Monthly Archives: June 2017

If youve heard about octopuses cleverly escaping their tanks, stealing cameras, and opening jars from the inside then youve also probably had nightmares about a cephalopod takeover. And as if the tentacled creatures werent unnerving enough, now it appears they can manipulate their own genetic information.

A study published inCell this past April showed octopuses and their cephalopod cousins have the unique ability to alter their RNA, a key element of DNA, to better adapt to their environments. To briefly catch you up on Biology 101, DNA is the nucleic acid carrying all the information needed to build every aspect of your body. Though also a type of nucleic acid, RNA is more of a paperboy, carrying all the information in the DNA to the rest of the cytoplasm, allowing the genetic instructions to become reality.

However, according to Popular Science, certain bases (which bind and form certain proteins) can be swapped out with different bases to create different proteins. Eli Eisenberg, a co-author of the study and biophysicist at Tel Aviv University in Israel, told the outlet, About 25 years ago, people identified the first example of RNA editing in mammals. There were a few cases where you'd see the DNA saying one thing and then see the actual protein was different.

Even humans have been known to use this adaptive hack, albeit rarely. This likely has to do with the fact that there are only about 1,000 locations within human DNA that allow for RNA editing to take place and fewer than 50 spots where that editing would have any noticeable effect on human physiology. Squids, on the other hand, have roughly 11,000 genetic opportunities for RNA editing, despite having the same total number of genes as humans, Popular Science reports.

Using previous research as a platform, the authors of this most recent study took a deep dive into the editing capabilities of cephalopods and found the sea creatures use this advantage to adjust to temperature shifts and expand their brainpower. And unlike DNA adaptations, which become fixed over generations, RNA changes can alter an individuals behavior several times within one lifetime. Put simply, dont be surprised if an octopus outwits you its in their genes.

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These Animals Figured Out How To Change Their Own DNA - GOOD Magazine

A host of proteins and other molecules sit on the strands of our DNA, controlling which genes are read out and used by cells and which remain silent. This aggregation of genetic material and controlling molecules, called chromatin, makes up the chromosomes in our cell nuclei; its control over which genes are expressed or not is what determines the difference between a skin cell and a neuron, and often between a healthy cell and a cancerous one.

Parts of the genome are only loosely coiled in the nucleus, allowing cells to access the genes inside, but large sections are compacted very densely, preventing the genes form being read until their region of the genome is unfolded again. These compacted regions, known as heterochromatin, are formed by a protein known as HP1 and similar proteins, but exactly how HP1 segregates this off-limits DNA from the rest of the nucleus has been largely a mystery, until now.

In a new study by UC San Francisco researchers published in the journal Nature on June 22, 2017, what looked at first like a failed experiment instead revealed the intriguing possibility that HP1 binds to stretches of DNA and pulls it into droplets that shield the genetic material inside from the molecular machinery of the nucleus that reads and translates the genome.

This provides a very simple explanation for how cells prevent access to genes, said Geeta Narlikar, Ph.D., professor of biochemistry and biophysics and senior author of the study.

Narlikars graduate student Adam Larson was trying to purify HP1, and noticed that the liquid in his samples was growing cloudy. For protein scientists, this is typically bad news, said Narlikar: it suggests that proteins that should dissolve in water are instead clumping together into a useless mass.

But Larson thought the clumps might actually be useful. After all, previous work had shown that the role of HP1 is to sequester long strands of DNA into very small volumes. What if this was exactly the sort of clumping he was seeing in the tube?

Larson took his samples to the lab across the hall from Narlikars, where Roger Cooke, PhD, professor emeritus of biochemistry and biophysics, helped him examine under the microscope what could have been just a tangled molecular mess. Instead, Larson and Cooke saw clouds of delicate droplets floating around in the water, like a freshly shaken mix of oil and vinegar.

HP1 had a reputation as a difficult protein to work with get any solution too concentrated, and the protein would clump out. But if the protein was supposed to clump, said Narlikar, a lot of things we couldnt explain started to make sense.

Narlikar speculates that other scientists may have seen the same cloudiness before, but thinking it was simply a ruined sample, never pursued it like Larson did. It demonstrates the power of curiosity-driven research, she said.

To see how and why the HP1 formed droplets, the team produced different mutant versions of the protein, watching which separated out. By watching which parts of the protein were important for forming droplets, and using X-rays to monitor changes in the proteins shape, the team found that the protein nearly doubles in length when small phosphate residues are added in cetain locations. The molecule literally opens up, said Narlikar. I was surprised at the size of the change.

This opening-up exposes electrically charged regions of the protein, which stick together, turning dissolved pairs of proteins into long chains that clump together into droplets. Just as balsamic vinegars dark and flavorful molecules dont seep into the oil of a salad dressing without some extra effort by the chef, the molecules for reading DNA dont seep into the HP1 droplets.

The fact that such a drastic change in shape comes from such a small modification may allow the cell to tightly regulate where and when HP1 silences genes, said Narlikar. The changes come quickly and robustly too using a technology employed by Sy Redding, PhD a Sandler Fellow, the team created a curtain of DNA molecules pulled straight by fluid flowing around them, then added HP1 and watched the protein compress the DNA into tiny droplets, folding it up against the flow.

People have been seeing for over a hundred years that you get these dense regions of DNA in the nucleus, said Madeline Keenen, the Ph.D. student who ran the curtain experiment. Now were seeing the actual mechanism.

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From Strands to Droplets: New Insights into DNA Control - Bioscience Technology

Hundreds of Broward cases are in doubt over prosecutors' favorite scientific evidence: DNA.

Illustration by Chris Whetzel

Late last year, as he served a life sentence in prison, Ernesto Behrens received a notice informing him of problems discovered at the crime lab that had examined DNA in his case. Behrens, who was convicted of armed sexual battery in Broward County in 2000, immediately filed a flurry of motions asking for the evidence to be reviewed.

But Judge Andrew Siegel quickly denied the motion without even granting a hearing.

Months after hundreds of cases were thrown into question over improper DNA interpretation at the Broward Sheriff's Office Crime Laboratory, Behrens' case has become a point of contention between prosecutors and public defenders.

Prosecutors say that his case wasn't affected by the DNA problem and that the notice might have been sent in error. The public defender's office, however, argues the judge's ruling shows that defendants aren't getting a fair shake at challenging the potentially tainted DNA evidence and that a much more thorough review is needed.

"The State Attorney's Office should also be looking at justice, and if there's one person sitting in jail or one person that was wrongly convicted based on faulty DNA, they should also be looking to right that conviction," Assistant Public Defender Gordon Weekes says.

The lab issue,which New Times detailed in a feature storylast month, surfaced in 2015. Forensic consultant Tiffany Roy reviewed evidence from a knife handle and realized it was ruled conclusive when it should have been inconclusive. Roy complained to the agency that accredits the lab, the American Society of Crime Lab Directors (ASCLD), which investigated and agreed with her.

At issuewas DNA evidence based on complex samples, in which the genetic material comes from multiple people. Complex samples require a complicated analysis to determine which portion of DNA belongs to which person.When the DNA is minuscule or degraded, pieces can be missing or seem to exist where they do not.

Because so much of that evidence is up to interpretation, the science can become more subjective and different experts often arrive at varying conclusions. That subjectivity led ASCLD in 2010 to issue new thresholds for interpreting DNA and calculating the odds that a particular person left DNA at a crime scene. Crime labs across the nation are grappling with the changes: Some are retesting thousands of cases to make sure old evidence was sound.

At the Broward crime lab, complex DNA processing was stopped after ASCLD issued its findings last year. The State Attorney's Office then began sending notices about the issue to 2,000 defendants in cases that were resolved since 1999 where any type of DNA was involved.

"We don't have the resources to go through every case," Chief Assistant State Attorney Jeff Marcus says. "And Ithink the public defender's office would not accept our opinion if we said, 'No, everything's fine; don't worry about it.' So our obligation is to tell them what the problem was."

After the State Attorney's Office notified defendants about the issue, the public defender's office followed up with fill-in-the-blank motions that can be used to challenge convictions. About 20 defendants have begun that process.But defendants are not entitled to representation for postconviction relief, so unless they can afford an attorney, they have to go through it alone.

Weekes argues that's an unfair burden when both the legal system and the science behind DNA are so complicated. He's highly critical of the way the State Attorney's Office has handled the crime lab problems, saying it does little to ensure the evidence was correct in cases that might have been affected. Even if a defendant files his own motion to double-check the evidence, a judge can still summarily deny it.

"They know that there are needles, and they put ten stacks of haystacks on top of those needles and said, 'It's up to you guys that potentially are entitled to relief to figure out where your needle lies,'" Weekes says of prosecutors.

Marcus defends the actions taken by the State Attorney's Office, pointing out that defendants can appeal judges' decisions which is what Behrens ended up doing. But in that case, Marcus says, the DNA was not complex and predates crime lab issues. Behrens, who was also convicted of armed battery in 1992, has filed numerous appeals over his years behind bars, none of which have been granted.

Weekes says the public defender's office plans to call for a committee of DNA experts and attorneys to look into the closed cases, as was done in other jurisdictions that faced similar issues. On that point, his office and the State Attorney's Office appear to agree: Marcus says prosecutors would be in favor of increased funding for some type of organization to conduct a review.

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Broward Judges Aren't Letting Defendants Challenge Bad DNA Evidence, Critics Say - Miami New Times

More and more people are taking DNA tests to get an insight into their genetic ancestries. Like everyone else, when I took mine earlier this year I was excited over the prospects of confirming (or questioning) the information Id already gathered through family lore and my own research.

The result? Absolutely no surprises ho-hum! But I did realize something new and interesting. My DNA results are readily explainable in terms of historic ethnic movements.

Heres how my experience applies to you. If you study up on history of the past 1,500 years or so, you have a good shot at learning how the strands of your DNA ended up combined in yourself.

In my case, the bulk of the DNA (57 percent) is listed as Irish. Thats what I expected. Both lines of my family arrived in America from Ireland in the mid-1800s.

But how did I end up with 18 percent Great Britain? Heres where family lore is the key. Id been told decades ago that my mothers paternal line started not in Ireland but in Britain, with the earliest record being my mega-great-grandparents living there in the 14th century.

It was about 200 years later that a direct ancestor left Britain for Scotland, with one of his descendants about 250 years afterward moving to Ireland and marrying there, a pair of moves that increased the Celtic (Irish and Scottish) content of my total DNA way beyond the British content.

Now, how to explain the 12 percent Western Europe? When I look at ancestry.coms map with ancestral lands circled, I see that Western Europe seems to be largely the coast of France. Didnt the Norman French invade England in 1066, settling down and, in time, marrying into the local populace?

Theres another circle up in the Baltic Sea area. If you remember your history courses, youll recall that groups from that area chiefly Anglos, Saxons, Jutes and Vikings invaded ancient Britain in early Christian times and, guess what, merged over the years with the local population of native Britons and Celts (ancestors of the Irish).

Some small oddities remain, but in tiny percentages. I see circles for central Europe and the Iberian peninsula. Does that mean that Ive got some Austrian and Spanish?

No, I dont think so. History shows that the Celts who eventually dominated in Ireland, Scotland and Wales arose in central Europe, with some moving down to what later became Spain and Portugal. The most likely explanation is that descendants of the ancient Celts share a good deal of the original Celtic DNA even today, no matter where their ancestors have been living for the last 1,500 years or so.

The test offers more precise results than Id thought it would. It even shows that my Irish/Celtic DNA is divided between the northeast of Ireland (from which my maternal line emigrated) and the northwest (from which my paternal line emigrated).

So, when my parents married in 1941, my father brought a largely Irish/Celtic DNA that had begun in central Europe, while my mother brought a polyglot mix of British, Baltic, French and Irish/Celtic. That blend would account for the predominance of Irish/Celtic in my own DNA, with substantial but lesser amounts of the rest.

Want the same experience? Head on down to the Northeast Pennsylvania Genealogical Society. At 6 p.m. on July 12 theyll have people there to help you take the ancestry.com DNA test. Regular price is $99. Theyre at the Hanover Green Cemetery building, Main Road, Hanover Township.

Tom Mooney Out on a Limb

http://timesleader.com/wp-content/uploads/2017/06/web1_TOM_MOONEY-3.jpgTom Mooney Out on a Limb

Tom Mooney is a Times Leader genealogy columnist. Reach him at [emailprotected]

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Out on a limb: DNA test can help trace family history, cultural ... - Wilkes Barre Times-Leader