--- Log opened Sun Jun 30 00:00:39 2024
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09:53 < geneh2> just a reminder, STEP-NC exists https://en.wikipedia.org/wiki/STEP-NC
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16:34 < hprmbridge> kanzure> "Comparative prospects of imaging methods for whole-brain mammalian connectomics" https://arxiv.org/abs/2405.10488v1
16:34 < hprmbridge> kanzure> https://logancollinsblog.com/
16:37 < hprmbridge> kanzure> "The case for emulating insect brains using anatomical “wiring diagrams” equipped with biophysical models of neuronal activity" https://link.springer.com/article/10.1007/s00422-019-00810-z
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17:03 < docl> I wonder if gluteraldehyde fixation reversal mechanisms could be lab evolved in bacteria somehow
17:04 < hprmbridge> kanzure> id imagine a membrane defense first
17:04 < hprmbridge> kanzure> you'd have to inject with microinjection
17:06 < docl> maybe every time it evolves a membrane defense you catalogue that as a thing to select out
17:06 < docl> also every time it evolves a rapid breakdown mechanism
17:07 < hprmbridge> kanzure> I think you would just be selecting for those weird bacteria with the weird lifecycle dessication states or something
17:07 < hprmbridge> kanzure> forgot the name of this
17:17 < docl> extremophiles?
17:19 < docl> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262776/ // Tolerance to Glutaraldehyde in Escherichia coli Mediated by Overexpression of the Aldehyde Reductase YqhD by YqhC
17:20 < docl> what we probably don't want to select for in this context, we want the bacteria to consistently have some of the crosslinking happen and impair fitness
17:24 < docl> also we want mechanisms to clear it off of cytostructures and chromatin so maybe yeast instead of e coli
17:37 < docl> yeast that can shrug off glutaraldehyde would be kind of dangerous, given how it is used as a broad spectrum biocide. useful if you could translate the mechanism to human cells though
17:38 < docl> (if it achieves fixation reversal for enough biostructures to restore viability, I mean)
18:04 < docl> hmm. it seems like there is a bootstrapping problem. if you have a cell capable of rebooting after complete fixation, by reversing just what's absolutely necessary (chromosomes, at least one type of ribosome, at least one ATP synthesis path, probably a few other things) it can eventually rebuild itself enough to replicate. then later mutations to reverse more things would be conserved by selection.
18:06 < docl> that's assuming you can't have a mechanism that targets GA crosslinking generalistically, which seems dubious since GA is such a small molecule
18:28 < docl> maybe this context demands a novel organelle that can protect its contents from fixation and has its own DNA, internal ribosome, ATP stores, etc. mitochondria as starting point perhaps
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21:23 < docl> https://syntheticyeast.github.io/
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--- Log closed Mon Jul 01 00:00:40 2024