Alternative Exon Usage Selectively Determines Both Tissue Distribution and Subcellular Localization of the acyl-CoA Thioesterase 7 Gene Products.

Acyl-CoA thioesterases (ACOTs) catalyze the hydrolysis of acyl-CoAs to free fatty acids and coenzyme A. Recent studies have demonstrated that one gene named Acot7, reported to be mainly expressed in brain and testis, is transcribed in several different isoforms by alternative usage of first exons. Strongly decreased levels of ACOT7 activity and protein in both mitochondria and cytosol was reported in patients diagnosed with fatty acid oxidation defects, linking ACOT7 function to regulation of fatty acid oxidation in other tissues. In this study, we have identified five possible first exons in mouse Acot7 (Acot7a-e) and show that all five first exons are transcribed in a tissue specific manner. Taken together, these data show that the Acot7 gene is expressed as multiple isoforms in a tissue specific manner, and that expression in tissues other than brain and testis is likely to play important roles in fatty acid metabolism

Activation of brain interleukin-1β in schizophrenia

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On the origine of the Boson peak

We show that the phonon-saddle transition in the ensemble of generalized inherent structures (minima and saddles) happens at the same point as the dynamical phase transition in glasses, that has been studied in the framework of the mode coupling approximation. The Boson peak observed in glasses at low temperature is a remanent of this transition.Comment: Proceeding of the Pisa conference September 2002, 13 pages+ 4 figures, To be publiched by Journal of Physic

Microplastic in Surface Waters of Urban Rivers: Concentration, Sources, and Associated Bacterial Assemblages

The ecological dynamics of microplastic (\u3c5 mm) are well documented in marine ecosystems, but the sources, abundance, and ecological role of microplastic in rivers are unknown and likely to be substantial. Microplastic fibers (e.g., synthetic fabrics) and pellets (e.g., abrasives in personal care products) are abundant in wastewater treatment plant (WWTP) effluent, and can serve as a point source of microplastic in rivers. The buoyancy, hydrophobic surface, and long transport distance of microplastic make it a novel substrate for the selection and dispersal of unique microbial assemblages. We measured microplastic concentration and bacterial assemblage composition on microplastic and natural surfaces upstream and downstream of WWTP effluent sites at nine rivers in Illinois, United States. Microplastic concentration was higher downstream of WWTP effluent outfall sites in all but two rivers. Pellets, fibers, and fragments were the dominant microplastic types, and polymers were identified as polypropylene, polyethylene, and polystyrene. Mean microplastic flux was 1,338,757 pieces per day, although the flux was highly variable among nine sites (min = 15,520 per day, max = 4,721,709 per day). High-throughput sequencing of 16S rRNA genes showed bacterial assemblage composition was significantly different among microplastic, seston, and water column substrates. Microplastic bacterial assemblages had lower taxon richness, diversity, and evenness than those on other substrates, and microplastic selected for taxa that may degrade plastic polymers (e.g., Pseudomonas) and those representing common human intestinal pathogens (e.g., Arcobacter). Effluent from WWTPs in rivers is an important component of the global plastic “life cycle,” and microplastic serves as a novel substrate that selects and transports distinct bacterial assemblages in urban rivers. Rates of microplastic deposition, consumption by stream biota, and the metabolic capacity of microplastic biofilms in rivers are unknown and merit further research

A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease

Peer reviewedPublisher PD

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/

Oral and Fecal Campylobacter concisus Strains Perturb Barrier Function by Apoptosis Induction in HT-29/B6 Intestinal Epithelial Cells

Campylobacter concisus infections of the gastrointestinal tract can be accompanied by diarrhea and inflammation, whereas colonization of the human oral cavity might have a commensal nature. We focus on the pathophysiology of C. concisus and the effects of different clinical oral and fecal C. concisus strains on human HT-29/B6 colon cells. Six oral and eight fecal strains of C. concisus were isolated. Mucus-producing HT-29/B6 epithelial monolayers were infected with the C. concisus strains. Transepithelial electrical resistance (Rt) and tracer fluxes of different molecule size were measured in Ussing chambers. Tight junction (TJ) protein expression was determined by Western blotting, and subcellular TJ distribution was analyzed by confocal laser-scanning microscopy. Apoptosis induction was examined by TUNEL-staining and Western blot of caspase-3 activation. All strains invaded confluent HT-29/B6 cells and impaired epithelial barrier function, characterized by a time- and dose-dependent decrease in Rt either after infection from the apical side but even more from the basolateral compartment. TJ protein expression changes were sparse, only in apoptotic areas of infected monolayers TJ proteins were redistributed. Solely the barrier-forming TJ protein claudin-5 showed a reduced expression level to 66±8% (P<0.05), by expression regulation from the gene. Concomitantly, Lactate dehydrogenase release was elevated to 3.1±0.3% versus 0.7±0.1% in control (P<0.001), suggesting cytotoxic effects. Furthermore, oral and fecal C. concisus strains elevated apoptotic events to 5-fold. C. concisus-infected monolayers revealed an increased permeability for 332 Da fluorescein (1.74±0.13 vs. 0.56±0.17 10−6 cm/s in control, P<0.05) but showed no difference in permeability for 4 kDa FITC-dextran (FD-4). The same was true in camptothecin-exposed monolayers, where camptothecin was used for apoptosis induction

Pseudopotential study of binding properties of solids within generalized gradient approximations: The role of core-valence exchange-correlation

In ab initio pseudopotential calculations within density-functional theory the nonlinear exchange-correlation interaction between valence and core electrons is often treated linearly through the pseudopotential. We discuss the accuracy and limitations of this approximation regarding a comparison of the local density approximation (LDA) and generalized gradient approximations (GGA), which we find to describe core-valence exchange-correlation markedly different. (1) Evaluating the binding properties of a number of typical solids we demonstrate that the pseudopotential approach and namely the linearization of core-valence exchange-correlation are both accurate and limited in the same way in GGA as in LDA. (2) Examining the practice to carry out GGA calculations using pseudopotentials derived within LDA we show that the ensuing results differ significantly from those obtained using pseudopotentials derived within GGA. As principal source of these differences we identify the distinct behavior of core-valence exchange-correlation in LDA and GGA which, accordingly, contributes substantially to the GGA induced changes of calculated binding properties.Comment: 13 pages, 6 figures, submitted to Phys. Rev. B, other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm