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dcf2

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Interesting article in Science a few weeks ago from the Doudna lab (Nobel in Chemistry 2020 for CRISPR-Cas genome editing). They used structure-based phylogeny (instead of sequence-based) to investigate CRISPR-Cas13 (RNA editing) evolution. Targeted RNA editing has 1001 potential uses including helping individuals with genetic disease without genome editing - thus much less ethically challenging.


Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.
 
dcf2 said:
Interesting article in Science a few weeks ago from the Doudna lab (Nobel in Chemistry 2020 for CRISPR-Cas genome editing). They used structure-based phylogeny (instead of sequence-based) to investigate CRISPR-Cas13 (RNA editing) evolution. Targeted RNA editing has 1001 potential uses including helping individuals with genetic disease without genome editing - thus much less ethically challenging.


Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.
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OK. To define key terms.

Somatic cell: cell in a tissue in the body. It doesn't pass information to progeny except possibly through microRNA (epigenetics)
Germ cell: egg, sperm. They pass DNA onto progeny

CRISPR - cas9: Gene editing made of RNA and an enzyme. It is used to repair gene mutations or damage in somatic cells today. Can specifically target code within a gene in somatic cells where there is a problem/mistake rather than replacing or removing entire gene sections typical of most gene therapy. Theoretically, it could be used on germ cells. CRISPR editing can be systemic or tissue-specific.

Gene Editing

crisprtx.com crisprtx.com

However, CRISPR does edit DNA. For example, CRISPR is being used to correct mutations in the dystrophin gene of Duchenne muscular dystrophy experimentally. CRISPR technology has moved up the pipeline into clinical trails for a number of diseases.

 
Ideal timing and a great idea for a topic.

If anyone is unaware of Professor Dave on YT, he covers a wide range of subjects. He also has some fantastic de-bunk videos, which I expect many in this community will love.

 
AlphaFold 3 has been recently released.

Simplifying background - AlphaFold algorithms use Deep Learning to predict molecular structures. AlphaFold 3 is a significant step forward in that in can predict complex structures like protein interactions with nucleic acids or small molecules (drugs). AlphaFold has been used to predict ~200 Million protein structures (essentially the known space) whereas the total number of experimentally solved structures (X-ray, Cryo-EM, other) over the last many decades is about 200 Thousand.

This should be open access should anyone want to read the paper in Nature: Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3
Accurate structure prediction of biomolecular interactions with AlphaFold 3 - Nature - Interesting that most of the authors are directly working with Google.

DOE National Labs and other supercomputer facilities make these computational resources available - e.g., (https://www.pnas.org/doi/10.1073/pnas.2311888121) but we are likely entering an area in which parts of the science become functionally difficult to reproduce (too expensive computationally) as well as widening the haves and have nots divide on resources.
 
Texas loaded up with earthquakes the last week
The rash of earthquakes is not naturally occurring, as Texas in general is not a very seismically active part of the country. Instead, it is"almost 99% likely" to be linked to local oil fields, Rubinstein said.
 
mpaer said:
Texas loaded up with earthquakes the last week
The rash of earthquakes is not naturally occurring, as Texas in general is not a very seismically active part of the country. Instead, it is"almost 99% likely" to be linked to local oil fields, Rubinstein said.
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So are you saying Texas is being Oklahomafied, with all the quakes?
Link:
 

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05C40 said:
So are you saying Texas is being Oklahomafied, with all the quakes?
Link:
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As a young man I would have scoffed at this, but as I’ve gained real world experience it makes sense that emptying caverns/spaces that were full of crude oil might have some weird effects on how weight is distributed and probably 100 other things I’m not aware of.

Climate change is similar. Why is it so hard for people to realize that dumping trash, chemicals, exhaust into a closed system is going to cause a lot of issues with cascading effects.
 
dcf2 said:
AlphaFold 3 has been recently released.

Simplifying background - AlphaFold algorithms use Deep Learning to predict molecular structures. AlphaFold 3 is a significant step forward in that in can predict complex structures like protein interactions with nucleic acids or small molecules (drugs). AlphaFold has been used to predict ~200 Million protein structures (essentially the known space) whereas the total number of experimentally solved structures (X-ray, Cryo-EM, other) over the last many decades is about 200 Thousand.

This should be open access should anyone want to read the paper in Nature: Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3
Accurate structure prediction of biomolecular interactions with AlphaFold 3 - Nature - Interesting that most of the authors are directly working with Google.

DOE National Labs and other supercomputer facilities make these computational resources available - e.g., (https://www.pnas.org/doi/10.1073/pnas.2311888121) but we are likely entering an area in which parts of the science become functionally difficult to reproduce (too expensive computationally) as well as widening the haves and have nots divide on resources.
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I was reading recently how AI helped solve the “protein folding” problem. That’s what this is?
 
ronjon said:
It’s the fracking. Blowing things up underground is no way to keep things stable. I don’t think regular oil pumping causes this.
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quPRUC.gif
 
Geisterfahrer said:
I was reading recently how AI helped solve the “protein folding” problem. That’s what this is?
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I would not say solved but yes this is the toolset that has advanced understanding of protein folding in a way that structural and mechanistic biology has been wanting for decades.
 
Probably the best YouTube channel with one of the most important lessons about how cultural and social constructions put the brakes on progress:

 
CallMeTyler said:
Some in the community might find this interesting.

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That's a hell of a job rendering that visualization... but... It's driving me bananas that the day night cycle is not synced to the rate of spin of the globe. One rotation equals one day night cycle dammit!
 
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