Homology modeling and assigned functional annotation of an uncharacterized antitoxin protein from Streptomyces xinghaiensis

Streptomyces xinghaiensis is a Gram-positive, aerobic and non-motile bacterium. The bacterial genome is known. Therefore, it is of interest to study the uncharacterized proteins in the genome. An uncharacterized protein (gi|518540893|86 residues) in the genome was selected for a comprehensive computational sequence-structure-function analysis using available data and tools. Subcellular localization of the targeted protein with conserved residues and assigned secondary structures is documented. Sequence homology search against the protein data bank (PDB) and non-redundant GenBank proteins using BLASTp showed different homologous proteins with known antitoxin function. A homology model of the target protein was developed using a known template (PDB ID: 3CTO:A) with 62% sequence similarity in HHpred after assessment using programs PROCHECK and QMEAN6. The predicted active site using CASTp is analyzed for assigned anti-toxin function. This information finds specific utility in annotating the said uncharacterized protein in the bacterial genome.     

Prevalence and Correlates of Smokeless Tobacco Consumption among Married Women in Rural Bangladesh

Objective

To estimate the prevalence and identify correlates of smokeless tobacco consumption among married rural women with a history of at least one pregnancy in Madaripur, Bangladesh.

Materials and Methods

We conducted a cross-sectional survey using an interviewer administered, pre-tested, semi-structured questionnaire. All women living in the study area, aged 18 years and above with at least one pregnancy in their lifetime, who were on the electoral roll and agreed to participate were included in the study. Information on socio-demographic characteristics and smokeless tobacco consumption was collected. Smokeless tobacco consumption was categorized as ‘Current’, ‘Ever but not current’ and ‘Never’. Associations between smokeless tobacco consumption and the explanatory variables were estimated using simple and multiple binary logistic regression.

Results

8074 women participated (response rate 99.9%). The prevalence of ‘Current consumption’, ‘Ever consumption but not current’, and ‘Never consumption’ was 25%, 44% and 31%, respectively. The mean age at first use was 31.5 years. 87% of current consumers reported using either Shadapata or Hakimpuree Jarda. Current consumption was associated with age, level of education, religion, occupation, being an income earner, marital status, and age at first use of smokeless tobacco. After adjustment for demographic variables, current consumption was associated with being over 25 years of age, a lower level of education, being an income earner, being Muslim, and being divorced, separated or widowed.

Conclusion

The prevalence of smokeless tobacco consumption is high among rural women in Bangladesh and the age of onset is considerably older than that for smoking. Smokeless tobacco consumption is likely to be producing a considerable burden of non-communicable disease in Bangladesh. Smokeless tobacco control strategies should be implemented.     

Plasmid-Mediated Sulfamethoxazole Resistance Encoded by the sul2 Gene in the Multidrug-Resistant Shigella flexneri 2a Isolated from Patients with Acute Diarrhea in Dhaka,Bangladesh

In this study, mechanisms of plasmid-mediated sulfamethoxazole resistances in the clinical strains of multi-drug resistant (MDR) Shigella flexneri 2a were elucidated for the first time in Bangladesh. From 2006 to 2011, a total of 200 S. flexneri 2a strains were randomly selected from the stock of the Enteric and Food Microbiology Laboratory of icddr,b. Antimicrobial susceptibility of the strains showed 73%, 98%, 93%, 58%, 98%, 64% and 4% resistance to trimethoprim-sulfamethoxazole, nalidixic acid, ampicillin, erythromycin, tetracycline, ciprofloxacin and ceftriaxone respectively. Plasmid profiling revealed heterogeneous patterns and interestingly, all the trimethoprim-sulfamethoxazole resistant (SXT^R) strains yielded a distinct 4.3 MDa plasmid compared to that of the trimethoprim-sulfamethoxazole susceptible (SXT^S) strains. Curing of this 4.3 MDa plasmid resulted in the susceptibility to sulfamethoxazole alone suggesting the involvement of this plasmid in the resistance of sulfamethoxazole. Moreover, PCR analysis showed the presence of sul2 gene in SXT^R strains which is absent in SXT^S strains as well as in the 4.3 MDa plasmid-cured derivatives, confirming the involvement of sul2 in the resistance of sulfamethoxazole. Furthermore, pulsed-field gel electrophoresis (PFGE) analysis revealed that both the SXT^R and SXT^S strains were clonal. This study will significantly contributes to the knowledge on acquired drug resistance of the mostly prevalent S. flexneri 2a and further warrants continuous monitoring of the prevalence and correlation of this resistance determinants amongst the clinical isolates of Shigella and other enteric pathogens around the world to provide effective clinical management of the disease.     

Pharmacological insights into Merremia vitifolia (Burm.f.) Hallier f. leaf for its antioxidant,thrombolytic, anti-arthritic and anti-nociceptive potential

Merremia vitifolia (Burm.f.) Hallier f., an ethnomedicinally important plant, used in the tribal areas to treat various ailments including fever, headache, eye inflammation, rheumatism, dysentery, jaundice and urinary diseases. The present study explored the biological efficacy of the aqueous fraction of M. vitifolia leaves (AFMV) through in vitro and in vivo experimental models. The thrombolytic and anti-arthritic effects of AFMV were evaluated by using the clot lysis technique and inhibition of protein denaturation technique, respectively. The anti-nociceptive activity of AFMV was investigated in Swiss Albino mice by acetic acid-induced writhing test and formalin-induced paw licking test. The antioxidant activities of AFMV, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical and total reducing power, were also tested. The qualitative phytochemical assays exhibited AFMV contains secondary metabolites such as alkaloid, carbohydrate, flavonoid, tannin, triterpenoids and phenols. In addition, AFMV showed strong antioxidant effects with the highest scavenging activity (IC₅₀ 146.61 µg/mL) and reducing power was increased with a dose-dependent manner. AFMV also revealed notable clot lysis effect and substantial anti-arthritic activity at higher doses (500 µg/mL) as compared with the control. The results demonstrated a promising reduction of the number of writhing and duration of paw licking in acetic acid-induced writhing test and formalin-induced paw licking test in a dose-dependent manner, respectively. In conclusion, AFMV provides the scientific basis of its folkloric usage, suggesting it as the vital source of dietary supplement.     

Investigating pollination strategies in disturbed habitats: the case of the narrow-endemic toadflax Linaria tonzigii (Plantaginaceae) on mountain screes

Plant Ecology - Plant mating systems may reflect an adaptation to a habitat type, with self-pollination being potentially common in unstable and disturbed conditions. We investigated the...     

Timing of enteral feeding in cerebral malaria in resource-poor settings: a randomized trial

Background

Early start of enteral feeding is an established treatment strategy in intubated patients in intensive care since it reduces invasive bacterial infections and length of hospital stay. There is equipoise whether early enteral feeding is also beneficial in non-intubated patients with cerebral malaria in resource poor settings. We hypothesized that the risk of aspiration pneumonia might outweigh the potential benefits of earlier recovery and prevention of hypoglycaemia.

Method and Findings

A randomized trial of early (day of admission) versus late (after 60 hours in adults or 36 hours in children) start of enteral feeding was undertaken in patients with cerebral malaria in Chittagong, Bangladesh from May 2008 to August 2009. The primary outcome measures were incidence of aspiration pneumonia, hypoglycaemia and coma recovery time. The trial was terminated after inclusion of 56 patients because of a high incidence of aspiration pneumonia in the early feeding group (9/27 (33%)), compared to the late feeding group (0/29 (0%)), p = 0.001). One patient in the late feeding group, and none in the early group, had hypoglycaemia during admission. There was no significant difference in overall mortality (9/27 (33%) vs 6/29 (21%), p = 0.370), but mortality was 5/9 (56%) in patients with aspiration pneumonia.

Conclusions

In conclusion, early start of enteral feeding is detrimental in non-intubated patients with cerebral malaria in many resource-poor settings. Evidence gathered in resource rich settings is not necessarily transferable to resource-poor settings.

Trial Registration

Controlled-Trials.com ISRCTN57488577     

Micropropagation of Abelmoschus esculentus L. (Moench.) for disease free plantlets through meristem culture

Protocol was established for mass in vitro propagation of okra using meristem culture. Meristems (0.3–0.5 mm in size) were isolated from shoot tips of three-week old in vitro grown seedlings. Isolated meristems were established rapidly in MS liquid medium containing 1.0 mg/l of BAP. For shoot development from primarily established meristem, semisolid MS medium having the same concentration of BAP was found to be the most effective. Rapid shoot multiplication of mericlone was achieved from node cutting cultured in 1.0 mg/l plus 0.5 mg/l GA₃, and a maximum of nine shoots were found from each node. Effective root development from the developed plantlets was successful in 1.0 mg/l IBA. More than 75% of the micropropagated mericlones plantlets were successfully acclimatised in soil up to maturity and found to be healthy.     

iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features

Linear B-cell epitopes are critically important for immunological applications, such as vaccine design, immunodiagnostic test, and antibody production, as well as disease diagnosis and therapy. The accurate identification of linear B-cell epitopes remains challenging despite several decades of research. In this work, we have developed a novel predictor, Identification of Linear B-cell Epitope (iLBE), by integrating evolutionary and sequence-based features. The successive feature vectors were optimized by a Wilcoxon-rank sum test. Then the random forest (RF) algorithm using the optimal consecutive feature vectors was applied to predict linear B-cell epitopes. We combined the RF scores by the logistic regression to enhance the prediction accuracy. iLBE yielded an area under curve score of 0.809 on the training dataset and outperformed other prediction models on a comprehensive independent dataset. iLBE is a powerful computational tool to identify the linear B-cell epitopes and would help to develop penetrating diagnostic tests. A web application with curated datasets for iLBE is freely accessible at http://kurata14.bio.kyutech.ac.jp/iLBE/.     

NDUFA4 Mutations Underlie Dysfunction of a Cytochrome c Oxidase Subunit Linked to Human Neurological Disease

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Reproduction,Growth, Mortality and Yield of the Goatfish Upeneus sulphureus in Northern Bay of Bengal,Bangladesh

Journal of Ichthyology - Information on stock condition and reproductive biology are important for fisheries conservation and management planning. This study examined reproduction, growth,...