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Your search keyword '"Nair, Mridul B."' showing total 9 results
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9 results on '"Nair, Mridul B."'

1. Genome-Wide DNA Methylation Profiling in Early Stage I Lung Adenocarcinoma Reveals Predictive Aberrant Methylation in the Promoter Region of the Long Noncoding RNA PLUT: An Exploratory Study

Author

Kim-Wanner, Soo-Zin, Assenov, Yassen, Nair, Mridul B., Weichenhan, Dieter, Benner, Axel, Becker, Natalia, Landwehr, Katharina, Kuner, Ruprecht, Sültmann, Holger, Esteller, Manel, Koch, Ina, Lindner, Michael, Meister, Michael, Thomas, Michael, Bieg, Matthias, Klingmüller, Ursula, Schlesner, Matthias, Warth, Arne, Brors, Benedikt, Seifried, Erhard, Bönig, Halvard, Plass, Christoph, Risch, Angela, and Muley, Thomas

Published
2020
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2. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.

Author

Vega, Fernando E, Brown, Stuart M, Chen, Hao, Shen, Eric, Nair, Mridul B, Ceja-Navarro, Javier A, Brodie, Eoin L, Infante, Francisco, Dowd, Patrick F, and Pain, Arnab

Subjects
Animals, Weevils, Coffea, Crops, Agricultural, Caffeine, Cytochrome P-450 Enzyme System, Enzymes, Carboxylesterase, ATP-Binding Cassette Transporters, Insect Proteins, RNA, Untranslated, Phylogeny, Gene Transfer, Horizontal, Multigene Family, Female, Genome, Insect, Inactivation, Metabolic, Infectious Diseases, Genetics, Crops, Agricultural, RNA, Untranslated, Gene Transfer, Horizontal, Genome, Insect, Inactivation, Metabolic, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.

Published
2015

3. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Author

Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Bessa, Theolis Barbosa, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis, Minh Ha, Dang, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, and Clark, Taane G.

Published
2018
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6. Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Author

Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Bessa, Theolis Barbosa, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis, Ha, Dang Minh, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Sousa, Erivelton Oliveira, Streicher, Elizabeth M., Van Helden, Paul, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, and Clark, Taane G.

Published
2018
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7. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Author

King Abdullah University of Science and Technology, Wellcome Trust, Burroughs Wellcome Fund, Fundação para a Ciência e a Tecnologia (Portugal), Fundação Calouste Gulbenkian, European Society of Clinical Microbiology and Infectious Diseases, Medical Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Japan Agency for Medical Research and Development, Coll, Francesc [0000-0002-7882-2325], Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Barbosa Bessa, Theolis, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis Louis, Ha, Dang Minh, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, Clark, Taane G., King Abdullah University of Science and Technology, Wellcome Trust, Burroughs Wellcome Fund, Fundação para a Ciência e a Tecnologia (Portugal), Fundação Calouste Gulbenkian, European Society of Clinical Microbiology and Infectious Diseases, Medical Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Japan Agency for Medical Research and Development, Coll, Francesc [0000-0002-7882-2325], Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Barbosa Bessa, Theolis, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis Louis, Ha, Dang Minh, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, and Clark, Taane G.

Abstract

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

Published
2018

8. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

Author

Biotechnology and Biological Sciences Research Council (UK), National Health and Medical Research Council (Australia), Newton Fund, Medical Research Council (UK), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Coll, Francesc [0000-0002-7882-2325], Phelan, Jody, Coll, Francesc, McNerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin L., Pain, Arnab, Rigouts, Leen, Clark, Taane G., Biotechnology and Biological Sciences Research Council (UK), National Health and Medical Research Council (Australia), Newton Fund, Medical Research Council (UK), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Coll, Francesc [0000-0002-7882-2325], Phelan, Jody, Coll, Francesc, McNerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin L., Pain, Arnab, Rigouts, Leen, and Clark, Taane G.

Abstract

Background: Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. Methods: To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. Results: The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. Conclusions: Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistan

Published
2016

9. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

Author

Phelan, Jody, primary, Coll, Francesc, additional, McNerney, Ruth, additional, Ascher, David B., additional, Pires, Douglas E. V., additional, Furnham, Nick, additional, Coeck, Nele, additional, Hill-Cawthorne, Grant A., additional, Nair, Mridul B., additional, Mallard, Kim, additional, Ramsay, Andrew, additional, Campino, Susana, additional, Hibberd, Martin L., additional, Pain, Arnab, additional, Rigouts, Leen, additional, and Clark, Taane G., additional

Published
2016
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