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Understanding the “Horizontal Dimension” of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains

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Journal of Computer Science & Technology 2010年第1期25卷 82-94页

作者： Gloria Rendon Mao-Feng Ger Ruth Kantorovitz Shreedhar natarajan Jeffrey Tilson Eric Jakobsson National Center for Supercomputing Applications University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Center for Biophysics and Computational Biology University of Illinois at Urbana-Champaign Department of Mathematics University of Illinois at Urbana-Champaign Department of Biology University of Pennsylvania Renaissance Computing Institute

Protein evolution proceeds by two distinct processes： 1） individual mutation and selection for adaptive mutations and 2） rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used （and continues to use） domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of “horizontal” protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.

关键词： domain-based discovery domain-based orthology domain interactions InterPro MEME/MAST

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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

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An artificial neural network based deep collocation method for the solution of transient linear and nonlinear partial differential equations

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Frontiers of Structural and Civil Engineering 2024年第8期18卷 1296-1310页

作者： Abhishek MISHRA Cosmin ANITESCU Pattabhi Ramaiah BUDARAPU Sundararajan natarajan Pandu Rang vUNDAvILLI Timon RABCZUK School of Mechanical Sciences Indian Institute of TechnologyBhubaneswar 752050India Institute of Structural Mechanics Bauhaus University of WeimarWeimar 99423Germany Department of Mechanical Engineering Indian Institute of Technology MadrasChennai 600036India

A combined deep machine learning(DML)and collocation based approach to solve the partial differential equations using artificial neural networks is *** developed method is applied to solve problems governed by the Sine–Gordon equation(SGE),the scalar wave equation and *** methods are studied:one is a space-time formulation and the other is a semi-discrete method based on an implicit Runge–Kutta(RK)time *** methodology is implemented using the Tensorflow framework and it is tested on several numerical *** on the results,the relative normalized error was observed to be less than 5%in all cases.

关键词： collocation method artificial neural networks deep machine learning Sine-Gordon equation transient wave equation dynamic scalar and elasto-dynamic equation Runge-Kutta method

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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

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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

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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

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Optimization of Friction and Wear Behaviour in Hybrid Metal Matrix Composites Using Taguchi Technique

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Journal of Minerals and Materials Characterization and Engineering 2012年第8期11卷 757-768页

作者： v. C. Uvaraja N. natarajan Department of Mechanical Engineering Bannari Amman Institute of Technology Sathyamangalam India RvS Faculty of Engineering Coimbatore India

Al-7075 alloy-base matrix, reinforced with mixtures of silicon carbide (SiC) and boron carbide (B4C) particles, know as hybrid composites have been fabricated by stir casting technique (liquid metallurgy route) and optimized at different parameters like sliding speed, applied load, sliding time, and percentage of reinforcement by Taguchi method. The specimens were examined by Rockwell hardness test machine, Pin on Disc, Scanning Electron Microscope (SEM) and Optical Microscope. A plan of experiment generated through Taguchi’s technique is used to conduct experiments based on L27 orthogonal array. The developed ANOvA and the regression equations were used to find the optimum wear as well as co-efficient of friction under the influence of sliding speed, applied load, sliding time and percentage of reinforcement. The dry sliding wear resistance was analyzed on the basis of “smaller the best”. Finally, confirmation tests were carried out to verify the experimental results.

关键词： Hybrid Metal Matrix Composites Stir-Cast Dry Sliding Wear Orthogonal Array Taguchi Technique Analysis of variance

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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

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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

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ALK expression,prognostic significance,and its association with MYCN expression in MYCN non-amplified neuroblastoma

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World Journal of Pediatrics 2022年第4期18卷 285-293页

作者： Dinesh Babu Somasundaram Sheeja Aravindan Nandita Gupta Zhongxin Yu Ashley Baker natarajan Aravindan Department of Radiation Oncology BMSB 311CRadiation Biology LaboratoryUniversity of Oklahoma Health Sciences Center940 Stanton L.Young BoulevardOklahoma CityOK 73104USA Stephenson Cancer Center Oklahoma CityOKUSA Plainsboro NJUSA Department of Pathology BMSB 311CRadiation Biology LaboratoryUniversity of Oklahoma Health Sciences Center940 Stanton L.Young BoulevardOklahoma CityOK 73104USA Department of Pediatrics University of Oklahoma Health Sciences CenterOklahoma CityOKUSA

Neuroblastoma(NB),the most common cancer at infancy,is derived from a selective sympathoadrenal lineage of the neural crest cells[1-3].The majority of NB is found in children younger than 5 years(median age:2 years)and is rare in children older than 10 *** NB accounts for only 5-6%of the childhood cancers,it heavily contributes(about 15%)to pediatric cancer deaths[4,5].

关键词： neuroblastoma MYCN cancer

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