The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulphite reduction system

Assimilatory and dissimilatory sulphite reductions are key reactions in the biogeochemical sulphur cycle and several distinct sirohaem-containing sulphite reductases have been characterized. Here, we describe that the Epsilonproteobacterium Wolinella succinogenes is able to grow by sulphite respiration (yielding sulphide) with formate as electron donor. Sulphite is reduced by MccA, a prototypical member of an emerging new class of periplasmic cytochrome c sulphite reductases that, phylogenetically, belongs to a multihaem cytochrome c superfamily whose members play crucial roles in the global sulphur and nitrogen cycles. Within this family, MccA represents an unconventional octahaem cytochrome c containing a special haem c group that is bound via two cysteine residues arranged in a unique CX(15)CH haem c binding motif. The phenotypes of numerous W.succinogenes mutants producing MccA variants underlined the structural importance of this motif. Several open reading frames of the mcc gene cluster were individually inactivated and characterization of the corresponding mutants indicated that the predicted iron-sulphur protein MccC, the putative quinol dehydrogenase MccD (a member of the NrfD/PsrC family) as well as a peptidyl-prolyl cis-trans isomerase, MccB, are essential for sulphite respiration. MccA synthesis in W. succinogenes was found to be induced by sulphite (but not by thiosulphate or sulphide) and repressed in the presence of fumarate or nitrate. Based on the results, a sophisticated model of respiratory sulphite reduction by the Mcc system is presented.     

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

MOTIVATION: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. RESULTS: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.     

Effect of nutrition on fatty acid profiles of riverine, lacustrine, and aquaculture-raised salmonids of pre-alpine habitats

We examined trophic positions and fatty acid concentrations of riverine, lacustrine, and aquaculture diet and fish in Austrian pre-alpine aquatic ecosystems. It was hypothesized that dietary fatty acid (FA) profiles largely influence the FA composition of the salmonids Salvelinus alpinus, Salmo trutta, and Oncorhynchus mykiss. We analyzed trophic positions using stable isotopes (δ¹⁵N) and tested for correlations with polyunsaturated fatty acid (PUFA) concentrations. Gut content analysis revealed benthos (rivers), pellets (aquaculture), and zooplankton (lakes) as the predominant diet source. Results of dorsal muscle tissues analysis showed that the omega-3 PUFA, docosahexaenoic acid (DHA; 22:6n − 3), was the mostly retained PUFA in all fish of all ecosystems, yet with the highest concentrations in S. alpinus from aquaculture (mean: 20 mg DHA/g dry weight). Moreover, we found that eicosapentaenoic acid (EPA; 20:5n − 3) in fish of natural habitats (rivers, lakes) was the second most abundant PUFA (3–5 mg/g DW), whereas aquaculture-raised fish had higher concentrations of the omega-6 linoleic acid (18:2n – 6; 9–11 mg/g DW) than EPA. In addition, PUFA patterns showed that higher omega-3/-6 ratios in aquacultures than in both riverine and lacustrine fish. Data of this pilot field study suggest that salmonids did not seem to directly adjust their PUFA to dietary PUFA profiles in either natural habitats or aquaculture and that some alterations of PUFA are plausible. Finally, we suggest that trophic positions of these freshwater salmonids do not predict PUFA concentrations in their dorsal muscle tissues.     

IL-1β and TNF-α alter the glycophenotype of primary human chondrocytes in vitro

Despite the significance of glycoproteins for extracellular matrix assembly in cartilage tissue, little is known about the regulation of the chondrocyte glycophenotype under inflammatory conditions. The present study aimed to assess the effect of IL-1β and TNF-α on specific features of the glycophenotype of primary human chondrocytes in vitro. Using LC-MS, we found that both cytokines increased overall sialylation of N- and O-glycans and induced a shift towards α-(2→3)-linked sialic acid residues in chondrocyte glycoproteins. These results were supported by quantitative PCR showing increased expression of α-(2→3) sialyltransferases in treated cells. Moreover, we found that both IL-1β and TNF-α induced a considerable shift from oligomannosidic glycans towards complex-type N-glycans. In contrast, core α-(1→6)-fucosylation of chondrocyte N-glycans was found to be reduced particularly by TNF-α. In summary, inflammatory conditions induce specific alterations of the chondrocyte glycophenotype which might affect cell-matrix interactions or the function of endogenous lectins.     

α-actinin-4 is essential for maintaining the spreading, motility and contractility of fibroblasts

Background

α-Actinins cross-link actin filaments, with this cross-linking activity regulating the formation of focal adhesions, intracellular tension, and cell migration. Most non-muscle cells such as fibroblasts express two isoforms, α-actinin-1 (ACTN1) and α-actinin-4 (ACTN4). The high homology between these two isoforms would suggest redundancy of their function, but recent studies have suggested different regulatory roles. Interestingly, ACTN4 is phosphorylated upon growth factor stimulation, and this loosens its interaction with actin.

Methodology/Principal Findings

Using molecular, biochemical and cellular techniques, we probed the cellular functions of ACTN4 in fibroblasts. Knockdown of ACTN4 expression in murine lung fibroblasts significantly impaired cell migration, spreading, adhesion, and proliferation. Surprisingly, knockdown of ACTN4 enhanced cellular compaction and contraction force, and increased cellular and nuclear cross-sectional area. These results, except the increased contractility, are consistent with a putative role of ACTN4 in cytokinesis. For the transcellular tension, knockdown of ACTN4 significantly increased the expression of myosin light chain 2, a element of the contractility machinery. Re-expression of wild type human ACTN4 in ACTN4 knockdown murine lung fibroblasts reverted cell spreading, cellular and nuclear cross-sectional area, and contractility back towards baseline, demonstrating that the defect was due to absence of ACTN4.

Significance

These results suggest that ACTN4 is essential for maintaining normal spreading, motility, cellular and nuclear cross-sectional area, and contractility of murine lung fibroblasts by maintaining the balance between transcellular contractility and cell-substratum adhesion.     

Analysis ofl-alanine:2-oxoglutarate aminotransferase isozymes in maize

Isozyme analysis ofl-alanine:2-oxoglutarate aminotransferase (ALT) in maize indicates that there are three genes encoding this enzyme activity. Two of the gene products interact with each other to form heterodimers, while the third gene product does not interact with the other two. Another isozyme that appears after gel electrophoresis and ALT staining is shown to be glutamate dehydrogenase-1. Anaerobic treatment does not result in increased ALT levels, indicating that the previously reported increase in alanine levels caused by this treatment may be due to increases in the level of pyruvate, a substrate of ALT.D. A. Russell was partially supported by a graduate student fellowship from the Division of Biology and Biomedical Sciences, Washington University. V. M. Peschke was partially supported by a postdoctoral fellowship from Monsanto. This research was supported by NIH Grant R01 GM34740.     

Diet of the golden eagle Aquila chrysaetos during the breeding season in Sweden

During a five-year period, 1975–1979, a total of 2881 prey individuals of 65 prey species were collected at 162 golden eagle nests from northern Sweden and from the island of Gotland. In northern Sweden birds are taken in higher numbers than mammals but calculated as weight the two categories are of equal importance, The main prey during the breeding season are capercaillie, black grouse, willow grouse, ptarmigan, mountain hare and reindeer fawns which together form 91% of the total food biomass. The capercaillie and the black grouse are taken more in the southern part of the coniferous region than in the northern. In contrast, in northern areas, reindeer fawns are more preyed upon than in the South, Ptarmigan and willow grouse are the most commonly captured prey species in mountain areas. The total number of reindeer fawns taken (dead and/or alive) by the Swedish golden eagle population during one summer is estimated at 600 individuals. On Gotland the golden eagles take mammals more often than in its northern distribution area. Rabbit and hedgehog arc the most important species.