SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

BACKGROUND: Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic counterparts. However, in silico methods for predicting BY-kinases have not been developed yet. Since these enzymes are involved in key regulatory processes, and are promising targets for anti-bacterial drug design, it is desirable to develop a simple and easily interpretable predictor to gain new insights into bacterial tyrosine phosphorylation. This study proposes a novel SCMBYK method for predicting and characterizing BY-kinases. RESULTS: A dataset consisting of 797 BY-kinases and 783 non-BY-kinases was established to design the SCMBYK predictor, which achieved training and test accuracies of 97.55 and 96.73%, respectively. Furthermore, the leave-one-phylum-out method was used to predict specific bacterial phyla hosts of target sequences, gaining 97.39% average test accuracy. After analyzing SCMBYK-derived propensity scores, four characteristics of BY-kinases were determined: 1) BY-kinases tend to be composed of α-helices; 2) the amino-acid content of extracellular regions of BY-kinases is expected to be dominated by residues such as Val, Ile, Phe and Tyr; 3) BY-kinases structurally resemble nuclear proteins; 4) different domains play different roles in triggering BY-kinase activity. CONCLUSIONS: The SCMBYK predictor is an effective method for identification of possible BY-kinases. Furthermore, it can be used as a part of a novel drug repurposing method, which recognizes putative BY-kinases and matches them to approved drugs. Among other results, our analysis revealed that azathioprine could suppress the virulence of M. tuberculosis, and thus be considered as a potential antibiotic for tuberculosis treatment.

An alcohol training program improves Chinese nurses' knowledge, self-efficacy, and practice: a randomized controlled trial.

BACKGROUND: Excessive alcohol use has been associated with health, social and legal problems. Helping health care providers to manage hazardous or harmful drinkers is an important worldwide issue. Alcohol is a legal and accessible substance in Taiwan and is viewed as an acceptable drink for relieving stress and enhancing socialization in Chinese culture. These cultural factors may contribute to drinking problems being easily ignored and to lack of alcohol training programs for health care providers. METHODS: For this randomized controlled clinical trial with 1- and 3-month posttests, six hospitals were randomly selected throughout Taiwan and were randomly assigned to an experimental or control group. In these hospitals, nurses were selected from the Emergency Department, psychiatric, and gastrointestinal medical-surgical units where most patients with alcohol problems are seen. For the experimental group, nurses received a 1.5-hour alcohol training program consisting of an introduction to alcohol, factors influencing alcohol drinking, impacts of high-risk drinking on a person, as well as introduction to and practice of the Alcohol Use Disorders Identification Test and brief alcohol intervention. The program also discussed Taiwanese nurses' perceived barriers and facilitators to intervening for problem alcohol use. Teaching strategies included lecture, discussion, demonstration, practice, role-playing, and sharing experiences. The control group did not receive any training. Data were collected at pretest, 1-month, and 3-month posttests using a self-report questionnaire on knowledge, self-efficacy, clinical practice scales, and a demographic form. RESULTS: The study was completed by 395 nurses, including 191 nurses in the experimental group and 204 nurses in the control group. Knowledge scores significantly improved in the experimental group at the 1- and 3-month posttests but not for the control group. Similarly, nurses' self-efficacy and clinical practice scores significantly improved in the experimental group at the 3-month posttest but not for the control group. CONCLUSIONS: Our results suggest that the alcohol training program could be used to enhance nurses' alcohol knowledge, self-efficacy, and clinical practice not only in Taiwan but also other countries.

Prevalence of melioidosis in the Er-Ren River Basin, Taiwan: implications for transmission.

An increase in melioidosis cases compared to other areas in Taiwan was observed in the Er-Ren River Basin, southwestern Taiwan, from November 2001 to August 2006. The objective of this study was to determine the association between the level of exposure to Burkholderia pseudomallei and the incidence rate of melioidosis and to survey the transmission modes of B. pseudomallei in the Er-Ren River Basin. The serosurveillance of melioidosis gave seropositivity rates of 36.6%, 21.6%, and 10.9%, respectively, for residents in regions A, B, and C within the Er-Ren Basin area. Culture and PCR-based detection of B. pseudomallei from soil demonstrated that the geographical distribution of this bacterium was confined to a particular site in region B. The distribution of seropositive titers was significantly associated with the incidence rate of melioidosis (120, 68, or 36 incidence cases per 100,000 population in region A, B, or C in 2005), whereas it did not correlate with the geographical distribution of B. pseudomallei within the soil. A survey of transmission modes showed that residents with seropositivity were linked to factors such as having confronted flooding and having walked barefoot on soil, which are potential risk factors associated with exposure to B. pseudomallei. Our findings indicated that the Er-Ren River Basin in Taiwan has the potential to become a high-prevalence area for melioidosis. This is the first report that documents a high prevalence of melioidosis in an area north of latitude 20 degrees N.

Down-regulation of human NDR gene in megakaryocytic differentiation of erythroleukemia K562 cells.

To study the control of hematopoietic cell differentiation, a human negative differentiation regulator (NDR) gene was identified by the comparative analysis of differentially expressed genes in hemato-lymphoid tissues. NDR is expressed preferentially in the adult bone marrow, fetal liver and testis. Immunocytochemistry with anti-NDR antiserum showed the presence of NDR in human erythroleukemia K562 cell line and CD34+ cells sorted from the umbilical cord blood. When fused to the green fluorescent protein (GFP), NDR was directed to the nucleus of mouse 3T3 and K562 cells. Fusion protein with a deletion from residues 7 to 87 was detected in the cytoplasm. NDR appeared not to affect the proliferation of K562 cells when overly expressed. However, its expression was down-regulated during megakaryocytic differentiation of K562 cells induced by 12-O-tetradecanoylphorbol-13-acetate (TPA). Down-regulation of NDR correlated well with up-regulation of megakaryocytic markers, CD41 and CD61. Overexpression of the nuclear NDR-GFP in K562 cells inhibited the expression of CD41 and CD61 in megakaryocytic differentiation. Treatment of K562 cells with GF-109203X (GFX), an antagonist of the protein kinase C (PKC), blocked NDR down-regulation, up-regulated expression of CD41/CD61 and TPA-induced megakaryocytic differentiation. These results suggest a novel function of nuclear NDR protein in regulating hematopoietic cell development.