Improved gossip protocol for blockchain applications

Cluster Computing - Blockchain is a distributed digital ledger consisting of sequence of blocks. These blocks are groups of transactions that make up a sequence where each block contains the...     

Cover Image,Volume 116, Number 2, February 2019

A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method called RiSLnet (Rapid i dentification of Smart mutant Library using residue network) to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, that is, T4 lysozyme, ribonuclease H, barnase, and cold shock protein B. Our method predicted beneficial mutations in thermal stability with ~62% average accuracy when the thermal stability of the mutants was compared with the ones in the Protherm database. It was further applied to lysine decarboxylase (CadA) to experimentally confirm its accuracy and effectiveness. RiSLnet identified mutations increasing the thermal stability of CadA with the accuracy of ~60% and significantly reduced the number of candidate residues (~99%) for mutation. Finally, combinatorial mutations designed by RiSLnet and in silico saturation mutagenesis yielded a thermally stable triple mutant with the half-life (T _1/2) of 114.9 min at 58°C, which is approximately twofold higher than that of the wild-type.     

A New Species of Protoachlya Upadhyay & Khulbe

Protoachlya nainitalensis isolated from mixed oak forest soil (Quercus leucotrichophora & Q. floribunda) is described herein. The species is characterised by elongated, cylindrical, smooth walled zoosporangia; spherical and smooth walled oogonia with androgynous and rarely diclinous branches of antheridia. A simplified key of the known Protoachlya species has also been established.     

Assessment of peroxidase isozyme marker-based model for cross identifications in hybrids (F(1)) of urdbean [ Vigna mungo (L.) Hepper

Four hybrids (4 F₁s) were chosen out of crosses in the urdbean [Vigna mungo (L.) Hepper, 2n = 22] having contrasting morphological characters. Zymograms for isozyme peroxidase were drawn from the patterns obtained from parents and their respective F₁ hybrids on the basis of relative similarities to parental bands. The selfed or crossed nature of hybrid pods was determined from the zymograms and their analysis. The number of bands and their intensities gave an idea about the extent of crossing in F₁ populations. Genetic identity (I) values were indicative of their selfed nature. Dendrograms were constructed on the basis of genetic identity values to display the relative similarities between the populations. Analysis was based on individual pods to confirm their hybrid or selfed nature. Possible use of this technique for identification of F₁ pods and elimination of selfed pods might be implemented to shorten the breeding operations during crossing.     

Preincubation of Mesorhizobium ciceri with flavonoids improves its nodule occupancy

Strains ofM. ciceri, symbionts of chickpea (Cicer arietinum) were incubated with the flavonoids naringenin, daidzein and quercetin which have earlier been reported as inducers and inhibitors ofnodABC-lacZ fusion ofM. ciceri. Preincubation ofM. ciceri with naringenin and daidzein (100 nmol/L) for 1 d improved the competitive ability of the inoculated strain while preincubation with quercetin decreased the nodule occupancy of inoculated strain under sterile conditions. Under nonsterile conditions induced strains of Rcd 301 and HT-6 formed by 23 and 18% more nodules, respectively, than untreated control. Quercetin-treated strains showed by 13–20% fewer nodules than untreated controls. Therefore, it is possible to regulate the competitive ability of inoculated strains by flavonoid treatment.     

Differential action of iodine on mitochondria from human tumoral- and extra-tumoral tissue in inducing the release of apoptogenic proteins

Iodide is actively concentrated in the thyroid gland for thyroid hormone biosynthesis. Excess iodine has been observed to induce apoptosis in thyrocytes and mammary cells. The mechanism of iodine induced apoptosis is poorly understood. Among various cell organelles, mitochondria is known to provide conducive environment for the organification of iodine, i.e. iodination of different proteins. Mitochondria also play a central role in execution of apoptosis. To study the role of mitochondria in iodine induced apoptosis, we investigated the direct interaction of iodine and human breast mitochondria vis-a-vis its role in the initiation of apoptosis in vitro. We observed that mitochondria isolated from the tumor (TT) and extra-tumoral tissue (ET) of human breast display significant uptake of iodine. Mitochondrial proteins were observed to be predominantly iodinated in ET but not in TT mitochondria. Treatment with iodine showed an increase in mitochondrial permeability transition of TT and decrease in ET. Iodine induced released factor(s) other than cytochrome c from tumor mitochondria initiate(s) apoptosis in vitro, while those from ET mitochondria were non-apoptogenic in nature. To our knowledge, this is first report demonstrating that iodine acts differentially on mitochondria of tumor and extratumoral origin to release apoptogenic proteins from TT and has a protective effect on ET.     

Asbestos-induced pulmonary toxicity: role of DNA damage and apoptosis

Asbestos causes asbestosis and various malignancies by mechanisms that are not clearly defined. Here, we review the accumulating evidence showing that asbestos is directly genotoxic by inducing DNA strand breaks (DNA-SB) and apoptosis in relevant lung target cells. Although the exact mechanisms by which asbestos causes DNA damage and apoptosis are not firmly established, some of the implicated mechanisms include the generation of iron-derived reactive oxygen species (ROS) as well as reactive nitrogen species (RNS), alteration in the mitochondrial function, and activation of the death receptor pathway. We focus on the accumulating evidence implicating ROS. DNA repair mechanisms have a key role in limiting the extent of DNA damage. Recent studies show that asbestos activates DNA repair enzymes such as apurinic/apyrimidinic endonuclease (APE) and poly (ADP-ribose) polymerase (PARP). Asbestos-induced neoplastic transformation may result in the setting where DNA damage overwhelms DNA repair in the face of a persistent proliferative signal. Strategies aimed at limiting asbestos-induced oxidative stress may reduce DNA damage and, as such, prevent malignant transformation.     

Predicting stable functional peptides from the intergenic space of E. coli

Expression of synthetic proteins from intergenic regions of E. coli and their functional association was recently demonstrated (Dhar et al. in J Biol Eng 3:2, 2009. doi:10.1186/1754-1611-3-2). This gave birth to the question: if one can make ‘user-defined’ genes from non-coding genome—how big is the artificially translatable genome? (Dinger et al. in PLoS Comput Biol 4, 2008; Frith et al. in RNA Biol 3(1):40–48, 2006a; Frith et al. in PLoS Genet 2(4):e52, 2006b). To answer this question, we performed a bioinformatics study of all reported E. coli intergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500 E. coli intergenic sequences were computationally translated into ‘protein sequence equivalents’ and matched against all known proteins. Sequences that did not show any resemblance were used for building a comprehensive profile in terms of their structure, function, localization, interactions, stability so on. A total of 362 protein sequences showed evidence of stable tertiary conformations encoded by the intergenic sequences of E. coli genome. Experimental studies are underway to confirm some of the key predictions. This study points to a vast untapped repository of functional molecules lying undiscovered in the non-expressed genome of various organisms.     

Transfecting pDNA to E. coli DH5α using bovine serum albumin nanoparticles as a delivery vehicle

We describe the formulation of bovine serum albumin nanoparticles (BSA‐NPs) by the coacervation method using surfactants. Plasmids (pUC18, pUC18egfp and pBBR1MCS‐2) isolated from E. coli were incorporated into the BSA matrix by incubating in albumin solution prior to formulation of NPs. Plasmid incorporation was calculated by % yield, entrapment efficiency, DNA loading capacity and release of entrapped DNA by comparing with blank NPs. BSA‐DNA binding studies were carried out by using fluorescence spectroscopy and Fourier Transform Infra Red Spectroscopy (FT‐IR). The surface charge distribution of the NPs loaded with plasmid was calculated using zeta potential. The photoluminescence of BSA‐NPs was quenched when loaded with pDNA, confirming the interaction of DNA with BSA. Altogether, these results provide evidences for the excellent DNA carrying efficiency of BSA‐NPs without loss of plasmid's integrity. The NPs were used to transfect E. coli DH5α strain lacking ampicillin resistance. They, however, showed ampicillin resistance subsequent to transfection with plasmid encoding ampicillin resistance gene. Effect of transfection was confirmed by confocal microscopy and by the isolation of the plasmid by agarose gel electrophoresis from the transfected bacterial culture. This study clearly demonstrates the efficacy of BSA‐NPs as delivery vehicle for pDNA transfection. Copyright © 2014 John Wiley & Sons, Ltd.     

Mechanistic insights into mode of action of potent natural antagonists of BACE-1 for checking Alzheimer’s plaque pathology

Alzheimer’s is a neurodegenerative disorder resulting in memory loss and decline in cognitive abilities. Accumulation of extracellular beta amyloidal plaques is one of the major pathology associated with this disease. β-Secretase or BACE-1 performs the initial and rate limiting step of amyloidic pathway in which 37–43 amino acid long peptides are generated which aggregate to form plaques. Inhibition of this enzyme offers a viable prospect to check the growth of these plaques. Numerous efforts have been made in recent years for the generation of BACE-1 inhibitors but many of them failed during the preclinical or clinical trials due to drug related or drug induced toxicity. In the present work, we have used computational methods to screen a large dataset of natural compounds to search for small molecules having BACE-1 inhibitory activity with low toxicity to normal cells. Molecular dynamics simulations were performed to analyze molecular interactions between the screened compounds and the active residues of the enzyme. Herein, we report two natural compounds of inhibitory nature active against β-secretase enzyme of amyloidic pathway and are potent lead molecules against Alzheimer’s disease.