Monthly Archives: April 2017

DNA(Photo: Associated Press)

Arguments swirled around a bill that would allow police to collectDNA samples from people arrested for felonies, but who had not yet been convicted.Then Senate President Pro TemDavid Long, R-Fort Wayne,stepped in to call off the vigorous debate.

"We've got a lot of work today," Long said, pressing the senators to vote on the motion to concur.

It passed 36-13. Now, the bill goes to the desk of Gov. Eric Holcomb.

But the fevered debate which only happened because the measure had to return to the Senate to concur on a minor House change indicates that the use of DNA, while a staple of police investigations for decades, evokes privacy concerns among some Hoosiers.

Also happening in the legislature:Lawmakers push to revive domestic violence gun bill

Will Holcomb sign abortion legislation?

Revenue forecast adds money to state budget talks

If signed into law by the governor, Senate Enrolled Act 322, authored by Sen. Erin Houchin, R-Salem,will broaden Indiana's DNA database, which supporters say will aid police in solving violent crimes such as rape, as well as clear those who may be innocent.

Right now, the state collects DNA upon conviction of crime. But come the end of the year, the proposal would allow police to take a sample upon arrest, making Indiana the 31ststateto do so.

As the bill traveled through the House and the Senate, lawmakers added a number of safeguards to protect innocent people from getting their DNA ensnared by the government through a false arrest. Thechanges came as opponents of the bill raised privacy concerns, predicting a Big Brother-like future of government intrusion oncitizens using their genetic material.

More on DNA collection:Should police take a DNA sample when making arrests?

Sen. Greg Taylor, D-Indianapolis,suggested that a DNA database could be breached, and used to frame people for crimes they didn't commit.

"If somebody gets your DNA and puts it at a crime scene, you're in trouble," Taylor said.

But supporters of the bill called such scenarios hyperbole, and argued that the practice in which DNA is taken with a cheek swab is similar to fingerprinting. The U.S. Supreme Court in a 5-4 decision in 2013 ruled that collecting DNA upon arrest is constitutionaland does not violate a suspect's Fourth Amendment rights against unreasonable search and seizure.

Sen. Brandt Hershman, R-Wheatfield, said some of the arguments from opponents "throw up hypotheticals that border on the silly."

"My fingerprints were taken when Itook the bar, and I didn't commit a crime," he said.

Lawmakers have proposed similar bills in past years, all of which failed to gain traction.

That changedlate last year when police closed two high-profile cases the slaying of an elderly man and attacks on two police stations because of a DNA sample taken on arrestin Ohio.

Before he was accused of shooting and killing an 82-year-old Zionsville man and firing shots at two police stations, Damoine Wilcoxson was arrested for a felony in Indiana, but not convicted. He also was arrested in Ohio, where a DNA sample was taken and placed into a database for comparison to other cases.

While investigating the two cases, police matched a DNA sample taken from a letter left at the scenes of the police station attacks to one in the Ohio database taken from Wilcoxson. Detectives then connected the slaying and the police station attacks with ballistic evidence. Police and prosecutors credited Ohio's expanded DNA database for solving the crimes.

However, some lawmakers were reluctant to expand the DNA database too far.

A similar bill authored by Rep. Greg Steuerwald, R-Avon,advanced in the House, and lawmakers worked together to add protections in the bills. For example, police can only take a DNA sample if a judge has found probable cause for an arrest, according to an amendment. Lawmakers also outlined a number of scenarios in which an individual can remove his or her DNA.

An individual can remove a DNA sample from the database when:

But it is the job of the suspect, not the government, to initiate the process for removal. This was a provision that some opponents took issue with, stating that removal should be automatic if an arrest does not stand. In past hearings, Steuerwald argued that the person charged would have the most incentive to follow up.

The measure requires police to inform a suspect of the removal process when taking a DNA sample. Then, if the circumstances qualify, the individual would fill out a form to expunge the DNA from the system.

Holcomb now has the option to sign or veto the bill, or allow it into law without his signature. Stephanie Wilson, a spokeswoman for the governor, said he is tracking all bills that head to his desk.

"He will consider carefully before making a decision," she said.

Steuerwald said he is confident the governor will sign the bill.

"This is one of the greatest law enforcement tools we have done here this entire session," he said.

Call IndyStar reporter Madeline Buckley at (317) 444-6083. Follow her on Twitter:@Mabuckley88.

Read or Share this story: http://indy.st/2pdF0HN

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DNA collection bill heads to governor's desk - Indianapolis Star

Some anglers won't have to tell big fish stories after their success April 8 on trout fishing opening day. iPhone video by Peggy Wright Peggy Wright

Map shows the two sites where samples were taken in the DNA fish hstudy(Photo: Courtesy of the Rockefeller University/Monmouth University)

For the first time, scientists have recorded a spring fish migration by conducting DNA tests on water samples.

The work was a collaboration ofRockefeller University and the Urban Coast Institute at Monmouth University.

According to the study's report, environmental DNA called eDNA,collectedfrom one-litersamples drawn weekly from New York's East and Hudson rivers over six months last year, revealed the presence or absence of several key fish species passing through the water on each test day.

READ: Fishermen not on board with Hudson Canyon sanctuary

READ:State prepares plan to dredge Little Egg Inlet

The bits of DNA recovered found the presence of menhaden, herring species, black sea bass, striped bass, tautog (blackfish), mummichog, bay anchovy, bluefish, oyster toadfish, Atlantic silverside, and conger eel. In total it found the presence of 42species.

Using eDNAisa way to monitor fish migrations that involves a fraction of the effort and cost of trawling, all without harming the fish, the study said.

It also said itcan be used toestimate the abundance and distribution of diverse fish species and other forms of marine life in the dark waters of rivers, lakes, and seas.

It has some kinks, for example, some DNA could not be exactlydistinguished, notably some in the herring family,

The testsalsoturned up DNA of fish species that are not found in New York waters but are commonly eaten by New Yorkers, such as tilapia, red snapper, and salmon.

It lead the researchers to conclude of those species DNA entered via the wastewater system.

Dan Radel: 732-643-4072; dradel@gannettnj.com

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DNA used to track fish in Hudson and East rivers - Asbury Park Press - Asbury Park Press

World's media focusing in on upcoming executions

Michael Buckner, KTHV 7:17 PM. CDT April 13, 2017

LITTLE ROCK, Ark. (KTHV) - The Innocence Project has asked an Arkansas circuit court to grant new DNA testing to death row inmate Stacey Johnson. The inmate is one of seven men set to be executed in a 10-day span starting on April 17.

The Innocence Project is a non-profit legal organization that works to exonerate those who may have been wrongly convicted. Their most famous case was the original exoneration of Steven Avery, who served 18 years in prison for a sexual assault he never committed.

In a press release, the group said newer DNA testing has "never been performed" in Johnson's case and could potentially prove he is innocent of the crime he's been charged with.

Johnson was convicted of the murder of Carol Heath in April of 1993. She was found only wearing a t-shirt. The evidence shows she was stabbed in the throat and raped. Johnson has maintained his innocence throughout his entire time in prison.

"While opinions are divided on whether the death penalty is a reasonable form of punishment, I hope we can all agree that no one should be put to death where DNA testing could prove innocence," said Karen Thompson, a staff attorney with the Innocence Project, "especially in situations like this one where potentially probative evidence from the crime scene was never even submitted for DNA testing despite a defense request."

Heath's purse was later on found at highway rest stop, where DNA tests proved the purse was stained in her blood.

The Innocence Project said that Johnson's case "rested largely on biological evidence and the testimony of the victim's 6-year-old daughter, Ashley Heath, who identified Johnson as the killer." His first conviction was overturned once the 6-year-old had been found "not mentally competent" to testify because of her age.

In Johnson's second conviction, the daughter's testimony was allowed. The conviction was later affirmed by the Arkansas Supreme Court in a 4-3 decision. In the dissenting opinion, Justice Robert L. Brown said the daughter began seeing a new therapist during the second trial and Johnson's counsel were denied access to these new therapist's evaluation of the child.

"Had defense counsel been privy to [the therapist's] records," Brown said in his dissent, "he would have been able to delve into [her] conclusions that Ashley's stories were profoundly inconsistent and that she had been under considerable pressure from her family and the prosecutor to convict Stacey Johnson."

The Innocence Project said that the defense was able to unseal those records and confirm that the child's therapist "believed her to be incompetent."

The group is requesting new DNA testing because his trial at the time didn't allow for testing of the sexual assault evidence. They say while Johnson's DNA matches to hairs found at the Heath's apartment, he admitted to visting the location previously.

"This early generation DNA testing also provided no results identifying the murderer on the shirts left at the highway rest stop, swabbingsof bite marks found on the victim's breasts, and other relevant items," the press release said.

The group also asserted that Heath's boyfriend at the time had a history of domestic assault, but police never investigated him as a potential suspect. During the trial, it came to light that his previous abuse charges included biting his ex-wife's breasts.

"This is not some sort of last-minute, hail mary pass," said Bryce Benjet with the Innocence Project. "Johnson asked for DNA testing in earlier appeals, but those requests were denied by State and federal courts. There have been revolutionary advancements in DNA testing since this case was initially investigated which could tell once and for all who actually committed this crime."

The motion filed on Thursday asks the Sevier County Circuit Court Judge to grant Johnson a hearing. If the hearing is granted, the group will present their evidence as to why the new DNA testing should be approved.

2017 KTHV-TV

KTHV

7 inmates in 10 days.

KTHV

Arkansas has never used midazolam, the sedative at center of execution debate

KTHV

Stop the execution madness in Arkansas: John Grisham

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Innocence Project asks Arkansas court to grant DNA testing in Stacey Johnson case - THV 11

Viruses reproduce by infiltrating living cells and taking over the biological machinery inside. Its an insidious process that can leave the host with a life-threatening illness, a mild fever, or no ill effects at all. Recent advances in medical science have allowed humans to combat viruses like never before, but a new study from researchers at Rockefeller University shows how our primate ancestors may have waged war on a virus with only the weapon of evolution.

Viruses dont leave behind fossil evidence, but sometimes their DNA can survive as part of their victims, and thats where the team went looking in this case. Thestudy focuses on an ancient virus known as HERV-T, which began infecting primates some 32 to 43 million years ago. HERV-T is a retrovirus (just like HIV), which means it carried its genetic material around as RNA. Eukaryotic cells (like ours) are DNA-based, so one of the first things HERV-T did upon gaining access to a cell was turn its RNA into DNA, then it stuffed it into the cells DNA to be duplicated.

HERV-T has long since gone extinct, but the researchers were able to find its remains in the genetic material of various primates. The germline cells like fetal cells, sperm progenitors, and eggs that were infected with HERV-T passed the viral genes down over the eons. This is what allowed the team to construct a timeline for the rise and fall of HERV-T, and find out how our ancestors might have killed it.

When HERV-T began popping up in primates around 40 million years ago, it used a protein on host cells called MCT1 to gain access. The virus used a protein called ancHTenv to link up with that protein, like a key in a lock. The team also found a remarkably well-preserved version of that protein hiding in the DNA of primates (including humans), which theyve named hsaHTenv. Its not uncommon for organisms to pick up a bit of nucleic acid here and there from viruses, but the nature of this gene suggests some interesting possibilities. The team used the remaining genetic code to reconstruct the ancient virus protein and study its function, which was a scientific first.

The life cycle of a retrovirus.

Scientists postulate that hsaHTenv was captured by our hominid ancestors cells around 19 million years ago. This gene was used by cells to produce the key protein of the virus independent of the virus itself. This in turn allowed cells to immunize themselves. Basically, hsaHTenv could bind to MCT1 particles in the cell, preventing them from being added to the cells membrane. With no MCT1 on the surface, the virus had no way to infect the cell. In the space of a few million years, HERV-T died out as its pool of hosts shrunk.

Not all researchers are convinced by the data, but such is the nature of science. Its possible the presence of hsaHTenv in primate genomes is due to some other factor, not its use as a weapon against ancient retroviruses. Still, its a fascinating hypothesis that warrants further study.

Now read: How DNA sequencing works

Original post:
Ancient DNA showcases a war between our hominid ancestors and viruses - ExtremeTech

INDIANAPOLIS Hoosiers arrested for any felony, starting in 2018, likely will have their DNA collected by cheek swab and their genetic record stored in a state police database.

State Sen. Erin Houchin, R-Salem, the sponsor of Senate Enrolled Act 322, said taking a DNA sample from every person arrested for a felony, instead of only those convicted of felonies, will help police solve more crimes similar to fingerprinting.

Opponents argued the DNA sampling is an illegal search, since police can use the DNA records for investigatory purposes, and not just identification.

"Our Constitution is pretty clear that you can't go and take things from people without a warrant to conduct an investigation. But here we're doing that," said state Sen. Mike Young, R-Indianapolis.

The legislation does contain a process for removing an individual's DNA from the database if the person is not convicted of a felony.

It passed the Senate, 36-13, and the House, 84-13.

Gov. Eric Holcomb now must decide whether to sign the measure into law.

Read more:
Indiana may create DNA record on every person arrested for felony ... - nwitimes.com

April 13, 2017 by Liz Ahlberg Touchstone University of Illinois researchers developed a method to detect and map DNA methylation, which can be a sign of cancer, by threading the DNA through a tiny hole in a thin sheet of conductive material with a current running through it. Credit: Aditya Sarathy

Detecting cancer early, just as changes are beginning in DNA, could enhance diagnosis and treatment as well as further our understanding of the disease. A new study by University of Illinois researchers describes a method to detect, count and map tiny additions to DNA called methylations, which can be a warning sign of cancer, with unprecedented resolution.

The method threads DNA strands through a tiny hole, called a nanopore, in an atomically thin sheet of material with an electrical current running through it. The study was published in the inaugural issue of the journal npj 2D Materials and Applications, a new journal from Nature Press.

"One or a few methylations is not a big deal, but if there are many of them and they are packed close together, then it's bad," said study leader Jean-Pierre Leburton, a professor of electrical and computer engineering at Illinois. "DNA methylation is actually a starting process for cancer. So we want to detect how many of them there are and how close together they are. That can tell us at which stage the cancer is."

Other attempts at using nanopores to detect methylation have been limited in resolution. Researchers begin by punching a tiny hole in a flat sheet of material only one atom or molecule thick. The pore is submerged in a salt solution and an electrical current is applied to drive the DNA molecule through the pore. Dips in the current alert researchers that a methyl group is passing through. However, when two or three are close together, the pore interprets it as one signal, Leburton said.

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The Illinois group tried a slightly different approach. They applied a current directly to the conductive sheet surrounding the pore. Working with Klaus Schulten, a professor of physics at Illinois, Leburton's group at Illinois' Beckman Institute for Advanced Science and Technology used advanced computer simulations to test applying current to different flat materials, such as graphene and molybdenum disulfide, as methylated DNA was threaded through.

"Our simulations indicate that measuring the current through the membrane instead of just the solution around it is much more precise," Leburton said. "If you have two methylations close together, even only 10 base pairs away, you continue to see two dips and no overlapping. We also can map where they are on the strand, so we can see how many there are and where they are."

Leburton's group is working with collaborators to improve DNA threading, to cut down on noise in the electrical signal and to perform experiments to verify their simulations.

Explore further: Semiconductor membrane mimics biological behavior of ion channels

More information: Hu Qiu et al, Detection and mapping of DNA methylation with 2D material nanopores, npj 2D Materials and Applications (2017). DOI: 10.1038/s41699-017-0005-7

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Researchers at the National Institute of Standards and Technology (NIST) have simulated a new concept for rapid, accurate gene sequencing by pulling a DNA molecule through a tiny, chemically activated hole in graphenean ...

Detecting cancer early, just as changes are beginning in DNA, could enhance diagnosis and treatment as well as further our understanding of the disease. A new study by University of Illinois researchers describes a method ...

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Nanopores could map small changes in DNA that signal big shifts in cancer - Phys.Org