8 Publications by Aditya Jain

• Edit publication 1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway

  publication title1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway

  publication dateMay 17, 2017  publication descriptionPublic Health Genome
  publication descriptionThe one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders.

  Other authors

   
  See publication 1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism PathwaySee publication
• Edit publication Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.

  publication titleCategorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.

  publication dateAug 2015  publication descriptionElsevier, Infection, Genetics and Evolution
  publication descriptionIn the erythrocytes, malaria parasite entry and infection is mediated through complex membrane sorting and signaling processes. We investigated the effects of single-locus and multilocus interactions to test the hypothesis that the members of the GPCR family genes, adenosine A2a receptor (ADORA2A) and G-protein coupled receptor kinase5 (GRK5), may contribute to the pathogenesis of malaria caused by Plasmodium falciparum (Pf) independently or through complex interactions. In a case-control study of adults, individuals affected by Pf malaria (complicated n=168; uncomplicated n=282) and healthy controls (n=450) were tested for their association to four known SNPs in GRK5 (rs2230345, rs2275036, rs4752307 and rs11198918) and two in ADORA2A (rs9624472 and rs5751876) genes with malaria susceptibility, using techniques of polymerase chain reaction-restriction fragment length polymorphisms and direct DNA sequencing. Single-locus analysis showed significant association of 2 SNPs; rs5751876 (OR=3.2(2.0-5.2); p=0.0006) of ADORA2A and rs2230345 (OR=0.3(0.2-0.5); p=0.0006) of GRK5 with malaria. . The study provides evidence for the role of ADORA2A and GRK5 that might influence the etiology of malaria infection.

  Other authors

    
  See publication Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.See publication
• Edit publication Genetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.

  publication titleGenetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.

  publication dateDec 24, 2013  publication descriptionGENE
  publication descriptionEstablishing genetic basis of Idiopathic generalized epilepsies (IGE) is challenging because of their complex inheritance pattern and genetic heterogeneity. Kir4.1 inwardly rectifying channel (KCNJ10) is one of the independent genes reported to be associated with seizure susceptibility. In the current study we have performed a comprehensive in silico analysis of genetic variants in KCNJ10gene at functional and structural level along with a case-control analysis for the association ofrs1130183 (R271C) polymorphism in Indian patients with IGE. Age and sex matched 108epileptic patients and normal healthy controls were examined. Genotyping of KCNJ10rs1130183variation was performed using PCR-RFLP method. The risk association was determined by using odds ratio and 95% confidence interval. Functional effects of non-synonymous SNPs (nsSNPs) in KCNJ10 gene were analyzed using SIFT PolyPhen-2, I-Mutant 2.0, PANTHER and FASTSNP. Subsequently, homology modeling of protein three dimensional (3D) structures was performed using Modeller tool (9.10v) and compared the native protein with mutant for assessment of structure and stability. SIFT, PolyPhen-2, I-Mutant 2.0 and PANTHER collectively showed rs1130183, rs1130182 and rs137853073 SNPs inKCNJ10 gene affect protein structure and function. There was a considerable variation in the Root Mean Square Deviation (RMSD) value between the native and mutant structure (1.17Ǻ). Association analysis indicate KCNJ10rs1130183 did not contribute to risk of seizure susceptibility in Indian patients with IGE (OR- 0.38; 95%CI, 0.07-2.05) and T allele frequency (0.02%) was in concordance with dbSNP reports. This study identifies potential SNPs that may contribute to seizure susceptibility and further studies with the selected SNPs in larger number of samples and their functional analysis is required for understanding the variants of KCNJ10with seizure susceptibility.

  Other author

  
  See publication Genetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.See publication
• Edit publication Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors

  publication titleMolecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors

  publication dateSep 2013  publication descriptionJournal of Pharmacy Research
  publication descriptionAim : Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme which plays a key role in fatty acid biosynthesis via production of melonyl-CoA as an essential substrate. It is involved in homeostasis of fatty acids inside the system using both up and down regulating mechanisms. Apart from this In silico analysis of its catalytic site and regulatory sites make it a potential target for herbicidal and insecticidal drug targeting. Currently the 3D structure of Acetyl-CoA carboxylase (ACC) from Jatropha curcas has not been solved in Protein Data Bank (PDB). Hence the aim of the present study is to build the 3D structure of Acetyl-CoA carboxylase (ACC) from J. curcas also to perform a virtual screening for the identification of the effective inhibitors using molecular docking studies.
  Methods: Homology modeling has been used to determine the 3D structure of Acetyl-CoA carboxylase (ACC) from J. curcas. Structure validation and molecular docking studies has been carried out using Procheck and Molegro Virtual Docker respectively.
  Results: Ramachandran Plot confirmed quality of modeled structures along with main chain and side chain parameters. Out of 309 residues in SPDBV model, 244 were in core region 19 residues were in additional allowed region, 2 residues were in generous allowed region and no residues were in disallowed region.
  Conclusion: Energy minimization for SPDBV model thermodynamically proved accepted structure with energy of −12,063.024 kJ/mol. The model further can be subjected to pharmacodynamic and pharmacokinetic studies. Molecular docking studies identified few established herbicides which could be promising inhibitors of Acetyl-CoA carboxylase (ACC). Efforts to screen and identify ACC inhibitors using flexible molecular docking resulted in Pinoxaden from Phenylpyrazole class as the most effective inhibitor with rerank = −81.436 and RMSD = 0.31.

  Other authors

     
  See publication Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitorsSee publication
• Edit publication Identification and characterization of foodborne pathogen Listeria monocytogenes strain Pyde1 and Pyde2 using 16S rRNA gene sequencing

  publication titleIdentification and characterization of foodborne pathogen Listeria monocytogenes strain Pyde1 and Pyde2 using 16S rRNA gene sequencing

  publication dateAug 22, 2013  publication descriptionJournal of Pharmacy Research. Elsevier. Volume 6, Issue 7, July 2013, Pages 736–741
  publication descriptionAbstract
  Aim: Listeria monocytogenes acts as a pathogen for humans and animals, mainly causing, neonatal sepsis, abortions in pregnant females and severe infections such as septicemia and meningoencephalitis in susceptible hosts. Current study was aimed to identify novel strains of L. monocytogenes from retail chicken, beef meat and seafood samples.
  Methods: In order to identify the strain, extraction and amplification of genomic DNA, 16S rRNA sequence analysis was carried out. Phylogenetic trees were constructed using dnapars and dnaml available in Phylip. The secondary structures of 16S rRNA gene sequence were predicted using UNAFOLD, a Linux based software.
  Results: The results obtained were found to be a novel foodborne pathogens, which was further named L. monocytogenes strain Pyde1 and L. monocytogenes strain Pyde2, after characterization the sequence of isolate was deposited in GenBank with accession numbers ‘KC852899’ and ‘KC852900’ respectively. The Gibb's free energy of the secondary structures of L. monocytogenes strain Pyde1 and Pyde2 were −275.60 and −282.20 kcal/mol seems to be more stable in the present investigation.
  Conclusion: The described results of phylogenetic distinctiveness and phenotypic disparities indicate that strain 2b represents a novel strain of foodborne pathogens within L. monocytogenes species, for which the name L. monocytogenes strain Pyde1 and L. monocytogenes strain Pyde2 is proposed.

  Other authors

    
  See publication Identification and characterization of foodborne pathogen Listeria monocytogenes strain Pyde1 and Pyde2 using 16S rRNA gene sequencingSee publication
• Edit publication Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

  publication titleScreening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

  publication dateMay 12, 2013  publication descriptionEuropean Journal of Biological Sciences 5 (3): 68-76
  publication descriptionBacillus anthracis is a gram positive bacterium and the etiologic agent of anthrax, a common disease
  of livestock and, occasionally, of humans and the only obligate pathogen within the genus Bacillus. Hence the
  aim of the current study was to identify the novel antigenic peptides from the whole plasmid PX01 proteins of
  Bacillus anthracis. The plasmid proteome were analyzed using various online bioinformatics algorithms.
  The current study performed based on two facts i) the toxicity of B. anthracis is by secretion of exotoxins
  encoded from plasmid pX01 into the host cell and ii) the plasmid pX01 has a distinct 70kbp region. Hence the
  work was initiated by considering the proteins that are secreted out of the B. anthracis cell via the classical
  pathway. The proteins were analyzed for the transmembranes, antigenecity and their regions followed by
  two protein blasts across the human and bacillus database. The blast against the human database showing
  their absence in humans confirmed their antigenecity for humans and blast across bacillus had shown the
  B. anthracis specificity. The complete plasmid genome had 1695 protein entries at the genbank. At the end 10
  potential proteins were found using the Bioinformatics algorithms. During the process two other observations
  were found, one showing an antigenic protein sequence specific to nearly 100 Bacillus species and the second
  was a protein sequence that had low similarity for the well-identified breast cancer gene BRCA1.

  Other authors

   
  See publication Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics ApproachSee publication
• Edit publication Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

  publication titleScreening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

  publication dateMar 5, 2013  publication descriptionEuropean Journal of Biological Sciences (EJBS)
  publication descriptionBacillus anthracis is a gram positive bacterium and the etiologic agent of anthrax, a common disease
  of livestock and, occasionally, of humans and the only obligate pathogen within the genus Bacillus. Hence the
  aim of the current study was to identify the novel antigenic peptides from the whole plasmid PX01 proteins of
  Bacillus anthracis. The plasmid proteome were analyzed using various online bioinformatics algorithms.
  The current study performed based on two facts i) the toxicity of B. anthracis is by secretion of exotoxins
  encoded from plasmid pX01 into the host cell and ii) the plasmid pX01 has a distinct 70kbp region. Hence the
  work was initiated by considering the proteins that are secreted out of the B. anthracis cell via the classical
  pathway. The proteins were analyzed for the transmembranes, antigenecity and their regions followed by
  two protein blasts across the human and bacillus database. The blast against the human database showing
  their absence in humans confirmed their antigenecity for humans and blast across bacillus had shown the
  B. anthracis specificity. The complete plasmid genome had 1695 protein entries at the genbank. At the end 10
  potential proteins were found using the Bioinformatics algorithms. During the process two other observations
  were found, one showing an antigenic protein sequence specific to nearly 100 Bacillus species and the second
  was a protein sequence that had low similarity for the well-identified breast cancer gene BRCA1

  Other authors

   
  See publication Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics ApproachSee publication
• Edit publication Comparative modeling of 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum– A potent target of malaria

  publication titleComparative modeling of 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum– A potent target of malaria

  publication dateJan 2, 2009  publication descriptionIJBR [INTERNATIONAL JOURNAL OF BIOINFORMATIC]
  publication descriptionPlasmodium falciparum causing malaria is yet reigning against drug design community when it
  comes to survival and defense. Continuous evolution and drug resistant character is foremost basis of
  parasite’s versatility. 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum is discovered
  decisive in fatty acid synthesis machinery. Objectives of enzyme inhibition need structural characterization
  from its 3D structure. In present studies molecular modeling of 3-oxoacyl-acyl-carrier protein synthase I/II is
  achieved using in silico comparative modeling. ICM Molsoft algorithm was adopted for comparative
  modeling which provides an accurate and efficient module to build loops and side chains found non-identical
  in sequence. Energy parameters fell in thermodynamically stability zone. Modeled structure revealed
  appreciable measures when validated. Ramachandran plot signified the present work undertaken through
  conformational parameters ? (phi) and ? (psi) angles calculated from model with 83.2% residues in most
  favoured region. Further PROCHECK results confirmed acceptance of model through main and side-chain
  values. Root mean square distance of planarity found below 0.01. Beside some bad contacts, bond angles
  and bond lengths confer qualitative part of work. Structure of 3-oxoacyl-acyl-carrier protein synthase I/II can
  be important tool for structure based drug designing techniques to impel the search of new efficient
  inhibitors. Comparison of similar structures of parasite can further reveal mutational trends to study their
  evolution patterns.

  Other authors

   
  See publication Comparative modeling of 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum– A potent target of malariaSee publication

ADITYA has 5 projects