MEM-FET: Essential protein prediction using membership feature and machine learning approach

Proteins are played key roles in different functionalities in our daily life. All functional roles of a protein are a bit enhanced in interaction compared to individuals. Identification of essential proteins of an organism is a time consume and costly task during observation in the wet lab. The results of observation in wet lab always ensure high reliability and accuracy in the biological ground. Essential protein prediction using computational approaches is an alternative choice in research. It proves its significance rapidly in day-to-day life as well as reduces the experimental cost of wet lab effectively. Existing computational methods were implemented using Protein interaction networks (PPIN), Sequence, Gene Expression Dataset (GED), Gene Ontology (GO), Orthologous groups, and Subcellular localized datasets. Machine learning has diverse categories of features that enable to model and predict essential macromolecules of understudied organisms. A novel methodology MEM-FET (membership feature) is predicted based on features, that is, edge clustering coefficient, Average clustering coefficient, subcellular localization, and Gene Ontology within a compartment of common neighbors. The accuracy (ACC) values of the predicted true positive (TP) essential proteins are 0.79, 0.74, 0.78, and 0.71 for YHQ, YMIPS, YDIP, and YMBD datasets. An enriched set of essential proteins are also predicted using the MEM-FET algorithm. Ensemble ML also validated the proposed model with an accuracy of 60%. It has been predicted that MEM-FET algorithms outperform other existing algorithms with an ACC value of 80% for the yeast dataset.     

Protoberberine Alkaloids Berberine,Palmatine, and Coralyne Binding to Poly(dT)⋅(Poly(dA)⋅Poly(dT)) Triplex: Comparative Structural Aspects and Energetics Profiles of the Interaction

The interaction of bioactive protoberberine alkaloids berberine, palmatine, and coralyne with the DNA triplex poly(dT)⋅(poly(dA)⋅poly(dT)) was studied using biophysical and calorimetric techniques. All three alkaloids bound the triplex cooperatively. Berberine and palmatine predominantly stabilized the triplex structure, while coralyne stabilized both triplex and duplex structures as inferred from optical thermal melting profiles. Fluorescence quenching, polarization, and viscometric studies hinted at an intercalative mode of binding for the alkaloids to the triplex, coralyne being more strongly intercalated compared to partial intercalation of berberine and palmatine. The overall affinity of coralyne was two order higher (2.29×10⁷ M ⁻¹) than that of berberine (3.43×10⁵ M ⁻¹) and palmatine (2.34×10⁵ M ⁻¹). Isothermal titration calorimetric studies revealed that the binding to the triplex was favored by negative enthalpy change (ΔH=−3.34 kcal/mol) with favorable entropy contribution (TΔS = 4.07 kcal/mol) for berberine, favored by almost equal negative enthalpy (ΔH =−3.88 kcal/mol) and entropy changes (TΔS = 3.37 kcal/mol) for palmatine, but driven by large enthalpy contributions (ΔH =−25.62 kcal/mol and TΔS =−15.21 kcal/mol) for coralyne. These results provide new insights on the binding of isoquinoline alkaloids to the DNA triplex structure.     

A low-cost medium for mannitol production by Lactobacillus intermedius NRRL B-3693

The production of mannitol by Lactobacillus intermedius NNRL B-3693 using molasses as an inexpensive carbon source was evaluated. The bacterium produced mannitol (104 g/l) from molasses and fructose syrups (1:1; total sugars, 150 g/l; fructose:glucose 4:1) in 16 h. Several kinds of inexpensive organic and inorganic nitrogen sources and corn steep liquor were evaluated for their potential to replace more expensive nitrogen sources derived from Bacto-peptone and yeast extract. Soy peptone D (5 g/l) and corn steep liquor (50 g/l) were found to be suitable substitutes for Bacto-peptone (5 g/l) and Bacto-yeast extract (5 g/l), respectively. The bacterium produced 105 g mannitol per liter from the molasses and fructose syrup (1:1, total sugars 150 g/l; fructose:glucose 4:1) in 22 h using a combination of soy peptone D (5 g/l) and corn steep liquor (50 g/l). This is the first report on the production of mannitol by fermentation using molasses and corn steep liquor.Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

Cluster-randomised controlled trial of community mobilisation in Mumbai slums to improve care during pregnancy, delivery, postpartum and for the newborn

Background

Chronic back pain is a major public health problem and the primary reason patients seek acupuncture treatment. Therefore, an objective assessment of acupuncture efficacy is critical for making informed decisions about its appropriate role for patients with this common condition. This study addresses methodological shortcomings that have plagued previous studies evaluating acupuncture for chronic low back pain.

Methods and Design

A total of 640 participants (160 in each of four arms) between the ages of 18 and 70 years of age who have low back pain lasting at least 3 months will be recruited from integrated health care delivery systems in Seattle and Oakland. They will be randomized to one of two forms of Traditional Chinese Medical (TCM) acupuncture needling (individualized or standardized), a "control" group (simulated acupuncture), or to continued usual medical care. Ten treatments will be provided over 7 weeks. Study participants and the "Diagnostician" acupuncturists who evaluate participants and propose individualized treatments will be masked to the acupuncture treatment actually assigned each participant. The "Therapist" acupuncturists providing the treatments will not be masked but will have limited verbal interaction with participants. The primary outcomes, standard measures of dysfunction and bothersomeness of low back pain, will be assessed at baseline, and after 8, 26, and 52 weeks by telephone interviewers masked to treatment assignment. General health status, satisfaction with back care, days of back-related disability, and use and costs of healthcare services for back pain will also be measured. The primary analysis comparing outcomes by randomized treatment assignment will be analysis of covariance adjusted for baseline value. For both primary outcome measures, this trial will have 99% power to detect the presence of a minimal clinically significant difference among all four treatment groups and over 80% power for most pairwise comparisons. Secondary analyses will compare the proportions of participants in each group that improve by a clinically meaningful amount.

Conclusion

Results of this trial will help clarify the value of acupuncture needling as a treatment for chronic low back pain.

Trial registration

Clinical Trials.gov NCT00065585.     

Trypanosoma brucei: differential requirement of membrane potential for import of proteins into mitochondria in two developmental stages

Trypanosome alternative oxidase (TAO) and the cytochrome oxidase (COX) are two developmentally regulated terminal oxidases of the mitochondrial electron transport chain in Trypanosoma brucei. Here, we have compared the import of TAO and cytochrome oxidase subunit IV (COIV), two stage-specific nuclear encoded mitochondrial proteins, into the bloodstream and procyclic form mitochondria of T. brucei to understand the import processes in two different developmental stages. Under in vitro conditions TAO and COIV were imported and processed into isolated mitochondria from both the bloodstream and procyclic forms. With mitochondria isolated from the procyclic form, the import of TAO and COIV was dependent on the mitochondrial inner membrane potential (delta psi) and required protein(s) on the outer membrane. Import of these proteins also depended on the presence of both internal and external ATP. However, import of TAO and COIV into isolated mitochondria from the bloodstream form was not inhibited after the mitochondrial delta psi was dissipated by valinomycin, CCCP, or valinomycin and oligomycin in combination. In contrast, import of these proteins into bloodstream mitochondria was abolished after the hydrolysis of ATP by apyrase or removal of the ATP and ATP-generating system, suggesting that import is dependent on the presence of external ATP. Together, these data suggest that nuclear encoded proteins such as TAO and COIV are imported in the mitochondria of the bloodstream and the procyclic forms via different mechanism. Differential import conditions of nuclear encoded mitochondrial proteins of T. brucei possibly help it to adapt to different life forms.     

Fostering Maternal and Newborn Care in India the Yashoda Way: Does This Improve Maternal and Newborn Care Practices during Institutional Delivery?

Background

The Yashoda program, named after a legendary foster-mother in Indian mythology, under the Norway-India Partnership Initiative was launched as a pilot program in 2008 to improve the quality of maternal and neonatal care at facilities in select districts of India. Yashodas were placed mainly at district hospitals, which are high delivery load facilities, to provide support and care to mothers and newborns during their stay at these facilities. This study presents the results from the evaluation of this intervention in two states in India.

Methods

Data collection methods included in-depth interviews with healthcare providers and mothers and a survey of mothers who had recently delivered within a quasi-experimental design. Fifty IDIs were done and 1,652 mothers who had delivered in the past three months were surveyed during 2010 and 2011.

Results

A significantly higher proportion of mothers at facilities with Yashodas (55 percent to 97 percent) received counseling on immunization, breastfeeding, family planning, danger signs, and nutrition compared to those in control districts (34 percent to 66 percent). Mothers in intervention facilities were four to five times more likely to receive postnatal checks than mothers in control facilities. Among mothers who underwent cesarean sections, initiation of breastfeeding within five hours was 50 percent higher in intervention facilities. Mothers and families also reported increased support, care and respect at intervention facilities.

Conclusion

Yashoda as mothers'' aide thus seems to be an effective intervention to improve quality of maternal and newborn care in India. Scaling up of this intervention is recommended in district hospitals and other facilities with high volume of deliveries.     

1alpha, 25-Dihydroxyvitamin D3 suppresses the effect of streptozotocin-induced diabetes during chemical rat liver carcinogenesis

The effect of streptozotocin-induced diabetes in male Sprague-Dawley rats was investigated to ascertain whether it has had any modulating role in hepatocarcinogenesis. Hepatocarcinogenesis was initiated with a single sub-necrogenic dose of diethylnitrosamine (DEN) (125 mg/kg body weight, i.p.) whilst acute diabetes was produced with a single i.p. injection of streptozotocin (STZ) (65 mg/kg body weight). STZ was administered either before or after initiation with DEN at 3-week intervals. With this basic experimental regimen, the effect of an antioxidant vitamin, 1alpha, 25-dihydroxyvitamin D3 (VD) (0.3 microg/ 0.1 ml propylene glycol per os twice a week), was investigated with effect from 4 weeks prior to the exposure of DEN or STZ. Primary routine histopathology, hepatic nodular morphometric analysis and major preneoplastic antioxidant and drug metabolising enzymes were tested either with or without VD treatment in different experimental and control groups. Observation of the hepatic nodulogenesis, pathology and level of the antioxidant and drug metabolising enzyme pattern of the tissue showed a marked protection in different experimental groups of rats treated with VD. It may be that VD could elicit an anticarcinogenic potential in the aforesaid regimen by resetting the effects of these biomarkers induced by DEN and/or STZ. We further propose that STZ, when administered 3 weeks after DEN, caused massive damage where its action in vivo could be comparable with any known promoter that could propel the process of carcinogenesis more efficiently than when it was applied before the carcinogen.