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The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes

Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50–60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388–112,709 unique archaic fragments that cover 38.0–48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types—perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.

Pocket-sized device tests DNA in blood samples for genetic conditions

It is now possible to use a cheap, lightweight and smartphone-powered DNA detector to identify DNA in blood, urine and other samples, on the spot.

At the moment, testing to identify DNA is usually done in laboratories using expensive, specialised equipment. To make this process faster and cheaper, Ming Chen at the Army Medical University in China and his colleagues developed a portable DNA detector made of 3D-printed parts that attach to a standard smartphone.

CRISPR combines with stem cell therapy to reverse diabetes in mice

For a few years now, scientists at Washington University have been working on techniques to turn stem cells into pancreatic beta cells as a way of addressing insulin shortages in diabetics. After some promising recent strides, the team is now reporting another exciting breakthrough, combining this technique with the CRISPR gene-editing tool to reverse the disease in mice.

The pancreas contains what are known as beta cells, which secrete insulin as a way of tempering spikes in blood-sugar levels. But in those with diabetes, these beta cells either die off or don’t function as they should, which means sufferers have to rely on diet and or regular insulin injections to manage their blood-sugar levels instead.

One of the ways scientists are working to replenish these stocks of pancreatic beta cells is by making them out of human stem cells, which are versatile, blank slate-like cells that can mature into almost any type of cell in the human body. The Washington University team has operated at the vanguard of this technology with a number of key breakthroughs, most recently with a cell implantation technique that “functionally cured” mice with diabetes.

Coronavirus: Why Oxford university is so confident in an early vaccine win

The Oxford scientists are extraordinarily confident that their vaccine against the coronavirus will work.

The government’s chief medical officer insists a jab is still 12 to 18 months off and some form of social distancing will be needed until it’s in widespread use.

Their confidence is built on past success. The same vaccine technology has been used on other diseases, including the related coronavirus MERS, as well as Ebola.

ChAdOx1, pronounced “Chaddox-one”, is a version of a common cold virus that has been modified not only so that it doesn’t cause symptoms, but also so it carries some genetic material of the coronavirus.


Past success of the technology Oxford University is using for the COVID-19 vaccine is why they think it can be ready by September.

Whole genome sequencing reveals genetic structural secrets of schizophrenia

:ooooo.


Most research about the genetics of schizophrenia has sought to understand the role that genes play in the development and heritability of schizophrenia. Many discoveries have been made, but there have been many missing pieces. Now, UNC School of Medicine scientists have conducted the largest-ever whole genome sequencing study of schizophrenia to provide a more complete picture of the role the human genome plays in this disease.

Published in Nature Communications, the study co-led by senior author Jin Szatkiewicz, PhD, associate professor in the UNC Department of Genetics, suggests that rare structural genetic variants could play a role in schizophrenia.

“Our results suggest that ultra-rare structural variants that affect the boundaries of a specific genome structure increase risk for schizophrenia,” Szatkiewicz said. “Alterations in these boundaries may lead to dysregulation of gene expression, and we think future mechanistic studies could determine the precise functional effects these variants have on biology.”

Smartphone-powered device tests blood samples for genetic conditions

It is now possible to use a cheap, lightweight and smartphone-powered DNA detector to identify DNA in blood, urine and other samples, on the spot.

At the moment, testing to identify DNA is done in laboratories using expensive, specialised equipment. To make this process faster and cheaper, Ming Chen at the Army Medical University in China and his colleagues developed a portable DNA detector made of 3D-printed parts that attach to a standard smartphone.

Reversing diabetes with CRISPR and patient-derived stem cells

Now, scientists at Washington University in St. Louis have developed a way to use gene editing system CRISPR-Cas9 to edit a mutation in human-induced pluripotent stem cells (iPSCs) and then turn them into beta cells. When transplanted into mice, the cells reversed preexisting diabetes in a lasting way, according to results published in the journal Science Translational Medicine.

While the researchers used cells from patients with Wolfram syndrome—a rare childhood diabetes caused by mutations in the WFS1 gene—they argue that the combination of a gene therapy with stem cells could potentially treat other forms of diabetes as well.

Virtual Event

DNA may not be life’s instruction book—just a jumbled list of ingredients

The common view of heredity is that all information passed down from one generation to the next is stored in an organism’s DNA. But Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, disagrees.

In two new papers, Jose argues that DNA is just the ingredient list, not the set of instructions used to build and maintain a living organism. The instructions, he says, are much more complicated, and they’re stored in the that regulate a cell’s DNA and other functioning systems.

Jose outlined a new theoretical framework for heredity, which was developed through 20 years of research on genetics and epigenetics, in peer-reviewed papers in the Journal of the Royal Society Interface and the journal BioEssays. Both papers were published on April 22, 2020.

Body part regeneration: How science can make the jump from fantasy to reality

Salamanders and lizards can regrow limbs. Certain worms and other creatures can generate just about any lost part — including a head — and the latest genetics research on body part regeneration is encouraging.


Since they are adult stem cells that have reverted back to a less developed — more pluripotent — state, iPSCs remind scientists of the stem cells that enable lizards to regrow limbs, and zebrafish to regrow hearts. When it comes to limbs, the understanding the regrowth process could help scientists promote nerve regeneration in cases when a limb is severely damaged, but not physically lost. Nerves of the human peripheral nervous system do have the ability to regrow, but whether this actually happens depends on the extent of the injury, so understanding the stem cell physiology in zebrafish and other animals could help clinicians fill the gap. The knowledge gained also could impact development of treatments aimed at promoting nerve regrowth in the central nervous system, for instance in the spinal cord after an injury.

Caveats

Even where regeneration is natural for humans, numerous regeneration cycles can put a person at greater risk of cancer. In the liver, for instance, disease can result in liver cancer largely because the organ produces new cells to replace the damaged ones. This is what happens in cirrhosis and after certain viral conditions when there are periods when regeneration overtakes liver deterioration. Prometheus avoided this fate, but we don’t know how well the process would work in humans, if a regenerative system based on iPSCs or some other types of stem cell is used clinically on a large scale. Regenerative medicine is promising and exciting to hear about. But we are at a very early stage, and reports on limb regrowth should be taken with caution.

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