Structure and activity of DmmA, a marine haloalkane dehalogenase

DmmA is a haloalkane dehalogenase (HLD) identified and characterized from the metagenomic DNA of a marine microbial consortium. Dehalogenase activity was detected with 1,3‐dibromopropane as substrate, with steady‐state kinetic parameters typical of HLDs ( K m = 0.24 ± 0.05 mM, k cat = 2.4 ± 0.1 s −1 ). The 2.2‐Å crystal structure of DmmA revealed a fold and active site similar to other HLDs, but with a substantially larger active site binding pocket, suggestive of an ability to act on bulky substrates. This enhanced cavity was shown to accept a range of linear and cyclic substrates, suggesting that DmmA will contribute to the expanding industrial applications of HLDs. PDB Code(s): 3U1TPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90241/1/PRO_2009_sm_suppinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90241/2/2009_ftp.pd

Brevianes Revisited

Breviones are a new family of secondary metabolites that were originally isolated from the New Zealand endemic fungus Penicillium brevicompactum var. Dierckx. These compounds are generally characterized by a new carbon skeleton, known as breviane, which that has three possible structural variations, such as breviane, abeo-breviane, and abeo-norbreviane. Brevianes present a basic diterpenic tricyclic core that is mevalonic in origin and is similar to that of perhydrophenanthrene. The core bears four methyl groups at positions C4, C8, C10, and C13 and has defined stereochemistry at positions C5, C8, C9, C10, and C14. The C1'-C7' side chain has been proposed to have a polyketide biosynthetic origin and is joined to the diterpenic moiety through carbons C2'-C15'. The cyclization and lactonization of this part of the molecule leads to the characteristic breviane spiranic ring fused to the α-pyrone

Unitary Standard Model from Spontaneous Dimensional Reduction and Weak Boson Scattering at the LHC

Spontaneous dimensional reduction (SDR) is a striking phenomenon predicted by a number of quantum gravity approaches which all indicate that the spacetime dimensions get reduced at high energies. In this work, we formulate an effective theory of electroweak interactions based upon the standard model, incorporating the spontaneous reduction of space-dimensions at TeV scale. The electroweak gauge symmetry is nonlinearly realized with or without a Higgs boson. We demonstrate that the SDR ensures good high energy behavior and predicts unitary weak boson scattering. For a light Higgs boson of mass 125GeV, the TeV-scale SDR gives a natural solution to the hierarchy problem. Such a light Higgs boson can have induced anomalous gauge couplings from the TeV-scale SDR. We find that the corresponding WW scattering cross sections become unitary at TeV scale, but exhibit different behaviors from that of the 4d standard model. These can be discriminated by the WW scattering experiments at the LHC.Comment: 38pp, Eur.Phys.J.(in Press); extended discussions for testing non-SM Higgs boson(125GeV) via WW scattering; minor clarifications added; references added; a concise companion is given in the short PLB letter arXiv:1301.457

Les Houches 2013: Physics at TeV Colliders: Standard Model Working Group Report

This Report summarizes the proceedings of the 2013 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt primarily with (1) the techniques for calculating standard model multi-leg NLO and NNLO QCD and NLO EW cross sections and (2) the comparison of those cross sections with LHC data from Run 1, and projections for future measurements in Run 2.Comment: Proceedings of the Standard Model Working Group of the 2013 Les Houches Workshop, Physics at TeV Colliders, Les houches 3-21 June 2013. 200 page

Marine Cyanobacteria Compounds with Anticancer Properties: Implication of Apoptosis

Marine cyanobacteria have been proved to be an important source of potential anticancer drugs. Although several compounds were found to be cytotoxic to cancer cells in culture, the pathways by which cells are affected are still poorly elucidated. For some compounds, cancer cell death was attributed to an implication of apoptosis through morphological apoptotic features, implication of caspases and proteins of the Bcl-2 family, and other mechanisms such as interference with microtubules dynamics, cell cycle arrest and inhibition of proteases other than caspases

The Kolumbo submarine volcano of Santorini island is a large pool of bacterial strains with antimicrobial activity

Microbes in hydrothermal vents with their unique secondary metabolism may represent an untapped potential source of new natural products. In this study, samples were collected from the hydrothermal field of Kolumbo submarine volcano in the Aegean Sea, in order to isolate bacteria with antimicrobial activity. Eight hundred and thirty-two aerobic heterotrophic bacteria were isolated and then differentiated through BOX-PCR analysis at the strain level into 230 genomic fingerprints, which were screened against 13 different type strains (pathogenic and nonpathogenic) of Gram-positive, Gram-negative bacteria and fungi. Forty-two out of 176 bioactive-producing genotypes (76 %) exhibited antimicrobial activity against at least four different type strains and were selected for 16S rDNA sequencing and screening for nonribosomal peptide (NRPS) and polyketide (PKS) synthases genes. The isolates were assigned to genus Bacillus and Proteobacteria, and 20 strains harbored either NRPS, PKS type I or both genes. This is the first report on the diversity of culturable mesophilic bacteria associated with antimicrobial activity from Kolumbo area; the extremely high proportion of antimicrobial-producing strains suggested that this unique environment may represent a potential reservoir of novel bioactive compounds

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes