99 results on '"Jayavel, Sridhar"'
Search Results
2. Surface Modification and Engineering of Nanoscale Absorbent and Their Composite
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Aravind, D., Diwahar, P., Bharathi, M., Prakalathan, K., Prasanth, M. S., Jayavel, Sridhar, Araujo, Paulo, Series Editor, Gomes Sousa Filho, Antonio, Editorial Board Member, Doorn, Stephen K., Editorial Board Member, Franklin, Aaron D., Editorial Board Member, Hartschuh, Achim, Editorial Board Member, Tharini, J., editor, and Thomas, Sabu, editor
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- 2024
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3. Complete sequence and characterization of the Mobula tarapacana (Sicklefin Devilray) mitochondrial genome and its phylogenetic implications
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Chandrasekaran, Kumar, Dhinakarasamy, Inbakandan, Jayavel, Sridhar, Rajendran, Thirugnanasambandam, Bhoopathy, Subashni, Gopal, Dharani, Ramalingam, Kirubagaran, and Ajmal Khan, Seyed
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- 2022
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4. Importance of wastewater-based epidemiology for detecting and monitoring SARS-CoV-2
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Jayavel Sridhar, Rahul Parit, Govindaraju Boopalakrishnan, M Johni Rexliene, Rajkumar Praveen, and Balaji Viswananathan
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Environmental engineering ,TA170-171 ,Chemical engineering ,TP155-156 - Abstract
Coronavirus disease caused by the SARS-CoV-2 virus has emerged as a global challenge in terms of health and disease monitoring. COVID-19 infection is mainly spread through the SARS-CoV-2 infection leading to the development of mild to severe clinical manifestations. The virus binds to its cognate receptor ACE2 which is widely expressed among different tissues in the body. Notably, SARS-CoV-2 shedding in the fecal samples has been reported through the screening of sewage water across various countries. Wastewater screening for the presence of SARS-CoV-2 provides an alternative method to monitor infection threat, variant identification, and clinical evaluation to restrict the virus progression. Multiple cohort studies have reported the application of wastewater treatment approaches and epidemiological significance in terms of virus monitoring. Thus, the manuscript outlines consolidated and systematic information regarding the application of wastewater-based epidemiology in terms of monitoring and managing a viral disease outbreak like COVID-19.
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- 2022
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5. Fabrication of Ag/Ag2O incorporated graphitic carbon nitride based ZnO nanocomposite for enhanced Z-scheme photocatalytic performance of various organic pollutants and bacterial disinfection
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Vignesh, Shanmugam, Eniya, Palaniyasan, Srinivasan, Manickam, Kalyana Sundar, Jeyaperumal, Li, Haitao, Jayavel, Sridhar, Pandiaraman, Mariappan, Manthrammel, M. Aslam, Shkir, Mohd., and Palanivel, Baskaran
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- 2021
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6. PVA and PMMA nano-composites: a review on strategies, applications and future prospects
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Kalyani Palanichamy, Muthupandeeswari Anandan, Jayavel Sridhar, Varagunapandiyan Natarajan, and Aravind Dhandapani
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polymer ,nanofiller ,nanocomposite ,PVA ,PMMA ,matrices ,Materials of engineering and construction. Mechanics of materials ,TA401-492 ,Chemical technology ,TP1-1185 - Abstract
Nanotechnology has facilitated unique ways of developing novel nano-composites. In that sense, polymer-based nano-composites are being extensively researched for their outstanding properties as a result of incorporating nano-fillers in the polymer matrix. They have activated enormous research interests owing to their potential in addressing environmental issues, packaging, optics, electronics, battery electrolytes, pneumatic actuation, molecular separations, sensors, biomedical applications, etc Hence, the authors intend to consolidate reported information about these polymer matrices, diverse inorganic nanofillers, and nano-filled polymer composites for improvement in properties and future advanced applications. The review exhaustively covers 15 years of literature on theoretical, experimental, and application aspects of PVA & PMMA-based nano-composites, mainly focusing on inorganic oxide-based fillers. It also summarizes the structure-property correlations that govern their performance. Hence this review is hoped to provide the readers with stimulating insights on strategies, noteworthy challenges, and future opportunities/prospects in developing polymer nano-composites that may cater to the need of our society and scientific industries as well.
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- 2023
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7. Encapsulation of Amphotericin B into Quercetin Based Silver Nanoparticles: Preparation, Characterization and Preliminary Investigation of Antiparasitic Activity
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Sundar, Anukragah, Arunachalam, Sankarganesh, Jayavel, Sridhar, Muthulakshmi, Lakshmanan, Ghosh, Arindam, Series Editor, Chua, Daniel, Series Editor, de Souza, Flavio Leandro, Series Editor, Aktas, Oral Cenk, Series Editor, Han, Yafang, Series Editor, Gong, Jianghong, Series Editor, Rajan, Mariappan, editor, Anand, Krishnan, editor, and Chuturgoon, Anil, editor
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- 2019
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8. Construction of high efficient g-C3N4 nanosheets combined with Bi2MoO6-Ag photocatalysts for visible-light-driven photocatalytic activity and inactivation of bacterias
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Shanmugam, Vignesh, Muppudathi, Anna Lakshmi, Jayavel, Sridhar, and Jeyaperumal, Kalyana Sundar
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- 2020
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9. Comparative analysis of fatty acid profiles through transesterification in macroalgae from Gulf of Mannar reveal Ulva lactuca for potent edible oil synthesis
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Ashwini Karuppaswamy, Jayavel Sridhar, and M. Pandi
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General Nursing ,Education - Abstract
Selective macroalgae comprising green algae (Ulva lactuca), brown algae (Padina gymnosphora, Sargassam wightii, Turbinaria ornate) and red algae (Gracilaria corticata, Halimeda macrolopa, Halymenia dilatata, Gracilaria crassa) were collected from Gulf of Mannar, India. Taxonomic and molecular identification affirmed the identity of the microalgal species. Free fatty acids and Fatty Acid Methyl Ester (FAME) synthesis by transesterification was assessed for cataloguing the edible oil source from the various macroalgae collected. Lipid components were extracted employing various solvents namely, Hexane, Chloroform: methanol (2:1), Chloroform: hexane (1:1), Chloroform: hexane (1:2) and Dichloromethane: methanol (2:1). The effects of different solvents based on Soxhlet extraction were preceded and GC-MS was utilized for cataloguing the various lipid components in the macroalgae. Furthermore, in vitro anticancer activity against the hepatocellular carcinoma cell line, HepG2 indicate 15.6µg/ml concentration showed significant cytotoxicity compared to control. Thus, the present report emphasizes the optimal role of Ulva lactuca as a potential edible oil source supplement, along with pharmaceutical and neutraceutical benefits.
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- 2022
10. Encapsulation of Amphotericin B into Quercetin Based Silver Nanoparticles: Preparation, Characterization and Preliminary Investigation of Antiparasitic Activity
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Sundar, Anukragah, primary, Arunachalam, Sankarganesh, additional, Jayavel, Sridhar, additional, and Muthulakshmi, Lakshmanan, additional
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- 2019
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11. PVA and PMMA nano-composites: a review on strategies, applications and future prospects
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Palanichamy, Kalyani, primary, Anandan, Muthupandeeswari, additional, Jayavel, Sridhar, additional, Natarajan, Varagunapandiyan, additional, and Aravind, Dhandapani, additional
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- 2023
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12. Mno2 Nanorods as Novel Electrochemical Sensor for the Detection of Nitrobenzene
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Chellappa, Vasanthi, primary, Jeyapragasam, Tharini, additional, Devi, J. Meena, additional, Jayavel, Sridhar, additional, and Jamespandi, Annaraj, additional
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- 2023
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13. Dynamic shock wave driven simultaneous crystallographic and molecular switching between α-Fe
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A, Sivakumar, A, Rita, S, Sahaya Jude Dhas, K P J, Reddy, Raju Suresh, Kumar, Abdulrahman I, Almansour, Shubhadip, Chakraborty, K, Moovendaran, Jayavel, Sridhar, and S A, Martin Britto Dhas
- Abstract
Switchable nanostructured materials with a low-cost and fast processing have diverse practical applications in the modern electronic industries, but such materials are highly scarce. Hence, there is a great demand for identifying the externally stimulated solid-state switchable phase transition materials for several industrial applications. In this paper, we present the experimentally observed solid-state molecular level switchable phase transitions of nanocrystalline iron oxide materials: {α-Fe
- Published
- 2022
14. Dynamic shock wave driven simultaneous crystallographic and molecular switching between alpha-Fe2O3 and Fe3O4 nanoparticles - a new finding
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A. Sivakumar, A. Rita, S. Sahaya Jude Dhas, K. P. J. Reddy, Raju Suresh Kumar, Abdulrahman I. Almansour, Shubhadip Chakraborty, K. Moovendaran, Jayavel Sridhar, S. A. Martin Britto Dhas, Sacred Heart College, Tirupattur, Indian Institute of Science, King Saud University [Riyadh] (KSU), Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institute of Physics, Academia Sinica, Madurai Kamaraj University, Department of Science and Technology (DST), India [SR/FST/College-2017/130], and King Saud University, Riyadh, Saudi Arabia [RSP-2021/142]
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Inorganic Chemistry ,[PHYS]Physics [physics] - Abstract
International audience; Switchable nanostructured materials with a low-cost and fast processing have diverse practical applications in the modern electronic industries, but such materials are highly scarce. Hence, there is a great demand for identifying the externally stimulated solid-state switchable phase transition materials for several industrial applications. In this paper, we present the experimentally observed solid-state molecular level switchable phase transitions of nanocrystalline iron oxide materials: {alpha-Fe2O3 (R-3c) to Fe3O4 (Fd-3m) and Fe3O4 (Fd-3m) to alpha-Fe2O3 (R-3c)} under dynamic shock wave loaded conditions, and the results were evaluated by diffraction, and vibrational and optical spectroscopic techniques. To date, this is most probably the first report which demonstrates the simultaneous molecular and crystallographic switchable-phase-transitions enforced by dynamic shock waves such that the title material is proposed for sensors and molecular switching applications.
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- 2022
15. Junker: An Intergenic Explorer for Bacterial Genomes.
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Jayavel Sridhar, Radhakrishnan Sabarinathan, Shanmugam Siva Balan, Ziauddin Ahamed Rafi, Paramasamy Gunasekaran, and Kanagaraj Sekar
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- 2011
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16. Computational Small RNA Prediction in Bacteria
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Jayavel Sridhar and Paramasamy Gunasekaran
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Biology (General) ,QH301-705.5 - Published
- 2013
17. PsRNA: A Computing Engine for the Comparative Identification of Putative Small RNA Locations within Intergenic Regions.
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Jayavel Sridhar, Govindaraj Sowmiya, Kanagaraj Sekar, and Ziauddin Ahamed Rafi
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- 2010
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18. sRNAbase: A Web Resource for Small RNAs in Enterobacteriaceae\m{1}.
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Sivasankaran Sathesh-Kumar, Jayavel Sridhar, and Ziauddin Ahamed Rafi
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- 2010
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19. Dynamic Shock Wave Driven Simultaneous Crystallographic and Molecular Switching between α-Fe2O3 and Fe3O4 nanoparticles- A new finding
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Sivakumar, A., primary, Rita, A, additional, Dhas, S. Sahaya Jude, additional, Reddy, K. P.J., additional, Kumar, Raju, additional, Almansour, Abdulrahman Ibrahim, additional, Chakraborty, Shubhadip, additional, Moovendaran, K, additional, Jayavel, Sridhar, additional, and Dhas, Martin Britto, additional
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- 2022
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20. Process optimization and production kinetics for cellulase production by Trichoderma viride VKF3
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Nathan, Vinod Kumar, Esther Rani, Mary, Rathinasamy, Gunaseeli, Dhiraviam, Kannan Narayanan, and Jayavel, Sridhar
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- 2014
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21. Identification of Novel Genomic Islands Associated with Small RNAs.
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Jayavel Sridhar and Ziauddin Ahamed Rafi
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- 2007
22. Deriving tropical gynoecious inbred backcross lines from exotic pickling cucumber using marker assisted backcross breeding
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Boopalakrishnan, G, primary, Jayavel, Sridhar, additional, Behera, Tusar Kanti, additional, Munshi, Anilabha Das, additional, Kumari, Shilpi, additional, and Kumar, Sachin, additional
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- 2021
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23. Computational and functional analysis of β-lactam resistance in Zymomonas mobilis
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Sheik Abdul Kader, Sheik Asraf, Ayyasamy, Mahalakshmi, Narayanan, Rajnish K., Jayavel, Sridhar, and Paramasamy, Gunasekaran
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- 2013
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24. Application of derivative voltammetry in the quantitative determination of alloxan at single-walled carbon nanotubes modified electrode
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Kumaraguru Duraimurugan, Arun Prasad Murthy, Jayavel Sridhar, and Jagannathan Madhavan
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Detection limit ,endocrine system ,endocrine system diseases ,General Chemical Engineering ,nutritional and metabolic diseases ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Electrochemistry ,01 natural sciences ,0104 chemical sciences ,law.invention ,chemistry.chemical_compound ,chemistry ,law ,Alloxan ,Electrode ,Uric acid ,0210 nano-technology ,Voltammetry ,Derivative (chemistry) ,Nuclear chemistry - Abstract
Alloxan is a glucose analogue produced by the oxidation of uric acid and assumes physiological significance owing to its toxicity and diabetes inducing nature. Foods tainted with alloxan are considered as a leading cause of diabetes. Hence, real time quantification of alloxan is mandatory to estimate the diabetogenic risk of food samples. Electrochemical activity of alloxan at various carbon nanomaterials has been used for the quantitative determination of alloxan in neutral and acid media. This method has made use of derivative technique that does not require further instrumentation but has remarkably improved the sensitivity. Alloxan has exhibited the highest electrochemical activity at single-walled carbon nanotubes among the investigated carbon nanomaterials. The redox activity of alloxan has disappeared in the conventional voltammogram at a concentration of 3 × 10−6 M, whereas, prominent peaks have been observed well below 3 × 10−7 M in derivative voltammograms. Linear calibration graphs have been constructed in the concentration range between 3 × 10−3 and 3 × 10−7 M both in neutral and acid media. The detection limits of alloxan in neutral and acid media are 5 × 10−8 and 1 × 10−7 M respectively.
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- 2019
25. Transcriptome based identification of silver stress responsive sRNAs from Bacillus cereus ATCC14579
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Manickam Gayathri and Jayavel Sridhar
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0303 health sciences ,Bacillus cereus ATCC 14579 ,Microarray ,030306 microbiology ,Microarray analysis techniques ,Promoter ,General Medicine ,Computational biology ,Biology ,biology.organism_classification ,Silver stress ,Transcriptome ,03 medical and health sciences ,Intergenic region ,Terminator (genetics) ,Cereus ,Transfer RNA ,sRNA ,Research Article ,030304 developmental biology - Abstract
Microbes modulate their metabolic and physiological mechanisms in response to changing environmental conditions. It is our interest to identify small regulatory RNAs using microarray expression data (GSE26043) obtained from B. cereus ATCC 14579 in AgNO3 stress. By definition, expression of transcripts from the Intergenic Regions (IGR) with >=2 fold under silver stress is predicted as novel small RNAs. Computational analysis of the IGR expression levels extracted from the available microarray data help in the identification of stress responsive sRNAs with rare promoters (Sigma 24, 28, 32, 54 and 70) followed by terminator signals predicted using the sRNAscanner tool. We predicted 1512 sRNA specific regions on both positive and negative strands collectively. Thus, a non-redundant high scoring unique 860 sRNAs with distinct promoter (S24: 83, S28: 86, S32: 31, S54: 57, S70: 223, sRNA_specific_S70: 380) and terminator signals are reported. These unique computationally predicted sRNA regions were verified with the highly expressing IGRs from the microarray data. It should be noted that 14 sRNAs reported in earlier studies were also found in this dataset. This study has reported 71 additional sRNAs from the transcriptome under metal stress response. Hence, we use global transcriptomics data for the identification of novel sRNAs in B. cereus. We described a general model using a procedure for the identification of small regulatory RNAs using microarray expression data with appropriate cross validation modules. It is found that some sRNAs reported in this study were found to have multiple rare promoters. This opens the possibility of sRNA activation under multiple stress condition. These sRNA data reported in this study should be characterized for their mRNA targets and molecular functional networks in future investigations.
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- 2019
26. Computational studies on new Leishmanial drug targets against Quercetin.
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Sivaranjani, Kanagaraj Jyothi V., Pavithra, U., Jayavel, Sridhar, and Muthulakshmi, Lakshmanan
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QUERCETIN ,LEISHMANIASIS treatment ,NUCLEIC acids ,MOLECULAR docking ,DRUG target - Abstract
Leishmaniasis, a parasitic disease caused by Leishmania parasite which resides in the infected sand flies. Control of Leishmaniasis remains a source of grave concern worldwide. Studies on Leishmaniasis triggered because of its outbreak in tropical and subtropical regions of Asia, East Africa and South America. There is an urgent need for new therapeutic interventions such as vaccine and new drug targets as it develops resistance towards the available drugs. Quercetin, a derivative of polyphenolic flavonoid exhibits various biological activities by interacting with proteins and nucleic acids. In this study, computational analysis was performed to identify the potential drug target of Quercetin in Leishmania species by molecular docking. The newly predicted targets were subjected for subcellular localization prediction and determined the protein-protein interaction networks that would aid in the development of anti-Leishmanial drugs. This study helps in the identification of targets and development of anti-Leishmanial drugs. [ABSTRACT FROM AUTHOR]
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- 2022
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27. Association of ACE inhibitors and angiotensin type II blockers with ACE2 overexpression in COVID-19 comorbidities: A pathway-based analytical study
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Parit, Rahul, primary and Jayavel, Sridhar, additional
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- 2021
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28. Computational studies on molecular interactions of 6-thioguanosine analogs with anthrax toxin receptor 1
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Singh, Nitin K., Pakkkianathan, Britto C., Kumar, Manish, Daddam, Jayssima R., Jayavel, Sridhar, Kannan, Mani, Pillai, Girinath G., and Krishnan, Muthukalingan
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- 2012
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29. Computational protein design and protein-ligand interaction studies for the improvement of organophosphorus degrading potential of Deinococcus radiodurans
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Prabu Manoharan and Jayavel Sridhar
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Models, Molecular ,0301 basic medicine ,Mutant ,Protein design ,Molecular Conformation ,Ligands ,Protein Engineering ,Catalysis ,Structure-Activity Relationship ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Hydrolase ,Materials Chemistry ,Physical and Theoretical Chemistry ,Spectroscopy ,chemistry.chemical_classification ,Binding Sites ,biology ,Chemistry ,Hydrolysis ,Organophosphate ,Computational Biology ,Deinococcus radiodurans ,Protein engineering ,biology.organism_classification ,Computer Graphics and Computer-Aided Design ,Organophosphates ,030104 developmental biology ,Enzyme ,Biochemistry ,Mutation ,Deinococcus ,Protein Binding ,Protein ligand - Abstract
The organophosphorus hydrolase enzyme is involved in the catalyzing reaction that involve hydrolysis of organophosphate toxic compounds. An enzyme from Deinococcus radiodurans reported as homologous to phosphotriesterase and show activity against organophosphate. In the past activity of this enzyme is low and efforts made to improve the activity by experimental mutation study. However only very few organophosphates tested against very few catalytic site mutations. In order to improve the catalytic power of the organophosphorus hydrolase enzyme, we carried out systematic functional hotspot based protein engineering strategy. The mutants tested against 46 know organophosphate compounds using molecular docking study. Finally, we carried out an extensive molecular docking study to predict the binding of 46 organophosphate compounds to wild-type protein and mutant organophosphorus hydrolase enzyme. At the end we are able to improve the degrading potential of organophosphorus hydrolase enzyme against organophosphate toxic compounds. This preliminary study and the outcome would be useful guide for the experimental scientist involved in the bioremediation of toxic organophosphate compounds.
- Published
- 2018
30. sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes.
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Jayavel Sridhar, Narmada Sambaturu, Radhakrishnan Sabarinathan, Hong-Yu Ou, Zixin Deng, Kanagaraj Sekar, Ziauddin Ahamed Rafi, and Kumar Rajakumar
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Medicine ,Science - Abstract
BACKGROUND: Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. METHODOLOGY/PRINCIPAL FINDINGS: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. CONCLUSIONS/SIGNIFICANCE: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that approximately 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.
- Published
- 2010
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31. Correction: sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes.
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Jayavel Sridhar, Narmada Sambaturu, Radhakrishna Sabarinathan, Hong-Yu Ou, Zixin Deng, Kanagaraj Sekar, Ziauddin Ahamed Rafi, and Kumar Rajakumar
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Medicine ,Science - Published
- 2010
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32. Mapping and linkage analysis of epistatic QTLs for gynoecious trait (F) in cucumber (Cucumis sativusL.)
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G., Boopalakrishnan, primary, Jayavel, Sridhar, additional, Behera, Tusar Kanti, additional, Munshi, Anilabha Das, additional, Choudhary, Harshwardhan, additional, Singh, Anupam, additional, and Pandey, Manoj Kumar, additional
- Published
- 2020
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33. Genetic diversity and evolutionary dynamics of dengue isolates from India
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Jayavel Sridhar and Johni Rexliene
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Genetics ,Serotype ,Antigenicity ,Genetic diversity ,viruses ,virus diseases ,Dengue virus ,Biology ,medicine.disease_cause ,medicine.disease ,Virus ,Dengue fever ,Infectious Diseases ,Virology ,Genotype ,medicine ,Original Article ,Selection (genetic algorithm) - Abstract
Dengue virus (DENV) is the mosquito borne virus which causes Dengue Haemorrhagic Fever and Dengue Shock Syndrome. It consists of four distinct serotypes (DENV 1–4). DENV 1, 3 and 4 were classified into five genotypes (GI–GV), where as DENV-2 belongs to American and Cosmopolitan genotypes. Dengue virus is most prevalent in south and Southeast Asia including India. This study was initiated to study the genetic diversity and evolution among the Dengue isolates in India. Pairwise comparison of amino acid sequences among the serotypes has shown that DENV-3 is having less sequence diversity compared to other serotypes having differences in their amino acid numbers. We have analyzed the 50 Indian strains and 19 of those strains have been identified as recombinant strains by using RDP4 package, which are then excluded for future selection. Episodic positive selection of DENV was obtained using MEME with P value is ≤ 5. Positive selection on several codons was used to correlate the genetic diversity between serotypes. This study clearly established that diversity of amino acids and inter genotypic recombination of strains are the major cause for antigenicity variation and evolution of DENV within India. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13337-019-00538-1) contains supplementary material, which is available to authorized users.
- Published
- 2019
34. Mapping and linkage analysis of epistatic QTLs for gynoecious trait (F) in cucumber (Cucumis sativus L.).
- Author
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G., Boopalakrishnan, Jayavel, Sridhar, Behera, Tusar Kanti, Munshi, Anilabha Das, Choudhary, Harshwardhan, Singh, Anupam, and Pandey, Manoj Kumar
- Subjects
CUCUMBERS ,MICROSATELLITE repeats ,PHENOTYPIC plasticity ,CARTOGRAPHY software - Abstract
The QTL mapping for gynoecy in cucmber (Cucumis sativus L.)was carried out by using backcross populations (BC
1 F2 & BC1 F3 ) of a cross using two inbred lines; one monoecious with multiple (≥ 5) lateral branching habit cv. Pusa Uday (Indian slicing type) and gynoecious exotic line Gy14 (American pickling type) with few lateral branches (1–2). QTL detection was performed by employing QTL Ici mapping software (version 4.1) of the two mapping populations. We detected seven gynoecious QTLs in two genomic regions (chromosome 5 and 6), on which three significant QTLs (qGyn 5.1, qGyn 6.5 and qGyn 6.6) had higher LOD score (10.5, 26.2, and 24.5) and phenotypic variance (5.9, 14.5 and 14.5%) in BC1 F2 population. However, two significant QTLs (qGyn 5.1 and qGyn 6.1) accounted for gynoecism which could explain 22.90 and 12.88% of the phenotypic variation with the LOD score of 15.86 and 11.82 in linkage group 5 and 6, respectively in BC1 F3 population. Out of 82 simple sequence repeats (SSR) markers, three (SSR00233, SSR15516 and SSR13251) was found tightly linked and flanked to gynoecious trait QTLs (qGyn6.5 and qGyn6.6) in BC1 F2 population at <1.5 cM, which could be used for marker-assisted selection (MAS) in cucumber improvement programmes. In order to increase the productivity of Indian cucumber, the introgressed Indian gynoecious cucumber lines derived from an exotic genetic background using MAS may be directly used as a variety or parent of hybrid. [ABSTRACT FROM AUTHOR]- Published
- 2021
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35. Identification of Recombination and Positively Selected Genes in Brucella
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Paramasamy Gunasekaran, Jayavel Sridhar, Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, and Jeyaprakash Rajendhran
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Comparative genomics ,Genetics ,Natural selection ,Intracellular parasite ,Brucella ,Biology ,bacterial infections and mycoses ,biology.organism_classification ,Microbiology ,Genome ,Original Article ,Homologous recombination ,Gene ,Recombination - Abstract
Brucella is a facultative intracellular bacterium belongs to the class alpha proteobacteria. It causes zoonotic disease brucellosis to wide range of animals. Brucella species are highly conserved in nucleotide level. Here, we employed a comparative genomics approach to examine the role of homologous recombination and positive selection in the evolution of Brucella. For the analysis, we have selected 19 complete genomes from 8 species of Brucella. Among the 1599 core genome predicted, 24 genes were showing signals of recombination but no significant breakpoint was found. The analysis revealed that recombination events are less frequent and the impact of recombination occurred is negligible on the evolution of Brucella. This leads to the view that Brucella is clonally evolved. On other hand, 56 genes (3.5 % of core genome) were showing signals of positive selection. Results suggest that natural selection plays an important role in the evolution of Brucella. Some of the genes that are responsible for the pathogenesis of Brucella were found positively selected, presumably due to their role in avoidance of the host immune system.
- Published
- 2015
36. Draft Genome Sequence of Paracoccus sp. MKU1, a New Bacterial Strain Isolated from an Industrial Effluent with Potential for Bioremediation
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Balasubramaniem Ashokkumar, Kamaldeen Nasrin Nisha, Jayavel Sridhar, and Perumal Varalakshmi
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Whole genome sequencing ,Paracoccus sp ,Short Research Communication ,Biology ,biology.organism_classification ,dimethylformamide ,Industrial effluent ,Genome ,Bacterial strain ,Microbiology ,Paracoccus sp. MKU1 ,Bioremediation ,bacteria ,xenobiotics ,genome ,Bacteria ,degradation - Abstract
Paracoccus sp. MKU1, a novel dimethylformamide degrading bacterial strain was originally isolated from an industrial effluent, Tirupur region, Tamil Nadu, India. Here, we report the draft genome sequence of Paracoccus sp. MKU1, which could provide the genetic insights on its evolution and application of this versatile bacterium for effective degradation of xenobiotics and thus in bioremediation.
- Published
- 2016
37. Pan-Genome of Brucella Species
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Paramasamy Gunasekaran, Jayavel Sridhar, Udayakumar S. Vishnu, Jeyaprakash Rajendhran, and Jagadesan Sankarasubramanian
- Subjects
Genetics ,biology ,Operon ,Pan-genome ,Virulence ,Chromosome ,Gene pool ,Brucella ,biology.organism_classification ,Microbiology ,Gene ,Genome - Abstract
Whole-genome sequencing of bacterial pathogens has high impact on diagnosis and development of prophylaxis to human and veterinary disease. To study the genetic variations and relatedness among Brucella spp., we have examined the pan-genomic content of 18 Brucella complete genomes from NCBI using GView and Panseq server. Multiple sequence alignment of 16S rRNA gene sequences and multiple genome alignment of all 18 Brucella spp. showed high conservation at the nucleotide level. The core, accessory and unique gene content of Brucella spp. were estimated to be 2473, 7972 and 235 respectively. The presence of strain specific region in chromosome 1 of B. melitensis M5-90 and chromosome 2 of B. microti CCM 4915, B. pinnipedialis B2/94, and B. suis ATCC 23445 were identified. In addition, a stretch of genetic pool harboring 206 strain specific coding genes trans-located from chromosome 1 to chromosome 2 were also identified in the genome of B. suis ATCC 23445. Pan-genome analysis has also revealed the integration of strain specific 23 CDS (57.82 Kb) and 6 CDS (12 Kb) in B. pinnipedialis B2/94 and B. microti CCM 4915, respectively. Major pathogenic determinants like virB operon, non-classical lipopolysaccharide, two-component system BvrR/BvrS and cyclic β-1, 2-glucan synthase were unanimously found in all Brucella spp.. The virulence genes such as flagella, type III secretion system, hemolysins, outer membrane proteins, acvB, MViN and genes involved in eryrthritol metabolism were found in the accessory genome, which may guide the host specificity.
- Published
- 2014
38. Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region
- Author
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Natesan Sundaresan, Johnpaul Muthumary, Enthai Jagan Ganeshan, Mohan Pandi, Jayavel Sridhar, Kathamuthu GokulRaj, and Pandi Rajapriya
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Systematics ,4SALE ,Phylogenetic tree ,biology ,ProfDistS ,General Medicine ,Hypothesis ,biology.organism_classification ,Plant use of endophytic fungi in defense ,Monophyly ,Emericella ,Sequence-secondary structure ,MEGA 5.1 ,Botany ,Endophytes ,ITS ,Internal transcribed spacer ,Cochliobolus ,Cladosporium - Abstract
Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal plants and characterized based on ITS2 sequence – secondary structure analysis. ITS2 secondary structures were elucidated with minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic relationships at different taxonomic levels due to their lesser length.
- Published
- 2014
39. Indole Alkaloids as New Leads for the Design and Development of Novel DPP-IV Inhibitors for the Treatment of Diabetes
- Author
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Dhiraviam, Kannan Narayanan, primary, Balasubramanian, Suganthana, additional, and Jayavel, Sridhar, additional
- Published
- 2018
- Full Text
- View/download PDF
40. Modeling and structural analysis of cellulases using Clostridium thermocellum as template
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Mary Esther Rani, Narayanan Kannan, R. Gunaseeli, Nathan Vinod Kumar, and Jayavel Sridhar
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biology ,Chemistry ,Stereochemistry ,Trichoderma longibrachiatum ,Active site ,General Medicine ,computer.file_format ,Cellulase ,Hypothesis ,Protein Data Bank ,biology.organism_classification ,Microbiology ,Pseudoalteromonas haloplanktis ,biology.protein ,Clostridium thermocellum ,Homology modeling ,computer ,Protein secondary structure - Abstract
Cellulase is one of the most widely distributed enzymes with wide application. They are involved in conversion of biomass into simpler sugars. Cellulase of Trichoderma longibrachiatum, a known cellulolytic fungus was compared with Clostridium thermocellum [AAA23226.1] cellulase. Blastp was performed with AAA23226.1 as query sequence to obtain nine similar sequences from NCBI protein data bank. The physicochemical properties of cellulase were analyzed using ExPASy's ProtParam tool namely ProtParam, SOPMA and GOR IV. Homology modeling was done using SWISS MODEL and checked quality by RMSD values using VMD1.9.1. Active sites of each model were predicted using automated active site prediction server of SCFBio. Study revealed instability of cellulase of two eukaryotic strains namely Trichoderma longibrachiatum [CAA43059.1] and Melanocarpus albomyces [CAD56665.1]. The negative GRAVY score value of cellulases ensured better interaction and activity in aqueous phase. It was found that molecular weight (M. Wt) ranges between 25-127.56 kDa. Iso-electric point (pI) of cellulases was found to be acidic in nature. GOR IV and SOPMA were used to predict secondary structure of cellulase, which showed that random coil, was dominated. Neighbor joining tree with C. thermocellum [AAA23226.1] cellulase as root showed that cellulases of Thermoaerobacter subterraneus [ZP_07835928] and C. thermocellum [CAA4305.1] were more similar to eukaryotic cellulases supported by least boot strap values. Pseudoalteromonas haloplanktis cellulase was found to be the ideal model supported by least RMSD score among the predicted structures. Trichoderma longibrachiatum cellulase was found to be the best compared to other cellulases, which possess high number of active sites with ASN and THR rich active sites. CYS residues were also present ensuring stable interaction and better bonding. Hydrophilic residues were found high in active sites of all analyzed models and template.
- Published
- 2012
41. PanGeT: Pan-genomics tool
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Jayavel Sridhar, Kanagaraj Sekar, Daliah Michael, and Iyyappan Yuvaraj
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0301 basic medicine ,Genetics ,Genome evolution ,Proteome ,030106 microbiology ,Pan-genome ,Salmonella enterica ,Genomics ,General Medicine ,Computational biology ,Biology ,Genome ,Mycobacterium ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,Species Specificity ,Minimal genome ,Clade ,Gene ,Genome, Bacterial ,Software - Abstract
A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines. The root of pan-genomic studies, however, is to identify the core genes, dispensable genes and strain specific genes across the genomes belonging to a clade. To this end, we have developed a tool, "PanGeT - Pan-genomics Tool" to compute the 'pan-genome' based on comparisons at the genome as well as the proteome levels. This automated tool is implemented using LaTeX libraries for effective visualization of overall pan-genome through graphical plots. Links to retrieve sequence information and functional annotations have also been provided. PanGeT can be downloaded from http://pranag.physics.iisc.ernet.in/PanGeT/ or https://github.com/PanGeTv1/PanGeT.
- Published
- 2016
42. Omics of Brucella: Species-Specific sRNA-Mediated Gene Ontology Regulatory Networks Identified by Computational Biology
- Author
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Jagadesan Sankarasubramanian, Jeyaprakash Rajendhran, Paramasamy Gunasekaran, Jayavel Sridhar, and Udayakumar S. Vishnu
- Subjects
0301 basic medicine ,Brucella suis ,030106 microbiology ,Brucella abortus ,Brucella ,Computational biology ,Biology ,Biochemistry ,03 medical and health sciences ,Gene expression ,Genetics ,Brucella melitensis ,Molecular Biology ,Gene ,Computational Biology ,biology.organism_classification ,RNA, Bacterial ,030104 developmental biology ,Gene Ontology ,Infectious disease (medical specialty) ,Transfer RNA ,Molecular Medicine ,Bacteria ,Biotechnology - Abstract
Brucella is an intracellular bacterium that causes the zoonotic infectious disease, brucellosis. Brucella species are currently intensively studied with a view to developing novel global health diagnostics and therapeutics. In this context, small RNAs (sRNAs) are one of the emerging topical areas; they play significant roles in regulating gene expression and cellular processes in bacteria. In the present study, we forecast sRNAs in three Brucella species that infect humans, namely Brucella melitensis, Brucella abortus, and Brucella suis, using a computational biology analysis. We combined two bioinformatic algorithms, SIPHT and sRNAscanner. In B. melitensis 16M, 21 sRNA candidates were identified, of which 14 were novel. Similarly, 14 sRNAs were identified in B. abortus, of which four were novel. In B. suis, 16 sRNAs were identified, and five of them were novel. TargetRNA2 software predicted the putative target genes that could be regulated by the identified sRNAs. The identified mRNA targets are involved in carbohydrate, amino acid, lipid, nucleotide, and coenzyme metabolism and transport, energy production and conversion, replication, recombination, repair, and transcription. Additionally, the Gene Ontology (GO) network analysis revealed the species-specific, sRNA-based regulatory networks in B. melitensis, B. abortus, and B. suis. Taken together, although sRNAs are veritable modulators of gene expression in prokaryotes, there are few reports on the significance of sRNAs in Brucella. This report begins to address this literature gap by offering a series of initial observations based on computational biology to pave the way for future experimental analysis of sRNAs and their targets to explain the complex pathogenesis of Brucella.
- Published
- 2016
43. Molecular modeling and structural analysis of nAChR variants uncovers the mechanism of resistance to snake toxins
- Author
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Venkatesan Suryanarayanan, N C Manimaran, Sanjeev Kumar Singh, Jayavel Sridhar, and D Gunasekaran
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Protein Conformation, alpha-Helical ,0301 basic medicine ,Glycosylation ,Herpestidae ,Stereochemistry ,In silico ,Neurotoxins ,Snake Bites ,Molecular Dynamics Simulation ,Receptors, Nicotinic ,Biology ,Crystallography, X-Ray ,Naja haje ,complex mixtures ,Mice ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Structural Biology ,medicine ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Binding site ,Molecular Biology ,G alpha subunit ,Acetylcholine receptor ,Binding Sites ,Sequence Homology, Amino Acid ,Shrews ,Colubridae ,General Medicine ,Bungarotoxins ,Alpha-neurotoxin ,Molecular Docking Simulation ,030104 developmental biology ,Nicotinic agonist ,chemistry ,Biochemistry ,nervous system ,Hedgehogs ,Thermodynamics ,Protein Conformation, beta-Strand ,Sequence Alignment ,030217 neurology & neurosurgery ,Acetylcholine ,Protein Binding ,medicine.drug - Abstract
Nicotinic acetylcholine receptors (nAChRs) are neuromuscular proteins responsible for muscle contraction upon binding with chemical stimulant acetylcholine (ACh). The α-neurotoxins of snake mimic the structure of ACh and attacks nAChRs, which block the flow of ACh and leads to numbness and paralysis. The toxin-binding site of alpha subunit in the nAChRs is highly conserved throughout chordate lineages with few exceptions in resistance organisms. In this study, we have analyzed the sequence and structures of toxin-binding/resistant nAChRs and their interaction stability with toxins through molecular docking and molecular dynamics simulation (MDS). We have reported the potential glycosylation residues within the toxin-binding cleft adding sugar moieties through N-linked glycosylation in resistant organisms. Residue variations at key positions alter the secondary structure of binding cleft, which might interfere with toxin binding and it could be one of the possible explanations for the resistance to snake venoms. Analysis of nAChR-α-neurotoxin complexes has confirmed the key interacting residues. In addition, drastic variation in the binding stability of Mongoose nAChR-α-Bungarotoxin (α-BTX) and human nAChR-α-BTX complexes were found at specific phase of MDS. Our findings suggest that specific mutations in the binding site of toxin are potentially preventing the formation of stable complex of receptor-toxin, which might lead to mechanism of resistance. This in silico study on the binding cleft of nAChR and the findings of interacting residues will assist in designing potential inhibitors as therapeutic targets.
- Published
- 2016
- Full Text
- View/download PDF
44. Computational prediction of secretion systems and secretomes of Brucella: identification of novel type IV effectors and their interaction with the host
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Jagadesan Sankarasubramanian, Jayavel Sridhar, Jeyaprakash Rajendhran, Paramasamy Gunasekaran, Udayakumar S. Vishnu, and Vasudevan Dinakaran
- Subjects
0301 basic medicine ,Proteome ,Operon ,Type V Secretion Systems ,030106 microbiology ,Brucella ,Genome ,Models, Biological ,Microbiology ,Type IV Secretion Systems ,03 medical and health sciences ,Bacterial Proteins ,Protein Interaction Mapping ,Animals ,Humans ,Secretion ,Computer Simulation ,Protein Interaction Maps ,Molecular Biology ,Gene ,Bacterial Secretion Systems ,Type I Secretion Systems ,biology ,Effector ,Intracellular parasite ,biology.organism_classification ,Protein Transport ,Host-Pathogen Interactions ,Metabolic Networks and Pathways ,Biotechnology - Abstract
Brucella spp. are facultative intracellular pathogens that cause brucellosis in various mammals including humans. Brucella survive inside the host cells by forming vacuoles and subverting host defence systems. This study was aimed to predict the secretion systems and the secretomes of Brucella spp. from 39 complete genome sequences available in the databases. Furthermore, an attempt was made to identify the type IV secretion effectors and their interactions with host proteins. We predicted the secretion systems of Brucella by the KEGG pathway and SecReT4. Brucella secretomes and type IV effectors (T4SEs) were predicted through genome-wide screening using JVirGel and S4TE, respectively. Protein–protein interactions of Brucella T4SEs with their hosts were analyzed by HPIDB 2.0. Genes coding for Sec and Tat pathways of secretion and type I (T1SS), type IV (T4SS) and type V (T5SS) secretion systems were identified and they are conserved in all the species of Brucella. In addition to the well-known VirB operon coding for the type IV secretion system (T4SS), we have identified the presence of additional genes showing homology with T4SS of other organisms. On the whole, 10.26 to 14.94% of total proteomes were found to be either secreted (secretome) or membrane associated (membrane proteome). Approximately, 1.7 to 3.0% of total proteomes were identified as type IV secretion effectors (T4SEs). Prediction of protein–protein interactions showed 29 and 36 host–pathogen specific interactions between Bos taurus (cattle)–B. abortus and Ovis aries (sheep)–B. melitensis, respectively. Functional characterization of the predicted T4SEs and their interactions with their respective hosts may reveal the secrets of host specificity of Brucella.
- Published
- 2015
45. Small RNA Identification in Enterobacteriaceae Using Synteny and Genomic Backbone Retention II
- Author
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Jayavel Sridhar, Sivasankaran Sathesh Kumar, and Ziauddin Ahamed Rafi
- Subjects
Genetics ,Small RNA ,RNA, Untranslated ,Sequence Analysis, RNA ,Molecular Sequence Data ,RNA ,Rfam ,Biology ,Non-coding RNA ,Synteny ,Biochemistry ,Genome ,Enterobacteriaceae ,Molecular Medicine ,Small nucleolar RNA ,Molecular Biology ,Gene ,Genome, Bacterial ,Biotechnology - Abstract
Small RNAs are bacterial counterparts of noncoding RNAs. Increasing evidence being added in the literature indicates that these small RNAs play major roles in prokaryotes both at the transcriptome and proteome levels. Based on comparative genomic studies, we present manually curated small RNA regions in 25 recently completed genomes from Enterobacteriaceae. The study is a continuation of our earlier work that uses the presence of small RNAs sandwiched between specific conserved flanking genes retaining genomic backbone and gene synteny. Based on this study, a total of 931 identified sRNA/sRNA regions are reported. This data contains 498 small RNA homologs, 80 putative small RNA regions containing partial stretches of homologous sequences, and 353 putative nonhomologous sRNA regions. This homologs/partial homologs includes, 84 putative small RNA homologous regions retaining at least one of the conserved flanking genes pair which may possibly act as hotspots for genetic pool insertion/deletion in genomes. Nonhomologous CsrB sRNA region reported by us in Yersinia pseudotuberculosis IP32953 has been experimentally confirmed by Kulkarni's group and sraH and ryeE sRNAs from Erwinia carotovora subsp. atroseptica SCRI1043 recently added to the Rfam database are indicative proof of our positive approach.
- Published
- 2009
46. CsrA interacting small RNAs in Haemophilus spp genomes: a theoretical analysis
- Author
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Jayavel Sridhar, Ziauddin Ahamed Rafi, and Kanagaraj Sekar
- Subjects
Small RNA ,RNA, Untranslated ,Haemophilus ,Biology ,Biochemistry ,Microbiology ,Genome ,Bacterial genetics ,Intergenic region ,Consensus Sequence ,Escherichia coli ,Genetics ,Consensus sequence ,Vibrio cholerae ,Molecular Biology ,Gene ,Regulator gene ,Binding Sites ,Computational Biology ,RNA-Binding Proteins ,RNA ,General Medicine ,RNA, Bacterial ,Pseudomonas aeruginosa ,Genome, Bacterial ,Protein Binding - Abstract
The csrA is a carbon storage regulator gene that encodes a protein with multiple RNA interaction sites. Bacterial non-coding small RNAs like csrB, csrC and their counterparts in diverse bacterial genus are identified to control the regulatory activities of CsrA and its orthologs. An attempt has been made in this study to identify 'novel' non-coding small RNAs that are involved in the regulatory activities of csrA gene. All CsrA-interacting small RNAs are computationally fingerprinted to have multiple occurrence of 7-nucleotide CsrA interacting repeats [CAGGA(U/A/C)G] along with a 18-nucleotide upstream binding site. However, in several of the genomes like Haemophilus spp, the upstream binding site is not identified. The current methodology overcomes this difficulty by identifying small RNA-specific orphan transcriptional units within the intergenic regions of the genome. The results could identify all known CsrA-interacting small RNAs in E. coli, Vibrio cholerae and Pseudomonas aeruginosa genomes and additionally has picked six new possible CsrA-interacting small RNA regions in E. coli. Our computational analysis indicates that known rygD and rprA sRNAs in E. coli could possibly interact with CsrA proteins. The study is extended to three of the Haemophilus genomes that could identify seven new possible CsrA interacting small RNAs.
- Published
- 2009
47. Functional annotations in bacterial genomes based on small RNA signatures
- Author
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Jayavel Sridhar and Ziauddin Ahamed Rafi
- Subjects
Bio-ontology ,Genetics ,Small RNA ,Genome evolution ,Computational genomics ,KO ,RNA ,General Medicine ,Bacterial genome size ,Hypothesis ,functional annotation ,Biology ,Genome ,KOBAS ,flanking genes ,KEGG ,sRNA ,Gene - Abstract
One of the key challenges in computational genomics is annotating coding genes and identification of regulatory RNAs in complete genomes. An attempt is made in this study which uses the regulatory RNA locations and their conserved flanking genes identified within the genomic backbone of template genome to search for similar RNA locations in query genomes. The search is based on recently reported coexistence of small RNAs and their conserved flanking genes in related genomes. Based on our study, 54 additional sRNA locations and functions of 96 uncharacterized genes are predicted in two draft genomes viz., Serratia marcesens Db1 and Yersinia enterocolitica 8081. Although most of the identified additional small RNA regions and their corresponding flanking genes are homologous in nature, the proposed anchoring technique could successfully identify four non-homologous small RNA regions in Y. enterocolitica genome also. The KEGG Orthology (KO) based automated functional predictions confirms the predicted functions of 65 flanking genes having defined KO numbers, out of the total 96 predictions made by this method. This coexistence based method shows more sensitivity than controlled vocabularies in locating orthologous gene pairs even in the absence of defined Orthology numbers. All functional predictions made by this study in Y. enterocolitica 8081 were confirmed by the recently published complete genome sequence and annotations. This study also reports the possible regions of gene rearrangements in these two genomes and further characterization of such RNA regions could shed more light on their possible role in genome evolution.
- Published
- 2008
48. Small RNA Identification inEnterobacteriaceaeUsing Synteny and Genomic Backbone Retention
- Author
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Jayavel, Sridhar and Ziauddin Ahamed, Rafi
- Subjects
Base Sequence ,Molecular Sequence Data ,Computational Biology ,Genomics ,Synteny ,Biochemistry ,RNA, Bacterial ,Enterobacteriaceae ,Genetic Techniques ,Multigene Family ,Escherichia coli ,Genetics ,Molecular Medicine ,Molecular Biology ,Genome, Bacterial ,Biotechnology - Abstract
Genomic screens for small RNA candidates in Enterobacteriacae genomes were carried out with existing small RNA sequences, conserved flanking genes, and genomic backbone information. The small RNA sequences and contexts from E. coli K12 formed the basis of the search. Sequence identity identified 117 additional small RNA homologs in related genomes. Motifs of continuous sequence stretches added another 48 sRNA regions, termed partial homologs. However, this study is unique in identifying 160 nonhomologous sRNA loci in related genomes based on the conserved flanking gene synteny and the backbone retention information obtained from KEGG-SSDB. Gene synteny and genomic backbone continuity were observed to be correlated with all of the sRNAs in related genomes. This search is the first of its kind toward identification of functionally important regions using gene order and back-bone information. A disruption in flanking gene order or genomic backbone indicates a possible hotspot for alien gene pool integration. This study reports both occurrence of multiple copies of a sRNA and co-occurrence of different sRNAs between a pair of conserved flanking genes. In general, synteny and genomic backbone retention information can be added as additional search criteria toward the design of precise bioinformatics tools for sRNA, gene identification, and gene functional annotations in related genomes.
- Published
- 2007
49. Draft Genome Sequence of Brucella abortus Virulent Strain 544
- Author
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D. K. Singh, Jagadesan Sankarasubramanian, Ashok Kumar, Udayakumar S. Vishnu, Amod Tiwari, Jayavel Sridhar, Paramasamy Gunasekaran, and Jeyaprakash Rajendhran
- Subjects
Genetics ,Whole genome sequencing ,Brucella abortus ,Strain (chemistry) ,RNA ,Virulence ,Prokaryotes ,Biology ,Molecular Biology ,C content ,Gene ,Genome - Abstract
Here, we present the draft genome sequence and annotation of Brucella abortus virulent strain 544. The genome of this strain is 3,289,405 bp long, with 57.2% G+C content. A total of 3,259 protein-coding genes and 60 RNA genes were predicted.
- Published
- 2015
50. BrucellaBase: Genome information resource
- Author
-
Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jeyaprakash Rajendhran, L.K.M. Abdul Khader, Paramasamy Gunasekaran, and Jayavel Sridhar
- Subjects
0301 basic medicine ,Microbiology (medical) ,030106 microbiology ,Brucella ,Computational biology ,Microbiology ,Genome ,Zoonotic disease ,03 medical and health sciences ,Information resource ,Species Specificity ,Phylogenetics ,Databases, Genetic ,Genetics ,Typing ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Internet ,biology ,Phylogenetic tree ,Base Sequence ,bacterial infections and mycoses ,biology.organism_classification ,Bacterial Typing Techniques ,Infectious Diseases ,Multilocus sequence typing ,Genome, Bacterial ,Multilocus Sequence Typing - Abstract
Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html.
- Published
- 2015
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