The Experts below are selected from a list of 65499 Experts worldwide ranked by ideXlab platform
Patrick A Limbach - One of the best experts on this subject based on the ideXlab platform.
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evaluating the reproducibility of quantifying modified nucleosides from Ribonucleic Acids by lc uv ms
Journal of Chromatography B, 2013Co-Authors: Susan P Russell, Patrick A LimbachAbstract:Post-transcriptional chemical covalent modification of adenosine, guanosine, uridine and cytidine occurs frequently in all types of Ribonucleic Acids (RNAs). In ribosomal RNA (rRNA) and transfer RNA (tRNA) these modifications make important contributions to RNA structure and stability and to the accuracy and efficiency of protein translation. The functional dynamics, synergistic nature and regulatory roles of these posttranscriptional nucleoside modifications within the cell are not well characterized. These modifications are present at very low levels and isolation of individual nucleosides for analysis requires a complex multi-step approach. The focus of this study is to characterize the reproducibility of a liquid chromatography method used to isolate and quantitatively characterize modified nucleosides in tRNA and rRNA when nucleoside detection is performed using ultraviolet and mass spectrometric detection (UV and MS, respectively). Despite the analytical challenges of sample isolation and dynamic range, quantitative profiling of modified nucleosides obtained from bacterial tRNAs and rRNAs is feasible at relative standard deviations of 5% RSD or less.
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mass spectrometry sequencing of transfer Ribonucleic Acids by the comparative analysis of rna digests card approach
Analyst, 2013Co-Authors: Patrick A LimbachAbstract:The comparative analysis of Ribonucleic acid digests (CARD) approach for sequencing of transfer Ribonucleic Acids (tRNAs) is described. This method is enabled by the differential labeling of two tRNA populations. A set of reference tRNAs, whose complete sequences including modifications are known, are labeled with 16O during enzymatic digestion. The second (candidate) set of tRNAs, whose sequence information is desired, is labeled with 18O. By combining the two digests, digestion products that share the same sequence between the reference and candidate will appear as doublets separated by 2 Da. Sequence or modification differences between the two will generate singlets that can be further characterized to identify how the candidate sequence differs from the reference. Using CARD, ca. 80% of the tRNAs from the bacterium Citrobacter koseri can be sequenced using ribonuclease T1 with Escherichia coli tRNAs as the reference. During these studies, we also discovered a sequence error for Escherichia coli tRNA-Thr1, and use this method to confirm the correct sequence for that tRNA.
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method for comparative analysis of Ribonucleic Acids using isotope labeling and mass spectrometry
Analytical Chemistry, 2012Co-Authors: Patrick A LimbachAbstract:Here, we describe a method for the comparative analysis of Ribonucleic Acids (RNAs). This method allows sequence or modification information from a previously uncharacterized RNA to be obtained by direct comparison with a reference RNA, whose sequence or modification information is known. This simple and rapid method is enabled by the differential labeling of two RNA samples. One sample, the reference RNA, is labeled with 16O during enzymatic digestion. The second sample, the candidate or unknown RNA, is labeled with 18O. By combining the two digests, digestion products that share the same sequence or post-transcriptional modification(s) between the reference and candidate will appear as doublets separated by 2 Da. Sequence or modification differences between the two will generate singlets that can be further characterized to identify how the candidate sequence differs from the reference. We illustrate the application of this approach for sequencing individual RNAs and demonstrate how this method can be u...
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quantitation of Ribonucleic Acids using 18o labeling and mass spectrometry
Analytical Chemistry, 2005Co-Authors: Zhaojing Meng, Patrick A LimbachAbstract:A previous limitation in the analysis of Ribonucleic Acids (RNAs) by mass spectrometry (MS) has been the inability to obtain quantitative information relating to total RNA, RNA subunits, and undermodified nucleosides in a straightforward manner. Here, a simple and rapid method has been developed for the relative quantitation of small RNAs using 18O labeling and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). One RNA sample is digested with RNase T1 in 18O-labeled (“heavy”) water with the 18O being incorporated at the 3‘-phosphate end of oligonucleotides upon hydrolysis. A second RNA sample is digested with RNase T1 in normal (“light”) water. The two samples are then combined and analyzed by MALDI-MS. Relative ion abundances of the light- and heavy-water digestion products, which are separated by 2 Da due to the isotopic mass of 18O, reveal relative quantitation information from the two RNA samples. The accuracy and reproducibility of this approach were tested on 18 known RNA samp...
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molecular mass measurement of intact Ribonucleic Acids via electrospray ionization quadrupole mass spectrometry
Journal of the American Society for Mass Spectrometry, 1995Co-Authors: Patrick A Limbach, Pamela F Crain, James A MccloskeyAbstract:The use of electrospray ionization mass spectrometry for the accurate determination of molecular masses of polynucleotides and small nucleic Acids is developed. The common problem of gas phase cation adduction that is particularly prevalent in the mass spectrometric analysis of nucleic Acids is reduced through the use of ammonium acetate precipitations and by the addition of chemical additives that compete for adduct ions in solution. The addition of chelating agents such as trans-1,2-diaminocyclohexane-N,N,N,′,N′-tetraacetic acid to remove divalent metal ions and triethylamine to displace monovalent cations from the analyte, in conjunction with ammonium acetate precipitation, reduces cation adduction to levels that permit accurate mass analysis (mass errors of less than 0.01%) without further complex cleanup procedures. The potential utility of accurate mass measurements of small Ribonucleic Acids is discussed.
Emiko Senba - One of the best experts on this subject based on the ideXlab platform.
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localization of leukemia inhibitory factor and interleukin 6 messenger Ribonucleic Acids in regenerating rat skeletal muscle
Muscle & Nerve, 1998Co-Authors: Katsuya Kami, Emiko SenbaAbstract:In the present study, we characterized both temporal and spatial expression patterns of leukemia inhibitory factor (LIF) and interleukin-6 (IL-6) messenger Ribonucleic Acids (mRNAs) in injured skeletal muscle using in situ hybridization. LIF and IL-6 mRNAs were expressed in mononucleated cells and damaged muscle cells. Further, signals for LIF mRNA were also detected in Schwann cell-like cells of intramuscular nerves. These results suggest that the earliest events involved in the repair of injured muscles and nerves may be triggered by these cytokines.
Volker A Erdmann - One of the best experts on this subject based on the ideXlab platform.
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5s ribosomal rna database y2k
Nucleic Acids Research, 2000Co-Authors: Maciej Szymanski, Miroslawa Z Barciszewska, Jan Barciszewski, Volker A ErdmannAbstract:This paper presents the updated version (Y2K) of the database of ribosomal 5S Ribonucleic Acids (5S rRNA) and their genes (5S rDNA), http://rose.man/poznan. pl/5SData/index.html . This edition of the database contains 1985 primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms.
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5s ribosomal rna data bank
Nucleic Acids Research, 1999Co-Authors: Maciej Szymanski, Miroslawa Z Barciszewska, Jan Barciszewski, Volker A ErdmannAbstract:This paper presents the updated version of the data base of ribosomal 5S Ribonucleic Acids (5S rRNA) and their genes (5S rDNA). This edition of the data bank contains 1889 primary structures of 5S rRNA and 5S rDNA. These include 60 archaebacterial, 439 eubacterial, 63 plastid, 9 mitochondrial and 1318 eukaryotic sequences. The nucleotide sequences of 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of organisms. The sequences stored in the database can be viewed and retrieved using the taxonomic browser at the URL: http://rose.man.poznan.pl/5SData/5SRNA.html++ +
Michiaki Hamada - One of the best experts on this subject based on the ideXlab platform.
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computational approaches for alternative and transient secondary structures of Ribonucleic Acids
Briefings in Functional Genomics, 2018Co-Authors: Tsukasa Fukunaga, Michiaki HamadaAbstract:Transient and alternative structures of Ribonucleic Acids (RNAs) play essential roles in various regulatory processes, such as translation regulation in living cells. Because experimental analyses for RNA structures are difficult and time-consuming, computational approaches based on RNA secondary structures are promising. In this article, we review computational methods for detecting and analyzing transient/alternative secondary structures of RNAs, including static approaches based on probabilistic distributions of RNA secondary structures and dynamic approaches such as kinetic folding and folding pathway predictions.
Katsuya Kami - One of the best experts on this subject based on the ideXlab platform.
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localization of leukemia inhibitory factor and interleukin 6 messenger Ribonucleic Acids in regenerating rat skeletal muscle
Muscle & Nerve, 1998Co-Authors: Katsuya Kami, Emiko SenbaAbstract:In the present study, we characterized both temporal and spatial expression patterns of leukemia inhibitory factor (LIF) and interleukin-6 (IL-6) messenger Ribonucleic Acids (mRNAs) in injured skeletal muscle using in situ hybridization. LIF and IL-6 mRNAs were expressed in mononucleated cells and damaged muscle cells. Further, signals for LIF mRNA were also detected in Schwann cell-like cells of intramuscular nerves. These results suggest that the earliest events involved in the repair of injured muscles and nerves may be triggered by these cytokines.
