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Computational identification and analysis of neurodegenerative disease associated protein kinases in hominid genomes

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Genes & Diseases 2016年第3期3卷 228-237页

作者： Saranya Jayapalan Devika Subramanian Jeyakumar natarajan Data Mining and Text Mining Lab Department of BioinformaticsBharathiar UniversityCoimbatoreIndia

Protein kinases play an important role in the incidence of neurodegenerative *** their incidence in non-human primates is found to be very *** differences among the genomes might influence the disease *** present study deals with finding the genetic differences of protein kinases in humans and their three closest evolutionary partners chimpanzee,gorilla and orangutan for three neurodegenerative diseases namely,Alzheimer’s,Parkinson’s and Huntington’s *** total 47 human protein kinases associated with three neurodegenerative diseases and their orthologs from other three nonhuman primates were identified and analyzed for any possible susceptibility factors in *** sequence alignment and pairwise sequence alignment revealed that,18 human protein kinases including DYRK1A,RPS6KB1,and GRK6 contained significant indels and *** phosphorylation site analysis revealed that eight kinases including MARK2 and LTK contained sites of phosphorylation exclusive to human genomes which could be particular candidates in determining disease susceptibility between human and non-human *** pathway analysis of these eight kinases and their targets revealed that these kinases could have long range consequences in important signaling pathways which are associated with neurodegenerative diseases.

关键词： Hominids Interaction analysis Neurodegenerative diseases Phosphorylation sites Protein kinases

Investigation on mechanical properties of aluminium 7075-boron carbide-coconut shell fly ash reinforced hybrid metal matrix composites

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China Foundry 2018年第6期15卷 449-456页

作者： Balasubramani Subramaniam Balaji natarajan Balasubramanian Kaliyaperumal Samson Jerold Samuel Chelladurai Department of Mechanical Engineering Sri Eshwar College of EngineeringCoimbatore-641202Tamilnadulndia Department of Mechanical Engineering Sri Krishna College of Engineering and TechnologyCoimbatore-641008India

The present research work reports the fabrication and evaluation of the mechanical properties of hybrid aluminium matrix composites(HAMC). Aluminium 7075(Al7075) alloy was reinforced with particles of boron carbide(B_4 C) and coconut shell fly ash(CSFA). Al7075 matrix composites were fabricated by stir casting method. The samples of Al7075 HAMC were fabricated with different weight percentages of(0, 3, 6, 9 and 12 wt.%) B_4 C and 3 wt.% of CSFA. The mechanical properties discussed in this work are hardness, tensile strength, and impact strength. Hardness of the composites increased 33% by reinforcements of 12 wt.% B_4 C and 3 wt.% CSFA in aluminium 7075 alloy. The tensile strength of the composites increased 66% by the addition of 9 wt.% B_4 C and 3 wt.% CSFA in aluminium 7075 alloy. Further addition of reinforcements decreased the tensile strength of the composites. Elongation of the composites decreased while increasing B_4 C and CSFA reinforcements in the matrix. The impact energy of the composites increased up to 2.3 J with 9 wt.% B_4 C and 3 wt.% CSFA addition in aluminium alloy. Further addition of reinforcement decreased the impact strength of the composites. The optical micrographs disclosed the homogeneous distribution of reinforcement particles(B_4 C and CSFA) in Al7075 matrix. The homogeneously distributed B_4 C and CSFA particles added as reinforcement in the Al7075 alloy contributed to the improvement of hardness, tensile strength, and impact strength of the composites.

关键词： aluminium 7075 boron carbide fly ash casting hardness tensile strength impact energy

Cytogenetic studies of chromium(Ⅲ) oxide nanoparticles on Allium cepa root tip cells

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Journal of Environmental Sciences 2015年第12期27卷 150-157页

作者： Deepak Kumar A.Rajeshwari Pradeep Singh Jadon Gouri Chaudhuri Anita Mukherjee natarajan Chandrasekaran Amitava Mukherjee Centre for Nanobiotechnology VIT University Centre of Advanced Study Department of BotanyUniversity of Calcutta

The current study evaluates the cytogenetic effects of chromium（Ⅲ） oxide nanoparticles on the root cells of Allium *** root tip cells of *** were treated with the aqueous dispersions of Cr2O3 nanoparticles（NPs） at five different concentrations（0.01,0.1,1,10,and 100 μg/m L） for 4 *** colloidal stability of the nanoparticle suspensions during the exposure period were ascertained by particle size *** 4 hr exposure to Cr2O3 NPs,a significant decrease in mitotic index（MI） from 35.56%（Control） to 35.26%（0.01 μg/m L）,34.64%（0.1 μg/m L）,32.73%（1 μg/m L）,29.6%（10 μg/m L） and 20.92%（100 μg/m L） was *** optical,fluorescence and confocal laser scanning microscopic analyses demonstrated specific chromosomal aberrations such as-chromosome stickiness,chromosome breaks,laggard chromosome,clumped chromosome,multipolar phases,nuclear notch,and nuclear bud at different exposure *** concentration-dependent internalization/bio-uptake of Cr2O3 NPs may have contributed to the enhanced production of anti oxidant enzyme,superoxide dismutase to counteract the oxidative stress,which in turn resulted in observed chromosomal aberrations and cytogenetic *** results suggest that *** root tip assay can be successfully applied for evaluating environmental risk of Cr2O3 NPs over a wide range of concentrations.

关键词： A.cepa Bio-uptake Chromosomal aberration C2O3 nanoparticles Mitotic index SOD

Effect of fracture-skin on virus transport in fractured porous media

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Geoscience Frontiers 2012年第6期3卷 893-900页

作者： N.natarajan G.Suresh Kumar EWRE Division Department of Civil EngineeringIndian Institute of TechnologyMadrasChennai 36India Department of Ocean Engineering Indian Institute of TechnologyMadrasChennai 36India

A numerical model is developed for describing the transport of virus in a fracture-matrix coupled system with fracture-skin. An advective dispersive virus transport equation, including first- order sorption and inactivation constant is used for simulating the movement of viruses. Implicit finite-difference numerical technique is used to solve the coupled non-linear governing equations for the triple continuum model consisting of fracture, fracture-skin and the rock-matrix. A varying grid is adopted at the fracture and fracture-skin interface to capture the mass transfer. Sensitivity analysis was performed to investigate the effect of various properties of the fracture-skin as well as viruses on the virus concentration in the fractured formation with fracture-skin. Simulation results suggest that the virus concentration in the fracture decreases with increment in the fracture-skin porosity, fracture-skin diffu- sion coefficient, mass transfer coefficient, inactivation constant and sorption distribution coefficient, and with reduction in the fracture aperture.

关键词： Fracture-skin Virus transport Rock-matrix Fracture

Phase transformation and crystal growth behavior of 8mol%(SmO1.5, GdO1.5, and YO1.5) stabilized ZrO2 powders

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International Journal of Minerals,Metallurgy and Materials 2017年第7期24卷 842-849页

作者： R.Mahendran S.P.Kumaresh Babu S.natarajan S.Manivannan A.Vallimanalan Department of Metallurgical and Materials Engineering National Institute of Technology Tirchirappalli 620015 Tamil Nadu india

Nanocrystalline powders of ZrO_2–8mol%SmO1.5（8Sm SZ）, ZrO_2–8mol%GdO1.5（8Gd SZ）, and ZrO_2–8mol%YO1.5（8YSZ） were prepared by a simple reverse-coprecipitation technique. Differential thermal analysis/thermogravimetry（DTA/TG）, Fourier transform infrared spectroscopy（FTIR）, X-ray diffraction（XRD）, Raman spectroscopy, and high-resolution transmission electron microscopy（HRTEM） were used to study the phase transformation and crystal growth behavior. The DTA results showed that the ZrO_2 freeze-dried precipitates crystallized at 529, 465, and 467°C in the case of 8Sm SZ, 8Gd SZ, and 8YSZ, respectively. The XRD and Raman results confirmed the presence of tetragonal ZrO_2 when the dried precipitates were calcined in the temperature range from 600 to 1000°C for 2 h. The crystallite size increased with increasing calcination temperature. The activation energies were calculated as 12.39, 12.45, and 16.59 k J/mol for 8Sm SZ, 8Gd SZ, and 8YSZ respectively.

关键词： zirconia thermal analysis reverse coprecipitation activation energy

Depletion of BBS Protein LZTFL1 Affects Growth and Causes Retinal Degeneration in Mice

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Journal of Genetics and Genomics 2016年第6期43卷 381-391页

作者： Jiangsong Jiang Kanyarat Promchan Hong Jiang Parirokh Awasthi Heather Marshall Adam Harned Ven natarajan Laboratory of Molecular Cell Biology Leidos Biomedical ResearchInc.Frederick National Laboratory for Cancer ResearchFrederickMD 21702USA Transgenic Mouse Model Laboratory Leidos Biomedical ResearchInc.Frederick National Laboratory for Cancer ResearchFrederickMD 21702USA Electron Microscopy Laboratory Leidos Biomedical ResearehInc.Frederick National Laboratory for Cancer ResearchFrederickMD 21702USA

Bardet-Biedl syndrome（BBS） is a heterogeneous disease characterized by deficiencies in various organs that are caused by defects in genes involved in the genesis, structural maintenance, and protein trafficking of cilia. Leucine zipper transcription factor-like 1（LZTFL1）has been identified as a BBS protein（BBS17）, because patients with mutations in this gene exhibit the common BBS phenotypes. In this study, we generated a knockout mouse model to investigate the effects of LZTFL1 depletion. Lztfl1 knockout mice were born with low birth weight, reached similar weight to those of wild-type mice at 10 weeks of age, and later gained more weight than their wild-type counterparts. LZTFL1 was localized to the primary cilium of kidney cells, and the absence of LZTFL1 increased the ciliary localization of BBS9. Moreover, in the retinas of Lztfl1 knockout mice, the photoreceptor outer segment was shortened, the distal axoneme of photoreceptor connecting cilium was significantly enlarged, and rhodopsin was targeted to the outer nuclear layer. TUNEL assay showed that many of these abnormal photoreceptor cells in Lztfl1 knockout mice underwent apoptosis. Interestingly, the absence of LZTFL1 caused an abnormal increase of the adaptor protein complex 1（AP1） in some photoreceptor cells. Based on these data, we conclude that LZTFL1 is a cilium protein and regulates animal weight and photoreceptor connecting cilium function probably by controlling microtubule assembly and protein trafficking in cilia.

关键词： LZTFL1 Cilium BBSome BBS17 Retina AP-1

In vitro evaluation of free radical scavenging activity of Codariocalyx motorius root extract

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Asian Pacific Journal of Tropical Medicine 2013年第3期6卷 188-194页

作者： Uma Chidambaram Vanitha Pachamuthu Suganya natarajan Bhakkiyalakshmi Elango Suriyanarayanan Kunga Mohan Ramkumar Department of Biotechnology School of BioengineeringSRM UniversityKattankulathur-603 203TamilnaduIndia Department of Water and Health JSS UniversityMysore-570015KarnatakaIndia

Objective:To determine the phenolic content in Codariocalyx motorius root extract and to evaluate its antioxidant properties using various in vitro assay ***:The antioxidant activity was evaluated based on scavenging of 1,1—diphenyl—2—picrylhydrazyl,hydroxyl radicals,superoxide anions,nitric oxide,hydrogen peroxide,peroxvnilrile,reducing power and by inhibition oi lipid peroxidation which was estimated in terms of thiohurhituric acid reactive ***:The root extract of the Codariocalyx motorius(***) exhibited potent total antioxidant activity that increased with increasing amount of extract concentration,which was compared with standard drug such as *** *** at different *** different concentrations of the extracts showed inhibition on lipid *** addition,the extracts had effective reducing power,free radical scavenging, super oxide anion scavenging,nitric oxide scavenging,lipid peroxidation,and total phenolic content depending on *** correlation between total phenolic contents and scavenging potential of different reactive oxygen species(r^2=0.83 1 -0.978) indicated the polyphenols as the main ***:Codariocalyx motorius(***) root possess the highly active antioxidant substance which can be used for the treatment of oxidative stress-related diseases.

关键词： Codariocalyx motorius Antioxidant activity Medicinal plants Polyphenols

Analysis of Protein-Ligand Interactions of SARS-CoV-2 Against Selective Drug Using Deep Neural Networks

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Big Data Mining and Analytics 2021年第2期4卷 76-83页

作者： natarajan Yuvaraj Kannan Srihari Selvaraj Chandragandhi Rajan Arshath Raja Gaurav Dhiman Amandeep Kaur St.Peter’s Institute of Higher Education and Research Information Communication Technology AcademyChennai 600096India Department of Computer Science and Engineering SNS College of Engineering641107India Department of Computer Science and Engineering Jagannath Educational Health and Charitable Trust College of Engineering and TechnologyCoimbatore 641105India B.S.Abdur Rahman Crescent Institute of Science and Technology Chennai 600048India Department of Computer Science Government Bikram College of CommercePatiala 147001India Department of Computer Science and Engineering Sri Guru Granth Sahib World UniversityFatehgarh 140406India

In recent time, data analysis using machine learning accelerates optimized solutions on clinical healthcare systems. The machine learning methods greatly offer an efficient prediction ability in diagnosis system alternative with the clinicians. Most of the systems operate on the extracted features from the patients and most of the predicted cases are accurate. However, in recent time, the prevalence of COVID-19 has emerged the global healthcare industry to find a new drug that suppresses the pandemic outbreak. In this paper, we design a Deep Neural Network(DNN)model that accurately finds the protein-ligand interactions with the drug used. The DNN senses the response of protein-ligand interactions for a specific drug and identifies which drug makes the interaction that combats effectively the virus. With limited genome sequence of Indian patients submitted to the GISAID database, we find that the DNN system is effective in identifying the protein-ligand interactions for a specific drug.

关键词： Deep Neural Network(DNN) coronavirus protein-ligand interactions deep learning clinical healthcare system

Implementing the Node Based Smoothed Finite Element Method as User Element in Abaqus for Linear and Nonlinear Elasticity

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Computers, Materials & Continua 2019年第8期61卷 481-502页

作者： S.Kshrisagar A.Francis J.J.Yee S.natarajan C.K.Lee Integrated Modelling and Simulation Lab Department of Mechanical EngineeringIndian Institute of Technology MadrasChennai600036India The Department of Architectural Engineering Dong-A UniversityS04-0302Engineering 237Nakdongdaero 550beon-gilSaha-guBusan49315Korea National Research Center for Disaster-free&Safe Ocean City Dong-A UniversityS04-0311-3Engineering 237Nakdong-daero 550beon-gilSaha-guBusan49315Korea

In this paper,the node based smoothed-strain Abaqus user element(UEL)in the framework of finite element method is *** basic idea behind of the node based smoothed finite element(NSFEM)is that finite element cells are divided into subcells and subcells construct the smoothing domain associated with each node of a finite element cell[Liu,Dai and Nguyen-Thoi(2007)].Therefore,the numerical integration is globally performed over smoothing *** is demonstrated that the proposed UEL retains all the advantages of the NSFEM,i.e.,upper bound solution,overly soft stiffness and free from locking in compressible and nearly-incompressible *** this work,the constant strain triangular(CST)elements are used to construct node based smoothing domains,since any complex two dimensional domains can be discretized using CST *** additional challenge is successfully addressed in this *** efficacy and robustness of the proposed work is obtained by several benchmark problems in both linear and nonlinear *** developed UEL and the associated files can be downloaded from https://***/nsundar/NSFEM.

关键词： Smoothed finite element method(SFEM) node based SFEM(NSFEM) linear and nonlinear elasticity Abaqus UEL(user elements) compressible and nearlyincompressible materials