Tag: biotech

CRISPR

CRISPR allows for much better genetic engineering than previous approaches and is a huge deal. It even works in human cells. Probably Nobel prize material.
2015-06-11: 1000x CRISPR

It is now possible to record a human genome (differences relative to a reference is only 2 megabytes. This is instead of 9 terabytes for a human genome with image data. CRISPR improvements are getting to 1 off target in 1 in 100 trillion (10^14) to 1 in 10 million trillion (10^19)

2015-11-11: CRISPR is the real deal

Editas plans to deliver the CRISPR technology as a gene therapy. The treatment will involve injecting into the retina a soup of viruses loaded with the DNA instructions needed to manufacture the components of CRISPR, including a protein that can cut a gene at a precise location. To treat LCA, the company intends to delete 1000 DNA letters from CEP290 in a patient’s photoreceptor cells.

2015-11-12: CRISPR Monsanto Problem

CRISPR is far too important to become entangled in the same web of confusion that has made G.M.O.s such a toxic issue. We ought to have learned something from those troubling and extended shouting matches; scientists, politicians, and everyone else needs to join in on this debate now. Society has no choice but to come to terms with both the potential benefits and the possible risks. That will require a big change: today, there isn’t even really a regulatory mechanism capable of governing products like CRISPR.

2016-03-09: Improvements to CRISPR subtypes like Cpf1 and now Cas9 are happening very quickly. This should reduce errors and increase the power of these gene editing technologies.
2016-10-14: CRISPR corrects sickle cells

Sickle cell disease is a genetic disorder caused by a mutation in one of the hemoglobin genes, which causes deformation of red blood cells and results in occlusion of blood vessels, severe pain crises, and progressive organ injury. To correct the mutation that causes this disease, DeWitt et al. modified hematopoietic stem cells from sickle cell disease patients using a CRISPR/Cas9 gene editing approach. The authors showed that the corrected cells successfully engrafted in a mouse model and produced enough normal hemoglobin to have a potential clinical benefit in the setting of sickle cell disease.

2018-04-26: Improving CRISPR accuracy 10000x

The use of bridged nucleic acids to guide Cas9 can improve its specificity by over 10000x in certain instances — a dramatic improvement.

2019-02-27: Doudna on CRISPR

Do you think that the medical applications of CRISPR in themselves can inform basic science?

For sure. CRISPR technology has been widely adopted by all kinds of scientists, including people like me. I was never doing anything with genome editing before CRISPR came along.

In my lab we’ve had a project over the last few years working on Huntington’s chorea, a degenerative neurological disease. The mutation that causes the disease is a single codon — 3 base pairs in the DNA — that gets repeated many times. If the codon gets repeated too many times, it leads to a defective protein that causes this disease. That’s been known for a long time, but the challenge was, how do you fix it?

We’ve been working on a way to deliver the CRISPR into mouse neuronal cells to make the necessary edits. But one of the curious things that’s come out of that line of work is that we found that only neuronal cells in the mouse brain were getting edited, not [the supportive glial] cells called astrocytes.

These cells are a lot smaller, so it could be that they don’t have enough surface area to take up the CRISPR protein efficiently. Or maybe they don’t respond to DNA cutting and editing in the same way as other cells.

2019-03-01: CRISPR error rates. Gene Editing Is Trickier Than Expected

how many errors are too many? Cells are prone to making their own mistakes—on the order of 1 every 1M-100M base pairs, with more for skin cells, and fewer for sperm and eggs. Does it matter if an overactive gene editor makes that number closer to 1 in 500K?

2019-05-07: CRISPR Inhibitor

The number of stories and journal articles about how CRISPR DNA-editing technology works, has worked, and is planned to work are beyond counting. How about an article about how to stop it in its tracks? That’s this one, just published in Cell from a multicenter team in Cambridge and New York. It describes a screening program for small-molecule inhibitors of S. pyogenes Cas9 (spCas9), because one would want some ways (not all of which currently exist) to turn its effects off in given places and at given times.

2019-10-04: CRISPR documentary

The teaser zooms in on the stomach-stabbing self-experimentations of biohackers like Josiah Zayner and Aaron Traywick. DIY Crispr is just one subplot in the larger narrative about what happens when nature can be minutely controlled, when humans might even preside over their own evolution. Their cameras also follow scientists like Jennifer Doudna and Kevin Esvelt and the first patients in an experimental gene therapy trial to treat hereditary blindness. “Our main hope is to create a discussion around these technologies. People might come away excited. Or they might be scared. But at least that means they’re talking and learning and understanding what’s coming.”

2019-12-18: CRISPR in Humans?

One of the most compelling arguments against CRISPR gene editing, namely the potential for misuse, can also be considered the most compelling argument for CRISPR gene editing. Banning progress on gene editing technology may create a black market, but the continuation of research on gene editing will allow the scientific community to control its use and ensure patient safety

2022-03-07: Another similar claim of a 4000x improvement. The new paper doesn’t mention BNANC, so who knows if these improvements stack. Probably not.

Researchers discovered how some of these errors can happen. Usually, the Cas9 protein is hunting for a specific sequence of 20 letters in the DNA code, but if it finds one where 18 out of 20 match its target, it might make its edit anyway. To find out why this occurs, the team used cryo-electron microscopy to observe what Cas9 is doing when it interacts with a mismatched sequence. To their surprise, they discovered a strange finger-like structure that had never been observed before. This finger reached out and stabilized the DNA sequence so the protein could still make its edit. Having uncovered this mechanism, the team tweaked this finger so that it no longer stabilized the DNA, instead pushing away from it. That prevents Cas9 from editing that sequence, making the tool 4000x less likely to produce off-target mutations. The team calls the new protein SuperFi-Cas9.


2023-01-19: CRISPR Cas12a2

“With this new system we’re seeing a structure and function unlike anything that’s been observed in CRISPR systems to date”.

While other CRISPR systems bind to their target sequence, make their cut, and then stop, when Cas12a2 binds to its target, it seems to “activate,” transforming in shape.

“It’s a change in structure that’s extraordinary to observe — a phenomenon that elicits audible gasps from fellow scientists”. Once activated, the protein can bind to any genetic material that comes near it, whether its single-stranded RNA, single-stranded DNA, or double-stranded DNA. Cas12a2 then starts shredding the material, making multiple cuts in indiscriminate locations.

Because the genetic material can belong to the bacteria itself, the result can be cellular death. CRISPR causes the infected cell to self-destruct — rather than let it become a virus factory.

2023-04-01: A much better drug delivery

Microbiologists were learning more about an unusual group of bacteria that use molecular spikes to pierce a hole in the membranes of host cells. The bacteria then transport proteins through the perforation and into the cell, exploiting the host’s physiology in their favor. Using the artificial-intelligence program AlphaFold, which predicts protein structures, the team designed ways to modify the tail fibre so that it would recognize mouse and human cells instead. They then loaded the syringes with various proteins, including Cas9 and toxins that could be used to kill cancer cells, and delivered them into human cells grown in the lab, and into the brains of mice. Similar to the early days of CRISPR–Cas9 research, the bacterial syringes are studied by only a handful of labs, and their roles in microbial ecology are only beginning to be understood.

2023-12-15: There are far better technologies like base and prime editing, than CRISPR.

That’s really what inspired us to develop base editing in 2016 and then prime editing in 2019. These are methods that allow you to change a DNA sequence of your choosing into a different sequence of your choosing, where you get to specify the sequence that comes out of the editing process. And that means you can, for the first time in a general way, programmable change a DNA sequence, a mutation that causes a genetic disease, for example, into a healthy sequence back into the normal, the so-called wild type sequence, for example. So base editors work by actually performing chemistry on an individual DNA base, rearranging the atoms of that base to become a different base.

100 years of dog tinkering

Idiocracy is already here, for dogs.

The Basset Hound has gotten lower, has suffered changes to its rear leg structure, has excessive skin, vertebra problems, droopy eyes prone to entropion and ectropion and excessively large ears. No dog breed has ever been improved by the capricious and arbitrary decision that a shorter/longer/flatter/bigger/smaller/curlier “whatever” is better. Condemning a dog to a lifetime of suffering for the sake of looks is not an improvement; it is torture.

2021-11-08: Another look at extinct dog breeds:

After more than 30 ka by the side of their human companions, and the development of 100s of different types, all around the globe – for different climates, hobbies, tastes, and professions – dogs were suddenly at the mercy of shows and sporting events. “There are a number of dogs that the Victorians kind of abandoned. If dogs don’t get a following in a dog show, then they kind of disappear. Nobody breeds them, nobody buys them, nobody shows them.” The era saw a kind of mass extinction of dogs which had been in existence for ka.

Factor V fixes

“The data from 23andMe helped to rule out more worrisome diagnoses and stave off more invasive treatments”. Doctors ultimately removed the clot as they took out part of his liver, and the intervention cured the fevers.

interesting, the factor v mutation has been the most useful bit in my own 23andme data too.

Researchers have identified new genetic associations for blood clots, one of the leading causes of death worldwide. On top of finding these genetic associations, this new paper also offered a model for conducting future research into this difficult-to-study condition by using self-reported data from 23andMe research participants answering questions about their own history of blood clots.

Mitochondrial outsourcing

Genetically, the mitochondrion has lost all but a handful of its 4000 bacterial genes, down to 37 in humans. Over many generations, the mitochondria outsource their genes to the nucleus. Is this starting to sound familiar? We have been outsourcing our intelligence, and our humanity, to machines for centuries. As we invent each new computer task, we define it away as not “really” human. The real question is, what will be the essential human thing left that we contribute to the machines we inhabit?

Ethics arbitrage

In China, a research project aims to find the roots of intelligence in our DNA; searching for the supersmart

it would appear that the biggest sequencing lab in the world has no qualms about research that would not pass ethics approval in the west. of course, the results of that research will not be ignored by the west, how convenient.