECT dataset while other folds are not represented at all. However, SCOP and CATH also have their own problems such as the labor-intensiveness of the update process and the problem of determining whether all folds are equally or sufficiently distant. We discuss areas where further work is required.     

Structural characterization of proteins using residue environments

A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S-BLEST quickly identifies similar amino acid environments using a K-nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S-BLEST on X-ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors.     

Inorganic carbon limitation and mixotrophic growth in Chlamydomonas from an acidic mining lake

Plankton communities in acidic mining lakes (pH 2.5-3.3) are species-poor because they face extreme environmental conditions, e.g. 150mg l(-1) Fe2+ +Fe3+. We investigated the growth characteristics of the dominant pigmented species, the flagellate Chlamydomonas acidophila, in semi-continuous culture experiments under in situ conditions. The following hypotheses were tested: (1) Low inorganic carbon (IC) concentrations in the epilimnion (e.g. 0.3 mg l(-1)) arising from the low pH limit phototrophic growth (H-1); (2) the additional use of dissolved organic carbon (mixotrophy) leads to higher growth rates under IC-limitation (H-2), and (3) phagotrophy is not relevant (H-3). H-1 was supported as the culture experiments, in situ PAR and IC concentrations indicated that IC potentially limited phototrophic growth in the mixed surface layers. H-2 was also supported: mixotrophic growth always exceeded pure phototrophic growth even when photosynthesis was saturated. Dark growth in filtered lake water illuminated prior to inoculation provided evidence that Chlamydomonas was able to use the natural DOC. The alga did not grow on bacteria, thus confirming H-3. Chlamydomonas exhibited a remarkable resistance to starvation in the dark. The compensation light intensity (ca. 20 micromol photons m(-2) s(-1)) and the maximum phototrophic growth (1.50 d(-1)) fell within the range of algae from non-acidic waters. Overall, Chlamydomonas, a typical r-strategist in circum-neutral systems, showed characteristics of a K-strategist in the stable, acidic lake environment in achieving moderate growth rates and minimizing metabolic losses.     

Small-scale Gold Mining in the Puyango River Basin,Southern Ecuador: A Study of Environmental Impacts andHuman Exposures

This study addresses the impact of small-scale gold mining on the environment and communities of the Puyango River basin in the southwest of Ecuador between 1999 and 2001. Our primary objectives were to measure mercury, manganese, and lead in the river, to identify pathways of population exposure, and biological indicators of human exposure. A multi-method design at the catchment scale was applied to the analysis of water, sediments, and particulate matter for mercury, lead, and manganese over two different seasons. A household survey was undertaken, and individuals were assessed for lead (blood samples), and for mercury (urine and hair samples). River water samples had high concentrations of particulate matter (700 mg/L). Mercury and lead levels in water at the gold processing plants were very high in both seasons (250 ng Hg/L and 160 μg Pb/L). Mercury and lead, there was a downstream gradient with the areas adjacent to the gold processing plants having the highest levels. In Portovelo, the Upper Basin city, 14% of the population reported occupational exposure to inorganic mercury. Although no one in Portovelo consumes water from the river, 10% of the population consume local fish. This contrasts the Lower Basin where 98% of the population consume fish, and 100% use river water for drinking and cooking. Lead blood levels over 20 μg/dl were found in 39.4% of the study population and blood mercury over 10 μg/L only in 10.0%. Urinary mercury over 4 μg/L was found in 66.5% of the examined persons. Hair methylmercury did not exceed the safe limit of 2 μg/g, the mean concentration was 1.2 μg/g. Mining activity and erosion contributes to heavy-metal contamination (mercury, lead, and manganese) throughout the Puyango Basin. The relation between environmental contamination is complex and further research is being conducted to understand these relations.     

Towards Efficient Isolation of R Gene Orthologs from Multiple Genotypes: Optimization of Long Range-PCR

Resistance (R) genes and the proteins they encode are key components of the defense system of plants. The exploration of R gene diversity enables the study of R gene evolution and may facilitate the isolation of new and functional alleles. Most cloned R genes occur in clusters of related sequences. Thus, the development of a tool for reliable recovery of orthologous R gene sequences to the exclusion of paralogous sequences will facilitate R gene diversity analysis. The late blight resistance gene RB is a single functional locus embedded within a cluster of related sequences. Previously, the functional RB allele was cloned from wild potato using a Long Range-PCR (LR-PCR) technique, suggesting this method may be a promising tool for recovery of R gene orthologs in other genotypes. Using the RB gene as a model, we explored the limitations and improved three technical aspects of LR-PCR for multi-genotype applications. We present improved primers for the recovery of the RB locus and have identified efficient DNA extraction procedures and reliable amplification systems. We document that consensus sequences built from three independently generated LR-PCR clones can be up to 100% accurate. Our results show encouraging advances toward successful application of LR-PCR for isolating alleles from orthologous R gene loci.