PubAg

Main content area

You searched for: Author "Sharma, Cynthia M." Remove constraint Author: "Sharma, Cynthia M." Subject transcription (genetics) Remove constraint Subject: transcription (genetics)
Start Over

Search

11  Search Results

1 - 11 of 11
Number of results to display per page

Search Results

1. Differential RNA-seq: the approach behind and the biological insight gained

Author:
Sharma, Cynthia M,   et al.   ; Vogel, Jörg;     Show all 2 Author
Source:
Current Opinion in Microbiology 2014 v.19 pp. 97-105
ISSN:
1369-5274
Subject:
Helicobacter pylori; eukaryotic cells; gene expression regulation; genetic engineering; non-coding RNA; operon; pathogens; prokaryotic cells; qualitative analysis; sequence analysis; transcription (genetics); transcriptome; transcriptomics
Abstract:
... RNA-sequencing has revolutionized the quantitative and qualitative analysis of transcriptomes in both prokaryotes and eukaryotes. It provides a generic approach for gene expression profiling, annotation of transcript boundaries and operons, as well as identifying novel transcripts including small noncoding RNA molecules and antisense RNAs. We recently developed a differential RNA-seq (dRNA-seq) me ...
DOI:
10.1016/j.mib.2014.06.010

2. Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

Author:
Sharma, Cynthia M.,   et al.   ; Bischler, Thorsten; Tan, Hock Siew; Nieselt, Kay;     Show all 4 Authors
Source:
Methods 2015 v.86 pp. 89-101
ISSN:
1046-2023
Subject:
Helicobacter pylori; RNA; bacteria; cDNA libraries; complementary DNA; high-throughput nucleotide sequencing; humans; operon; pathogens; transcription (genetics); transcriptome
Abstract:
... The global mapping of transcription boundaries is a key step in the elucidation of the full complement of transcriptional features of an organism. It facilitates the annotation of operons and untranslated regions as well as novel transcripts, including cis- and trans-encoded small RNAs (sRNAs). So called RNA sequencing (RNA-seq) based on deep sequencing of cDNAs has greatly facilitated transcript ...
DOI:
10.1016/j.ymeth.2015.06.012

3. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

Author:
Sharma, Cynthia M.,   et al.   ; Papenfort, Kai; Förstner, Konrad U.; Cong, Jian-Ping; Bassler, Bonnie L.;     Show all 5 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2015 v.112 no.7 pp. E766
ISSN:
0027-8424
Subject:
Vibrio cholerae; biofilm; group behavior; humans; messenger RNA; pathogens; transcription (genetics); transcription factors
Abstract:
... Quorum sensing (QS) is a process of cell-to-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence and biofilm formation in Vibrio cholerae , the causative agent of cholera disease. Differential RNA sequencing (RNA-seq) of wild-type V. cholerae and a locked low-cell-density QS-mutant strain identified 7,240 transcriptional start s ...
DOI:
10.1073/pnas.1500203112
PubMed:
25646441
PubMed Central:
PMC4343088

4. Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori

Author:
Sharma, Cynthia M.,   et al.   ; Müller, Stephan A.; Pernitzsch, Sandy R.; Haange, Sven-Bastiaan; Uetz, Peter; von Bergen, Martin; Kalkhof, Stefan;     Show all 7 Authors
Source:
Journal of proteomics 2015 v.126 pp. 34-45
ISSN:
1874-3919
Subject:
Helicobacter pylori; amino acids; antibiotics; arginase; bacteria; biopsy; cell death; cell division; chronic diseases; coculture; fractionation; immune evasion; isotope labeling; mucus; outer membrane proteins; oxygen; pathogens; patients; protein metabolism; proteome; proteomics; stable isotopes; stomach; transcription (genetics); translation (genetics); tumor necrosis factor-alpha
Abstract:
... Helicobacter pylori (H. pylori) is a ε-proteobacterium that colonizes the stomach of about half of the world's population. Persistent infections have been associated with several gastric diseases. Mainly rod- or spiral shaped but also coccoid H. pylori forms have been isolated from mucus layer biopsies of patients. It is still being debated whether the coccoid form can be transformed back into the ...
DOI:
10.1016/j.jprot.2015.05.011

5. Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

Author:
Sharma, Cynthia M.,   et al.   ; Thomason, Maureen K.; Bischler, Thorsten; Eisenbart, Sara K.; Förstner, Konrad U.; Zhang, Aixia; Herbig, Alexander; Nieselt, Kay; Storz, Gisela;     Show all 9 Authors
Source:
Journal of bacteriology 2015 v.197 no.1 pp. 18-28
ISSN:
0021-9193
Subject:
Escherichia coli; RNA; algorithms; bacteriology; complementary DNA; genes; mutation; prediction; ribonucleases; surveys; transcription (genetics); transcriptome
Abstract:
... While the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional ...
DOI:
10.1128/JB.02096-14
PubMed:
25266388
PubMed Central:
PMC4288677

6. The transcriptional landscape of Chlamydia pneumoniae

Author:
Sharma, Cynthia M,   et al.   ; Albrecht, Marco; Dittrich, Marcus T; Müller, Tobias; Reinhardt, Richard; Vogel, Jörg; Rudel, Thomas;     Show all 7 Authors
Source:
Genome biology 2011 v.12 no.10 pp. 2689
ISSN:
1474-760X
Subject:
Chlamydia; Chlamydophila pneumoniae; RNA; bacteria; complementary DNA; genetic engineering; nucleotide sequences; operon; pathogens; transcription (genetics); transcriptome
Abstract:
... BACKGROUND: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae. RESULTS: Using a different ...
DOI:
10.1186/gb-2011-12-10-r98
PubMed:
21989159
PubMed Central:
PMC3333780

7. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Author:
Sharma, Cynthia M.,   et al.   ; Albrecht, Marco; Reinhardt, Richard; Vogel, Jörg; Rudel, Thomas;     Show all 5 Authors
Source:
Nucleic acids research 2010 v.38 no.3 pp. 868-877
ISSN:
0305-1048
Subject:
Chlamydia trachomatis; bacteria; complementary DNA; genes; genetic engineering; high-throughput nucleotide sequencing; non-coding RNA; nucleotide sequences; pathogens; transcription (genetics); transcriptome
Abstract:
... Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, r ...
DOI:
10.1093/nar/gkp1032
PubMed:
19923228
PubMed Central:
PMC2817459

8. Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability

Author:
Sharma, Cynthia M.,   et al.   ; Jäger, Dominik; Thomsen, Jens; Ehlers, Claudia; Vogel, Jörg; Schmitz, Ruth A.;     Show all 6 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2009 v.106 no.51 pp. 21878-21882
ISSN:
0027-8424
Subject:
5' untranslated regions; Methanosarcina mazei; acetates; binding sites; carbon dioxide; gene expression regulation; genes; greenhouse gases; high-throughput nucleotide sequencing; intergenic DNA; methane; methanol; nitrogen; open reading frames; promoter regions; transcription (genetics); transcriptome; transposition (genetics)
Abstract:
... Methanosarcina mazei and related mesophilic archaea are the only organisms fermenting acetate, methylamines, and methanol to methane and carbon dioxide, contributing significantly to greenhouse gas production. The biochemistry of these metabolic processes is well studied, and genome sequences are available, yet little is known about the overall transcriptional organization and the noncoding region ...
DOI:
10.1073/pnas.0909051106
PubMed:
19996181
PubMed Central:
PMC2799843

9. Functional Characterization of the RNA Chaperone Hfq in the Opportunistic Human Pathogen Stenotrophomonas maltophilia

Author:
Sharma, Cynthia M.,   et al.   ; Roscetto, Emanuela; Angrisano, Tiziana; Costa, Valerio; Casalino, Mariassunta; Förstner, Konrad U.; Di Nocera, Pier Paolo; De Gregorio, Eliana;     Show all 8 Authors
Source:
Journal of bacteriology 2012 v.194 no.21 pp. 5864-5874
ISSN:
0021-9193
Subject:
RNA-binding proteins; Stenotrophomonas maltophilia; adhesion; anti-infective agents; biochemical pathways; biofilm; cell movement; enzymes; epithelial cells; genes; humans; immunocompromised population; macrophages; messenger RNA; mutants; pathogens; prokaryotic cells; sequence analysis; transcription (genetics); transmembrane proteins
Abstract:
... Hfq is an RNA-binding protein known to regulate a variety of cellular processes by interacting with small RNAs (sRNAs) and mRNAs in prokaryotes. Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immunocompromised hosts. We constructed an hfq deletion mutant (Δhfq) of S. maltophilia and compared the behaviors of wild-type and Δhfq S. maltophili ...
DOI:
10.1128/JB.00746-12
PubMed:
22923593
PubMed Central:
PMC3486118

10. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

Author:
Sharma, Cynthia M.,   et al.   ; Mitschke, Jan; Georg, Jens; Scholz, Ingeborg; Dienst, Dennis; Bantscheff, Jens; Voss, Björn; Steglich, Claudia; Wilde, Annegret; Vogel, Jörg; Hess, Wolfgang R.;     Show all 11 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.5 pp. 2124-2129
ISSN:
0027-8424
Subject:
Synechocystis; autotrophs; bioengineering; biofuels; energy; genes; intergenic DNA; messenger RNA; microarray technology; non-coding RNA; photosynthesis; solar energy; transcription (genetics)
Abstract:
... There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcr ...
DOI:
10.1073/pnas.1015154108
PubMed:
21245330
PubMed Central:
PMC3033270

11. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

Author:
Sharma, Cynthia M.,   et al.   ; Bohn, Chantal; Rigoulay, Candice; Chabelskaya, Svetlana; Marchais, Antonin; Skorski, Patricia; Borezée-Durant, Elise; Barbet, Romain; Jacquet, Eric; Jacq, Annick; Gautheret, Daniel; Felden, Brice; Vogel, Jörg; Bouloc, Philippe;     Show all 14 Authors
Source:
Nucleic acids research 2010 v.38 no.19 pp. 6620-6636
ISSN:
0305-1048
Subject:
ABC transporters; Staphylococcus aureus; carbon; citrates; enzymes; intergenic DNA; messenger RNA; metabolism; operon; pathogens; transcription (genetics)
Abstract:
... Using an experimental approach, we investigated the RNome of the pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among the latter, 10 are encoded in intergenic regions, three are generated by premature transcription termination associated with riboswitch activities, and one is expressed from the complementary strand of a transposase gene. The ...
DOI:
10.1093/nar/gkq462
PubMed:
20511587
PubMed Central:
PMC2965222