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Category: genetics – Page 71

Genomics is revolutionizing medicine and science, but current approaches still struggle to capture the breadth of human genetic diversity. Pangenomes that incorporate many people’s DNA could be the answer, and a new project thinks quantum computers will be a key enabler.

When the Human Genome Project published its first reference genome in 2001, it was based on DNA from just a handful of humans. While less than one percent of our DNA varies from person to person, this can still leave important gaps and limit what we can learn from genomic analyses.

That’s why the concept of a pangenome has become increasingly popular. This refers to a collection of genomic sequences from many different people that have been merged to cover a much greater range of human genetic possibilities.

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CRISPR was first discovered in bacteria as a defense mechanism, suggesting that nature hides a bounty of CRISPR components. For the past decade, scientists have screened different natural environments—for example, pond scum—to find other versions of the tool that could potentially increase its efficacy and precision. While successful, this strategy depends on what nature has to offer. Some benefits, such as a smaller size or greater longevity in the body, often come with trade-offs like lower activity or precision.

Rather than relying on evolution, can we fast-track better CRISPR tools with AI?

This week, Profluent, a startup based in California, outlined a strategy that uses AI to dream up a new universe of CRISPR gene editors. Based on large language models—the technology behind the popular ChatGPT—the AI designed several new gene-editing components.

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Jason Comander, MD, PhD, performs the procedure to deliver the CRISPR-based medicine as part of the BRILLIANCE trial in September 2020 at Mass Eye and Ear. Credit: Mass Eye and Ear.

All 14 trial participants, including 12 adults (ages 17 to 63) and two children (ages 10 and 14), were born with a form of Leber Congenital Amaurosis (LCA) caused by mutations in the centrosomal protein 290 (CEP290) gene. They underwent a single injection of a CRISPR/Cas9 genome editing medicine, EDIT-101 in one eye via a specialized surgical procedure. This trial, which included the first patient to ever receive a CRISPR-based investigational medicine directly inside the body, focused primarily on safety with a secondary analysis for efficacy.

No serious treatment or procedure-related adverse events were reported, nor were there any dose-limiting toxicities. For efficacy, the researchers looked at four measures: best-corrected visual acuity (BCVA); dark-adapted full-field stimulus testing (FST), visual function navigation (VNC, as measured by a maze participants completed), and vision-related quality of life.

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In episode 267 of the Stem Cell Podcast, we chat with Dr. Shankar Srinivas, a Professor of Developmental Biology in the Department of Physiology Anatomy and Genetics based in the Institute for Developmental and Regenerative Medicine at the University of Oxford. He is also a Zeitlyn Fellow and Tutor in Medicine at Jesus College. Using mouse and human embryos as model systems, his group looks at the control of patterning and morphogenesis during the establishment of the anterior-posterior axis, gastrulation, and early cardiogenesis. He discusses how tissues respond to forces during early development, characterizing cardiac progenitors, and training internationally.

Roundup Papers:
2:26 https://bit.ly/3yeD3ms.
7:14 https://bit.ly/4dKJ7nd.
19:06 https://go.nature.com/3V2SNSo.
27:10 https://go.nature.com/4dnC43H

38:40 Guest Interview.

#Cardiogenesis #DevelopmentalBiology.

Listen on Apple Podcasts: https://apple.co/2T8BhPA
Listen on Stitcher: https://bit.ly/3hGwsGA
Listen on Spotify: https://spoti.fi/3xFdENP

Official Website: https://stemcellpodcast.com/

Continue reading “The Stem Cell Podcast” | >

Remember all those low rate scifi horror movies with big snakes, let’s see if the bookie will take bet on when we have a first big one (on the run from the facility)

Scientists used CRISPR editing to make the world’s first genetically modified snakes, giving new insight into how the reptiles develop their patterned scales.

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Cells in the human body chat with each other all the time. One major way they communicate is by releasing tiny spheres called exosomes. These carry fats, proteins, and genetic material that help regulate everything from pregnancy and immune responses to heart health and kidney function.

Now, a new Columbia University study in Nature Nanotechnology demonstrated that these “nanobubbles” can deliver potent immunotherapy directly to tough-to-treat lung cancer tumors via inhalation.

“Exosomes work like text messages between cells, sending and receiving information,” said lead researcher Ke Cheng, PhD, professor of biomedical engineering at Columbia. “The significance of this study is that exosomes can bring mRNA-based treatment to lung cancer cells locally, unlike systemic chemotherapy that can have side effects throughout the body. And inhalation is totally noninvasive. You don’t need a nurse to use an IV needle to pierce your skin.”

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Scientists have recently discovered thousands of active RNA molecules that can control the human body.

By Philip Ball

Thomas Gingeras did not intend to upend basic ideas about how the human body works. In 2012 the geneticist, now at Cold Spring Harbor Laboratory in New York State, was one of a few hundred colleagues who were simply trying to put together a compendium of human DNA functions. Their ­project was called ENCODE, for the Encyclopedia of DNA Elements. About a decade earlier almost all of the three billion DNA building blocks that make up the human genome had been identified. Gingeras and the other ENCODE scientists were trying to figure out what all that DNA did.

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