Fluorescein-labeled β-Glucosidase as a Bacterial Stain

Fluorescein isothiocyanate-labeled beta-glucosidase was used as a simple staining reagent with selected gram-positive and gram-negative organisms. Staining in situ appeared to be dependent on the presence of accessible glycosidic-type linkages in the bacterial cell wall. Extensive wall damage or lysis did not occur when stained cells were suspended in washing and mounting solutions. The apparent specificity of labeled enzyme for wall substance was tested by blocking reactions, staining of isolated cell walls, and failure to stain substances lacking appropriate glycosidic linkages. Severe cell wall lesions were produced after prolonged contact with labeled enzyme, and this phenomenon may also be related to staining specificity. Gram-negative organisms and spores were poorly stained unless protected glycopeptide substrate was previously exposed by treatment of cells with thioglycolic acid or dilute alkaline sodium hypochlorite solution. A potential for staining tissues and cell lines may also exist. Some possible applications of labeled enzymes are briefly discussed.     

A Pleiotropic Phospholipid Biosynthetic Regulatory Mutation in Saccharomyces Cerevisiae Is Allelic to Sin3 (Sdi1, Ume4, Rpd1)

Three mutants were identified in a genetic screen using an INO1-lacZ fusion to detect altered INO1 regulation in Saccharomyces cerevisiae. These strains harbor mutations that render the cell unable to fully repress expression of INO1, the structural gene for inositol-1-phosphate synthase. The Cpe(-) (constitutive phospholipid gene expression) phenotype associated with these mutations segregated 2:2, indicating that it was the result of a single gene mutation. The mutations were shown to be recessive and allelic. A strain carrying the tightest of the three alleles was examined in detail and was found to express the set of co-regulated phospholipid structural genes (INO1, CHO1, CHO2 and OPI3) constitutively. The Cpe(-) mutants also exhibited a pleiotropic defect in sporulation. The mutations were mapped to the right arm of chromosome XV, close to the centromere, where it was discovered that they were allelic to the previously identified regulatory mutation sin3 (sdi1, ume4, rpd1, gam2). A sin3 null mutation failed to complement the mutation conferring the Cpe(-) phenotype. A mutant harboring a sin3 null allele exhibited the same altered INO1 expression pattern observed in strains carrying the Cpe(-) mutations isolated in this study.     

Comparison of the folding of 2-Keto-3-deoxy-6-phosphogluconate aldolase,triosephosphate isomerase and pyruvate kinase: Implications in molecular evolution

The 8-fold α/β barrel conformation of 2-keto-3-deoxy-6-phosphogluconate aldolase has been compared to that of triosephosphate isomerase and the A-domain of pyruvate kinase. There are eight supersecondary structure units (α/β) in each of these proteins, and the comparisons were carried out in orientations corresponding to each of the possible congruences, i.e. first to first, first to second,… of the supersecondary structure units. The comparison of the C_α structure of the main chain folding of the three enzymes indicated about 150 equivalences with rootmean-square differences of about 3.1 Å, with no orientational preference, including the aldolase with itself. In addition, there is no sequence homology between the aldolase and the isomerase, and no indication of gene duplication in the former. The lack of orientational preference among the three enzymes suggests convergence to a fold of exceptional stability. However, all three enzymes activate a CH bond adjacent to a carbonyl, and their active sites correspond to the f strand, F helix region of the α/β barrel, thus contradicting the foregoing and suggesting divergent evolution from a common precursor. Other and similar arguments are also presented for and against convergent evolution of these three strikingly similar enzymes.     

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma     

Urinary Metal Levels with Relation to Age,Occupation, and Smoking Habits of Male Inhabitants of Eastern Iran

Biological Trace Element Research - In low-income and middle-income countries such as Iran, smoking is becoming increasingly popular, especially among young people. This has led to additional...     

Suppressor of Cytokine Signaling (SOCS) 5 Utilises Distinct Domains for Regulation of JAK1 and Interaction with the Adaptor Protein Shc-1

Suppressor of Cytokine Signaling (SOCS)5 is thought to act as a tumour suppressor through negative regulation of JAK/STAT and epidermal growth factor (EGF) signaling. However, the mechanism/s by which SOCS5 acts on these two distinct pathways is unclear. We show for the first time that SOCS5 can interact directly with JAK via a unique, conserved region in its N-terminus, which we have termed the JAK interaction region (JIR). Co-expression of SOCS5 was able to specifically reduce JAK1 and JAK2 (but not JAK3 or TYK2) autophosphorylation and this function required both the conserved JIR and additional sequences within the long SOCS5 N-terminal region. We further demonstrate that SOCS5 can directly inhibit JAK1 kinase activity, although its mechanism of action appears distinct from that of SOCS1 and SOCS3. In addition, we identify phosphoTyr317 in Shc-1 as a high-affinity substrate for the SOCS5-SH2 domain and suggest that SOCS5 may negatively regulate EGF and growth factor-driven Shc-1 signaling by binding to this site. These findings suggest that different domains in SOCS5 contribute to two distinct mechanisms for regulation of cytokine and growth factor signaling.     

Disordered nucleiome: Abundance of intrinsic disorder in the DNA‐ and RNA‐binding proteins in 1121 species from Eukaryota,Bacteria and Archaea

Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty‐by‐association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (～548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA‐binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA‐binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation.     

A Novel Attempt to Standardize Results of CFD Simulations Basing on Spatial Configuration of Aortic Stent-Grafts

Currently, studies connected with Computational Fluid Dynamic (CFD) techniques focus on assessing hemodynamic of blood flow in vessels in different conditions e.g. after stent-graft’s placement. The paper propose a novel method of standardization of results obtained from calculations of stent-grafts'' “pushing forces” (cumulative WSS—Wall Shear Stress), and describes its usefulness in diagnostic process. AngioCT data from 27 patients were used to reconstruct 3D geometries of stent-grafts which next were used to create respective reference cylinders. We made an assumption that both the side surface and the height of a stent-graft and a reference cylinder were equal. The proposed algorithm in conjunction with a stent-graft “pushing forces” on an implant wall, allowed us to determine which spatial configuration of a stent-graft predispose to the higher risk of its migration. For stent-grafts close to cylindrical shape (shape factor φ close to 1) WSS value was about 267Pa, while for stent-grafts different from cylindrical shape (φ close to 2) WSS value was about 635Pa. It was also noticed that deformation in the stent-graft’s bifurcation part impaired blood flow hemodynamic. Concluding the proposed algorithm of standardization proved its usefulness in estimating the WSS values that may be useful in diagnostic process. Angular bends or tortuosity in bifurcations of an aortic implant should be considered in further studies of estimation of the risk of implantation failure.