The human gastric pathogen Helicobacter pylori has a potential acetone carboxylase that enhances its ability to colonize mice

<p>Abstract</p> <p>Background</p> <p><it>Helicobacter pylori </it>colonizes the human stomach and is the etiological agent of peptic ulcer disease. All three <it>H. pylori </it>strains that have been sequenced to date contain a potential operon whose products share homology with the subunits of acetone carboxylase (encoded by <it>acxABC</it>) from <it>Xanthobacter autotrophicus </it>strain Py2 and <it>Rhodobacter capsulatus </it>strain B10. Acetone carboxylase catalyzes the conversion of acetone to acetoacetate. Genes upstream of the putative <it>acxABC </it>operon encode enzymes that convert acetoacetate to acetoacetyl-CoA, which is metabolized further to generate two molecules of acetyl-CoA.</p> <p>Results</p> <p>To determine if the <it>H. pylori acxABC </it>operon has a role in host colonization the <it>acxB </it>homolog in the mouse-adapted <it>H. pylori </it>SS1 strain was inactivated with a chloramphenicol-resistance (<it>cat</it>) cassette. In mouse colonization studies the numbers of <it>H. pylori </it>recovered from mice inoculated with the <it>acxB:cat </it>mutant were generally one to two orders of magnitude lower than those recovered from mice inoculated with the parental strain. A statistical analysis of the data using a Wilcoxin Rank test indicated the differences in the numbers of <it>H. pylori </it>isolated from mice inoculated with the two strains were significant at the 99% confidence level. Levels of acetone associated with gastric tissue removed from uninfected mice were measured and found to range from 10–110 μmols per gram wet weight tissue.</p> <p>Conclusion</p> <p>The colonization defect of the <it>acxB:cat </it>mutant suggests a role for the <it>acxABC </it>operon in survival of the bacterium in the stomach. Products of the <it>H. pylori acxABC </it>operon may function primarily in acetone utilization or may catalyze a related reaction that is important for survival or growth in the host. <it>H. pylori </it>encounters significant levels of acetone in the stomach which it could use as a potential electron donor for microaerobic respiration.</p

PhytAMP: a database dedicated to antimicrobial plant peptides

Plants produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. Based on amino acid sequence homology, these peptides were classified mostly as α-defensins, thionins, lipid transfer proteins, cyclotides, snakins and hevein-like. Although many antimicrobial plant peptides are now well characterized, much information is still missing or is unavailable to potential users. The compilation of such information in one centralized resource, such as a database would therefore facilitate the study of the potential these peptide structures represent, for example, as alternatives in response to increasing antibiotic resistance or for increasing plant resistance to pathogens by genetic engineering. To achieve this goal, we developed a new database, PhytAMP, which contains valuable information on antimicrobial plant peptides, including taxonomic, microbiological and physicochemical data. Information is very easy to extract from this database and allows rapid prediction of structure/function relationships and target organisms and hence better exploitation of plant peptide biological activities in both the pharmaceutical and agricultural sectors. PhytAMP may be accessed free of charge at http://phytamp.pfba-lab.org

Characterizing the scent and chemical composition of Panthera leo marking fluid using solid-phase microextraction and multidimensional gas chromatography–mass spectrometry-olfactometry

Lions (Panthera leo) use chemical signaling to indicate health, reproductive status, and territorial ownership. To date, no study has reported on both scent and composition of marking fluid (MF) from P. leo. The objectives of this study were to: 1) develop a novel method for simultaneous chemical and scent identification of lion MF in its totality (urine + MF), 2) identify characteristic odorants responsible for the overall scent of MF as perceived by human panelists, and 3) compare the existing library of known odorous compounds characterized as eliciting behaviors in animals in order to understand potential functionality in lion behavior. Solid-phase microextraction and simultaneous chemical-sensory analyses with multidimensional gas-chromatography-mass spectrometry-olfactometry improved separating, isolating, and identifying mixed (MF, urine) compounds versus solvent-based extraction and chemical analyses. 2,5-Dimethylpyrazine, 4-methylphenol, and 3-methylcyclopentanone were isolated and identified as the compounds responsible for the characteristic odor of lion MF. Twenty-eight volatile organic compounds (VOCs) emitted from MF were identified, adding a new list of compounds previously unidentified in lion urine. New chemicals were identified in nine compound groups: ketones, aldehydes, amines, alcohols, aromatics, sulfur-containing compounds, phenyls, phenols, and volatile fatty acids. Twenty-three VOCs are known semiochemicals that are implicated in attraction, reproduction, and alarm-signaling behaviors in other species

Establishing bioinformatics research in the Asia Pacific

In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5(th )annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand) and Busan (South Korea). This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community