Toggling CRISPR Activity with a Chemical Switch

Researchers design a Cas9 enzyme that cuts DNA only in the presence of particular drug.

 

There are various ways to turn CRISPR/Cas9’s gene-editing activity on and off in cells, such as exposing tailor-made Cas9 enzymes to a particular type of light or to specific drugs. Each technique developed so far has drawbacks—either being complicated or irreversible. So researchers took inspiration from the Cre-recombinase-based method to control gene expression and built a “user-friendly” protocol for reversibly activating and inactivating CRISPR.

 

Read at TheScientist

DNA revelations from Ötzi the Iceman’s leather and furs

5,300-year-old mummy found in the Italian Alps wore clothes made from many different animals.

or the past two decades, scientists have analyzed every minute detail of Ötzi, a 5,300-year-old natural mummy found in the ice of the Italian Ötztal Alps. But one remaining mystery was the provenance of his clothing, made from leather and fur. Now, thanks to refined techniques in DNA sequencing, a team of scientists has identified how the clothing was made—and discovered something surprising about Ötzi’s domestic habits.

Ötzi lived during the Copper Age, when humans had been domesticating animals for a few thousand years, and our cutting-edge technologies included stone tools and fired pottery. From previous studies, we know that Ötzi was likely murdered by an arrow and a blow to the head. We also know he suffered from arthritis, and he ate a meal of deer and berries before he died.

The team’s new findings, published in Nature Scientific Reports, are as much a demonstration of DNA sequencing wizardry as they are about ancient fashion. It’s incredibly difficult to get genetic material out of tanned hides, because they’ve generally been scraped, heated, and exposed to fatty acids. Plus, the hides and furs themselves had disintegrated. But the researchers used several methods for extracting DNA from the hides that made up Ötzi’s shoelace, hat, loincloth, coats, leggings, and quiver. First they compared the strands of DNA they did find with other mapped genomes to identify species. Then the researchers targeted very small, specific regions in the DNA for reconstruction to learn more about the animals’ relationships with today’s domestic breeds.

 

Read at ArsTechnica

Large DNA study using 23andMe data finds 15 sites linked to depression

Scientists announced on Monday that they had pinpointed 15 locations in our DNA that are associated with depression, one of the most common mental health conditions and one that is estimated to cost the world billions in health-care costs and lost productivity.

Although gene association studies — which link DNA inherited from our parents to particular diseases, conditions or even habits such as vegetarianism — are published practically every week, this is a particularly important one. It’s the first large study on major depressive disorder in people of European descent, and it shows that the genes that may be involved in the condition correspond to those involved in the development of neurons in the brain. There is also overlap between the genetic regions implicated in depression and those that have been linked to other psychiatric disorders such as schizophrenia. This finding supports another key study published in April that focused on genetic factors related to well-being and depression, which found that the genetic variants for those genes had some “moderate” overlap with those with schizophrenia and bipolar disorder. This may suggest that scientists study these genes and traits jointly in future work.

The new study, published in Nature Genetics, involved an analysis of genetic variations of 75,607 people of European ancestry who self-reported having depression and 231,747 healthy controls.

 

Read at Washington Post

Meet Luca, the Ancestor of All Living Things

A surprisingly specific genetic portrait of the ancestor of all living things has been generated by scientists who say that the likeness sheds considerable light on the mystery of how life first emerged on Earth.

This venerable ancestor was a single-cell, bacterium-like organism. But it has a grand name, or at least an acronym. It is known as Luca, the Last Universal Common Ancestor, and is estimated to have lived some four billion years ago, when Earth was a mere 560 million years old.

The new finding sharpens the debate between those who believe life began in some extreme environment, such as in deep sea vents or the flanks of volcanoes, and others who favor more normal settings, such as the “warm little pond” proposed by Darwin.

Read at NYT

Branching Out Researchers create a new tree of life, largely composed of mystery bacteria.

Scientists have created a new tree of life showing the relationships among all known living things, which taxonomists typically classify into one of three domains: eukaryotes, bacteria, and archaea. One of this new tree’s largest branches consists of bacteria that are essentially new to science, according to a study published today (April 11) inNature Microbiology.

“The significant feature [of the tree] is so many of the major lineages have no isolated representatives”—that is, that none of their species been cultured individually in the laboratory, saidJillian Banfield of the University of California, Berkeley, who led the work. “Much of the world around us is populated by organisms we know nothing about,” she added.

“It’s a great step forward,” said the Florida Museum of Natural History’s Doug Soltis

 

Read at The Scientist

 

Scientists Map Bedbug Genome, Follow Pest Through NYC Subway

Scientists have mapped the genome of bedbugs in New York City, then traced fragments of the nefarious pests’ DNA through the subway system.

In the grubby recesses of hundreds of stations, they discovered surprising genetic diversity among the bloodsucking creatures. The next step is to figure out how the information can be put to good use, such as to develop better insecticides or blood thinners.

But these goals will take further medical research.

For now, the focus is on two main players in New York life: the subway and bedbugs.

Scientists already have found that genetic traces of bedbugs in northern Manhattan are more closely related to those in the island’s southern part, while there are bigger variations between the Upper East Side and Upper West Side.

Link to article

It’s time to rethink how we identify disease-causing microbes

Modern disease theory must account for communities of commensal bacteria.

 

At the turn of the last century, German physician Heinrich Koch identified four critical criteria for determining whether or not a particular microbe causes a disease. The ideas behind them were crucial for advancing medicine and formalizing the germ theory of disease. Over the last century, these postulates have been updated as medicine has advanced.

In what may end up being the most recent of these updates, biologists Allyson Byrd and Julia Segre propose some adjustments to these classic medical postulates intended to bring them in line with analytic techniques based on DNA sequencing and the most current understanding of bacterial communities. Just as the previous updates to Koch’s postulates did, these proposed amendments incorporate cutting-edge scientific knowledge and add nuance to our understanding of the causes of disease.

Koch’s original postulates are that, if a microorganism causes a disease, then:

  1. For every single case of the disease, the microorganism will be present.
  2. Healthy people will not carry the microorganism—if they did, they would be sick.
  3. The microorganism can be isolated and cultured in a lab, then used to infect new people.
  4. The microorganism can be re-isolated from a person who was experimentally infected.

Link to full article at ArsTechnica

Lager-brewing yeast was probably born twice

Genome of newly discovered parent species shows strains are separate crosses.

 

Guinness stout and Bud Lite differ in, to be conservative, several ways, but one is that they’re brewed with very different types of yeast. Lager isn’t just a beer style, it’s a yeast lifestyle. Humans have been brewing with ale yeast—Saccharomyces cerevisiae—for thousands of years. But it was less than 600 years ago that European brewers stumbled on lager yeast, which behaves very differently and produces that distinctive lager flavor.

 

Read full article at Ars Technica

Misunderstanding the genome:

A recent Ars feature story about genetic screening generated quite a lively debate in the discussion thread. However, it also underlined just how many misconceptions people have when it comes to genetics. Public perception hasn’t been helped by scientists overhyping their findings or by inaccurate portrayals in the media (GATTACA, anyone?). So today, I’m going to try to clear some common confusions.

Before moving recently to Ars full time, I spent six years working in the policy office of the National Human Genome Research Institute, the part of the National Institutes of Health responsible for the Human Genome Project (along with the UK’s Wellcome Trust). The job gave me a front row seat to the challenge of explaining a horribly complex topic, one where common assumptions are often counterfactual.

Maria Delany’s Ars article does a great job laying out how screening at-risk individuals for mutations in a pair of genes—BRCA1 and BRCA2—can spare people from developing cancer. Delany also explains why there isn’t unanimity among clinicians about rolling out BRCA testing at the population level. At first glance, such testing seems like a no brainer, right? Testing right now is targeted to at-risk groups, like women with a family history of breast cancer, but studies have found those mutations in people with no family history of the disease. If testing people for BRCA mutations finds them before cancer does, where’s the downside?

 

 

Full story at Ars Technica