https://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&feed=atom&action=historyAging in Single-celled Organisms: from Bacteria to the Whole Tree of Life/SabrinaSpencer - Revision history2024-03-29T15:24:15ZRevision history for this page on the wikiMediaWiki 1.35.6https://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5496&oldid=prevSabrinaSpencer at 04:10, February 13, 20202020-02-13T04:10:19Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:10, February 13, 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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><del class="diffchange diffchange-inline">Additional thoughts</del>: <del class="diffchange diffchange-inline"> We don</del>'<del class="diffchange diffchange-inline">t know </del>the <del class="diffchange diffchange-inline">currency </del>of <del class="diffchange diffchange-inline">aging, so we don</del>'<del class="diffchange diffchange-inline">t know if we should be measuring DNA damage</del>, <del class="diffchange diffchange-inline">telomere length</del>, <del class="diffchange diffchange-inline">protein aggregates</del>, etc. <del class="diffchange diffchange-inline"> </del>The <del class="diffchange diffchange-inline">best path forward is to measure all </del>the <del class="diffchange diffchange-inline">things we can in a single </del>cell <del class="diffchange diffchange-inline">and correlate </del>that <del class="diffchange diffchange-inline">with fitness</del>. <del class="diffchange diffchange-inline"> Measuring fitness </del>is <del class="diffchange diffchange-inline">hard</del>, <del class="diffchange diffchange-inline">so </del>instead we <del class="diffchange diffchange-inline">can use proliferation (</del>or <del class="diffchange diffchange-inline">lack thereof) as a proxy</del>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline">'''Meeting statements</ins>:'<ins class="diffchange diffchange-inline">''</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''Aging is </ins>the <ins class="diffchange diffchange-inline">cost organisms pay to have offspring that are free </ins>of <ins class="diffchange diffchange-inline">damage.'''</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''Aging is a spandrel''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># ''</ins>'<ins class="diffchange diffchange-inline">Aging is a consequence of the chemical reactions</ins>, <ins class="diffchange diffchange-inline">energy flux</ins>, <ins class="diffchange diffchange-inline">2nd law</ins>, etc. <ins class="diffchange diffchange-inline">needed for life.''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''Asymmetry is inevitable.''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''</ins>The <ins class="diffchange diffchange-inline">parent cell will be defined here as </ins>the cell that <ins class="diffchange diffchange-inline">accepts the majority of the damage</ins>.<ins class="diffchange diffchange-inline">''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''Which damaged components matter the most </ins>is <ins class="diffchange diffchange-inline">unclear (e.g. old pole protein, mitochondria, immortal strand)''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''Therefore</ins>, <ins class="diffchange diffchange-inline">there will be no universal marker for aging (more granular: damage) and what we need </ins>instead <ins class="diffchange diffchange-inline">is various functional definitions that are context dependent (when can </ins>we <ins class="diffchange diffchange-inline">project this onto fitness of vice versa)?''' </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline"># '''The major issue is that we don’t have the right data </ins>or <ins class="diffchange diffchange-inline">know what to measure? ie We don’t know the currency of aging</ins>.<ins class="diffchange diffchange-inline">'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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>
</table>SabrinaSpencerhttps://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5495&oldid=prevSabrinaSpencer at 19:32, February 12, 20202020-02-12T19:32:17Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:32, February 12, 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8" >Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>We don't know the currency of aging, so we don't know if we should be measuring DNA damage, telomere length, protein aggregates, etc. The best path forward is to measure all the things we can in a single cell and correlate that with fitness. Measuring fitness is hard, so instead we can use proliferation (or lack thereof) as a proxy.</div></td><td class='diff-marker'>+</td><td style="color: #202122; 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 class="diffchange diffchange-inline">Additional thoughts: </ins>We don't know the currency of aging, so we don't know if we should be measuring DNA damage, telomere length, protein aggregates, etc. The best path forward is to measure all the things we can in a single cell and correlate that with fitness. Measuring fitness is hard, so instead we can use proliferation (or lack thereof) as a proxy.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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>
</table>SabrinaSpencerhttps://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5493&oldid=prevSabrinaSpencer at 19:28, February 12, 20202020-02-12T19:28:21Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:28, February 12, 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>{{Attendee note</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>{{Attendee note</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;">|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; 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><del style="font-weight: bold; text-decoration: none;">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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 one thing that can currently be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates is our best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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: #202122; 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;">We don't know the currency of aging, so we don't know if we should be measuring DNA damage, telomere length, protein aggregates, etc. The best path forward is to measure all the things we can in a single cell and correlate that with fitness. Measuring fitness is hard, so instead we can use proliferation (or lack thereof) as a proxy.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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;">|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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>
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</table>SabrinaSpencerhttps://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5490&oldid=prevSabrinaSpencer at 19:21, February 12, 20202020-02-12T19:21:20Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:21, February 12, 2020</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>{{Attendee note</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>{{Attendee note</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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;">|Reference material notes=Baker DJ, Childs BG, Durik M, Wijers ME, Sieben CJ, Zhong J, Saltness RA, Jeganathan KB, Verzosa GC, Pezeshki A, Khazaie K, Miller JD, '''van Deursen JM'''. Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature. 2016 Feb 11; 530 (7589):184-9 Epub 2016 Feb 03</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; 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: #202122; 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;">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=26840489&query_hl=11&itool=pubmed_docsum</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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>SabrinaSpencerhttps://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5482&oldid=prevSabrinaSpencer at 14:38, February 12, 20202020-02-12T14:38:33Z<p></p>
<table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:38, February 12, 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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>|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>Of course, there are single-cell DNA damage markers, but as far as I know, they only mark current existing mismatches, damaged bases, single-strand or double-strand breaks etc, but not cumulative damage. <del class="diffchange diffchange-inline">Telomere </del>length and oxygen consumption rate are easily measured on a population level, but not in single cells. Tracking the immortal strand is technically difficult. For the epigenetic clock measured by DNA methylation, the conceptual link with deterioration of function is unclear. </div></td><td class='diff-marker'>+</td><td style="color: #202122; 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>Of course, there are single-cell DNA damage markers, but as far as I know, they only mark <ins class="diffchange diffchange-inline">'''</ins>current<ins class="diffchange diffchange-inline">''' </ins>existing mismatches, damaged bases, single-strand or double-strand breaks etc, but not <ins class="diffchange diffchange-inline">'''</ins>cumulative<ins class="diffchange diffchange-inline">''' </ins>damage. <ins class="diffchange diffchange-inline">The need for a cumulative/historical marker speaks to the idea Sri proposed that aging requires a cellular memory - something needs to be accumulated as cells age, otherwise cells would not know or have an age. While a snapshot of telomere length does contain a historical record, telomere </ins>length and oxygen consumption rate are easily measured on a population level, but not in single cells. <ins class="diffchange diffchange-inline">The single-cell aspect is important because while telomere length decreases with increasing passage number, Martin Picard showed that telomere length does not correlate with when a population hits its Hayflick limit. This may well be because what cells care about is the shortest telomere in a cell, not the population telomere length. </ins>Tracking the immortal strand is technically difficult. For the epigenetic clock measured by DNA methylation, the conceptual link with deterioration of function is unclear. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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>Then there's the ability to return to homeostasis as a general definition of aging, but how to measure that is <del class="diffchange diffchange-inline">completely </del>unclear <del class="diffchange diffchange-inline">to me</del>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; 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>Then there's the ability to return to homeostasis as a general definition of aging, but how to measure that is unclear.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; 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: #202122; 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: #202122; 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 one thing that can be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates <del class="diffchange diffchange-inline">are </del>best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons</div></td><td class='diff-marker'>+</td><td style="color: #202122; 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 one thing that can <ins class="diffchange diffchange-inline">currently </ins>be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates <ins class="diffchange diffchange-inline">is our </ins>best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
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</table>SabrinaSpencerhttps://centre.santafe.edu/complextime/w/index.php?title=Aging_in_Single-celled_Organisms:_from_Bacteria_to_the_Whole_Tree_of_Life/SabrinaSpencer&diff=5480&oldid=prevSabrinaSpencer: Created page with "{{Attendee note |Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of func..."2020-02-12T00:08:31Z<p>Created page with "{{Attendee note |Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of func..."</p>
<p><b>New page</b></p><div>{{Attendee note<br />
|Post-meeting summary=What is holding back the field of aging? First is a definition of aging, which we have generally agreed represents deterioration of function. Second then, is how to measure deterioration of function. We lack good markers for most relevant items at the single-cell level: 1. Cumulative DNA damage, 2. Telomere length, 3. Oxygen consumption rate, 4. Presence of original or newly replicated DNA strand. 5. epigenetic clock measured by DNA methylation.<br />
<br />
Of course, there are single-cell DNA damage markers, but as far as I know, they only mark current existing mismatches, damaged bases, single-strand or double-strand breaks etc, but not cumulative damage. Telomere length and oxygen consumption rate are easily measured on a population level, but not in single cells. Tracking the immortal strand is technically difficult. For the epigenetic clock measured by DNA methylation, the conceptual link with deterioration of function is unclear. <br />
<br />
Then there's the ability to return to homeostasis as a general definition of aging, but how to measure that is completely unclear to me.<br />
<br />
The one thing that can be measured in single cells both in a snapshot and over time is protein aggregation. Lin Chao measures this with IBPA-GFP. Maybe measuring protein aggregates are best bet since that is measurable and since it has been shown to cause dysfunction, particularly in neurons<br />
}}</div>SabrinaSpencer