http://www.openwetware.org/index.php?title=Pan:What_we_do&feed=atom&action=historyPan:What we do - Revision history2013-05-21T21:26:27ZRevision history for this page on the wikiMediaWiki 1.13.2http://www.openwetware.org/index.php?title=Pan:What_we_do&diff=614955&oldid=prevTaopan at 20:23, 20 July 20122012-07-20T20:23:33Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. It is commonly believed that translation deviating from the genetic code is avoided at all times. We discovered that mammalian cells can deliberately reprogram the genetic code through tRNA misacylation upon innate immune activation and chemically triggered oxidative stress. The reprogramming is regulated by fluctuating levels of reactive oxygen species (ROS) in the cell. We are investigating how regulated mis-translation is used as a mechanism for stress response.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. It is commonly believed that translation deviating from the genetic code is avoided at all times. We discovered that mammalian cells can deliberately reprogram the genetic code through tRNA misacylation upon innate immune activation and chemically triggered oxidative stress. The reprogramming is regulated by fluctuating levels of reactive oxygen species (ROS) in the cell. We are investigating how regulated mis-translation is used as a mechanism for stress response.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites from bacteria to humans. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. RNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Some modifications can be removed by cellular enzymes, leading to dynamic regulation of their function. We are <del class="diffchange diffchange-inline">developing genome-wide methods and applying these to study </del>the function of RNA modifications in cell growth, adaptation and development. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites from bacteria to humans. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. RNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Some modifications can be removed by cellular enzymes, leading to dynamic regulation of their function. We are <ins class="diffchange diffchange-inline">investigating </ins>the function of RNA modifications in cell growth, adaptation and development. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. </del>We are investigating how RNA folds during transcription to understand RNA folding in the cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We are <ins class="diffchange diffchange-inline">also </ins>investigating how RNA folds during transcription to understand RNA folding <ins class="diffchange diffchange-inline">and structural rearrangement </ins>in the cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Research positions|Research positions]] | [[Pan:Press|Press]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Research positions|Research positions]] | [[Pan:Press|Press]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=540145&oldid=prevTaopan at 14:27, 22 September 20112011-09-22T14:27:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are investigating how RNA folds during transcription to understand RNA folding in the cell.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are investigating how RNA folds during transcription to understand RNA folding in the cell.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | <ins class="diffchange diffchange-inline">[[Pan:Research positions|Research positions]] | [[Pan:Press|Press]] | </ins>[[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=540125&oldid=prevTaopan at 14:06, 22 September 20112011-09-22T14:06:21Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">tRNA is essential for protein synthesis and life. Genomes contain hundreds of tRNA genes. </del>Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and <del class="diffchange diffchange-inline">cellular </del>adaptation to new environments and to control gene expression <del class="diffchange diffchange-inline">in differentiated organisms</del>. We developed microarray methods that measure tRNA abundance, <del class="diffchange diffchange-inline">its </del>fraction of aminoacylation and misacylation at the genomic scale. We are exploring roles of tRNA in translational control <del class="diffchange diffchange-inline">in yeast and </del>in mammalian cells <del class="diffchange diffchange-inline">including cancer</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and adaptation to new environments and to control gene expression. We developed microarray methods that measure tRNA abundance, fraction of aminoacylation and misacylation at the genomic scale. We are exploring roles of tRNA in translational control in mammalian cells.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Over 100 types </del>of <del class="diffchange diffchange-inline">post-transcriptional modifications have been identified in thousands </del>of <del class="diffchange diffchange-inline">RNA sites </del>from <del class="diffchange diffchange-inline">bacteria </del>to <del class="diffchange diffchange-inline">man</del>. <del class="diffchange diffchange-inline">They include methylation of bases and </del>the <del class="diffchange diffchange-inline">ribose backbone, rotation </del>and <del class="diffchange diffchange-inline">reduction of uridine, base deamination, elaborate addition of ring structures and carbohydrate moieties, and so on</del>. <del class="diffchange diffchange-inline">RNA modification enzymes represent 1-2% </del>of <del class="diffchange diffchange-inline">all genes </del>in <del class="diffchange diffchange-inline">bacteria</del>. <del class="diffchange diffchange-inline">Hundreds of guide RNAs and dozens of proteins </del>are used <del class="diffchange diffchange-inline">to direct modifications in eukaryotic rRNAs. RNA modifications are involved in </del>stress response<del class="diffchange diffchange-inline">, environmental adaptation, antibiotic resistance and human neurology. We developed genomic methods that detect and quantify changes in modification fraction. We are applying these high throughput methods to study the function of RNA modifications at the genomic level during cell growth, adaptation and development</del>. <del class="diffchange diffchange-inline"> </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">A central tenet </ins>of <ins class="diffchange diffchange-inline">biology is the accurate flow </ins>of <ins class="diffchange diffchange-inline">information </ins>from <ins class="diffchange diffchange-inline">nucleic acids </ins>to <ins class="diffchange diffchange-inline">proteins through the genetic code</ins>. <ins class="diffchange diffchange-inline">It is commonly believed that translation deviating from </ins>the <ins class="diffchange diffchange-inline">genetic code is avoided at all times. We discovered that mammalian cells can deliberately reprogram the genetic code through tRNA misacylation upon innate immune activation </ins>and <ins class="diffchange diffchange-inline">chemically triggered oxidative stress</ins>. <ins class="diffchange diffchange-inline">The reprogramming is regulated by fluctuating levels </ins>of <ins class="diffchange diffchange-inline">reactive oxygen species (ROS) </ins>in <ins class="diffchange diffchange-inline">the cell</ins>. <ins class="diffchange diffchange-inline">We </ins>are <ins class="diffchange diffchange-inline">investigating how regulated mis-translation is </ins>used <ins class="diffchange diffchange-inline">as a mechanism for </ins>stress response.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are <del class="diffchange diffchange-inline">working on methods for folding studies of non-coding RNAs, and for structural determination using cryo-Electron Microscopy. Folding </del>during transcription <del class="diffchange diffchange-inline">is also studied </del>to understand <del class="diffchange diffchange-inline">non-coding </del>RNA folding in the cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites from bacteria to humans. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. RNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Some modifications can be removed by cellular enzymes, leading to dynamic regulation of their function. We are developing genome-wide methods and applying these to study the function of RNA modifications in cell growth, adaptation and development. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are <ins class="diffchange diffchange-inline">investigating how RNA folds </ins>during transcription to understand RNA folding in the cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=370171&oldid=prevTaopan at 22:19, 25 November 20092009-11-25T22:19:39Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>tRNA is essential for protein synthesis and life. <del class="diffchange diffchange-inline">Biological genomes </del>contain hundreds of tRNA genes. Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and cellular adaptation to new environments and to control gene expression in differentiated organisms. We developed microarray methods that measure tRNA abundance <del class="diffchange diffchange-inline">and </del>its fraction of aminoacylation at the genomic scale. We are exploring roles of tRNA in translational control in <del class="diffchange diffchange-inline">bacteria </del>and in mammalian cells including cancer.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>tRNA is essential for protein synthesis and life. <ins class="diffchange diffchange-inline">Genomes </ins>contain hundreds of tRNA genes. Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and cellular adaptation to new environments and to control gene expression in differentiated organisms. We developed microarray methods that measure tRNA abundance<ins class="diffchange diffchange-inline">, </ins>its fraction of aminoacylation <ins class="diffchange diffchange-inline">and misacylation </ins>at the genomic scale. We are exploring roles of tRNA in translational control in <ins class="diffchange diffchange-inline">yeast </ins>and in mammalian cells including cancer.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Over 100 types of post-transcriptional modifications have been identified in thousands of RNA sites from bacteria to man. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, elaborate addition of ring structures and carbohydrate moieties, and so on. RNA modification enzymes represent 1-2% of all genes in bacteria. Hundreds of guide RNAs and dozens of proteins are used to direct modifications in eukaryotic rRNAs. RNA modifications are involved in stress response, environmental adaptation, antibiotic resistance and human neurology. We developed <del class="diffchange diffchange-inline">a microarray method </del>that <del class="diffchange diffchange-inline">detects </del>and <del class="diffchange diffchange-inline">quantifies </del>changes in modification fraction <del class="diffchange diffchange-inline">at the genomic scale</del>. We are applying <del class="diffchange diffchange-inline">this </del>high throughput <del class="diffchange diffchange-inline">method </del>to study the function of RNA modifications at the genomic level during cell growth, adaptation and development. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Over 100 types of post-transcriptional modifications have been identified in thousands of RNA sites from bacteria to man. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, elaborate addition of ring structures and carbohydrate moieties, and so on. RNA modification enzymes represent 1-2% of all genes in bacteria. Hundreds of guide RNAs and dozens of proteins are used to direct modifications in eukaryotic rRNAs. RNA modifications are involved in stress response, environmental adaptation, antibiotic resistance and human neurology. We developed <ins class="diffchange diffchange-inline">genomic methods </ins>that <ins class="diffchange diffchange-inline">detect </ins>and <ins class="diffchange diffchange-inline">quantify </ins>changes in modification fraction. We are applying <ins class="diffchange diffchange-inline">these </ins>high throughput <ins class="diffchange diffchange-inline">methods </ins>to study the function of RNA modifications at the genomic level during cell growth, adaptation and development. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. <del class="diffchange diffchange-inline">Recent </del>estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are working on <del class="diffchange diffchange-inline">high throughput </del>methods for folding studies of non-coding RNAs, and for structural determination using cryo-Electron Microscopy. Folding during transcription is also studied to understand non-coding RNA folding in the cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Non-coding RNAs perform biological function without being translated into proteins. <ins class="diffchange diffchange-inline">Some </ins>estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are working on methods for folding studies of non-coding RNAs, and for structural determination using cryo-Electron Microscopy. Folding during transcription is also studied to understand non-coding RNA folding in the cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=218969&oldid=prevTaopan at 20:09, 7 July 20082008-07-07T20:09:53Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>tRNA is essential for protein synthesis and life. Biological genomes contain <del class="diffchange diffchange-inline">up to several hundred </del>tRNA genes. Translational regulation is related to the dynamic properties of <del class="diffchange diffchange-inline">each </del>tRNA that constantly change to facilitate stress response and cellular adaptation to new environments and to control gene expression in differentiated organisms. We <del class="diffchange diffchange-inline">have </del>developed <del class="diffchange diffchange-inline">tRNA microarrays </del>that measure <del class="diffchange diffchange-inline">the </del>abundance and <del class="diffchange diffchange-inline">the </del>fraction of aminoacylation <del class="diffchange diffchange-inline">of each tRNA</del>. <del class="diffchange diffchange-inline">Using these microarray technologies, we </del>are exploring <del class="diffchange diffchange-inline">the effect </del>of <del class="diffchange diffchange-inline">varying </del>tRNA <del class="diffchange diffchange-inline">concentration and aminoacylation fraction on translation </del>in bacteria and in <del class="diffchange diffchange-inline">cancer </del>cells. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>tRNA is essential for protein synthesis and life. Biological genomes contain <ins class="diffchange diffchange-inline">hundreds of </ins>tRNA genes. Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and cellular adaptation to new environments and to control gene expression in differentiated organisms. We developed <ins class="diffchange diffchange-inline">microarray methods </ins>that measure <ins class="diffchange diffchange-inline">tRNA </ins>abundance and <ins class="diffchange diffchange-inline">its </ins>fraction of aminoacylation <ins class="diffchange diffchange-inline">at the genomic scale</ins>. <ins class="diffchange diffchange-inline">We </ins>are exploring <ins class="diffchange diffchange-inline">roles </ins>of tRNA <ins class="diffchange diffchange-inline">in translational control </ins>in bacteria and in <ins class="diffchange diffchange-inline">mammalian </ins>cells <ins class="diffchange diffchange-inline">including cancer</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Over 100 <del class="diffchange diffchange-inline">chemical </del>types of post-transcriptional modifications have been identified in thousands of sites <del class="diffchange diffchange-inline">in RNAs </del>from bacteria to man. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, elaborate addition of ring structures and carbohydrate moieties, and so on. RNA modification enzymes represent 1-2% of all genes in bacteria. Hundreds of guide RNAs and dozens of proteins are used to direct modifications in eukaryotic rRNAs. RNA modifications are involved in stress response, environmental adaptation, antibiotic resistance and human neurology. We <del class="diffchange diffchange-inline">are working on </del>a <del class="diffchange diffchange-inline">general </del>microarray method that <del class="diffchange diffchange-inline">will detect </del>and <del class="diffchange diffchange-inline">quantify </del>the <del class="diffchange diffchange-inline">extent of modifications in any RNA</del>. We are applying this high throughput<del class="diffchange diffchange-inline">, microarray </del>method to study the function of RNA modifications at the genomic level during cell growth, adaptation and development. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Over 100 types of post-transcriptional modifications have been identified in thousands of <ins class="diffchange diffchange-inline">RNA </ins>sites from bacteria to man. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, elaborate addition of ring structures and carbohydrate moieties, and so on. RNA modification enzymes represent 1-2% of all genes in bacteria. Hundreds of guide RNAs and dozens of proteins are used to direct modifications in eukaryotic rRNAs. RNA modifications are involved in stress response, environmental adaptation, antibiotic resistance and human neurology. We <ins class="diffchange diffchange-inline">developed </ins>a microarray method that <ins class="diffchange diffchange-inline">detects </ins>and <ins class="diffchange diffchange-inline">quantifies changes in modification fraction at </ins>the <ins class="diffchange diffchange-inline">genomic scale</ins>. We are applying this high throughput method to study the function of RNA modifications at the genomic level during cell growth, adaptation and development. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The goals </del>of <del class="diffchange diffchange-inline">RNA folding are </del>to <del class="diffchange diffchange-inline">understand how RNA folds into defined structures and how RNA structures are stabilized</del>. We <del class="diffchange diffchange-inline">use a wide array </del>of <del class="diffchange diffchange-inline">biophysical</del>, structural <del class="diffchange diffchange-inline">and biochemical methods to elucidate the principles RNA folding and stability</del>. Folding during transcription is also studied to <del class="diffchange diffchange-inline">mimic </del>RNA folding in the cell.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Non-coding RNAs perform biological function without being translated into proteins. Recent estimates suggest that in human, the number </ins>of <ins class="diffchange diffchange-inline">non-coding RNAs may be comparable </ins>to <ins class="diffchange diffchange-inline">the number of coding RNAs</ins>. We <ins class="diffchange diffchange-inline">are working on high throughput methods for folding studies </ins>of <ins class="diffchange diffchange-inline">non-coding RNAs</ins>, <ins class="diffchange diffchange-inline">and for </ins>structural <ins class="diffchange diffchange-inline">determination using cryo-Electron Microscopy</ins>. Folding during transcription is also studied to <ins class="diffchange diffchange-inline">understand non-coding </ins>RNA folding in the cell.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=97414&oldid=prevTaopan at 17:26, 7 February 20072007-02-07T17:26:27Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Research Summary'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Research Summary'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Our research focuses on <del class="diffchange diffchange-inline">elucidating principles of RNA folding and </del>functional genomics of tRNA.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Our research focuses on functional genomics of tRNA<ins class="diffchange diffchange-inline">, RNA epigenetics and RNA folding</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The goals </del>of <del class="diffchange diffchange-inline">RNA folding studies are </del>to <del class="diffchange diffchange-inline">understand how RNA folds into defined structures </del>and to <del class="diffchange diffchange-inline">rationally design RNA structures of high stability</del>. We <del class="diffchange diffchange-inline">apply an array </del>of <del class="diffchange diffchange-inline">biophysical </del>and <del class="diffchange diffchange-inline">biochemical methods including single-molecule fluorescence spectroscopy to evaluate RNA folding </del>and <del class="diffchange diffchange-inline">stability. Folding during transcription is also studied to mimic RNA folding </del>in <del class="diffchange diffchange-inline">vivo</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">tRNA is essential for protein synthesis and life. Biological genomes contain up to several hundred tRNA genes. Translational regulation is related to the dynamic properties </ins>of <ins class="diffchange diffchange-inline">each tRNA that constantly change </ins>to <ins class="diffchange diffchange-inline">facilitate stress response </ins>and <ins class="diffchange diffchange-inline">cellular adaptation </ins>to <ins class="diffchange diffchange-inline">new environments and to control gene expression in differentiated organisms</ins>. We <ins class="diffchange diffchange-inline">have developed tRNA microarrays that measure the abundance and the fraction of aminoacylation of each tRNA. Using these microarray technologies, we are exploring the effect </ins>of <ins class="diffchange diffchange-inline">varying tRNA concentration </ins>and <ins class="diffchange diffchange-inline">aminoacylation fraction on translation in bacteria </ins>and in <ins class="diffchange diffchange-inline">cancer cells</ins>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Transfer RNA is essential for protein synthesis and life. Biological genomes contain 23 </del>- <del class="diffchange diffchange-inline">500 tRNA genes encoding 23 - 57 unique tRNA species. Translational regulation </del>of <del class="diffchange diffchange-inline">any protein is related </del>to <del class="diffchange diffchange-inline">three properties </del>of <del class="diffchange diffchange-inline">each tRNA: concentration</del>, <del class="diffchange diffchange-inline">fraction </del>of <del class="diffchange diffchange-inline">aminoacylation</del>, and <del class="diffchange diffchange-inline">post-transcriptional </del>modification. <del class="diffchange diffchange-inline">For example, highly abundant ribosomal proteins have strong codon biases that correlate with tRNA isoacceptors </del>of <del class="diffchange diffchange-inline">highest concentration</del>. <del class="diffchange diffchange-inline">Upon </del>environmental <del class="diffchange diffchange-inline">change</del>, the <del class="diffchange diffchange-inline">fraction </del>of <del class="diffchange diffchange-inline">aminoacylation can be selectively altered for each tRNA isoacceptor</del>, <del class="diffchange diffchange-inline">allowing more efficient translation </del>of <del class="diffchange diffchange-inline">regulatory proteins whose mRNAs contain unique sets of codons</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Over 100 chemical types of post</ins>-<ins class="diffchange diffchange-inline">transcriptional modifications have been identified in thousands </ins>of <ins class="diffchange diffchange-inline">sites in RNAs from bacteria </ins>to <ins class="diffchange diffchange-inline">man. They include methylation </ins>of <ins class="diffchange diffchange-inline">bases and the ribose backbone</ins>, <ins class="diffchange diffchange-inline">rotation and reduction </ins>of <ins class="diffchange diffchange-inline">uridine</ins>, <ins class="diffchange diffchange-inline">base deamination, elaborate addition of ring structures </ins>and <ins class="diffchange diffchange-inline">carbohydrate moieties, and so on. RNA </ins>modification <ins class="diffchange diffchange-inline">enzymes represent 1-2% of all genes in bacteria</ins>. <ins class="diffchange diffchange-inline">Hundreds </ins>of <ins class="diffchange diffchange-inline">guide RNAs and dozens of proteins are used to direct modifications in eukaryotic rRNAs</ins>. <ins class="diffchange diffchange-inline">RNA modifications are involved in stress response, </ins>environmental <ins class="diffchange diffchange-inline">adaptation</ins>, <ins class="diffchange diffchange-inline">antibiotic resistance and human neurology. We are working on a general microarray method that will detect and quantify </ins>the <ins class="diffchange diffchange-inline">extent </ins>of <ins class="diffchange diffchange-inline">modifications in any RNA. We are applying this high throughput</ins>, <ins class="diffchange diffchange-inline">microarray method to study the function </ins>of <ins class="diffchange diffchange-inline">RNA modifications at the genomic level during cell growth, adaptation and development</ins>. <ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">We have developed a microarray specifically tailored for tRNA. </del>The <del class="diffchange diffchange-inline">microarray allows the measurement </del>of <del class="diffchange diffchange-inline">relative concentration of each tRNA between two samples </del>and <del class="diffchange diffchange-inline">the absolute fraction </del>of <del class="diffchange diffchange-inline">aminoacylation of each tRNA in the same sample. Using this microarray</del>, <del class="diffchange diffchange-inline">we are exploring </del>the <del class="diffchange diffchange-inline">effect of varying tRNA concentration </del>and <del class="diffchange diffchange-inline">aminoacylation fraction on translation in bacteria and in cancer cells</del>. <del class="diffchange diffchange-inline">We are </del>also <del class="diffchange diffchange-inline">developing microarrays for quantitative measurements of all post-transcriptional modifications</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The <ins class="diffchange diffchange-inline">goals </ins>of <ins class="diffchange diffchange-inline">RNA folding are to understand how RNA folds into defined structures </ins>and <ins class="diffchange diffchange-inline">how RNA structures are stabilized. We use a wide array </ins>of <ins class="diffchange diffchange-inline">biophysical</ins>, <ins class="diffchange diffchange-inline">structural and biochemical methods to elucidate </ins>the <ins class="diffchange diffchange-inline">principles RNA folding </ins>and <ins class="diffchange diffchange-inline">stability</ins>. <ins class="diffchange diffchange-inline">Folding during transcription is </ins>also <ins class="diffchange diffchange-inline">studied to mimic RNA folding in the cell</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Taopanhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=97166&oldid=prevJzaborsk at 17:27, 6 February 20072007-02-06T17:27:06Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:<del class="diffchange diffchange-inline">Toapan</del>.<del class="diffchange diffchange-inline">gif</del>|left]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:<ins class="diffchange diffchange-inline">Taopan2</ins>.<ins class="diffchange diffchange-inline">jpg|275px</ins>|left]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Research Summary'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Research Summary'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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</table>Jzaborskhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=97089&oldid=prevJzaborsk at 04:10, 6 February 20072007-02-06T04:10:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><font color=#000000 size=2> </ins>[[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols<ins class="diffchange diffchange-inline">]] | [[Pan:Links|Links</ins>]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Jzaborskhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=97078&oldid=prevJzaborsk at 03:42, 6 February 20072007-02-06T03:42:18Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] <del class="diffchange diffchange-inline"> </del>[[Pan:Protocols|Protocols]] | [[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] <ins class="diffchange diffchange-inline">| </ins>[[Pan:Protocols|Protocols]] | [[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Jzaborskhttp://www.openwetware.org/index.php?title=Pan:What_we_do&diff=97075&oldid=prevJzaborsk at 03:41, 6 February 20072007-02-06T03:41:07Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>We have developed a microarray specifically tailored for tRNA. The microarray allows the measurement of relative concentration of each tRNA between two samples and the absolute fraction of aminoacylation of each tRNA in the same sample. Using this microarray, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells. We are also developing microarrays for quantitative measurements of all post-transcriptional modifications.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Pan Lab |Main]] <del class="diffchange diffchange-inline"> </del>[[Pan:What we do|What we do]] <del class="diffchange diffchange-inline"> </del>[[Pan:Who we are|Who we are]] <del class="diffchange diffchange-inline"> </del>[[Pan:Publications|Publications]] [[Pan:Protocols|Protocols]] <del class="diffchange diffchange-inline"> </del>[[Pan:Contact us|Contact us]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Pan Lab |Main]] <ins class="diffchange diffchange-inline">| </ins>[[Pan:What we do|What we do]] <ins class="diffchange diffchange-inline">| </ins>[[Pan:Who we are|Who we are]] <ins class="diffchange diffchange-inline">| </ins>[[Pan:Publications|Publications]] [[Pan:Protocols|Protocols]] <ins class="diffchange diffchange-inline">| </ins>[[Pan:Contact us|Contact us]]</div></td></tr>
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</table>Jzaborsk