CORRIE: enzyme sequence annotation with confidence estimates

Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate that the method is able to correctly re-annotate 91% of all Enzyme Classification (EC) classes with high coverage (755 out of 827). Only 44 enzyme classes are found to contain false positives, while the remaining 28 enzyme classes are not represented. We also show cases where the re-annotation procedure results in partial overlaps for those few enzyme classes where a certain inconsistency might appear between homologous proteins, mostly due to function specificity. Our results allow the interactive exploration of the EC hierarchy for known enzyme families as well as putative enzyme sequences that may need to be classified within the EC hierarchy. These aspects of our framework have been incorporated into a web-server, called CORRIE, which stands for Correspondence Indicator Estimation and allows the interactive prediction of a functional class for putative enzymes from sequence alone, supported by probabilistic measures in the context of the pre-calculated Correspondence Indicators of known enzymes with the functional classes of the EC hierarchy. The CORRIE server is available at: http://www.genomes.org/services/corrie/.     

Interrelated modulation of endothelial function in Behcet's disease by clinical activity and corticosteroid treatment

Corticosteroids are commonly used in empirical treatment of Behçet''s disease (BD), a systemic inflammatory condition associated with reversible endothelial dysfunction. In the present study we aimed to dissect the effects of clinical disease activity and chronic or short-term corticosteroid treatment on endothelial function in patients with BD. In a case-control, cross-sectional study, we assessed endothelial function by endothelium dependent flow mediated dilatation (FMD) at the brachial artery of 87 patients, who either were or were not receiving chronic corticosteroid treatment, and exhibiting variable clinical disease activity. Healthy individuals matched for age and sex served as controls. Endothelial function was also assessed in a prospective study of 11 patients before and after 7 days of treatment with prednisolone given at disease relapse (20 mg/day). In the cross-sectional component of the study, FMD was lower in patients than in control individuals (mean ± standard error: 4.1 ± 0.4% versus 5.7 ± 0.2%, P = 0.003), whereas there was a significant interaction between the effects of corticosteroids and disease activity on endothelial function (P = 0.014, two-factor analysis of variance). Among patients with inactive BD, those who were not treated with corticosteroids (n = 33) had FMD comparable to that in healthy control individuals, whereas those treated with corticosteroids (n = 15) had impaired endothelial function (P = 0.023 versus the respective control subgroup). In contrast, among patients with active BD, those who were not treated with corticosteroids (n = 20) had lower FMD than control individuals (P = 0.007), but in those who were receiving corticosteroids (n = 19) the FMD values were comparable to those in control individuals. Moreover, FMD was significantly improved after 7 days of prednisolone administration (3.7 ± 0.9% versus 7.6 ± 1.4%, P = 0.027). Taken together, these results imply that although corticosteroid treatment may impair endothelial function per se during the remission phase of the inflammatory process, it restores endothelial dysfunction during active BD by counteracting the harmful effects of relapsing inflammation.     

The Effect of 2-Ketobutyrate on Mitochondrial Substrate-Level Phosphorylation

Neurochemical Research - The reaction catalyzed by succinate-CoA ligase in the mitochondrial matrix yields a high-energy phosphate when operating towards hydrolysis of the thioester bond of...     

Chemical Priming with Salt and Urea Improves Germination and Seedling Growth of Black Cumin (Nigella sativa L.) under Osmotic Stress

Journal of Plant Growth Regulation - A common problem with vegetable production in saline areas is poor crop stand, but for black cumin (Nigella sativa L.) germination data are limited and...     

ROC graphs for assessing the ability of a diagnostic marker to detect three disease classes with an umbrella ordering

Receiver operating characteristic (ROC) curves and the area under these curves are commonly used to assess the ability of a continuous diagnostic marker (e.g., DNA methylation markers) to correctly classify subjects as having a particular disease or not (e.g., cancer). These approaches, however, are not applicable to settings where the gold standard yields more than two disease states or classes. ROC surfaces and the volume under the surfaces have been proposed for settings with more than two disease classes. These approaches, however, do not allow one to assess the ability of a marker to differentiate two disease classes from a third disease class without requiring a monotone order for the three disease classes under study. That is, existing approaches do not accommodate an umbrella ordering of disease classes. This article proposes the construction of an ROC graph that is applicable for an umbrella ordering. Furthermore, this article proposes that a summary measure for this umbrella ROC graph can be used to summarize the classification accuracy, and corresponding variance estimates can be obtained using U-statistics theory or bootstrap methods. The proposed methods are illustrated using data from a study assessing the ability of a DNA methylation marker to correctly classify lung specimens into three histologic classes: squamous cell carcinoma, large cell carcinoma, and nontumor lung.     

Spermidine triggering effect to the signal transduction through the AtoS–AtoC/Az two-component system in Escherichia coli

Recent analysis revealed that, in Escherichia coli the AtoS–AtoC/Az two-component system (TCS) and its target atoDAEB operon regulate the biosynthesis of short-chain poly-(R)-3-hydroxybutyrate (cPHB) biosynthesis, a biopolymer with many physiological roles, upon acetoacetate-mediated induction. We report here that spermidine further enhanced this effect, in E. coli that overproduces both components of the AtoS–AtoC/Az TCS, without altering their protein levels. However, bacteria that overproduce either AtoS or AtoC did not display this phenotype. The extrachromosomal introduction of AtoS–AtoC/Az in an E. coli ΔatoSC strain restored cPHB biosynthesis to the level of the atoSC⁺ cells, in the presence of the polyamine. Lack of enhanced cPHB production was observed in cells overproducing the TCS that did not have the atoDAEB operon. Spermidine attained the cPHB enhancement through the AtoC/Az response regulator phosphorylation, since atoC phosphorylation site mutants, which overproduce AtoS, accumulated less amounts of cPHB, compared to their wild-type counterparts. Exogenous addition of N⁸-acetyl-spermidine resulted in elevated amounts of cPHB but at lower levels than those attained upon spermidine addition. Furthermore, AtoS–AtoC/Az altered the intracellular distribution of cPHB according to the inducer recognized by the TCS. Overall, AtoS–AtoC/Az TCS was induced by spermidine to regulate both the biosynthesis and the intracellular distribution of cPHB in E. coli.     

Environmental influences on the spatial distribution of European hake (Merluccius merluccius) and red mullet (Mullus barbatus) in the Mediterranean

Generalised additive models (GAMs) were used to test the hypotheses that red mullet (Mullus barbatus) and hake (Merluccius merluccius) abundances are related to the bathymetry, spatial location and the temperature-based variability of the NE Mediterranean. Data were collected during a 2-year period (1996–1997) of quasi-synoptic sampling using demersal trawl surveys in the northern Aegean Sea. The results of this study supported these hypotheses. It was found that geographic position and sea bottom characteristics influence the temporal distribution patterns of red mullet and hake. Data are presented that reveal species-specific aggregation patterns and an important habitat utilisation of the area. The modelled species’ abundances showed a strongly non-linear dependence on the explanatory covariates. This study, although not directly dealing with spawning, also provided evidence that red mullet and hake demonstrate environmental and bathymetric preferences in the months posterior to spawning. Mean red mullet abundance was consistently highest in areas with warmer bottom waters in the east and west than in the centre, these areas having shallower depths (35–60 m) and bottom temperatures around 19°C. The red mullet appeared to avoid the cold bottom waters (<16°C) of the deeper regions. Results indicated that areas with the highest hake abundances were located in waters of ∼160 m having bottom temperature of ∼16°C and avoided the shallower waters (<70 m) regardless of their bottom temperature. The present findings also suggested that colder bottom waters at all depths were associated with lower-than-average hake abundance. Red mullet and hake preferences for areas with specific bathymetric and ocean environmental conditions are believed to be linked to the oceanography of the NE Mediterranean ecosystem.     

Whole-proteome genetic analysis of dependencies in assembly of a vertebrate kinetochore

Kinetochores orchestrate mitotic chromosome segregation. Here, we use quantitative mass spectrometry of mitotic chromosomes isolated from a comprehensive set of chicken DT40 mutants to examine the dependencies of 93 confirmed and putative kinetochore proteins for stable association with chromosomes. Clustering and network analysis reveal both known and unexpected aspects of coordinated behavior for members of kinetochore protein complexes. Surprisingly, CENP-T depends on CENP-N for chromosome localization. The Ndc80 complex exhibits robust correlations with all other complexes in a “core” kinetochore network. Ndc80 associated with CENP-T interacts with a cohort of Rod, zw10, and zwilch (RZZ)–interacting proteins that includes Spindly, Mad1, and CENP-E. This complex may coordinate microtubule binding with checkpoint signaling. Ndc80 associated with CENP-C forms the KMN (Knl1, Mis12, Ndc80) network and may be the microtubule-binding “workhorse” of the kinetochore. Our data also suggest that CENP-O and CENP-R may regulate the size of the inner kinetochore without influencing the assembly of the outer kinetochore.