Thousands of programmable DNA-cutters found in algae, snails and other organisms | Hacker News Reader

Thousands of programmable DNA-cutters found in algae, snails and other organisms

phys.org

158 pointsPaulHoule29 comments

“CRISPR-based genome editing tools developed by MIT professor and McGovern investigator Feng Zhang, Abudayyeh, Gootenberg, and others have changed the way scientists modify DNA, accelerating research and enabling the development of many experimental gene therapies.”

“Others” being Nobel laureates Jennifer Doudna and Emmanuel Charpatier - MIT and the Broad have long sought to minimize the work of these two women in the media for their own gain. Here again, a small but glaring example of their pettiness.

Could you elaborate for those of us not in the know?

I think it goes something like this: Doudna, et. al. were the first to discover and describe CRISPR in nature. Zhang, et. al. were the first to successfully develop ways to edit genomes with it.

Mojica is generally considered the "discoverer of CRISPR". Douda and Charpentier took that knowledge and made a specific genome editing system based on bacterial enzymes (Cas9) and demonstrated it working in bacteria. Zhang is generally considered the person who made it work in eukaryotes.

Biochemist Dr. Jennifer Doudna, from the University of California, Berkeley, submitted her patent application for the core CRISPR technology back in May 2012 after creating the tech along with Emmanuelle Charpentier.

But then biologist Feng Zhang from the Broad Institute of Harvard and MIT submitted a similar patent application in 2013--but he requested a fast-track process and received the official patent in April 2014. Zhang has since been awarded additional patents on the technology.

https://www.fiercebiotech.com/biotech/crispr-patent-battle-h...

Nobel Prize for CRISPR honors two great scientists – and leaves out many others

https://theconversation.com/nobel-prize-for-crispr-honors-tw...

CRISPR’s Nobel Prize winners defeated in key patent claim for genome editor

According to a ruling by an appeal board of the U.S. Patent and Trademark Office (USPTO), a different group, led by the Broad Institute of MIT and Harvard, made the “actual reduction to practice” of CRISPR’s ability to edit eukaryotic cells, including humans. This means companies developing CRISPR-based medicines must now negotiate with Broad and its partners, Harvard University and the Massachusetts Institute of Technology, for the use of the editor.

https://www.science.org/content/article/crispr-s-nobel-prize...

Small correction, it's Emmanuelle Charpatier.

Emmanuelle Charpentier

Yet another example of how the loss of biodiversity as a tragedy of the commons is one of the great failings of modern civilization.

How does that relate to the article?

The more we study life on Earth and its incredible diversity of form and function, the more we learn.

Over the past 4 billion years, our biosphere has developed the most fascinating and amazing array of “biotechnologies”. The vast majority of which we haven’t yet discovered.

Thus, the more we damage the biosphere, the more untapped knowledge we destroy.

The article presents a nice example of such “biotechnologies” which we have just discovered.

People might wonder, how much can scientists learn from snails and algae anyways? And is it even useful? The answer is, quite a lot, it turns out. And that knowledge often becomes invaluable, usually in ways we can’t predict.

The next revolutionary drug or medical treatment could be laying inside a plant or microbe that's about to go extinct.

Also, current revolutionary biomedical technologies, as was recently reported in relation to horseshoe crabs, whose blood is a necessary and irreplaceable medical ingredient, and who have survived several mass extinction events over the course of the species’ 500,000,000 years of existence—and yet humans over harvesting and failing to protect fisheries have caused unprecedented declines in their numbers causing real concern for their species survival.

> The next revolutionary drug or medical treatment could be laying inside a plant or microbe that's about to go extinct

I read this a lot. It feels a bit pat to me, but I am uneducated.

Is this any more true/likely than, e.g.:

  - There could be a lost diamond ring at the bottom of any septic tank
  - Any terminated pregnancy could have become the scientist who saved the world/cured cancer/etc

No matter how alien life on earth is, it is incredibly closely related to us compared to pretty much anything else. This is more like don't kill off half your family, they have kidneys, amongst millions of other things you don't even know about yet, that you night need.

That helps! Thank you.

Can someone explain in simple terms what is the usefulness of this finding?

biotech uses lots of random enzymes to "cut" DNA strands in different places to reassemble them how they need them, this discovery just means there are more available sources for them to use now so I'd guess it'll help make their lab work slightly less expensive.

Similar applications as CRISPR gene editing, except with a potentially lower rate of being rejected by the human immune system because it comes from other things than bacteria (CRISPR is from bacteria).

So these things have a better chance of be used to repair mutations in your genome live on the spot, rather than being constrained to being used in a test tube (which is still useful).

Cas9 immunity creates challenges for CRISPR gene editing therapies

https://www.nature.com/articles/s41467-018-05843-9

Other species have experimented with DNA editing and they turned out looking like balls of slime.

I hope we can un-slime them now to find out all of their secrets.

Any favorite examples?

The reason why mammals have a placenta and live birth is due to the incorporation of an ancient syncytium-producing retrovirus in our genomes.

Very interesting, Thank you for sharing. I just took a little look into this, and I'm definitely going to research it more.

Do you know of other cases similar to this, where a virus is incorporated into our genome? Or where I can look into it more?

You can find more about that in the lecture on retroviruses here:

https://www.youtube.com/watch?v=07Zu1sWKuuE&list=PLGhmZX2NKi...

Eventually, if we have enough differing examples, we may be understand how to edit DNA CRISPR style directly, without needing bacteria to do the actual splicing for us.

There’s usefulness but also the pure science that RNA is a highly versatile part of living systems. Specifically, RNA can play the role of a genetic coding material but it can also play the enzyme role that proteins play. It’s possible that before “life as we know it” existed there was an “RNA world” where RNA played the role that RNA plays today, plus the role of DNA, plus the role of proteins.

Thus there has to be a lot to learn about tricks RNA can play and also a large range of technical applications. There has been talk about pharmaceutical applications of RNA since the 1970s but it has taken decades for it to arrive, for instance now we have the mRNA vaccine platforms, RNA silencing pesticides and it may well turn out to be practical to engineer RNA enzymes so it’s an exciting area of practical research too.

Great.

In 20 years when my anti-DNA-virus scans for Zombie Viruses, it will have to check for thousands of executables.

The implication is that self-editing of genes is much more common than we suspected?

Is there there any HN like website dedicated for discussing topics like this?

Reply on news.ycombinator.com