Arcobacter molluscorum sp. nov., a new species isolated from shellfish

Nineteen bacteria isolates recovered from shellfish samples (mussels and oysters) showed a new and specific 16S rDNA-RFLP pattern with an Arcobacter identification method designed to recognize all species described up to 2008. These results suggested that they could belong to a new species. ERIC-PCR revealed that the 19 isolates belonged to 3 different strains. The sequence of the 16S rRNA gene of a representative strain (F98-3^T) showed 97.6% similarity with the closest species Arcobacter marinus followed by Arcobacter halophilus (95.6%) and Arcobacter mytili (94.7%). The phylogenetic analysis with the16S rRNA, rpoB, gyrB and hsp60 genes placed the shellfish strains within the same cluster as the three species mentioned (also isolated from saline habitats) but they formed an independent phylogenetic line. The DDH results between strain F98-3^T and A. marinus (54.8% ± 1.05), confirmed that it represents a new species. Several biochemical tests differentiated the shellfish isolates from all other Arcobacter species. Although the new species was different from A. mytili, they shared not only the same habitat (mussels) but also the characteristic of being so far the only Arcobacter species that are simultaneously negative for urea and indoxyl acetate hydrolysis. All results supported the classification of the shellfish strains as a new species, for which the name Arcobacter molluscorum sp. nov. with the type strain F98-3^T is proposed (=CECT 7696^T = LMG 25693^T).     

Predictors of outcome of dream work for East Asian volunteer clients: Dream factors, attachment anxiety, Asian values, and therapist input.

Eighty-eight East Asian volunteers were paired with 6 East Asian therapists who provided low or high input in single-dream sessions. Volunteer clients with poor initial functioning on the target problem associated with their dreams and high self-efficacy for working with dreams profited more from dream sessions than did their counterparts. Although no main effects were found for therapist input, volunteer clients who scored higher on attachment anxiety had better outcome in the low-input condition, whereas clients who scored lower on attachment anxiety had better outcome in the high-input condition. Volunteer clients with lower Asian values evaluated low-input sessions more positively, whereas volunteer clients with higher Asian values evaluated high-input sessions more positively. Implications for dream work and future research are suggested. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

In‐depth characterization of the tomato fruit pericarp proteome

Since the genome of Solanum lycopersicum L. was published in 2012, some studies have explored its proteome although with a limited depth. In this work, we present an extended characterization of the proteome of the tomato pericarp at its ripe red stage. Fractionation of tryptic peptides generated from pericarp proteins by off‐line high‐pH reverse‐phase phase chromatography in combination with LC‐MS/MS analysis on a Fisher Scientific Q Exactive and a Sciex Triple‐TOF 6600 resulted in the identification of 8588 proteins with a 1% FDR both at the peptide and protein levels. Proteins were mapped through GO and KEGG databases and a large number of the identified proteins were associated with cytoplasmic organelles and metabolic pathways categories. These results constitute one of the most extensive proteome datasets of tomato so far and provide an experimental confirmation of the existence of a high number of theoretically predicted proteins. All MS data are available in the ProteomeXchange repository with the dataset identifiers PXD004947 and PXD004932.     

1H, 15N and 13C chemical shift assignments of the C-Ala domain of the alanyl-tRNA synthetase of the psychrophilic bacterium Bizionia argentinensis sp. nov.

A gene encoding a protein classified as alanyl-tRNA synthetase (AlaRS) was found in the genome of the psychrophilic bacteria Bizionia argentinensis. The enzyme is constituted by three domains with an evolutionarily conserved modular arrangement: the N-terminal aminoacylation domain, the editing domain and the C-terminal domain (C-Ala). Herein we report the near complete NMR resonance assignment of the 122 amino acid C-Ala domain from B. argentinensis. The chemical shift data, reported for the first time for a C-Ala domain, constitute the basis for NMR structural studies aimed at elucidating the cold-adaptation mechanism of AlaRS.     

Dietary Squalene Increases High Density Lipoprotein-Cholesterol and Paraoxonase 1 and Decreases Oxidative Stress in Mice

Background and Purpose

Squalene, the main hydrocarbon in the unsaponifiable fraction of virgin olive oil, is involved in cholesterol synthesis and it has been reported to own antiatherosclerotic and antiesteatosic effects. However, the squalene''s role on lipid plasma parameters and the influence of genotype on this effect need to be addressed.

Experimental Approaches

Three male mouse models (wild-type, Apoa1- and Apoe- deficient) were fed chow semisynthetic diets enriched in squalene to provide a dose of 1 g/kg during 11 weeks. After this period, their plasma parameters and lipoprotein profiles were analyzed.

Key Results

Squalene administration at a dose of 1 g/kg showed decreased reactive oxygen species in lipoprotein fractions independently of the animal background and caused an specific increase in high density lipoprotein (HDL)-cholesterol levels, accompanied by an increase in phosphatidylcholine and paraoxonase 1 and no changes in apolipoproteins A1 and A4 in wild-type mice. In these mice, the cholesterol increase was due to its esterified form and associated with an increased hepatic expression of Lcat. These effects were not observed in absence of apolipoprotein A1. The increases in HDL- paraoxonase 1 were translated into decreased plasma malondialdehyde levels depending on the presence of Apolipoprotein A1.

Conclusions and Implications

Dietary squalene promotes changes in HDL- cholesterol and paraoxonase 1 and decreases reactive oxygen species in lipoproteins and plasma malondialdehyde levels, providing new benefits of its intake that might contribute to explain the properties of virgin olive oil, although the phenotype related to apolipoproteins A1 and E may be particularly relevant.     

Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint

Dna2 is a dual polarity exo/endonuclease, and 5′ to 3′ DNA helicase involved in Okazaki Fragment Processing (OFP) and Double-Strand Break (DSB) Repair. In yeast, DNA2 is an essential gene, as expected for a DNA replication protein. Suppression of the lethality of dna2Δ mutants has been found to occur by two mechanisms: overexpression of RAD27^scFEN1, encoding a 5′ to 3′ exo/endo nuclease that processes Okazaki fragments (OFs) for ligation, or deletion of PIF1, a 5′ to 3′ helicase involved in mitochondrial recombination, telomerase inhibition and OFP. Mapping of a novel, spontaneously arising suppressor of dna2Δ now reveals that mutation of rad9 and double mutation of rad9 mrc1 can also suppress the lethality of dna2Δ mutants. Interaction of dna2Δ and DNA damage checkpoint mutations provides insight as to why dna2Δ is lethal but rad27Δ is not, even though evidence shows that Rad27^ScFEN1 processes most of the Okazaki fragments, while Dna2 processes only a subset.Key words: yeast, RAD27, RAD9, RAD53, Okazaki fragment processing, DNA replication, exo1     

Molecular dynamics of the “hydrophobic patch” that immobilizes hydrophobin protein HFBII on silicon

The experimentally-observed stable, electrically-conducting interface formed between hydrophobin protein HFBII and silicon provides a model system for the Bio/ICT interfaces required for bionanoelectronics. The present work used molecular dynamics (MD) computer simulations to investigate the atom-scale details of the assembly and structure of the HFBII/silicon interface, using models on the order of 40,000 atoms to compute energy profiles for the full protein interacting with a bare Si(111) substrate in aqueous solution. Five nanoseconds of free, equilibrated dynamics were performed for six models with initial protein:silicon separations ranging from 1.2 to 0.2 nanometers in steps of 0.2 nm. Three of the models formed extensive protein:silicon van der Waals’s interfacial contacts. The model with 0.2 nm starting separation serves as an illustrative example of the dynamic interface created, whereby hydrophobic patch residues cycle between flat and more protruding patch conformations that favor respectively close inter-patch and close patch-surface contacts, with protein:surface separations cycling between 0.2 and 0.4 nm over the 5 ns of dynamics. Analysis of residue-based binding energies at the interface reveal three leucines Leu19, Leu21 and Leu63, together with isoleucine Ile22 and alanine Ala61, as the primary drivers towards adhesion on bare silicon, providing the atom-scale details of HFBII’s hydrophobic patch which in turn provides leads for the engineering of more tightly-coupled interfaces.