BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

WormBase: a multi-species resource for nematode biology and genomics

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system

Peptide metabolism in the lactococci and its regulation : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University

Aspects of peptide metabolism in the lactococci have been investigated to increase the understanding of how these nutritionally fastidious bacteria, which have a central role in the dairy manufacturing industry, are able to grow in a complex medium such as milk. Peptide metabolism by lactococci in milk encompasses the processes by which large oligopeptides, produced from milk-caseins by the extracellular activity of the cell wall-associated proteinase, are converted into an intracellular pool of metabolisable amino acids. This involves the activities of both membrane-bound transport systems and peptidases. Early research into lactococcal peptide utilisation has proposed significant differences between Lactococcus lactis strains with respect to the mechanisms by which these bacteria utilise peptides in their environment. More recent studies of the lactococcal peptide carrier systems, based on intensive studies of only a single strain, have proposed a major role for a carrier system capable of transporting di- and tripeptides, and a subsidiary role for another system transporting oligopeptides containing four or more residues. Yet to date, peptidases with an extracellular location capable of degrading the large casein-peptides into smaller peptides have not been isolated. This current study has attempted to investigate more fully the in vivo activity of the oligopeptide transport system, and to assess whether it may have a more fundamental role in peptide utilisation than previous work has suggested. For this study a model series of homologous peptides of increasing size from the dipeptide Val-Gly to the octapeptide Val-Gly7 , all based on the essential amino acid valine, was used. The larger peptides in this series, Val-Gly3 , Val-Gly4 and Val-Gly7 , were synthesised for this work. The ability of Lactococcus lactis subsp. cremoris E8 8 to transport these peptides, and to grow in a chemically defined medium where they constitute the sole source of the essential amino acid valine, was studied . Preliminary peptide uptake studies were also performed using oligopeptides derived from a proteolytic cleavage of β-casein. The collective results of these studies suggest that the upper size limit, and the relative activity of this transport system, may be sufficient to permit this strain to utilise relatively large casein-derived oligopeptides without the need for hydrolysis into smaller peptides and free amino acids. A comparative study of peptide transport by a number of Lactococcus lactis strains was undertaken to investigate previously published observations indicating significant differences in the mechanisms of peptide uptake between lactococcal strains. While the results of this comparative study are consistent with the general model proposing two separate peptide carrier systems, they have revealed that significant differences can exist between strains in the relative activities and possible substrate specificities of these transport systems consistent with previous work that the lactococci have only two peptide carrier systems. These observations imply the need for caution in extrapolating the results obtained from the study of a single strain to lactococci as a whole. In contrast to the finding of significant strain differences with respect to the relative rates of peptide transport, a comparative study of the relative activity of six different intracellular peptidases showed relatively few differences in peptidase activity between strains. An investigation was also carried out to assess whether the peptidases and transport systems involved in the utilisation of peptides were nutritionally regulated. No clear evidence was obtained for the significant induction of either the intracellular peptidase complement or the di-/tripeptide transport system. An attempt was also made to isolate a mutant of Lactococcus lactis subsp. cremoris E8 unable to utilise dipeptides, to assess whether the di-/tripeptide transport system or the intracellular dipeptidase of this strain were essential to casein utilisation. This attempt was not successful

On Map Representations of DNA

We have constructed graphical (qualitative and visual) representations of DNA sequences as 2D maps and their numerical (quantitative and computational) analysis. The maps are obtained by transforming the four-letter sequences (where letters represent the four nucleic bases) via a spiral representation over triangular and square cells grids into a four-color map. The so constructed maps are then represented by distance matrices. We consider the use of several matrix invariants as DNA descriptors for determining the degree of similarity of a selection of DNA sequences. (doi: 10.5562/cca2338

Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made