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24 results on '"Shi, Shundi"'

4. Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

Author

Stranges, P. Benjamin, Palla, Mirkó, Kalachikov, Sergey, Nivala, Jeff, Dorwart, Michael, Trans, Andrew, Kumar, Shiv, Porel, Mintu, Chien, Minchen, Tao, Chuanjuan, Morozova, Irina, Li, Zengmin, Shi, Shundi, Aberra, Aman, Arnold, Cleoma, Yang, Alexander, Aguirre, Anne, Harada, Eric T., Korenblum, Daniel, Pollard, James, Bhat, Ashwini, Gremyachinskiy, Dmitriy, Bibillo, Arek, Chen, Roger, Davis, Randy, Russo, James J., Fuller, Carl W., Roever, Stefan, Ju, Jingyue, and Church, George M.

Published
2016

5. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

Author

Fuller, Carl W., Kumar, Shiv, Porel, Mintu, Chien, Minchen, Bibillo, Arek, Stranges, P. Benjamin, Dorwart, Michael, Tao, Chuanjuan, Li, Zengmin, Guo, Wenjing, Shi, Shundi, Korenblum, Daniel, Trans, Andrew, Aguirre, Anne, Liu, Edward, Harada, Eric T., Pollard, James, Bhat, Ashwini, Cech, Cynthia, Yang, Alexander, Arnold, Cleoma, Palla, Mirkó, Hovis, Jennifer, Chen, Roger, Morozova, Irina, Kalachikov, Sergey, Russo, James J., Kasianowicz, John J., Davis, Randy, Roever, Stefan, Church, George M., and Ju, Jingyue

Published
2016

6. The Genomic Sequence of the Accidental Pathogen Legionella pneumophila

Author

Chien, Minchen, Morozova, Irina, Shi, Shundi, Sheng, Huitao, Chen, Jing, Gomez, Shawn M., Asamani, Gifty, Hill, Kendra, Nuara, John, Feder, Marc, Rineer, Justin, Greenberg, Joseph J., Steshenko, Valeria, Park, Samantha H., Zhao, Baohui, Teplitskaya, Elita, Edwards, John R., Pampou, Sergey, Georghiou, Anthi, Iannuccilli, William, Ulz, Michael E., Kim, Dae H., Geringer-Sameth, Alex, Goldsberry, Curtis, Morozov, Pavel, Fischer, Stuart G., Segal, Gil, Qu, Xiaoyan, Rzhetsky, Andrey, Zhang, Peisen, Cayanis, Eftihia, De Jong, Pieter J., Ju, Jingyue, Kalachikov, Sergey, Shuman, Howard A., and Russo, James J.

Published
2004

10. MLC-Seq: de novo Sequencing of Full-Length tRNAs and Quantitative Mapping of Multiple RNA Modifications

Author

Zhang, Shenglong, primary, Yuan, Xiaohong, additional, Su, Yue, additional, Zhang, Xudong, additional, Turkel, Spencer, additional, Shi, Shundi, additional, Wang, Xuanting, additional, Choi, Eun-Jin, additional, Wu, Wenzhe, additional, Liu, Haichuan, additional, Viner, Rosa, additional, Russo, James, additional, Li, Wenjia, additional, Bao, Xiaoyong, additional, and Chen, Qi, additional

Published
2021
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11. MLC Seq: De novo sequencing of full-length tRNA isoforms by mass ladder complementation

Author

Yuan, Xiaohong, primary, Su, Yue, additional, Zhang, Xudong, additional, Turkel, Spencer J., additional, Shi, Shundi, additional, Wang, Xuanting, additional, Choi, Eun-Jin, additional, Wu, Wenzhe, additional, Liu, Haichuan, additional, Viner, Rosa, additional, Russo, James J., additional, Li, Wenjia, additional, Bao, Xiaoyong, additional, Chen, Qi, additional, and Zhang, Shenglong, additional

Published
2021
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20. Mitochondrial single nucleotide polymorphism genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using cleavable biotinylated dideoxynucleotides

Author

Qiu, Chunmei, primary, Kumar, Shiv, additional, Guo, Jia, additional, Lu, Jiesheng, additional, Shi, Shundi, additional, Kalachikov, Sergey M., additional, Russo, James J., additional, Naini, Ali B., additional, Schon, Eric A., additional, and Ju, Jingyue, additional

Published
2012
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22. Comparative sequence analysis of the icm/dot genes in Legionella

Author

Morozova, Irina, Qu, Xiaoyan, Shi, Shundi, Asamani, Gifty, Greenberg, Joseph E., Shuman, Howard A., and Russo, James J.

Subjects
*LEGIONELLA pneumophila, *MACROPHAGES, *CYTOPLASM, *GENES
Abstract

The icm/dot genes in Legionella pneumophila are essential for the ability of the bacteria to survive within macrophages in lung infections such as Legionnaires’ disease, or amoebae in nature. The 22 genes of the complex, thought to encode a transport apparatus for transfer of effector molecules into the host cell cytoplasm, are located in two chromosomal loci. We demonstrate that these genes are present in all the L. pneumophila strains examined herein, but display a wide range of sequence variation among the different strains, none of which are clearly associated with virulence potential. The strains fall within seven phylogenetic groups, but discrepancies among the gene trees indicate a complicated evolutionary history for the icm/dot loci, with perhaps two independent gene acquisition events and subsequent genomic rearrangements. Significant findings include a probable t-SNARE domain in IcmG that may indicate a direct role for this putative inner membrane protein in altering the host’s membrane fusion machinery, a potential functional domain in the central hydrophobic portion of IcmK that may allow it to participate in forming the pore of the secretion complex, and strict conservation of the amino acid physicochemical characteristics in the IcmP region corresponding to the trbA domain that could play a role in molecular transfer. [Copyright &y& Elsevier]

Published
2004
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23. EXPRESSION AND DELETION ANALYSIS OF EcoRII ENDONUCLEASE AND METHYLASE GENE.

Author

Liu Jinyi, Zhao Xiaojuan, Meng Yan, Shen Jie, Xue Yueqiang, Shi Shundi, and Cai Youyu

Subjects
*ENDONUCLEASES, *METHYLTRANSFERASES
Abstract

Examines the expression and deletion of EcoRII restriction endonuclease and methyltransferase gene in China. Construction of unidirectional deletion subclones; Determination of deletion sites by sequencing; Components of the restriction-modification system.

Published
2001

24. A General LC-MS-Based Method for Direct and De Novo Sequencing of RNA Mixtures Containing both Canonical and Modified Nucleotides.

Author

Zhang N, Shi S, Yuan X, Ni W, Wang X, Yoo B, Jia TZ, Li W, and Zhang S

Subjects
5-Methylcytosine metabolism, Hydrophobic and Hydrophilic Interactions, Oligonucleotides genetics, Pseudouridine genetics, RNA Processing, Post-Transcriptional genetics, Uridine genetics, Chromatography, Liquid methods, Nucleotides genetics, RNA genetics, Sequence Analysis, RNA methods, Tandem Mass Spectrometry methods
Abstract

Mass spectrometry (MS)-based sequencing has advantages in direct sequencing of RNA, compared to cDNA-based RNA sequencing methods, as it is completely independent of enzymes and base complementarity errors in sample preparation. In addition, it allows for sequencing of different RNA modifications in a single study, rather than just one specific modification type per study. However, many technical challenges remain in de novo MS sequencing of RNA, making it difficult to MS sequence mixed RNAs or to differentiate isomeric modifications such as pseudouridine (Ψ) from uridine (U). Our recent study incorporates a two-dimensional hydrophobic end labeling strategy into MS-based sequencing (2D-HELS MS Seq) to systematically address the current challenges in MS sequencing of RNA, making it possible to directly and de novo sequence purified single RNA and mixed RNA containing both canonical and modified nucleotides. Here, we describe the method to sequence representative single-RNA and mixed-RNA oligonucleotides, each with a different sequence and/or containing modified nucleotides such as Ψ and 5-methylcytosine (m 5 C), using 2D-HELS MS Seq.

Published
2021
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