Life Sciences

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Shiv Nadar University

Tropical Calcific Pancreatitis (TCP) is a neglected juvenile form of chronic nonalcoholic pancreatitis. Cathepsin B (CTSB), a lysosomal protease involved in the cellular degradation process, has recently been studied as a potential candidate gene in the pathogenesis of TCP. According to the Cathepsin B hypothesis, mutated CTSB can lead to premature intracellular activation of trypsinogen, a key regulatory mechanism in pancreatitis. So far, CTSB mutations have been studied in pancreatitis and neurode-generative disorders, but little is known about the structural and functional effect of variants in CTSB. In this study, we investigated the effect of single nucleotide variants (SNVs) specifically associated with TCP, using molecular dynamics and simulation algorithms. There were two non-synonymous variants (L26V and S53G) of CTSB, located in the propeptide region. We tried to predict the effect of these variants on structure and function using multiple algorithms: SIFT, Polyphen2, PANTHER, SDM sever, i-Mutant2.0 suite, mCSM algorithm, and Vadar. Further, using databases like miRdbSNP, PolymiRTS, and miRNASNP, two SNPs in the 30UTR region were predicted to affect the miRNA binding sites. Structural mutated models of nsSNP mutants (L26V and S53G) were prepared by MODELLER v9.15 and evaluated using TM-Align, Verify 3D, ProSA and Ramachandran plot. The 3D mutated structures were simulated using GROMACS 5.0 to predict the impact of these SNPs on protein stability. The results from in silico analysis and molecular dynamics simulations suggested that these variants in the propeptide region of Cathepsin B could lead to structural and functional changes in the protein and thus could be pathogenic. Hence, the structural and functional analysis results have given interim conclusions that these variants can have a deleterious effect in TCP pathogenesis, either uniquely or in combination with other mutations. Thus, it could be extrapolated that Cathepsin B gene can be screened in samples from all TCP patients in future, to decipher the distribution of variants in patients. Copyright 2019 Singh et al.

(SoNS) School of Natural Sciences

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Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics

The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/. © 2019, The Author(s).

World University root node

Scientific Reports

Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

Present research efforts coupled with improved experimental techniques have provided voluminous genomic data. To convert this data into useful knowledge, novel tools for phenomenological and data driven modelling approaches are needed. This need has spurred initiation of a lot of rigorous efforts and has resulted in development of robust artificial intelligence (AI) and machine learning (ML) based models. While these paradigms individually and in synergistic combinations have been employed in various bioinformatics applications, the viral biology discipline has particularly benefitted most. These methodologies can efficiently handle single dimensional sequence to higher dimensional protein structures, microarray data, image and text data, experimental data emanating from spectroscopy, etc. Our analysis deals with ML tools like support vector machines (SVM), neural networks, deep neural networks, random forest, and decision tree. Analysis and interpretations are provided along with ample illustrations of their relevance to real-life applications. AI and evolutionary computing based tools like Genetic Algorithms, Ant Colony optimization, Particle swarm optimization and their applicability to viral biology problems are also discussed. Hybrid combination of these tools with ML techniques have resulted in simultaneous selection of informative attributes and high performance classification. This hybrid methodology has been discussed in detail. In this chapter we describe the applications artificial intelligence and machine learning in virology. While there are AI has a multitude of tools, the focus would be on a specific aspect of Ai, known as evolutionary and heuristic computing. These are mainly employed as an alternative paradigm of optimization. They are mainly nature inspired algorithms. Although very simple and straightforward to use they have been deputed to solve several problems successfully in different domains of science and engineering. Machine learning on the other hand deals with a mountain of available data, recognize hidden patterns useful and interesting to upgrade it to structure and knowledge. We provide examples of the power of AI and Machine learning with the illustration of several examples from different subdomains of viral biology. We will also provide examples where the synergistic combination of AI and ML has a been found to be a very potent tool for solving several important problems in viral biology. © Springer Nature Switzerland AG 2019. All rights reserved.

Center for Informatics

Global Virology III: Virology in the 21st Century

Applications of artificial intelligence and machine learning in viral biology

Deinococcus radiodurans exhibits growth medium-dependent morphological variation in cell shape, but there is no evidence whether this phenomenon is observed in other members of the Deinococcaceae family. In this study, we isolated a red-pigmented, aerobic, Deinococcus indicus strain DR1 from Dadri wetland, India. This D. indicus strain exhibited cell-morphology transition from rod-shaped cells to multicell chains in a growth-medium-dependent fashion. In response to addition of 1\% casamino acids in the minimal growth medium, rod-shaped cells formed multi-cell chains. Addition of all 20 amino acids to the minimal medium was able to recapitulate the phenotype. Specifically, a combination of L-methionine, L-lysine, L-aspartate, and L-threonine caused morphological alterations. The transition from rod shape to multi-cell chains is due to delay in daughter cell separation after cell division. Minimal medium supplemented with L-ornithine alone was able to cause cell morphology changes. Furthermore, a comparative UPLC analysis of PG fragments isolated from D. indicus cells propagated in different growth media revealed alterations in the PG composition. An increase in the overall cross-linkage of PG was observed in muropeptides from nutrient-rich TSB and NB media versus PYE medium. Overall our study highlights that environmental conditions influence PG composition and cell morphology in D. indicus. Copyright © 2019 Chauhan, Srivastava, Ritzl, Yennamalli, Cava and Priyadarshini. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Frontiers in Microbiology

Amino acid-dependent alterations in cell wall and cell morphology of deinococcus indicus DR1

Agriculture now is shifting in light of society's requirements. Where promising to provide as an instance, drinking water retention implanted area, which ensure superb services and products are very popular. Green houses have become for accomplishing those targets an answer; afterward back, problems that were tough can be prompted by a greenhouse for a technique for the farming. The increased section of these are discovered within the greenhouse setting states by which restraining the temperatures, and relative humidity (RH) would be the essential targets of technology. Accomplishing climate states that were proper to ensure that usage diminishing are the target of search for a significant long time. Programs in manage hypotheses are connected to manage the topics previously. The idea with the paper is to introduce an overview of control strategies that are diverse implemented in farming to manage rainwater setting requirements, revealing detriments and conditions of get a grip on levels that are to indicate a design approach according to outcome gained by assessments. © BEIESP.

International Journal of Recent Technology and Engineering

Green house control system: A research

In this work, we have developed novel multifunctional magnetic-polymeric nanoparticles (MMPNs) based ferrofluids by encapsulating oleylamine (OM)-coated hydrophobic superparamagnetic iron oxide nanoparticles (SPIONs) inside the poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) individually, and along with two drugs such as curcumin (Cur, a chemotherapeutic drug (CHD)), and/or verapamil (Ver, a calcium channel blocker (CCB)). Herein, several parameters such as weighed amount (wt\%) of PLGA polymer (i.e., Resomer), stabilizer (i.e., polyvinyl alcohol (PVA)), organic solvents, amount of the SPIONs (in liquid suspension and powder forms), and amount of the drugs (i.e., Cur or/and Ver) are varied during the encapsulation process to optimize the formulation of PLGA NPs. The resulting polymeric NPs including empty PLGA NPs (i.e., without SPIONs/drugs), and MMPNs such as SPIONs-loaded PLGA NPs, Cur-SPIONs-loaded PLGA NPs, Ver-SPIONs-loaded PLGA NPs, and Cur-Ver-SPIONs-loaded PLGA NPs have displayed (i) hydrodynamic diameters and zeta potentials in the range of 280.8–287.3 nm, and −21 to – 26 mV, respectively, and (ii) better encapsulation efficiency for the SPIONs/Cur/Ver. In addition, the MMPNs have exhibited (i) magnetization values in the range of 7.6–9.5 emu/g with superparamagnetic behaviour, (ii) concentration based time-dependent temperature raise up-to 42 °C (minimum therapeutic temperature in magnetic fluid hyperthermia (MFH)/thermotherapy) with heating efficacies i.e., specific absorption rate (SAR) and intrinsic loss power (ILP) values ranging from 7 to 36 W/gFe and 0.1–0.4 nHm2/kg, respectively and (iii) better cytocompatibility. Finally, the SPIONs and dual-drugs (Cur &amp;Ver) co-loaded PLGA NPs have shown enhanced therapeutic efficacy in HepG2 cancer cells via combined therapies (i.e., thermotherapy and chemotherapy), as compared to the individual therapy (i.e., thermotherapy or chemotherapy) using the SPIONs/Cur/Ver loaded PLGA NPs. Thus, the as-prepared SPIONs/dual-drugs co-loaded PLGA NPs (i.e., MMPNs based ferrofluids) are potential therapeutic candidates for multi-modal treatment of cancer in vitro using thermotherapy and chemotherapy. © 2019 Elsevier B.V.

Journal of Molecular Liquids

Multifunctional magnetic-polymeric nanoparticles based ferrofluids for multi-modal in vitro cancer treatment using thermotherapy and chemotherapy

THz spectroscopy is an attractive technique to study the interaction of proteins in water as it is highly sensitive to water mediated interactions. GroEL, a barrel shaped chaperonin known for assisting protein folding, is studied using THz-TDS technique for varying concentrations. Results show significant decrease in absorption with increasing concentrations demonstrating the formation of more bound water due to the presence of GroEL complex. © 2019 IEEE.

International Conference on Infrared, Millimeter, and Terahertz Waves, IRMMW-THz

Study of Protein Water Interactions in GroEL Molecular Chaperonins using Terahertz Spectroscopy

Riparian landscapes are characterized by heterogeneous geomorphological structures such as erosive and depositional habitats, and therefore, may have variable soil biophysical properties. The heterogeneity in geomorphological structures and related biophysical properties would exert spatial variations in the soil CO2 efflux (SCE). However, studies assessing the relative control of biophysical variables on the SCE under such complex landscapes of dry tropical ecosystems are limited. Therefore, we assessed the effect of heterogeneity in geomorphological structures on SCE, and identified the key biophysical variables governing SCE along the riparian landscapes. The SCE, soil organic C (SOC), microbial biomass C (MBC) and pH were found to vary significantly (P &lt; 0.05) along riparian habitats, and SCE was found 73% higher at erosive than depositional habitats. SOC was found as a prominent regulator of SCE which alone explained about 80% of the variability in SCE. Moreover, soil moisture, fine particles, pH and MBC also showed strong control on SCE along riparian landscapes. Stepwise regression analysis revealed that after excluding SOC as a main variable, soil moisture explained 32% of the variability in SCE at overall landscape level whereas fine particles and MBC explained 78% and 23% of the variability in SCE at erosive and depositional habitats, respectively. Overall, results indicate that erosive habitats are the major source of SCE, and variation in biophysical variables is greatly affecting the SCE at these habitats. Therefore, further assessment of interactions of SCE, soil biophysical parameters and their regulatory components such as hydrology, vegetation and anthropogenic activities at micro—(site and land-use) as well as macro—(landscape) scales would help to understand the soil C dynamics along the heterogeneous riparian landscapes under climate change scenarios. © 2019, Springer Nature Switzerland AG.

Aquatic Sciences

Geomorphologic heterogeneity influences dry-season soil CO2 efflux by mediating soil biophysical variables in a tropical river valley

Arsenic prevalence in the environment impelled many organisms to develop resistance over the course of evolution. Tolerance to arsenic, either as the pentavalent [As(V)] form or the trivalent form [As(III)], by bacteria has been well studied in prokaryotes, and the mechanism of action is well defined. However, in the rod-shaped arsenic tolerant Deinococcus indicus DR1, the key enzyme, arsenate reductase (ArsC) has not been well studied. ArsC of D. indicus belongs to the Grx-linked prokaryotic arsenate reductase family. While it shares homology with the well-studied ArsC of Escherichia coli having a catalytic cysteine (Cys 12) and arginine triad (Arg 60, 94, and 107), the active site of D.indicus ArsC contains four residues Glu 9, Asp 53, Arg 86, and Glu 100, and with complete absence of structurally equivalent residue for crucial Cys 12. Here, we report that the mechanism of action of ArsC of D. indicus is different as a result of convergent evolution and most likely able to detoxify As(V) using a mix of positively- and negatively-charged residues in its active site, unlike the residues of E. coli. This suggests toward the possibility of an alternative mechanism of As (V) degradation in bacteria. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

Journal of Molecular Modeling

Structure and function prediction of arsenate reductase from Deinococcus indicus DR1

Nuclear receptors (NRs) are transcription factors that bind to specific DNA sequences known as hormone response elements located upstream of their target genes. Transcriptional activity of NRs can be modulated by binding of the compatible ligand and transient interaction with cellular coregulators, functioning either as coactivators or as corepressors. Many coactivator proteins possess intrinsic histone acetyltransferase (HAT) activity that catalyzes the acetylation of specific lysine residues in histone tails and loosens the histone-DNA interaction, thereby facilitating access of transcriptional factors to the regulatory sequences of the DNA. Tat interactive protein 60 (TIP60), a member of the Mof-Ybf2-Sas2-TIP60 family of HAT protein, is a multifunctional coregulator that controls a number of physiological processes including apoptosis, DNA damage repair, and transcriptional regulation. Over the last two decades or so, TIP60 has been extensively studied for its role as NR coregulator, controlling various aspect of steroid receptor functions. The aim of this review is to summarize the findings on the role of TIP60 as a coregulator for different classes of NRs and its overall functional implications. We also discuss the latest studies linking TIP60 to NR-associated metabolic disorders and cancers for its potential use as a therapeutic drug target in future. Copyright © 2018 Endocrine Society.