An experimental metagenome data management and analysis system

The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m.     

Control of metallic corrosion through microbiological route

Involvement of biofilm or microorganisms in corrosion processes is widely acknowledged. Although majority of the studies on microbiologically induced corrosion (MIC) have concentrated on aerobic/anaerobic bacteria. There are numerous aerobic bacteria, which could hinder the corrosion process. The microbiologically produced exopolymers provide the structural frame work for the biofilm. These polymers combine with dissolved metal ions and form organometallic complexes. Generally heterotrophic bacteria contribute to three major processes: (i) synthesis of polymers (ii) accumulation of reserve materials like poly-beta-hydroxy butrate (iii) production of high molecular weight extracellular polysaccharides. Poly-beta-hydroxy butyrate is a polymer of D(-)beta-hydroxy butrate and has a molecular weight between 60,000 and 2,50,000. Some extracellular polymers also have higher molecular weights. It seems that higher molecular weight polymer acts as biocoating. In the present review, role of biochemistry on corrosion inhibition and possibilities of corrosion inhibition by various microbes are discussed. The role of bacteria on current demand during cathodic protection is also debated. In addition, some of the significant contributions made by CECRI in this promising area are highlighted.     

Enhancement and selective production of phoslactomycin B,a protein phosphatase IIa inhibitor,through identification and engineering of the corresponding biosynthetic gene cluster

Phoslactomycins (PLMs), potent and selective inhibitors of serine threonine phosphatases, are of interest for their antitumor and antiviral activity. Multiple analogs and low titers in the fermentation process have hampered the development of this class of natural products. The entire 75-kb PLM biosynthetic gene cluster of Streptomyces sp. HK-803 was cloned, sequenced, and analyzed. The loading domain and seven extension modules of the PLM polyketide synthase generate an unusual linear unsaturated polyketide chain containing both E- and Z-double bonds from a cyclohexanecarboxylic acid (CHC) primer. Hydroxylation of the CHC-derived side chain of the resulting PLM-B by PlmS2, and a subsequent esterification, produces the remaining PLM analogs. A new PCR targeting technology allowed rapid and facile allelic replacement of plmS2. The resulting mutant selectively produced the PLM-B, at 6-fold higher titers than the wild type strain. This mutant and the biosynthetic gene cluster will facilitate engineered microbial production of hybrid PLMs with improved properties.     

A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also,after an abrupt acceleration,in the elongation zone

A requirement for understanding morphogenesis is being able to quantify expansion at the cellular scale. Here, we present new software (RootflowRT) for measuring the expansion profile of a growing root at high spatial and temporal resolution. The software implements an image processing algorithm using a novel combination of optical flow methods for deformable motion. The algorithm operates on a stack of nine images with a given time interval between each (usually 10 s) and quantifies velocity confidently at most pixels of the image. The root does not need to be marked. The software calculates components of motion parallel and perpendicular to the local tangent of the root's midline. A variation of the software has been developed that reports the overall root growth rate versus time. Using this software, we find that the growth zone of the root can be divided into two distinct regions, an apical region where the rate of motion, i.e. velocity, rises gradually with position and a subapical region where velocity rises steeply with position. In both zones, velocity increases almost linearly with position, and the transition between zones is abrupt. We observed this pattern for roots of Arabidopsis, tomato (Lycopersicon lycopersicum), lettuce (Lactuca sativa), alyssum (Aurinia saxatilis), and timothy (Phleum pratense). These velocity profiles imply that relative elongation rate is regulated in a step-wise fashion, being low but roughly uniform within the meristem and then becoming high, but again roughly uniform, within the zone of elongation. The executable code for RootflowRT is available from the corresponding author on request.     

Stereochemistry of strictic acid and related furano-diterpenes from conyza japonica and grangea maderaspatana

Extraction of Conyza japonica gave strictic acid, ent-2β-hydroxy-15,16-epoxy-3,13(16),14-clerodatrien-18-oic acid and 5,7-dihydroxy-3,8,4′-trimethoxyflavone. Extraction of Grangea maderaspatana gave (-)-hardwickiic acid, ent-15,16-epoxy-1,3,13(16),14-clerodatetraen-18-oic acid and 3-hydroxy-8-acetoxypentadeca-1,9,14-trien-4,6-diyne. The structure of ent-2β-hydroxy-15,16-epoxy-3,13(16),14-cleroclatrien-18-oic acid was deduced by spectroscopic methods and by partial synthesis from (-)-hardwickiic acid and the stereochemistries of strictic acid and (ent-15,16-epoxy-1,3,13(16),14-clerodatraen-18-oic acid were established by correlation with ent-2β-hydroxy-15,16-epoxy-3,13(16),14-clerodatrien-18-oic acid.     

Biosynthesis of o-succinylbenzoic acid in Bacillus subtilis: identification of menD mutants and evidence against the involvement of the alpha-ketoglutarate dehydrogenase complex.

The biosynthesis of o-succinylbenzoic acid (OSB), the first aromatic intermediate involved in the biosynthesis of menaquinone (vitamin K2) is demonstrated for the first time in the gram-positive bacterium Bacillus subtilis. Cell extracts were found to contain isochorismate synthase, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase-alpha-ketoglutarate decarboxylase and o-succinylbenzoic acid synthase activities. An odhA mutant which lacks the decarboxylase component (usually termed E1, EC 1.2.4.2, oxoglutarate dehydrogenase [lipoamide]) of the alpha-ketoglutarate dehydrogenase complex was found to synthesize SHCHC and form succinic semialdehyde-thiamine pyrophosphate. Thus, the presence of an alternate alpha-ketoglutarate decarboxylase activity specifically involved in menaquinone biosynthesis is established for B. subtilis. A number of OSB-requiring mutants were also assayed for the presence of the various enzymes involved in the biosynthesis of OSB. All mutants were found to lack only the SHCHC synthase activity.     

Ammonium assimilation inNocardia asteroides

Specific enzymes of ammonium assimilation were measured in cell-free extracts ofNocardia asteroides grown in a synthetic medium with glutamate as the nitrogen source. Cell-free extracts had active glutamine synthetase (GS) and glutamate synthase (GOGAT) and alanine dehydrogenase (ADH) but glutamate dehydrogenase (GDH) could not be detected in the enzyme preparation. This shows that GS/GOGAT is the major pathway of ammonium assimilation inN. asteroides.     

Ent-norlabdane triols from Austroeupatorium inulaefolium

Two new ent-norlabdane triols were isolated from the above-ground parts of Austroeupatorium inulaefolium.     

(2S,1'S,2'R,3'R)-2(2'-Carboxy-3'-hydroxymethylcyclopropyl)glycine-[3H], a potent and selective radioligand for labeling group 2 and 3 metabotropic glutamate receptors

We report herein the synthesis of the tritium labeled isotopomer of 1 and its use as a radioligand to label mGlu8 receptors in rat forebrain membranes as well as cloned human recombinant mGlu receptors. [(3)H]-1 was synthesized by the NaBT(4) reduction of an activated analog of 5. [(3)H]-1 bound appreciably to recombinant human mGlu2, mGlu3 and mGlu8 receptors and to rat forebrain membranes and was displaced by L-glutamate and L-(+)-2 amino-4-phosphonobutyric acid. The results indicate that [(3)H]-1 should be a useful ligand for the study of mGluR2, 3, and 8 receptors in cloned cell lines and possibly brain tissue.