Tag: dna

Gene Deextinction

Bringing Col2A1 back:

While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

Same deal for IRGM:

The exact reason that IRGM was reborn in species such as humans and apes, but not monkeys, is not yet completely understood. We do know, however, that the fact that most humans have a working copy of IRGM is quite fortuitous. As mentioned above, the IRG genes are essential to controlling bacteria, specifically by maintaining the delicate balance of bacterial growth and immune control in our intestines. Recent research has shown that those without a working copy of IRGM have a greater risk of developing Crohn’s Disease, in which an individual’s immune system begins attacking the friendly bacteria living in our guts.

Glycerol nucleic acid

“Making GNA is not tricky, it’s just 3 steps, and with 3 carbon atoms, only 1 stereo center. It allows us to make these right and left-handed biomolecules. People have actually made left-handed DNA, but it is a synthetic nightmare. To use it for DNA nanotechnology could never work. It’s too high of a cost to make, so one could never get enough material.” The ability to make mirror image structures opens up new possibilities for making nanostructures. The research team also found a number of physical and chemical properties that were unique to GNA, including having a higher tolerance to heat than DNA nanostructures.

interesting. GNA is simpler and more robust

70 ka Human bottleneck

From one of my favorite projects, the Genographic Project.

Human beings may have had a brush with extinction 70 ka BP. The human population at that time was reduced to small isolated groups in Africa, apparently because of drought. The number of early humans may have shrunk as low as 2k before numbers began to expand again in the early Stone Age.

2023-08-31: And an even more severe, earlier bottleneck

Human ancestors in Africa were pushed to the brink of extinction 900 ka BP. It suggests a drastic reduction in the population of our ancestors well before our species, Homo sapiens, emerged. The population of breeding individuals was reduced to 1280 and didn’t expand again for 117 ka. “98.7% of human ancestors were lost”. The fossil record in Africa and Eurasia between 950 ka and 650 ka BP is patchy and that “the discovery of this bottleneck may explain the chronological gap”. “Of greater surprise is the estimated length of time that this small group survived. If this is correct, then one imagines that it would require a stable environment with sufficient resources and few stresses to the system.”

Ice Man

Wim Hof should be dead for doing the following: running a half-marathon in the Arctic Circle in his bare feet, climbing the Everest in his shorts, and diving under the ice at the North Pole. Here’s a fascinating story about a 48-year-old Dutchman nicknamed “The Ice Man” for his uncanny ability of withstanding fatally freezing temperatures:

Normally, when a person is exposed to freezing temperatures for a prolonged period of time, the body goes into survival mode, as its liquids begin to freeze.

Frostbite sets in, and in order to save the major organs, the body sacrifices blood flow to the extremities, cutting circulation from the fingers, toes, ears and nose to keep the blood flowing to the organs necessary for survival.

If not treated immediately, the damage to these extremities is irreversible. The other danger is hypothermia, an abnormally low body temperature. At 0 celsius, body functions start shutting down, and once that starts, you could be dead within minutes.

But Hof stayed in his tomb of ice for 72 minutes. Then, the ice was poured out of the tank, and Hof emerged, his skin still pink.

“He’s not moving, he’s not generating heat, he’s not dressed for it, and he’s immersed in ice water. And water will transmit heat 30x faster than air. It literally sucks the life right out of you. And yet, despite all those negative factors, Wim Hof was very calm, very comfortable the entire time that he was immersed in that water

scan that guys dna already

Engineering Biology

30 years into biotechnology, despite all of the successes and attention and hype, we still are inept when it comes to engineering the living world. We haven’t scratched the surface of it, and so the big question for me is, how do we make biology easy to engineer? For comparison, if you look at other examples of technology, there are many of them. Take modern electronics, during and following World War Two, people are building computers. Von Neumann is building a nice machine in the basement of the Institute for Advanced Study at Princeton. The official purpose of this machine is to design hydrogen bombs and compute the trajectories of munitions. And he of course is apparently running artificial life programs on it, because that’s what he’s more interested in Let’s say it was 1950. The Apple One, the personal computer is only 25 years later.

interview with drew endy, the guy behind parts.mit.edu

Protein Arrays

Existing protein arrays involve the tedious and lengthy process of expressing proteins in living cells followed by purifying, stabilizing, and spotting the samples. This process is a bottleneck in the preparation of the arrays. Moreover, functionally active proteins require careful manipulation, and the less that is needed the better. Our approach to developing a protein array, a Nucleic Acid-Programmable Protein Array (NAPPA), replaces the complex process of spotting purified proteins with the straightforward and much simpler process of spotting plasmid DNA. The system could produce any desired protein from synthesized DNA placed on the chip. It is another step in making protein production and engineering and biotechnology in general faster and cheaper.