Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae

Enorma massiliensis strain phI^T is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phI^T is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes.     

Lipase production by Serratia marcescens strain SN5gR isolated from the scat of lion-tailed macaque (Macaca silenus) in Silent Valley National Park, a biodiversity hotspot in India

An extracellular lipase-producing bacterium was isolated from a fecal sample of lion-tailed macaque (Macaca silenus), an endangered Old World monkey that is endemic to the Western Ghats of South India. Morphological, biochemical and molecular analyses identified the bacterium as Serratia marcescens. Production of lipase was investigated in shake-flask culture. Optimum tributyrin concentration of 1.5 % was found to be the most suitable triglyceride to increase lipase production (13.3 U ml^?1). The next best lipid source observed was olive oil (11.94 U ml^?1), followed by castor oil, coconut oil and palm oil. Analyzing the effect of different carbon sources on lipase production revealed that 2 % glucose yielded higher lipase production than the other tested carbon sources. Investigations on suitable nitrogen source for lipase production revealed that 2 % meat extract yielded higher lipase production. The most suitable trace element for maximum lipase production was zinc sulfate, followed by magnesium sulfate and copper sulfate. Partial characterization of the crude lipase revealed that pH 7.0 and a temperature of 40 °C gave optimal lipase activity. Enzymatic activity of the crude sample was retained over a wide temperature range (20–75 °C), and 70 % of enzyme activity was retained at 60 °C. Testing the effect of various organic solvents on lipase activity revealed that hexadecane increased lipase activity by 85 % over the control.     

Methodologies to decipher the cell secretome

The cell secretome is a collection of proteins consisting of transmembrane proteins (TM) and proteins secreted by cells into the extracellular space. A significant portion (~ 13–20%) of the human proteome consists of secretory proteins. The secretory proteins play important roles in cell migration, cell signaling and communication. There is a plethora of methodologies available like Serial Analysis of Gene Expression (SAGE), DNA microarrays, antibody arrays and bead-based arrays, mass spectrometry, RNA sequencing and yeast, bacterial and mammalian secretion traps to identify the cell secretomes. There are many advantages and disadvantages in using any of the above methods. This review aims to discuss the methodologies available along with their potential advantages and disadvantages to identify secretory proteins. This review is a part of a Special issue on The Secretome. This article is part of a Special Issue entitled: An Updated Secretome.     

Utilization of renewable agricultural residues for the production of extracellular halostable cellulase from newly isolated Halomonas sp. strain PS47

A newly isolated biopolymer-degrading halophilic bacterium, Halomonas sp. strain PS47, yielded higher cellulase activity (0.0076 U/ml) in mineral salt medium (MM63). Activity increased to 0.029 U/ml when carboxymethyl cellulose (0.5 % w/v) was used as carbon source and further to 0.138 U/ml when a combination of yeast extract and peptone was used as nitrogen source. Enzyme secretion was maximal during late exponential and stationary phases (0.15 U/ml, 48 h). Among different agro-residues (1 % w/v), wheat bran gave the highest activity (0.12 U/ml) at pH 7.5, 30 °C and 6 % (w/v) NaCl. The cellulase exhibited higher activity at pH 7.1 and 50 °C. The enzyme exhibited activity over a wide range of NaCl concentrations (0–4 M). Optimum activity was at 0–1 M NaCl. At 4 M NaCl, activity was reduced to 65 % of the initial value. The present investigation thus contributes to the limited information available on halostable cellulases.     

A computational approach to design energetic ionic liquids

The present work deals with the theoretical estimation of ion-pair binding energies and the energetic properties of four ion pairs formed by combining the 1-butyl-2,4-dinitro-3-methyl imidazolium ion with nitrate (I), perchlorate (II), dinitramide (III), or 3,5-dinitro-1,2,4-triazolate (IV) anions. The counterpoise-corrected ion-pair binding energies were calculated for each ion pair at the B3LYP/6-311+G(d,p) level of theory. Results show that the cation–anion interaction is strongest for ion pair I and weakest for IV, indicating that the nitrate (I) has a greater tendency to exist as a stable ionic salt whereas the 3,5-dinitro-1,2,4-triazolate (IV) may exist as an ionic liquid. Natural bond orbital (NBO) analysis and electrostatic potential (ESP) mapping revealed that charge transfer occurs in all of the ion pairs, but is greatest (0.25e) for ion pair I and smallest (0.03e) for IV, resulting in ion pair I being the least polarized. A nucleus-independent chemical shift (NICS) study revealed that the aromaticity of the 1-butyl-2,4-dinitro-3-methyl imidazolium ion significantly increases in ion pair IV, indicating that this has the greatest charge delocalization among all of the four ion pairs considered. Studies of thermodynamic and detonation properties showed that ion pair II is the most energetic ion pair in terms of its detonation velocity (D = 7.5 km s^?1) and detonation pressure (P = 23.1 GPa). It is also envisaged that ion pair IV would exist as an energetic azolium azolate type ionic liquid that could be conveniently used as a secondary explosive characterized by detonation parameters D and P of 6.9 km s^?1 and 19.3 GPa, respectively. These values are comparable to those of conventional explosives such as TNT.     

Comparative modeling of Rab6 proteins: identification of key residues and their interactions with guanine nucleotides

The cytoplasm of a eukaryotic cell consists of a wide variety of membrane bound cell organelles and continuous flow of proteins amongst these organelles is a major challenge and must be stringently maintained in order to continue the correct biochemical functioning inside a cell. The transportation of various proteins amongst these organelles is facilitated by a vast Tubulo-vesicular network mediated by carrier proteins. The Rabs belong to small G proteins super family involved in the regulation and vesicle transport in between the organelles by shuttling between the active GTP and inactive GDP bound states. In this paper we put forth the homology modeling and docking studies of Rab6A proteins (Mus musculus, Gallus gallus and Caenorhabditis elegans) with GTP, GMP-PNP and GDP molecules and a comparative study between these proteins is done to identify key residues out of which serine of the phosphate binding loop (P – loop) and aspartic acid showed prominent interactions with the GTP, GDP and GMP-PNP nucleotides and cogitate that aspartic acid might also help in the stabilization of the switch I region of the Rab proteins besides serine.     

Structure guided inhibitor designing of CDK2 and discovery of potential leads against cancer

On the basis of stereo specific information obtained from crystal structures of CDK2, indole and chromene analogues were designed by suitably substituting the pharmacophores on their moiety and docked with target protein for calculating binding affinities. The binding affinities are represented in glide score. (5E)-5-[(1-methyl-1H-indol-3-yl)methylidene]-2,4,6-trioxotetrahydro-2H-pyrimidin-1-ide (I₁), (5E)-5-(1H-indol-3-ylmethylidene)-2,4,6-trioxotetrahydro-2H-pyrimidin-1-ide (I₂) and 2-amino-4-(4-methyl phenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile (C₉) were selected for synthesis and biological testing based on vital interactions. (5E)-5-(1H-indol-3-ylmethylidene)-2,4,6-trioxotetrahydro-2H-pyrimidin-1-ide(I₂) and 2-amino-4-(4-methyl phenyl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile (C₉) were proved to be active against MCF-7 and HeLa cell lines.     

Theoretical investigation on the kinetics and branching ratio of the gas phase reaction of sevoflurane with Cl atom

The present work deals with the theoretical investigation on the Cl initiated H-atom abstraction reaction of sevoflurane, (CF₃)₂CHOCH₂F. A dual-level procedure has been adopted for studying the kinetics of the reaction. Geometrical optimization and frequency calculation were performed at DFT(BHandHLYP)/6-311G(d,p) while single-point energy calculation was made at CCSD(T)/6-311G(d,p) level of theory. The intrinsic reaction coordinate (IRC) calculation has also been performed to confirm the smooth transition from the reactant to product through the respective transition state. The rate constants were calculated using conventional transition state theory (TST). It has been found that 99 % of the reaction proceeded via the H-atom abstraction from the –CH₂F end of the sevoflurane. The rate constant of the dominant path is found to be 1.13 × 10^?13 cm³ molecule^?1 s^?1. This is in excellent agreement with the reported experimental rate constant of 1.10 × 10^?13 cm³ molecule^?1 s^?1 obtained by relative rate method using FTIR/Smog chamber and LP/LIF techniques.