Removal of odors from Swine wastewater by using microbial fuel cells

A single-chamber microbial fuel cell (MFC) was used to reduce 10 chemicals associated with odors by 99.76% (from 422 +/- 23 mug/ml) and three volatile organic acids (acetate, butyrate, and propionate) by >99%. The MFC produced a maximum of 228 mW/m(2) and removed 84% of the organic matter in 260 h. MFCs were therefore effective at both treatment and electricity generation.     

Genetic Influences on Metabolite Levels: A Comparison across Metabolomic Platforms

Metabolomic profiling is a powerful approach to characterize human metabolism and help understand common disease risk. Although multiple high-throughput technologies have been developed to assay the human metabolome, no technique is capable of capturing the entire human metabolism. Large-scale metabolomics data are being generated in multiple cohorts, but the datasets are typically profiled using different metabolomics platforms. Here, we compared analyses across two of the most frequently used metabolomic platforms, Biocrates and Metabolon, with the aim of assessing how complimentary metabolite profiles are across platforms. We profiled serum samples from 1,001 twins using both targeted (Biocrates, n = 160 metabolites) and non-targeted (Metabolon, n = 488 metabolites) mass spectrometry platforms. We compared metabolite distributions and performed genome-wide association analyses to identify shared genetic influences on metabolites across platforms. Comparison of 43 metabolites named for the same compound on both platforms indicated strong positive correlations, with few exceptions. Genome-wide association scans with high-throughput metabolic profiles were performed for each dataset and identified genetic variants at 7 loci associated with 16 unique metabolites on both platforms. The 16 metabolites showed consistent genetic associations and appear to be robustly measured across platforms. These included both metabolites named for the same compound across platforms as well as unique metabolites, of which 2 (nonanoylcarnitine (C9) [Biocrates]/Unknown metabolite X-13431 [Metabolon] and PC aa C28:1 [Biocrates]/1-stearoylglycerol [Metabolon]) are likely to represent the same or related biochemical entities. The results demonstrate the complementary nature of both platforms, and can be informative for future studies of comparative and integrative metabolomics analyses in samples profiled on different platforms.     

A hypothesis on the biological role of ABH,lewis and P blood group determinant structures in glycosphingolipids and glycoproteins

A hypothesis is presented that glycosphingolipids of circulating erythrocytes are membrane-packing substances providing for an energetically cheap carbohydrate protective coat at the cell surface. The glycosphingolipids should cover the membrane surface not occupied by functional glycoproteins. This role is envisaged for the globo series of glycosphingolipids which are P^k and P antigens of human blood. Glycosphingolipids of the neolacto series terminated with non-informative A, B, H. Lewis, P₁ antigenic structures as well as with sialic acid residues should serve the same purpose. These carbohydrate structures may be also used for conferring biological inertness on otherwise functionally active carbohydrate structures and provide protection for circulatory and membrane glycoproteins from proteolysis, denaturation and recognition of potentially antigenic sites of protein moieties by the immunosurveillance system of the body. At the external body surface the same carbohydrate structures may protect cells from the action of pathogenic microorganisms and other environmental factors. The roles of the above mentioned carbohydrate sequences on glycosphingolipids and glycoproteins in the development, tumorigenesis and evolution of blood group polymorphism are discussed.Abbreviations GP glycoprotein - GSL glycosphingolipid - GC glycoconjugate     

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates

Background

Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populations by genetic drift and that the origin of small subpopulations from larger populations can be fueled by biological innovations.

Results

We report three distinct groups of repetitive families preserved in the human genome that expanded and declined during the three previously described periods of regulatory innovations in vertebrate genomes. The first group originated prior to the evolutionary separation of the mammalian and bird lineages and the second one during subsequent diversification of the mammalian lineages prior to the origin of eutherian lineages. The third group of families is primate-specific.

Conclusions

The observed correlation implies a relationship between regulatory innovations and the origin of repetitive families. Consistent with our previous hypothesis, it is proposed that regulatory innovations fueled the origin of new subpopulations in which new repetitive families became fixed by genetic drift.

Reviewers

Eugene Koonin, I. King Jordan, Jürgen Brosius.     

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p‐Coumaric acid and related aromatic acids

Lignin comprises 15–25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP‐binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p‐coumarate, 3‐phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X‐ray crystal structures of protein–ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin‐derived aromatic compounds. The screens and structural data provide new functional assignments for these solute‐binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence‐based functional annotation methods for this family of proteins.Proteins 2013; 81:1709–1726. © 2013 Wiley Periodicals, Inc.     

Vasopressin V2 Receptor/Bioligand Interactions

Summary We predict some essential interactions between the V2 vasopressin renal receptor (V2R) and its agonists [Arg⁸]vasopressin (AVP) and [D-Arg⁸]vasopressin (DAVP), and the non-peptide antagonist OPC-31260. V2R controls antidiuresis and belongs to the superfamily of heptahelical transmembrane (7TM) G-protein-coupled receptors (GPCRs). The receptor was built, the ligands were docked and the structures relaxed using advanced molecular modeling techniques. Docked agonists and antagonists appear to prefer similar V2R compartments. A number of receptor amino acid residues are indicated, mainly in the TM3-TM7 helices, as potentially important in ligand binding. Many of these residues are invariant for either the GPCR superfamily or the subfamily of related (vasopressin V2R, V1aR and V1bR and oxytocin OR) receptors. Moreover, some of the equivalent residues in V1aR have already been found critical for ligand affinity [Mouillac et al., J. Biol. Chem., 270 (1995) 25771].     

Mapping of susceptibility and protective loci for acute GVHD in unrelated HLA-matched bone marrow transplantation donors and recipients using 155 microsatellite markers on chromosome 22

Despite matching donors and recipients for the human leukocyte antigens (HLAs) expressed by the major histocompatibility genomic region of the short arm of chromosome 6, several recipients still develop acute graft-versus-host disease (aGVHD) after bone marrow transplantation (BMT). This is possibly due to non-HLA gene polymorphisms, such as minor histocompatibility antigens (mHas) and genes coding for cytokines. However, a detailed genetic background for aGVHD has not yet been established. To find novel susceptibility and/or protective loci for aGVHD, a whole genome-wide association study of donors and recipients needs to be performed. As the first step to such a study, we retrospectively analyzed polymorphisms of 155 microsatellite markers spread across the long arm of chromosome 22 in 70 pairs of HLA-matched unrelated BMT donors and recipients. We performed individual typing and then compared the markers’ allele frequencies (1) between all the aGVHD (grades III and IV GVHD) and GVHD-free (grade 0 GVHD) groups in donors and recipients and (2) between the aGVHD and aGVHD-free groups in donor/recipient pairs that were matched and mismatched for the microsatellite marker’s allele. Screening of the microsatellite markers revealed five loci with a significant difference between the aGVHD and GVHD-free groups and revealed eight loci on chromosome 22, where the microsatellite allele mismatched markers were associated with aGVHD. This screening analysis suggests that several aGVHD-associated susceptible and protective loci exist on chromosome 22, which may encompass novel gene regions that need to be elucidated for their role in aGVHD.     

Oxidation of glycerol-3-phosphate in porcine and bovineadrenal cortex mitochondria

The capabilities of porcine adrenal cortex mitochondria to oxidize glycerol-3-phosphate (GP) were studied. In comparison with bovine adrenal cortex mitochondria, porcine mitochondria oxidized GP about three times more actively (18.9 vs 6.1 nmol O(2)/min per mg protein in the presence of ADP) and the activity of mitochondrial glycerol-3-phosphate dehydrogenase was about four times higher (33.4 vs 8.2 nmol/min per mg protein). In porcine adrenal cortex mitochondria we found similar values for succinate and GP oxidation both in the absence and presence of ADP or deoxycorticosterone (DOC). Rotenone sensitivity of DOC stimulation of GP oxidation indicated that porcine adrenal cortex mitochondria are able to oxidize GP and thus to generate NADPH from GP, presumably via reverse electron transport followed by energy-dependent NADH-NADP transhydrogenation.