https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&feed=atom&action=historyCommunityW303.html - Revision history2024-03-29T09:47:35ZRevision history for this page on the wikiMediaWiki 1.31.14https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400156&oldid=prevSba479 at 17:03, 11 June 20182018-06-11T17:03:22Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The original W303 strain is mutated in ''RAD5'' ([<del class="diffchange diffchange-inline">http</del>://www.yeastgenome.org/<del class="diffchange diffchange-inline">cgi-bin</del>/<del class="diffchange diffchange-inline">locus.fpl?locus=rad5 </del>''RAD5''], an G to R change at position 535 (''rad5-G535R'') - See [http://www.yeastgenome.org/reference/S000051944 Fan HY. ''et al.'' (1996)], Genetics 142:749-759. Two homologs of Rad5 have been identified in human cells, the [http://en.wikipedia.org/wiki/HLTF HLTF] and [https://en.wikipedia.org/wiki/SHPRH SHPRH] proteins, showing 39% and 21% similarities to Rad5, [http://www.ncbi.nlm.nih.gov/pubmed/20096653 Unk I., ''et al.'' (2010)]).</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The original W303 strain is mutated in ''RAD5'' ([<ins class="diffchange diffchange-inline">https</ins>://www.yeastgenome.org/<ins class="diffchange diffchange-inline">locus</ins>/<ins class="diffchange diffchange-inline">S000004022 </ins>''RAD5''], an G to R change at position 535 (''rad5-G535R'') - See [http://www.yeastgenome.org/reference/S000051944 Fan HY. ''et al.'' (1996)], Genetics 142:749-759. Two homologs of Rad5 have been identified in human cells, the [http://en.wikipedia.org/wiki/HLTF HLTF] and [https://en.wikipedia.org/wiki/SHPRH SHPRH] proteins, showing 39% and 21% similarities to Rad5, [http://www.ncbi.nlm.nih.gov/pubmed/20096653 Unk I., ''et al.'' (2010)]).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The change is subtle resulting in a phenotype in combination with ''soh1'' (Hannah Klein in the Fan paper), ''sir'' mutations--increased MMS resistance (David Sinclair, unpublished) and no effect on recombination, UV or X-ray sensitivities (Rothstein lab, unpublished).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The change is subtle resulting in a phenotype in combination with ''soh1'' (Hannah Klein in the Fan paper), ''sir'' mutations--increased MMS resistance (David Sinclair, unpublished) and no effect on recombination, UV or X-ray sensitivities (Rothstein lab, unpublished).</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400155&oldid=prevSba479 at 18:53, 30 May 20182018-05-30T18:53:39Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:53, 30 May 2018</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l19" >Line 19:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The ''rad5-G535R'' missense mutation does not cause any growth defect or gamma-ray sensitive phenotype. However, ''rad5-G535R'' strains displayed increased sensitivity to UV light at high doses when compared to wild-type strains, and ''rad52 rad5-G535R'' double mutants were more sensitive to UV light when compared to ''RAD52 rad5-G535R'' and ''rad52 RAD5'' single mutants. Levels of direct repeat recombination were not affected by the ''rad-G535R'' allele in ''rad1'', ''rad52'' or ''rfa1-D288Y'' backgrounds. The efficiency of plasmid gap repair (outline of the system: [https://www.yeastgenome.org/reference/S000049982 Bärtsch S. ''et al''  (2000)], Mol. Cell. Biol. Feb.; 20(4): 1194-1205) was not significantly affected by the ''rad5-G535R'' allele. Also, the ''rad5-G535R'' allele had no effect on the proportion of crossover and non-crossover events independent of whether the DNA donor for gap repair was of chromosomal or plasmid origin. These unpublished findings support the hypothesis that the weak DNA repair phenotype conferred by the ''rad5-G535R'' mutation is caused indirectly through interaction either with proteins of the transcription machinery ([https://www.yeastgenome.org/reference/S000071643 Kiakos K. ''et al'' (2002)] suggest as a possibility a role of Rad5 in facilitating transcription-coupled DNA repair, [http://en.wikipedia.org/wiki/Transcription-coupled_repair TCR], of DNA minor groove adducts) or with chromatin but not by direct involvement in recombination (Stephan Bärtsch and Naz Erdeniz, April 2000, unpublished; in July, 2000, [https://www.yeastgenome.org/reference/S000042429 Ulrich HD, and Jentsch S., (2000)] conclude that the Ubc13–Mms2 complex is recruited to the chromatin by Rad5 upon its accumulation in the nucleus in response to DNA damage).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* The ''rad5-G535R'' missense mutation does not cause any growth defect or gamma-ray sensitive phenotype. However, ''rad5-G535R'' strains displayed increased sensitivity to UV light at high doses when compared to wild-type strains, and ''rad52 rad5-G535R'' double mutants were more sensitive to UV light when compared to ''RAD52 rad5-G535R'' and ''rad52 RAD5'' single mutants. Levels of direct repeat recombination were not affected by the ''rad-G535R'' allele in ''rad1'', ''rad52'' or ''rfa1-D288Y'' backgrounds. The efficiency of plasmid gap repair (outline of the system: [https://www.yeastgenome.org/reference/S000049982 Bärtsch S. ''et al''  (2000)], Mol. Cell. Biol. Feb.; 20(4): 1194-1205) was not significantly affected by the ''rad5-G535R'' allele. Also, the ''rad5-G535R'' allele had no effect on the proportion of crossover and non-crossover events independent of whether the DNA donor for gap repair was of chromosomal or plasmid origin. These unpublished findings support the hypothesis that the weak DNA repair phenotype conferred by the ''rad5-G535R'' mutation is caused indirectly through interaction either with proteins of the transcription machinery ([https://www.yeastgenome.org/reference/S000071643 Kiakos K. ''et al'' (2002)] suggest as a possibility a role of Rad5 in facilitating transcription-coupled DNA repair, [http://en.wikipedia.org/wiki/Transcription-coupled_repair TCR], of DNA minor groove adducts) or with chromatin but not by direct involvement in recombination (Stephan Bärtsch and Naz Erdeniz, April 2000, unpublished; in July, 2000, [https://www.yeastgenome.org/reference/S000042429 Ulrich HD, and Jentsch S., (2000)] conclude that the Ubc13–Mms2 complex is recruited to the chromatin by Rad5 upon its accumulation in the nucleus in response to DNA damage).</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* Spore analysis of meiosis products showed a synthetic growth defect between ''rad5Δ and rad52Δ'' or ''rad5-G535R'' and ''rad52Δ'' in ''TLC1'' cells that was exacerbated in tlc1Δ cells. The authors concluded that Rad5 and Rad52 act in at least partially non-overlapping pathways to maintain the viability of telomerase negative cells ([https://www.ncbi.nlm.nih.gov/pubmed/24393774 Fallet E. ''et al.'' (2014)])</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Probably due to the ''rad5-G535R'' missense mutation in the W303 background strains, the sensitivity of the ''mrc1Δ'' mutant ([http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=mrc1 Mrc1] plays a role in mediating the DNA replication checkpoint, [https://www.yeastgenome.org/reference/S000073790 Osborn AJ, and Elledge SJ (2003)]  to 200 mM HU observed by [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] (viability about 80%) differed from that reported previously by [https://www.yeastgenome.org/reference/S000068879 Alcasabas AA. ''et al.'' (2001)] (viability about 30%). All strains constructed in the [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] study were derived from ''RAD5'' strain BY4741 (MKY0027 ''MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 mrc1Δ::LEU2'', [https://www.yeastgenome.org/reference/S000073860 Katou Y., ''et al.'' (2003)]). The ''mrc1-1'' Y1121 strain used by Alcasabas AA. ''et al.'' is isogenic with the W303-derived Y300 strain (''MATa trp1-1 ura3-1 his3- 11,15, leu2-3,112 ade2-1 can1-100'', [https://www.yeastgenome.org/reference/S000051282 Allen JB. ''et al.'' (1994)])</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Probably due to the ''rad5-G535R'' missense mutation in the W303 background strains, the sensitivity of the ''mrc1Δ'' mutant ([http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=mrc1 Mrc1] plays a role in mediating the DNA replication checkpoint, [https://www.yeastgenome.org/reference/S000073790 Osborn AJ, and Elledge SJ (2003)]  to 200 mM HU observed by [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] (viability about 80%) differed from that reported previously by [https://www.yeastgenome.org/reference/S000068879 Alcasabas AA. ''et al.'' (2001)] (viability about 30%). All strains constructed in the [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] study were derived from ''RAD5'' strain BY4741 (MKY0027 ''MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 mrc1Δ::LEU2'', [https://www.yeastgenome.org/reference/S000073860 Katou Y., ''et al.'' (2003)]). The ''mrc1-1'' Y1121 strain used by Alcasabas AA. ''et al.'' is isogenic with the W303-derived Y300 strain (''MATa trp1-1 ura3-1 his3- 11,15, leu2-3,112 ade2-1 can1-100'', [https://www.yeastgenome.org/reference/S000051282 Allen JB. ''et al.'' (1994)])</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400154&oldid=prevSba479 at 17:47, 23 May 20182018-05-23T17:47:43Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:47, 23 May 2018</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22" >Line 22:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Probably due to the ''rad5-G535R'' missense mutation in the W303 background strains, the sensitivity of the ''mrc1Δ'' mutant ([http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=mrc1 Mrc1] plays a role in mediating the DNA replication checkpoint, [https://www.yeastgenome.org/reference/S000073790 Osborn AJ, and Elledge SJ (2003)]  to 200 mM HU observed by [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] (viability about 80%) differed from that reported previously by [https://www.yeastgenome.org/reference/S000068879 Alcasabas AA. ''et al.'' (2001)] (viability about 30%). All strains constructed in the [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] study were derived from ''RAD5'' strain BY4741 (MKY0027 ''MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 mrc1Δ::LEU2'', [https://www.yeastgenome.org/reference/S000073860 Katou Y., ''et al.'' (2003)]). The ''mrc1-1'' Y1121 strain used by Alcasabas AA. ''et al.'' is isogenic with the W303-derived Y300 strain (''MATa trp1-1 ura3-1 his3- 11,15, leu2-3,112 ade2-1 can1-100'', [https://www.yeastgenome.org/reference/S000051282 Allen JB. ''et al.'' (1994)])</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Probably due to the ''rad5-G535R'' missense mutation in the W303 background strains, the sensitivity of the ''mrc1Δ'' mutant ([http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=mrc1 Mrc1] plays a role in mediating the DNA replication checkpoint, [https://www.yeastgenome.org/reference/S000073790 Osborn AJ, and Elledge SJ (2003)]  to 200 mM HU observed by [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] (viability about 80%) differed from that reported previously by [https://www.yeastgenome.org/reference/S000068879 Alcasabas AA. ''et al.'' (2001)] (viability about 30%). All strains constructed in the [https://www.yeastgenome.org/reference/S000134925 Komata M. ''et al.'' (2009)] study were derived from ''RAD5'' strain BY4741 (MKY0027 ''MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 mrc1Δ::LEU2'', [https://www.yeastgenome.org/reference/S000073860 Katou Y., ''et al.'' (2003)]). The ''mrc1-1'' Y1121 strain used by Alcasabas AA. ''et al.'' is isogenic with the W303-derived Y300 strain (''MATa trp1-1 ura3-1 his3- 11,15, leu2-3,112 ade2-1 can1-100'', [https://www.yeastgenome.org/reference/S000051282 Allen JB. ''et al.'' (1994)])</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* Diploid W303-based strains that harbor the ''rad5-535'' allele have a much higher rate of ''MET15'' (standard name [http://www.yeastgenome.org/locus/S000004294/overview ''MET17'']) loss of heterozygosity (LOH, brown colored sectors within a colony on lead nitrate plates) than other backgrounds, such as ''RAD5'' BY derivatives, and presumably than ''RAD5'' W303 derivatives. Not surprisingly, they also have a much higher level of extrachromosomal rDNA circles ([http://research.fhcrc.org/gottschling/en/protocols/yeast-protocols/lab-lore.html Lab Lore]; Dan Gottschling, personal communication, and Michael McMurray, unpublishd results; Stephan Bärtsch, in August 2012). In regard to the ''MET15'' locus, the Jef Boeke lab noticed a phenomenon occurring at the locus: frequent loss of heterozygosity (LOH). ''MET15'' is distal to the [<del class="diffchange diffchange-inline">http</del>://www.yeastgenome.org/<del class="diffchange diffchange-inline">cgi-bin</del>/<del class="diffchange diffchange-inline">locus.fpl?locus=rdn1 </del>''RDN1''] multigene locus on chromosome XII. When the rDNA repeats recombine mitotically, as they are prone to do, heterozygosity can be lost (e.g. mitotic unequal crossing-over). Preliminary estimates are approximately a 3% frequency of LOH ([http://www.bs.jhmi.edu/MBG/boekelab/Resources/Met15/Met15updt.html Met15 Update], Carla Connelly and Jef D. Boeke, unpublished observation, and personal communication; Stephan Bärtsch, in August 2013).</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* Diploid W303-based strains that harbor the ''rad5-535'' allele have a much higher rate of ''MET15'' (standard name [http://www.yeastgenome.org/locus/S000004294/overview ''MET17'']) loss of heterozygosity (LOH, brown colored sectors within a colony on lead nitrate plates) than other backgrounds, such as ''RAD5'' BY derivatives, and presumably than ''RAD5'' W303 derivatives. Not surprisingly, they also have a much higher level of extrachromosomal rDNA circles ([http://research.fhcrc.org/gottschling/en/protocols/yeast-protocols/lab-lore.html Lab Lore]; Dan Gottschling, personal communication, and Michael McMurray, unpublishd results; Stephan Bärtsch, in August 2012). In regard to the ''MET15'' locus, the Jef Boeke lab noticed a phenomenon occurring at the locus: frequent loss of heterozygosity (LOH). ''MET15'' is distal to the [<ins class="diffchange diffchange-inline">https</ins>://www.yeastgenome.org/<ins class="diffchange diffchange-inline">locus</ins>/<ins class="diffchange diffchange-inline">S000029411 </ins>''RDN1''] multigene locus on chromosome XII. When the rDNA repeats recombine mitotically, as they are prone to do, heterozygosity can be lost (e.g. mitotic unequal crossing-over). Preliminary estimates are approximately a 3% frequency of LOH ([http://www.bs.jhmi.edu/MBG/boekelab/Resources/Met15/Met15updt.html Met15 Update], Carla Connelly and Jef D. Boeke, unpublished observation, and personal communication; Stephan Bärtsch, in August 2013).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* A ''rad5-G535R'' strain did not show detectable chronic low dose ultraviolet light (CLUV) sensitivity, whereas the ATPase-deficient ''rad5-K538A'' mutant showed a CLUV hypersensitivity similar to that observed in a ''rad5'' deletion mutant ([https://www.yeastgenome.org/reference/S000128822 Hishida T. ''et al.'' (2008)], Nature 457 (7229): 612-615; Hishida T., personal communication; Stephan Bärtsch, in December 2008). The ''rad5-KT538/539AA''  (also known as '' rad5-GAA'' ) mutant was partially sensitive to UV irradiation and its ionizing radiation sensitivity was comparable to that of a ''rad5'' deletion strain ([https://www.yeastgenome.org/reference/S000086919 Chen S. ''et al.'' (2005)], Nucleic Acids Res.;33(18):5878-5886). Substitutions at position 535 from G to R, at position 538 from K to A, and at position 539 from T to A are predicted by [http://sift.bii.a-star.edu.sg/ SIFT] to affect protein function with a score of 0.00 (?); amino acids with probabilities < 0.05 are predicted to be deleterious. With an alternative, [http://provean.jcvi.org/index.php PROVEAN], the variant G535R results in a PROVEAN score of -7.850 (?); variants with a score equal to or below -2.5 are considered deleterious. [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] report for Rad5-G535R: This mutation is predicted to be probably damaging with a score of 1.000 (?) (sensitivity: 0.00; specificity: 1.00).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* A ''rad5-G535R'' strain did not show detectable chronic low dose ultraviolet light (CLUV) sensitivity, whereas the ATPase-deficient ''rad5-K538A'' mutant showed a CLUV hypersensitivity similar to that observed in a ''rad5'' deletion mutant ([https://www.yeastgenome.org/reference/S000128822 Hishida T. ''et al.'' (2008)], Nature 457 (7229): 612-615; Hishida T., personal communication; Stephan Bärtsch, in December 2008). The ''rad5-KT538/539AA''  (also known as '' rad5-GAA'' ) mutant was partially sensitive to UV irradiation and its ionizing radiation sensitivity was comparable to that of a ''rad5'' deletion strain ([https://www.yeastgenome.org/reference/S000086919 Chen S. ''et al.'' (2005)], Nucleic Acids Res.;33(18):5878-5886). Substitutions at position 535 from G to R, at position 538 from K to A, and at position 539 from T to A are predicted by [http://sift.bii.a-star.edu.sg/ SIFT] to affect protein function with a score of 0.00 (?); amino acids with probabilities < 0.05 are predicted to be deleterious. With an alternative, [http://provean.jcvi.org/index.php PROVEAN], the variant G535R results in a PROVEAN score of -7.850 (?); variants with a score equal to or below -2.5 are considered deleterious. [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] report for Rad5-G535R: This mutation is predicted to be probably damaging with a score of 1.000 (?) (sensitivity: 0.00; specificity: 1.00).</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400028&oldid=prevSba479 at 15:35, 18 April 20182018-04-18T15:35:21Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Kindly provided at SGD's request by Rodney Rothstein on March 10, 2005.''</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Kindly provided at SGD's request by Rodney Rothstein on March 10, 2005.''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>''Last additional information provided by Stephan Bärtsch on <del class="diffchange diffchange-inline">October 11</del>, <del class="diffchange diffchange-inline">2017</del>.''</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>''Last additional information provided by Stephan Bärtsch on <ins class="diffchange diffchange-inline">April 16</ins>, <ins class="diffchange diffchange-inline">2018</ins>.''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Choose your yeast strain carefully: the RAD5 gene matters [http://www.nature.com/articles/s41580-018-0005-2 Elserafy M. and El-Khamisy SF. (2018)], Nat Rev Mol Cell Biol. 2018 Apr 3. doi: 10.1038/s41580-018-0005-2. [Epub ahead of print]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Choose your yeast strain carefully: the RAD5 gene matters [http://www.nature.com/articles/s41580-018-0005-2 Elserafy M. and El-Khamisy SF. (2018)], Nat Rev Mol Cell Biol. 2018 Apr 3. doi: 10.1038/s41580-018-0005-2. [Epub ahead of print]</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400027&oldid=prevSba479 at 19:09, 16 April 20182018-04-16T19:09:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Rothstein R (2005) Information regarding the provenance of Saccharomyces  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Rothstein R (2005) Information regarding the provenance of Saccharomyces  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>cerevisiae strain W303 (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>cerevisiae strain W303 (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''<ins class="diffchange diffchange-inline"><</ins>Date accessed<ins class="diffchange diffchange-inline">></ins>'')  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Bärtsch S (2018) Biological effects of the yeast W303 ''rad5-G535R'' mutation (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Bärtsch S (2018) Biological effects of the yeast W303 ''rad5-G535R'' mutation (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''<ins class="diffchange diffchange-inline"><</ins>Date accessed<ins class="diffchange diffchange-inline">></ins>'')</div></td></tr>
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</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400026&oldid=prevSba479 at 14:13, 14 April 20182018-04-14T14:13:28Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>cerevisiae strain W303 (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>cerevisiae strain W303 (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Bärtsch S (<del class="diffchange diffchange-inline">2008</del>) Biological effects of the yeast W303 ''rad5-G535R'' mutation (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Bärtsch S (<ins class="diffchange diffchange-inline">2018</ins>) Biological effects of the yeast W303 ''rad5-G535R'' mutation (online) Available at: http://wiki.yeastgenome.org/index.php/CommunityW303.html (Accessed ''Date accessed'')</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
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</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=400025&oldid=prevSba479: /* Information regarding the Saccharomyces cerevisiae strain W303 */2018-04-14T13:44:18Z<p><span dir="auto"><span class="autocomment">Information regarding the Saccharomyces cerevisiae strain W303</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 13:44, 14 April 2018</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Last additional information provided by Stephan Bärtsch on October 11, 2017.''</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Last additional information provided by Stephan Bärtsch on October 11, 2017.''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Choose your yeast strain carefully: the RAD5 gene matters [http://www.nature.com/articles/s41580-018-0005-2 Elserafy M. and El-Khamisy SF. (2018)], Nat Rev Mol Cell Biol. 2018 Apr 3. doi: 10.1038/s41580-018-0005-2. [Epub ahead of print]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Suggested citation for this website:</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Suggested citation for this website:</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=399928&oldid=prevSba479 at 15:44, 20 October 20172017-10-20T15:44:08Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:44, 20 October 2017</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l33" >Line 33:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** In ''rad5-535''<nowiki>: 155 bp, 120 bp and 62 bp.</nowiki></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** In ''rad5-535''<nowiki>: 155 bp, 120 bp and 62 bp.</nowiki></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The ''RAD5'' wild type derivatives of W303 are W1588. [http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=RAD5&submit=Submit&rm=display_result ''RAD5/YLR032W S. cerevisiae'' Strain Sequence Alignment]  ([http://www.ncbi.nlm.nih.gov/pubmed/23487186, Annotation of multiple ''Saccharomyces cerevisiae'' strains at the Saccharomyces Genome Database], Engel SR, and Cherry JM., Database, Vol. 2013, Article ID bat012) [[File:Rad5_aa_yeast_strain_SeqAlign-tiff.jpg|thumb|alt=Rad5.|ClustalW ''S. cerevisiae'' strain amino acid sequence alignments covering W303 ''rad5-G535R'' region.]]  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The ''RAD5'' wild type derivatives of W303 are W1588. [http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=RAD5&submit=Submit&rm=display_result ''RAD5/YLR032W S. cerevisiae'' Strain Sequence Alignment]  ([http://www.ncbi.nlm.nih.gov/pubmed/23487186, Annotation of multiple ''Saccharomyces cerevisiae'' strains at the Saccharomyces Genome Database], Engel SR, and Cherry JM., Database, Vol. 2013, Article ID bat012) [[File:Rad5_aa_yeast_strain_SeqAlign-tiff.jpg|thumb|alt=Rad5.|ClustalW ''S. cerevisiae'' strain amino acid sequence alignments covering W303 ''rad5-G535R'' region.]]  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499129/ Matheson K. ''et al.''  (2017)] provide with a Whole-Genome Sequence and Variant Analysis of W303 high-quality, annotated genome sequences for comparative analyses and genome-wide studies. Interestingly, as they and R. Rothstein (personal communication with the authors) report, W303 was selected to have a higher sporulation efficiency than S288C (Gerke et al. 2006; <del class="diffchange diffchange-inline">(</del>Hong et al. 2008)  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499129/ Matheson K. ''et al.''  (2017)] provide with a Whole-Genome Sequence and Variant Analysis of W303 high-quality, annotated genome sequences for comparative analyses and genome-wide studies. Interestingly, as they and R. Rothstein (personal communication with the authors) report, W303 was selected<ins class="diffchange diffchange-inline">, besides to have a high transformation efficiency, </ins>to have a higher sporulation efficiency than S288C (Gerke et al. 2006; Hong et al. 2008)<ins class="diffchange diffchange-inline">. </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Some relevant information for W303: ===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Some relevant information for W303: ===</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=399927&oldid=prevSba479 at 15:15, 20 October 20172017-10-20T15:15:57Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:15, 20 October 2017</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l33" >Line 33:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** In ''rad5-535''<nowiki>: 155 bp, 120 bp and 62 bp.</nowiki></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** In ''rad5-535''<nowiki>: 155 bp, 120 bp and 62 bp.</nowiki></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The ''RAD5'' wild type derivatives of W303 are W1588. [http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=RAD5&submit=Submit&rm=display_result ''RAD5/YLR032W S. cerevisiae'' Strain Sequence Alignment]  ([http://www.ncbi.nlm.nih.gov/pubmed/23487186, Annotation of multiple ''Saccharomyces cerevisiae'' strains at the Saccharomyces Genome Database], Engel SR, and Cherry JM., Database, Vol. 2013, Article ID bat012) [[File:Rad5_aa_yeast_strain_SeqAlign-tiff.jpg|thumb|alt=Rad5.|ClustalW ''S. cerevisiae'' strain amino acid sequence alignments covering W303 ''rad5-G535R'' region.]]  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The ''RAD5'' wild type derivatives of W303 are W1588. [http://www.yeastgenome.org/cgi-bin/FUNGI/alignment.pl?locus=RAD5&submit=Submit&rm=display_result ''RAD5/YLR032W S. cerevisiae'' Strain Sequence Alignment]  ([http://www.ncbi.nlm.nih.gov/pubmed/23487186, Annotation of multiple ''Saccharomyces cerevisiae'' strains at the Saccharomyces Genome Database], Engel SR, and Cherry JM., Database, Vol. 2013, Article ID bat012) [[File:Rad5_aa_yeast_strain_SeqAlign-tiff.jpg|thumb|alt=Rad5.|ClustalW ''S. cerevisiae'' strain amino acid sequence alignments covering W303 ''rad5-G535R'' region.]]  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499129/ Matheson K. ''et al.''  (2017)] provide with a Whole-Genome Sequence and Variant Analysis of W303 high-quality, annotated genome sequences for comparative analyses and genome-wide studies.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>** [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499129/ Matheson K. ''et al.''  (2017)] provide with a Whole-Genome Sequence and Variant Analysis of W303 high-quality, annotated genome sequences for comparative analyses and genome-wide studies. <ins class="diffchange diffchange-inline">Interestingly, as they and R. Rothstein (personal communication with the authors) report, W303 was selected to have a higher sporulation efficiency than S288C (Gerke et al. 2006; (Hong et al. 2008) </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Some relevant information for W303: ===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Some relevant information for W303: ===</div></td></tr>
</table>Sba479https://wiki.yeastgenome.org/index.php?title=CommunityW303.html&diff=399926&oldid=prevSba479 at 18:02, 15 October 20172017-10-15T18:02:16Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:02, 15 October 2017</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l23" >Line 23:</td>
<td colspan="2" class="diff-lineno">Line 23:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Diploid W303-based strains that harbor the ''rad5-535'' allele have a much higher rate of ''MET15'' (standard name [http://www.yeastgenome.org/locus/S000004294/overview ''MET17'']) loss of heterozygosity (LOH, brown colored sectors within a colony on lead nitrate plates) than other backgrounds, such as ''RAD5'' BY derivatives, and presumably than ''RAD5'' W303 derivatives. Not surprisingly, they also have a much higher level of extrachromosomal rDNA circles ([http://research.fhcrc.org/gottschling/en/protocols/yeast-protocols/lab-lore.html Lab Lore]; Dan Gottschling, personal communication, and Michael McMurray, unpublishd results; Stephan Bärtsch, in August 2012). In regard to the ''MET15'' locus, the Jef Boeke lab noticed a phenomenon occurring at the locus: frequent loss of heterozygosity (LOH). ''MET15'' is distal to the [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=rdn1 ''RDN1''] multigene locus on chromosome XII. When the rDNA repeats recombine mitotically, as they are prone to do, heterozygosity can be lost (e.g. mitotic unequal crossing-over). Preliminary estimates are approximately a 3% frequency of LOH ([http://www.bs.jhmi.edu/MBG/boekelab/Resources/Met15/Met15updt.html Met15 Update], Carla Connelly and Jef D. Boeke, unpublished observation, and personal communication; Stephan Bärtsch, in August 2013).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Diploid W303-based strains that harbor the ''rad5-535'' allele have a much higher rate of ''MET15'' (standard name [http://www.yeastgenome.org/locus/S000004294/overview ''MET17'']) loss of heterozygosity (LOH, brown colored sectors within a colony on lead nitrate plates) than other backgrounds, such as ''RAD5'' BY derivatives, and presumably than ''RAD5'' W303 derivatives. Not surprisingly, they also have a much higher level of extrachromosomal rDNA circles ([http://research.fhcrc.org/gottschling/en/protocols/yeast-protocols/lab-lore.html Lab Lore]; Dan Gottschling, personal communication, and Michael McMurray, unpublishd results; Stephan Bärtsch, in August 2012). In regard to the ''MET15'' locus, the Jef Boeke lab noticed a phenomenon occurring at the locus: frequent loss of heterozygosity (LOH). ''MET15'' is distal to the [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=rdn1 ''RDN1''] multigene locus on chromosome XII. When the rDNA repeats recombine mitotically, as they are prone to do, heterozygosity can be lost (e.g. mitotic unequal crossing-over). Preliminary estimates are approximately a 3% frequency of LOH ([http://www.bs.jhmi.edu/MBG/boekelab/Resources/Met15/Met15updt.html Met15 Update], Carla Connelly and Jef D. Boeke, unpublished observation, and personal communication; Stephan Bärtsch, in August 2013).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* A ''rad5-G535R'' strain did not show detectable chronic low dose ultraviolet light (CLUV) sensitivity, whereas the ATPase-deficient ''rad5-K538A'' mutant showed a CLUV hypersensitivity similar to that observed in a ''rad5'' deletion mutant ([https://www.yeastgenome.org/reference/S000128822 Hishida T. ''et al.'' (2008)], Nature 457 (7229): 612-615; Hishida T., personal communication; Stephan Bärtsch, in December 2008). The ''rad5-KT538/539AA''  (also known as '' rad5-GAA'' ) mutant was partially sensitive to UV irradiation and its ionizing radiation sensitivity was comparable to that of a ''rad5'' deletion strain ([https://www.yeastgenome.org/reference/S000086919 Chen S. ''et al.'' (2005)], Nucleic Acids Res.;33(18):5878-5886). Substitutions at position 535 from G to R, at position 538 from K to A, and at position 539 from T to A are predicted by [http://sift.bii.a-star.edu.sg/ SIFT] to affect protein function with a score of 0.00 (?); amino acids with probabilities < 0.05 are predicted to be deleterious. With an alternative [http://provean.jcvi.org/index.php PROVEAN], the variant G535R results in a PROVEAN score of -7.850 (?); variants with a score equal to or below -2.5 are considered deleterious<del class="diffchange diffchange-inline">) </del>. [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] report for Rad5-G535R: This mutation is predicted to be probably damaging with a score of 1.000 (?) (sensitivity: 0.00; specificity: 1.00).</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* A ''rad5-G535R'' strain did not show detectable chronic low dose ultraviolet light (CLUV) sensitivity, whereas the ATPase-deficient ''rad5-K538A'' mutant showed a CLUV hypersensitivity similar to that observed in a ''rad5'' deletion mutant ([https://www.yeastgenome.org/reference/S000128822 Hishida T. ''et al.'' (2008)], Nature 457 (7229): 612-615; Hishida T., personal communication; Stephan Bärtsch, in December 2008). The ''rad5-KT538/539AA''  (also known as '' rad5-GAA'' ) mutant was partially sensitive to UV irradiation and its ionizing radiation sensitivity was comparable to that of a ''rad5'' deletion strain ([https://www.yeastgenome.org/reference/S000086919 Chen S. ''et al.'' (2005)], Nucleic Acids Res.;33(18):5878-5886). Substitutions at position 535 from G to R, at position 538 from K to A, and at position 539 from T to A are predicted by [http://sift.bii.a-star.edu.sg/ SIFT] to affect protein function with a score of 0.00 (?); amino acids with probabilities < 0.05 are predicted to be deleterious. With an alternative<ins class="diffchange diffchange-inline">, </ins>[http://provean.jcvi.org/index.php PROVEAN], the variant G535R results in a PROVEAN score of -7.850 (?); variants with a score equal to or below -2.5 are considered deleterious. [http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2] report for Rad5-G535R: This mutation is predicted to be probably damaging with a score of 1.000 (?) (sensitivity: 0.00; specificity: 1.00).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* To assay for its presence in any W303 derivative strain, one can do a PCR and digest the products with ''Mnl''I, as the mutation creates a ''Mnl''I site.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* To assay for its presence in any W303 derivative strain, one can do a PCR and digest the products with ''Mnl''I, as the mutation creates a ''Mnl''I site.</div></td></tr>
</table>Sba479