SearchDOGS Bacteria,Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes

We report the development of SearchDOGS Bacteria, software to automatically detect missing genes in annotated bacterial genomes by combining BLAST searches with comparative genomics. Having successfully applied the approach to yeast genomes, we redeveloped SearchDOGS to function as a standalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST and a synteny-based method; this is followed by a scan of the entire genome of each species for unannotated genes. Results are provided in a HTML interface, providing coordinates, BLAST results, syntenic location, omega values (Ka/Ks, where Ks is the number of synonymous substitutions per synonymous site and Ka is the number of nonsynonymous substitutions per nonsynonymous site) for protein conservation estimates, and other information for each candidate gene. Using SearchDOGS Bacteria, we identified 155 gene candidates in the Shigella boydii sb227 genome, including 56 candidates of length < 60 codons. SearchDOGS Bacteria has two major advantages over currently available annotation software. First, it outperforms current methods in terms of sensitivity and is highly effective at identifying small or highly diverged genes. Second, as a freely downloadable package, it can be used with unpublished or confidential data.     

Diselenides as universal oxidative folding catalysts of diverse proteins

Small-molecule diselenides show considerable potential as catalysts of oxidative protein folding. To explore their scope, diselenide-containing redox buffers were used to promote the folding of proteins that varied in properties such as size, overall tertiary structure, number of disulfide bonds, pI value, and difficulty of in vitro folding. Diselenides are able to catalyze the oxidative folding of all proteins tested, providing significant increases in both rate and yield relative to analogous disulfides. Compared to the disulfide-linked dimer of glutathione (the most commonly used oxidant for in vitro protein folding), selenoglutathione provided markedly improved efficiencies in the folding of biotechnologically important proteins such as hirudin, lysozyme, human epidermal growth factor and interferon α-2a. Selenoglutathione also enhances the renaturation of more challenging targets such as bovine serum albumin, whose native state contains 17 disulfide bonds, and the Fab fragment of an antibody. In the latter case, micromolar amounts of selenoglutathione are able to match the modest yield provided by a previously optimized redox buffer, which contains millimolar levels of glutathione. Taken together, the folding reactions of these diverse proteins exemplify the advantages and limitations of diselenide catalysts.     

On-line infrared spectroscopy for bioprocess monitoring

One of the major aims of bioprocess engineering is the real-time monitoring of important process variables. This is the basis of precise process control and is essential for high productivity as well as the exact documentation of the overall production process. Infrared spectroscopy is a powerful analytical technique to analyze a wide variety of organic compounds. Thus, infrared sensors are ideal instruments for bioprocess monitoring. The sensors are non-invasive, have no time delay due to sensor response times, and have no influence on the bioprocess itself. No sampling is necessary, and several components can be analyzed simultaneously. In general, the direct monitoring of substrates, products, metabolites, as well as the biomass itself is possible. In this review article, insights are provided into the different applications of infrared spectroscopy for bioprocess monitoring and the complex data interpretation. Different analytical techniques are presented as well as example applications in different areas.     

Differential expression of a novel gene <Emphasis Type="Italic">BRE</Emphasis> (TNFRSF1A modulator/BRCC45) in response to stress and biological signals

Stress-responsive genes play critical roles in many biological functions that includes apoptosis, survival, differentiation and regeneration. We have identified a novel stress-responsive gene called BRE which interacts with TNF-receptor-1 and blocks the apoptotic effect of TNF-α. BRE enhances tumor growth in vivo and is up-regulated in hepatocellular and esophageal carcinomas. BRE also regulates the ubiquitination of the DNA repair complex BRCC, and the synthesis of steroid hormones. Here, we examined BRE-mRNA in cells after treatments with UV and ionizing radiation (IR). UV and IR treatment alone suppressed BRE-mRNA levels by more than 90% at 24 h, while hydroxyurea, fluorodeoxyuridine, aphidicolin, known inhibitors of S-phase DNA synthesis, had no significant effect. BRE protein expression was unaltered in cells treated with TNF-α, Interleukin-1 and Dexamethasone, while a threefold increase was observed following chorionic gonadotropin exposure. Although BRE plays a regulatory role in many different pathways, yet its expression is apparently under very stringent control.