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Category: genetics – Page 338

Predicting gene expression with AI

Based on Transformers, our new architecture advances genetic research by improving the ability to predict how DNA sequence influences gene expression.

When the Human Genome Project succeeded in mapping the DNA sequence of the human genome, the international research community were excited by the opportunity to better understand the genetic instructions that influence human health and development. DNA carries the genetic information that determines everything from eye colour to susceptibility to certain diseases and disorders. The roughly 20,000 sections of DNA in the human body known as genes contain instructions about the amino acid sequence of proteins, which perform numerous essential functions in our cells. Yet these genes make up less than 2% of the genome. The remaining base pairs — which account for 98% of the 3 billion “letters” in the genome — are called “non-coding” and contain less well-understood instructions about when and where genes should be produced or expressed in the human body.

Scientists Have Successfully Recorded Data to DNA in a Few Short Minutes

Blowing older methods away, which can take hours and even days.

Global data production is estimated to reach 463 exabytes per day by 2025 — which is the equivalent of 212,765,957 DVDs per day, per the World Economic Forum.

Our existing data-storage systems, which can hold only so many 0s and 1s, and consume huge amounts of energy and space, cannot last us forever, putting us on the cusp of a serious data-storage problem that can only worsen over time. DNA-based data storage may come to the rescue as an alternative to hard drives since our genetic code is millions of times more efficient at storing information than current solutions. Now, in a breakthrough development, researchers at Northwestern University have devised a new method for recording information to DNA that takes minutes rather than hours or days.

Catching Criminals With Their Relative’s DNA

Your DNA is in a database.

Your genetic code is probably already in a database, without you ever giving a sample or permission. This video is sponsored by Brilliant. The first 200 people to sign up via https://brilliant.org/veritasium get 20% off a yearly subscription.

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A huge thanks to Paul Holes, Billy Jensen, Brett Williams, Dr Connie Bormans and Dr Doc Edge for being part of this video. Thanks to Verogen and Family Tree DNA for giving me access to film.

Thanks to Sonya Pemberton, Joe Hanson, Raquel Nuno, CGP Grey, and numerous Patreon supporters for helpful feedback on an earlier version of this video.

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Continue reading “Catching Criminals With Their Relative’s DNA” | >

Deleted coronavirus genome sequences trigger scientific intrigue

Efforts to study the early stages of the coronavirus pandemic have received help from a surprising source. A biologist in the United States has ‘excavated’ partial SARS-CoV-2 genome sequences from the beginnings of the pandemic’s probable epicentre in Wuhan, China, that were deposited — but later removed — from a US government database.

The partial genome sequences address an evolutionary conundrum about the early genetic diversity of the coronavirus SARS-CoV-2, although scientists emphasize that they do not shed light on its origins. Nor is it fully clear why researchers at Wuhan University asked for the sequences to be removed from the Sequence Read Archive (SRA), a repository for raw sequencing data maintained by the National Center for Biotechnology Information (NCBI), part of the US National Institutes of Health (NIH).

Partial SARS-CoV-2 sequences from early outbreaks in Wuhan were removed from a US government database by the scientists who deposited them.

3D Reconstruction Reveals the Faces of Three Ancient Egyptian Mummies

Residents of Abusir el-Meleq, an ancient Egyptian city south of Cairo, the men died between 1,380 B.C.E. and 450 C.E. A team from Parabon NanoLabs presented the trio’s facial reconstructions at the International Symposium on Human Identification in September.

“[T]his is the first time comprehensive DNA phenotyping has been performed on human DNA of this age,” says Parabon, a Virginia-based company that typically uses genetic analysis to help solve cold cases, in a statement.

To approximate the men’s faces, researchers used DNA phenotyping, which predicts individuals’ physical appearance based on genetic markers. (Phenotyping can suggest subjects’ skin, hair and eye color, but as Caitlin Curtis and James Hereward wrote for the Conversation in 2,018 the process has its limitations.) The team determined the mummies’ other characteristics through examination of their physical remains, reports Hannah Sparks for the New York Post.

A Biological ‘Time Machine’ With Human Cells Can Help Reverse Cancer

And, depending on how further studies progress, it could be implemented via gene therapy.

Early-stage pancreatic cancer has a ‘reset button’

“These findings open up the possibility of designing a new gene therapy or drug because now we can convert cancerous cells back into their normal state,” said Professor Bumsoo Han of Purdue’s mechanical engineering, who is also the program leader for the university’s Center for Cancer Research, in a blog post shared on the university’s official website. Han has also received a courtesy appointment in biomedical engineering, according to the post. The new time machine (speaking figuratively) from Han’s lab is a lifelike reproduction of a specific structure of the pancreas, called the acinus, which secretes and produces digestive enzymes into the small intestine. When pancreatic cancer strikes, it typically comes from chronic inflammation, which is caused by a mutation that tricks the digestive enzymes to begin digesting the pancreas itself. This is bad.

Scientists Rewired The Brain of a Mutant Worm Using Parts From a Hydra

Brains aren’t the easiest of organs to study, what with their delicate wiring and subtle whispering of neurotransmitter messages. Now, this research could be made a little easier, as we’ve learned we can swap some critical chemical systems with the host animal being none the wiser.

In a proof-of-concept study run by a team of US researchers, the microscopic worm Caenorhabditis elegans was genetically gifted pieces of a nervous system taken from a radically different creature – a curious freshwater organism known as Hydra.

The swap wasn’t unlike teaching a specific brain circuit a foreign language, and finding it performs its job just as well as before.

Mapping proteins could offer a clearer view of what’s driving cancer

Genetic information can be messy. Mapping proteins could offer a clearer view of what’s driving cancer.

Scientists have unveiled new maps of the protein networks underlying different types of cancer, offering a potentially clearer way to see what’s driving the disease and to find therapeutic targets.

Sequencing the genetic information of tumors can provide a trove of data about the mutations contained in those cancer cells. Some of those mutations help doctors figure out the best way to treat a patient, but others remain more of a mystery than a clear instruction manual. Many are exceedingly rare, or there are so many mutations it’s not clear what’s fueling the cancer.

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