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Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

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Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#51

Post by subroutine »

arca_vorago wrote: post #50
feelix wrote: post #21

Most of the DNA that suffers random mutations is non-coding DNA. It's completely unknown what effects, if any, modifying non-coding DNA might have as its use is unknown. I find it interesting that although anyone can experiment with CRISPR in their living room using something like this http://www.the-odin.com/ that no one has just tried modifying the non-coding DNA a lot and then observed any changes (or lack thereof…

Its been a few years since I left the genetics world behind, and I was just a sysadmin, but even then I'm pretty sure they had determined non coding regions to play a vital role in protein formation/folding.

How would non-coding DNA help with protein folding when translation happens outside the nucleus?

It's possible that upstream UTRs impact RNA transcription rates, but I'd be surprised if UTRs mediate protein folding.

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#52

Post by arca_vorago »

subroutine wrote: post #51
arca_vorago wrote: post #50

Earlier quoted context omitted.

Its been a few years since I left the genetics world behind, and I was just a sysadmin, but even then I'm pretty sure they had determined non coding regions to play a vital role in protein formation/folding.

How would non-coding DNA help with protein folding when translation happens outside the nucleus? It's possible that upstream UTRs impact RNA transcription rates, but I'd be surprised if UTRs mediate protein folding.

I wanted to say something about RNA so maybe your onto something, but alas, I may be simply wrong.

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#53

Post by cma »

leggomylibro wrote: post #27
feelix wrote: post #21

Most of the DNA that suffers random mutations is non-coding DNA. It's completely unknown what effects, if any, modifying non-coding DNA might have as its use is unknown. I find it interesting that although anyone can experiment with CRISPR in their living room using something like this http://www.the-odin.com/ that no one has just tried modifying the non-coding DNA a lot and then observed any changes (or lack thereof…

It's still fairly hard to do in a living room, if you want to do anything novel. You need probably low 4-figures of equipment first; a -20C freezer for DNA/buffer storage, small centrifuge, thermal cycler, some way of getting genes into a target, and incubation space for whatever you're modifying. Preferably you'll also have consistent temperature control and an extremely clean environment. You also need a source of…

> a -20C freezer for DNA/buffer storage,

How about dry ice from the grocery store?

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#54

Post by dragonwriter »

Blackthorn wrote: post #38
leggomylibro wrote: post #27

Earlier quoted context omitted.

It's still fairly hard to do in a living room, if you want to do anything novel. You need probably low 4-figures of equipment first; a -20C freezer for DNA/buffer storage, small centrifuge, thermal cycler, some way of getting genes into a target, and incubation space for whatever you're modifying. Preferably you'll also have consistent temperature control and an extremely clean environment. You also need a source of…

> And they've demonstrated an ability to take genes from things like jellyfish for e.g. autoluminescence, too. This almost feels like bikeshedding but...to be fair, pretty much the first thing anybody does with a new work organism in biotech is make it glow and it's been that way long before CRISPR! There's just something about it that people find irresistible.

> There's just something about it that people find irresistible.

It's cheap to verify and demonstrate success, so it's a natural first, or at least early, application.

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#55

Post by gopalv »

madengr wrote: post #42
leggomylibro wrote: post #27

Earlier quoted context omitted.

It's still fairly hard to do in a living room, if you want to do anything novel. You need probably low 4-figures of equipment first; a -20C freezer for DNA/buffer storage, small centrifuge, thermal cycler, some way of getting genes into a target, and incubation space for whatever you're modifying. Preferably you'll also have consistent temperature control and an extremely clean environment. You also need a source of…

Could the genes that produce THC be spliced into common lawn grass?

That is the stuff of urban legends ...

http://www.fleeb.com/rant/pot.html

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#56

Post by eicossa »

nonbel wrote: post #40
Amygaz wrote: post #37

Earlier quoted context omitted.

Any time before the advent of "supplementary materials" pretty much meant that you had nothing more than a highlight of the method. It was terrible indeed. However, even today I find that roughly half the publications are not worth the paper they are printed on, or the bandwidth to download them.

Check out pre-1940 papers (the year may be later depending on exact sub field). I've seen that they used to make it a point to include all the info (including raw data) to the point it was practical. Somewhere along the line the attitudes went wrong, I blame NHST personally.

NHST ? What's that ?

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#57

Post by Someone »

subroutine wrote: post #51
arca_vorago wrote: post #50

Earlier quoted context omitted.

Its been a few years since I left the genetics world behind, and I was just a sysadmin, but even then I'm pretty sure they had determined non coding regions to play a vital role in protein formation/folding.

How would non-coding DNA help with protein folding when translation happens outside the nucleus? It's possible that upstream UTRs impact RNA transcription rates, but I'd be surprised if UTRs mediate protein folding.

Non-coding = "not translated into proteins", not "isn't used". Some non-coding DNA produces non-coding RNA, including transfer RNAs (https://en.wikipedia.org/wiki/Non-coding_RNA), which help in protein construction.

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#58

Post by mpatobin »

dragonwriter wrote: post #54
Blackthorn wrote: post #38

Earlier quoted context omitted.

> And they've demonstrated an ability to take genes from things like jellyfish for e.g. autoluminescence, too. This almost feels like bikeshedding but...to be fair, pretty much the first thing anybody does with a new work organism in biotech is make it glow and it's been that way long before CRISPR! There's just something about it that people find irresistible.

> There's just something about it that people find irresistible. It's cheap to verify and demonstrate success, so it's a natural first, or at least early, application.

Its like making a todo app in a new language

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#59

Post by nonbel »

eicossa wrote: post #56
nonbel wrote: post #40

Earlier quoted context omitted.

Check out pre-1940 papers (the year may be later depending on exact sub field). I've seen that they used to make it a point to include all the info (including raw data) to the point it was practical. Somewhere along the line the attitudes went wrong, I blame NHST personally.

NHST ? What's that ?

I explained it and provided some references in an earlier post here: https://news.ycombinator.com/item?id=13483055

Here is another reference you could check: http://andrewgelman.com/2016/02/04/the-notorious-n-h-s-t-pre...

Re: Crack in CRISPR Facade After Unanticipated in Vivo Mutations Arise

#60

Post by subroutine »

Someone wrote: post #57
subroutine wrote: post #51

Earlier quoted context omitted.

How would non-coding DNA help with protein folding when translation happens outside the nucleus? It's possible that upstream UTRs impact RNA transcription rates, but I'd be surprised if UTRs mediate protein folding.

Non-coding = "not translated into proteins", not "isn't used". Some non-coding DNA produces non-coding RNA, including transfer RNAs ( https://en.wikipedia.org/wiki/Non-coding_RNA ), which help in protein construction.

This makes sense given we know that some nontranslated RNA has biological activity , like tRNA and rRNA. I was under the impression that "junk" DNA referred to DNA that was not transcribed.
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