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15 results on '"Chen, Donald S."'

5. Mpox in the New York Metropolitan area, Summer 2022

Author

Gnanaprakasam, Rachel, primary, Keller, Marina, additional, Glassman, Rebecca, additional, El‐Khoury, Marc, additional, Chen, Donald S, additional, Feola, Nicholas, additional, Feldman, Jared, additional, and Chaturvedi, Vishnu, additional

Published
2023
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7. Genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor

Author

Wiens, Gregory D., Rockey, Daniel D., Wu, Zaining, Chang, Jean, Levy, Ruth, Crane, Samuel, Chen, Donald S., Capri, Gina R., Burnett, Jeffrey R., Sudheesh, Ponnerassery S., Schipma, Matthew J., Burd, Henry, Bhattacharyya, Anamitra, Rhodes, Linda D., Kaul, Rajinder, and Strom, Mark S.

Subjects
Bacteria -- Genetic aspects, Bacteria -- Health aspects, Bacteria -- Research, Nucleotide sequence -- Research, Gene mutations -- Research, Biological sciences
Abstract

Renibacterium salmoninarum is the causative agent of bacterial kidney disease and a significant threat to healthy and sustainable production of salmonid fish worldwide. This pathogen is difficult to culture in vitro, genetic manipulation is challenging, and current therapies and preventative strategies are only marginally effective in preventing disease. The complete genome of R. salmoninarum ATCC 33209 was sequenced and shown to be a 3,155,250-bp circular chromosome that is predicted to contain 3,507 open-reading frames (ORFs). A total of 80 copies of three different insertion sequence elements are interspersed throughout the genome. Approximately 21% of the predicted ORFs have been inactivated via frameshifts, point mutations, insertion sequences, and putative deletions. The R. salmoninarum genome has extended regions of synteny to the Arthrobacter sp. strain FB24 and Arthrobacter aurescens TCI genomes, but it is approximately 1.9 Mb smaller than both Arthrobacter genomes and has a lower G+C content, suggesting that significant genome reduction has occurred since divergence from the last common ancestor. A limited set of putative virulence factors appear to have been acquired via horizontal transmission after divergence of the species; these factors include capsular polysaccharides, heme sequestration molecules, and the major secreted cell surface antigen p57 (also known as major soluble antigen). Examination of the genome revealed a number of ORFs homologous to antibiotic resistance genes, including genes encoding [beta]-lactamases, efflux proteins, macrolide glycosyltransferases, and rRNA methyltransferases. The genome sequence provides new insights into R. salmoninarum evolution and may facilitate identification of chemotherapeutic targets and vaccine candidates that can be used for prevention and treatment of infections in cultured salmonids.

Published
2008

8. 531. Practical and Evidence-Based Considerations for Implementation of Bacterial Whole-Genome Sequencing Within Longitudinal Infection Control Practice

Author

Chen, Donald S, primary, Quinn, Moira, additional, Sussner, Rita M, additional, Wang, Guiqing, additional, Fallon, John T, additional, Chanza, Melissa, additional, Doty, Alan J, additional, Ashworth, Judy L, additional, Kelleher, Steven W, additional, Holler, Devon J, additional, Fortunato-habib, Mary M, additional, Loving, Joshua, additional, Abdolahi, Amir, additional, Carmona, Juan J, additional, and Gross, Brian D, additional

Published
2019
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11. Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

Author

Rougeron, Virginie, primary, Tiedje, Kathryn E., additional, Chen, Donald S., additional, Rask, Thomas S., additional, Gamboa, Dionicia, additional, Maestre, Amanda, additional, Musset, Lise, additional, Legrand, Eric, additional, Noya, Oscar, additional, Yalcindag, Erhan, additional, Renaud, François, additional, Prugnolle, Franck, additional, and Day, Karen P., additional

Published
2017
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12. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

Author

Rask, Thomas Salhøj, Petersen, Bent, Chen, Donald S., Day, Karen P., Pedersen, Anders Gorm, Rask, Thomas Salhøj, Petersen, Bent, Chen, Donald S., Day, Karen P., and Pedersen, Anders Gorm

Abstract

Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data. This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon sequencing data, particularly where extensive prior knowledge is available about the obtained sequences, for example in analysis of the immunoglobulin VDJ region where Multipass can be combined with a model for the known recombining germline genes. Multipass is available for Roche 454 data at http://www.cbs.dtu.dk/services/MultiPass-1.0 , and the concept can potentially be implemented for other sequencing technologies as well.

Published
2016

15. A Molecular Epidemiological Study of var Gene Diversity to Characterize the Reservoir of Plasmodium falciparum in Humans in Africa

Author

Chen, Donald S., primary, Barry, Alyssa E., additional, Leliwa-Sytek, Aleksandra, additional, Smith, Terry-Ann, additional, Peterson, Ingrid, additional, Brown, Stuart M., additional, Migot-Nabias, Florence, additional, Deloron, Philippe, additional, Kortok, Moses M., additional, Marsh, Kevin, additional, Daily, Johanna P., additional, Ndiaye, Daouda, additional, Sarr, Ousmane, additional, Mboup, Souleymane, additional, and Day, Karen P., additional

Published
2011
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