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Category: genetics – Page 228

A Stanford University-led research team has set a new Guinness World Record for the fastest DNA sequencing technique using AI computing to accelerate workflow speed.

The research, led by Dr Euan Ashley, professor of medicine, genetics and biomedical data science at Stanford School of Medicine, in collaboration with Nvidia, Oxford Nanopore Technologies, Google, Baylor College of Medicine, and the University of California, achieved sequencing in just five hours and two minutes.

The study, published in The New England Journal of Medicine, involved speeding up every step of genome sequencing workflow by relying on new technology. This included using nanopore sequencing on Oxford Nanopore’s PromethION Flow Cells to generate more than 100 gigabases of data per hour, and Nvidia GPUs on Google Cloud to speed up the base calling and variant calling processes.

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An international team of researchers claim to have slowed the signs of aging in mice by resetting their cells to younger states, using a genetic treatment.

To the scientists, The Guardian reports, it’s a breakthrough in cell regeneration and therapeutic medicine that doesn’t seem to cause any unexpected issues in mice.

“We are elated that we can use this approach across the life span to slow down aging in normal animals,” said Juan Carlos Izpisua Belmonte, Salk Institute professor and co-corresponding author of a new study published in the journal Nature Aging, in a statement. “The technique is both safe and effective in mice.”

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To date, scientists have largely been in the dark with regard to how individual circuits operate in the highly branched networks of the brain. Mapping these networks is a complicated process, requiring precise measurement methods. For the first time, scientists from the Max Planck Institute for Biological Cybernetics in Tübingen, Germany, together with researchers from the Ernst Strüngmann Institute in Frankfurt and Newcastle University in England, have now functionally proven a so far poorly understood neural connection in the visual system of monkeys using optogenetic methods. To this end, individual neurons were genetically modified so that they became sensitive to a light stimulus.

For decades microstimulation was the method of choice for activating neurons – the method proved to be reliable and accurate. That is why it is also used medically for deep stimulation. The Tübingen-based scientists were now able to show that optogenetics, a biological technique still in its infancy, delivers comparable results.

With optogenetics it is possible to directly influence the activity of neurons by light. To do this are genetically modified with the help of viruses to express light-sensitive ion channels in their cell membrane. Through blue light pulses delivered directly into the brain, the modified neurons can then be systematically activated.

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From the time of Hippocrates, physicians have suspected a link between epilepsy and depression. Now, for the first time, scientists at Rutgers University-New Brunswick and Columbia University have found evidence that seizures and mood disorders such as depression may share the same genetic cause in some people with epilepsy, which may lead to better screening and treatment to improve patients’ quality of life.

The scientists studied dozens of unusual families with multiple relatives who had epilepsy, and compared the family members’ of with that of the U.S. population.

They found an increased incidence of mood disorders in persons who suffer from a type of the condition called focal epilepsy, in which begin in just one part of the brain. But mood disorders were not increased in people with generalized epilepsy, in which seizures start on both sides of the brain.

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Researchers created a mathematical framework to examine the genome and detect signatures of natural selection, deciphering the evolutionary past and future of non-coding DNA.

Despite the sheer number of genes that each human cell contains, these so-called “coding” DNA sequences comprise just 1% of our entire genome. The remaining 99% is made up of “non-coding” DNA — which, unlike coding DNA, does not carry the instructions to build proteins.

One vital function of this non-coding DNA, also called “regulatory” DNA, is to help turn genes on and off, controlling how much (if any) of a protein is made. Over time, as cells replicate their DNA to grow and divide, mutations often crop up in these non-coding regions — sometimes tweaking their function and changing the way they control gene expression. Many of these mutations are trivial, and some are even beneficial. Occasionally, though, they can be associated with increased risk of common diseases, such as type 2 diabetes, or more life-threatening ones, including cancer.

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A totipotent cell is a single cell that can give rise to a new organism, if given appropriate maternal support. Totipotent cells have many properties, but we do not know all of them yet. Researchers at Helmholtz Munich have now made a new discovery.

“We found out that in totipotent , the mother cells of stem cells, DNA replication occurs at a different pace compared to other more differentiated cells. It is much slower than in any other cell type we studied,” says Tsunetoshi Nakatani, first-author of the new study.

DNA replication, in fact, is one of the most important biological processes. Throughout the course of our lives, each time that a cell divides it generates an exact copy of its DNA so that the resulting daughter cells carry identical genetic material. This fundamental principle enables faithful inheritance of our genetic material.

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Can we turn up—or dial down—their fervor by tweaking their genes?

Enter a new kind of CRISPR. Known mostly as a multi-tool to cut, snip, edit, or otherwise kneecap an existing gene, this version—dubbed CRISPRa—forcibly turns genes on. Optimized by scientists at Gladstone Institutes and UC San Francisco, the tool is counterbalanced by CRISPRi—“i” for “interference,” which, you guessed it, interferes with the gene’s expression.

Though previously used in immortal cells grown in labs, this is the first time these CRISPR tools are rejiggered for cells extracted from our bodies. Together, the tools simultaneously screened nearly 20,000 genes in T cells isolated from humans, building a massive genetic translator—from genes to function—that maps how individual genes influence T cells.

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One of the especially promising therapies to appear in the realm of anti-aging research involves a set of molecules known as Yamanaka factors, which scientists have deployed to rejuvenate aging cells, trigger muscle regeneration and tackle glaucoma. New research at the Salk Institute has sought to build on these short-term and specific use cases by demonstrating how these molecules can reverse signs of aging in middle-aged and elderly mice, with no evidence of health problems following the extended treatment.

The Yamanaka factors at the center of this study are a set of four reprogramming molecules that can reset the molecular clock found in the cells of the body. They do so by returning unique patterns of chemicals known as epigenetic markers, which evolve through aging, to their original states.

This approach has been used to convert adult cells back into stem cells, that can then differentiate into different cell types. The Salk Institute team has previously used the approach to reverse signs of aging in mice with a premature aging disease, and improve the function of tissues found in the heart and brain. Separately, Stanford University scientists last year used the technique to give elderly mice the muscle strength of younger mice.

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The XPrize and other competitions are helping to advance science and technological innovation.

Over the years, we have had alumni go on to become successful academic scientists, company managers and entrepreneurs. The networks that the participants create with each other during the competition are useful to tap into throughout their careers. Recently, I also learnt that a winning team from 2020 decided to create a bioelectronics start-up, INIA Biosciences, that aims to use ultrasound to interact with the immune system to relieve chronic inflammatory diseases.

More companies and foundations are seeing the advantages of science competitions and are organizing innovation challenges. The organizers benefit from recruiting talented people, gaining fresh ideas and promoting an image of innovativeness. The participants are rewarded with training, network building and prize money. In addition to the Innovation Cup, we also organize events such as the €1 million Future Insight Prize, which is given out annually to honour and enable scientists solving key challenges of humanity.

MARJOLEIN CROOIJMANS: The judge

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