Identification of Penicillin-binding proteins employing support vector machines and random forest

Penicillin-Binding Proteins are peptidases that play an important role in cell-wall biogenesis in bacteria and thus maintaining bacterial infections. A wide class of β-lactam drugs are known to act on these proteins and inhibit bacterial infections by disrupting the cell-wall biogenesis pathway. Penicillin-Binding proteins have recently gained importance with the increase in the number of multi-drug resistant bacteria. In this work, we have collected a dataset of over 700 Penicillin-Binding and non-Penicillin Binding Proteins and extracted various sequence-related features. We then created models to classify the proteins into Penicillin-Binding and non-binding using supervised machine learning algorithms such as Support Vector Machines and Random Forest. We obtain a good classification performance for both the models using both the methods.     

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes

According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed''s features include chemical, pharmacological, biochemical and geographical information of the medicinal plant, scientifically relevant information of the plant, and the coherent research done on it in the field of diabetes. The database also includes the list of poly-herbal formulations which are used for treatment of diabetes in India.

Availability

http://www.indiamed.info     

Ni (II) adsorption onto Chrysanthemum indicum: Influencing factors,isotherms, kinetics,and thermodynamics

The study explores the adsorption potential of Chrysanthemum indicum biomass for nickel ion removal from aqueous solution. C. indicum flowers in raw (CIF-I) and biochar (CIF-II) forms were used as adsorbents in this study. Batch experiments were conducted to ascertain the optimum conditions of solution pH, adsorbent dosage, contact time, and temperature for varying initial Ni(II) ion concentrations. Surface area, surface morphology, and functionality of the adsorbents were characterized by Brunauer, Emmett, and Teller (BET) surface analysis, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and Fourier transform infrared spectroscopy (FTIR). Adsorption kinetics were modeled using pseudo-first order, pseudo-second order, Elovich, intraparticle diffusion, Bangham's, and Boyd's plot. The equilibrium data were modeled using Langmuir, Freundlich, Temkin, and Dubinin–Radushkevich (D-R) isotherm models. Experimental data provided the best fit to pseudo-second-order kinetic model and Langmuir isotherm model for the adsorption of Ni(II) ion on both CIF-I and CIF-II with maximum adsorption capacities of 23.97 and 44.02 mg g^?1, respectively. Thermodynamic analysis of the data proved the process to be spontaneous and endothermic in nature. Desorption studies were conducted to evaluate the possibility of reusing the adsorbents. Findings of the present study provide substantial evidence for the use of C. indicum flower as an eco-friendly and potential adsorbent for the removal of Ni(II) ions from aqueous solution.     

Cloning,Expression, Purification,and Characterization of Biologically Active Recombinant Hemagglutinin-33, Type A Botulinum Neurotoxin Associated Protein

Botulinum neurotoxin type A, the most toxic substance known to mankind, is produced by Clostridium botulinum type A as a complex with a group of neurotoxin-associated proteins (NAPs) through polycistronic expression of a clustered group of genes. Hemagglutinin-33 (Hn-33) is a 33 kDa subcomponent of NAPs, which is resistant to protease digestion, a feature likely to be involved in the protection of the botulinum neurotoxin from proteolysis. In order to fully understand the function of Hn-33, large amounts of Hn-33 will be needed without dealing with biosafety risks to grow large cultures of C. botulinum. There are difficulties to clone the genes with the high A + T contents produced by C. botulinum. We report here for the first time using the Gateway technology to clone functional Hn-33 that has been expressed in E. coli. The yield of the recombinant Hn-33 was about 12 mg per liter of E. coli culture. The recombinant Hn-33 folds well in aqueous solution as shown with circular dichroism spectra, resists temperature-denaturation, is totally resistant to trypsin proteolysis despite the presence of cleavage sites on the molecular surface, and maintains its biological activities comparable to the native Hn-33 hemagglutination.