Automated programming for bioinformatics algorithm deployment

Many bioinformatics solutions suffer from the lack of usable interface/platform from which results can be analyzed and visualized. Overcoming this hurdle would allow for more widespread dissemination of bioinformatics algorithms within the biological and medical communities. The algorithms should be accessible without extensive technical support or programming knowledge. Here, we propose a dynamic wizard platform that provides users with a Graphical User Interface (GUI) for most Java bioinformatics library toolkits. The application interface is generated in real-time based on the original source code. This platform lets developers focus on designing algorithms and biologists/physicians on testing hypotheses and analyzing results. AVAILABILITY: The open source code can be downloaded from: http://bcl.med.harvard.edu/proteomics/proj/APBA/.     

Isolation of a <Emphasis Type="Italic">Latimeria menadoensis</Emphasis><Emphasis Type="Italic">heat shock protein 70</Emphasis> (<Emphasis Type="Italic">Lmhsp70</Emphasis>) that has all the features of an inducible gene and encodes a functional molecular chaperone

Molecular chaperones facilitate the correct folding of other proteins, and heat shock proteins form one of the major classes of molecular chaperones. Heat shock protein 70 (Hsp70) has been extensively studied, and shown to be critically important for cellular protein homeostasis in almost all prokaryotic and eukaryotic systems studied to date. Since there have been very limited studies conducted on coelacanth chaperones, the main objective of this study was to genetically and biochemically characterize a coelacanth Hsp70. We have successfully isolated an Indonesian coelacanth (L. menadoensis) hsp70 gene, Lmhsp70, and found that it contained an intronless coding region and a potential upstream regulatory region. Lmhsp70 encoded a typical Hsp70 based on conserved structural and functional features, and the predicted upstream regulatory region was found to contain six potential promoter elements, and three potential heat shock elements (HSEs). The intronless nature of the coding region and the presence of HSEs suggested that Lmhsp70 was stress-inducible. Phylogenetic analyses provided further evidence that Lmhsp70 was probably inducible, and that it branched as a clade intermediate between bony fish and tetrapods. Recombinant LmHsp70 was successfully overproduced, purified and found to be functional using ATPase activity assays. Taken together, these data provide evidence for the first time that the coelacanth encodes a functional molecular chaperone system. K. W. Modisakeng and M. Jiwaji contributed equally to this study.     

Enhanced hydantoin-hydrolyzing enzyme activity in an Agrobacterium tumefaciens strain with two distinct N-carbamoylases

Hydantoin-hydrolyzing enzymes of Agrobacterium tumefaciens isolates such as strain RU-OR are used as biocatalysts in the commercial production of d-hydroxyphenylglycine via hydrolysis of d, l-p-hydroxyphenylhydantoin. Hydantoin-hydrolyzing enzyme activity in RU-OR cells is tightly regulated by nitrogen catabolite repression and is induced when hydantoin or a hydantoin-analogue is present in the growth medium. Previous studies have selected mutant strains which are inducer-independent and no longer subject to nitrogen catabolite expression. However, these mutants did not exhibit significantly higher levels of enzyme activity compared to the wild-type strain. In this study, we have focused on enhancing the levels of hydantoinase and N-carbamoylase activity in wild-type RU-OR cells by manipulating the growth medium or over-expressing the global nitrogen regulatory factors, NtrBC. We also show that this strain encodes two distinct d-selective N-carbamoylases. One enzyme is virtually identical to the other Agrobacterium N-carbamoylases while the second represents a new class of d-N-carbamoylases with potentially novel biocatalytic properties.