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The Evolutionary Perspective
Category Archives: DNA
Posted: February 25, 2017 at 2:51 pm
February 24, 2017 11:19 PM By Natasha Brown
PHILADELPHIA (CBS) Our region is filled with a mosaic of faces, diverse looks, ethnicities and languages abound.
Our differences are often pronounced, but professors at West Chester University are trying to start a different conversation, where diversity becomes more of a topic of finding similarities.
On campus, we met up with a group of curious students looking to delve into their ancestry. They found an outlet in Professor Anita Foemans diversity project.
The project started 10 years ago with a grant to look at diversity in a non-traditional way, Foeman said.
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A decade later and the availability and affordability of ancestry DNA tests has expanded her mission with students jumping at the chance to explore.
The way weve used it to get people to talk about race in a positive way, Foeman said. This project is humbling in that you start with yourself and the diversity within.
Some students have already gone through the process.
We went on a journey with these students as they began the process, submitting DNA samples, looking beyond the narrative theyve always been told about themselves. As they discover, there is more than meets the eye when they get their results.
I myself even decided to join in, exploring my own ancestry. After a few weeks, the ancestry DNA results were back. It was time for the big reveal.
My results: 59 percent African background and 40 percent European background. While one of the participants, Sarah, expected more Scandinavian roots, I didnt expect to find any.
Our results sparked lively conversations which is exactly the goal.
In our research so far, it doesnt change someones identity, but it does soften how they talk about race and diversity. At a time when headlines seem to suggest an ongoing racial divide in our country, Dr. Foeman is suggesting a new outlook, one DNA test at a time.
Natasha Brown is the Emmy Award-winning anchor for the weekend evening editions of Eyewitness News on CBS 3 and The CW Philly. Natasha joined CBS 3 as a general assignment reporter in December, 2002. She came to the station from Pittsbu…
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Professors Using DNA To Bridge Racial Divide, Focus On Our Similarities – CBS Local
Posted: February 24, 2017 at 5:54 pm
PRINCETON, Mass. — The highly-specialized DNA technology that investigators used to create a profile of a person of interest in the killing of Vanessa Marcotte could mean the difference between solving a crime and a cold case, CBS Boston reports.
Marcotte, a New York City Google employee, was 27 when she was killed while jogging near her parents Princeton home on August 7, 2016.
The technology has the potential to show police the killers face and give them desperately needed clues.
Worcester County District Attorney Joseph Early said Thursday that investigators used a combination of witness statements and a DNA profile developed with the help of scientists at private lab Parabon NanoLab to develop a description of a person of interest in the case. The person of interest is described as a Hispanic or Latino man, about 30 years old, with an athletic build, light or medium skin, and a shaved head or very short hair.
He added that the person of interest would have had scratches on his face, neck, hands and arms after the Aug. 7 attack, the Associated Press reports.
Early wouldnt say where investigators collected the DNA. When asked by a reporter whether the DNA was recovered from Marcottes fingernails, Early said, I cant speak to that, but he did have a lot of scratches.
Using a small amount of DNA, scientists at the Parabon NanoLab are able to predict certain physical features and develop a forensic profile of the person.
We focus on things that dont change with the environment, so we do pigmentation which is eye, hair, and skin color, as well as freckling, Dr. Ellen McRae Greytak, director of the Parabon NanoLab, told CBS Boston.
She added that the lab also focuses on the face and persons ancestry.
When investigators run out of options, Greytak said they contact her lab, oftentimes for help generating new leads on cold cases.
And what we do is we tell them of those 400 people in the area, you can eliminate 90-95 percent because they dont match this profile, Greytak said. And now you can focus on a manageable number of people.
From there, the investigators have more information to work with and become more hopeful of solving the case.
It is not yet possible to predict height and weight using the technology.
Anyone with information about the Vanessa Marcotte case is asked to call the Massachusetts State Police tipline at 508-453-7589.
2017 CBS Interactive Inc. All Rights Reserved.
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Vanessa Marcotte case: New DNA technology could help solve jogger’s slaying – CBS News
Posted: at 5:54 pm
Neanderthals went extinct 30,000 years ago, taking their precious genetic material with them. But their DNA lives on in their hybrid ancestors: modern-day humans.
smithsonian.com February 24, 2017 11:06AM
Neanderthals may have gone extinct 30,000 years ago, but they still live on inside us. Ever since scientists discovered that Neanderthal DNA comprises roughly 2 percent of the genomes of modern humans of European and Asian heritage, theyve speculated about how exactly those lingering genes affect us today. Now weve found that even though most humans hardly resemble Neanderthals in appearance, their DNA still influences how our genes work today.
Humans and Neanderthals began splitting on the evolutionary tree about 700,000 years ago, but continued to interbreed up until at least 50,000 years ago. Despite a genetic incompatibility that may have made reproduction difficult, enough hybrid human-Neanderthals were born to enshrine bits of their DNA throughout the human genome. Previous research has found that the Neanderthal DNA sequences and genes found in modern humans are linked to depression, fat metabolism and a host of other traits and conditions.
However, just because we can see a gene doesn’t mean we know how it works. Genes can be expressed at different strengths, and sometimes not at all. It all comes down to how that DNA is used by the RNA in our cells, which follows DNA’s instructions to make proteins. Cells can “regulate” various genes by choosing to use them, ignore them or modify them to make RNA. Unfortunately, unlike relatively permanent DNA, RNA is unstable and thus rarely found in fossils, making it difficult to analyze how the cells of extinct organisms actually utilized their DNA.
In a study published yesterday in the journal Cell, University of Washington genetics researcher Rajiv McCoy and co-authors got around the lack of ancient Neanderthal data by instead looking in their living descendants: today’s hybrid humans. “[We set out to use] gene expression from modern humans to get an idea of how gene flow from Neanderthals is impacting human gene expression,” says McCoy.
Using a dataset of the genomes of more than 400 deceased people, the researchers looked for instances of heterozygous genes: genes that are the result of a person inheriting a human gene from one parent and a Neanderthal gene from another. The dataset included samples of tissues from 52 different parts of the body, McCoys says, allowing the researchers to compare how human and Neanderthal genes were expressed in these different areas by comparing how much of each gene was transcribed into RNA.
Through analyzing these individuals with human and Neanderthal alleles, or gene variations, McCoy and his team found differences in human and Neanderthal gene expression in 25 percent of the areas they tested. Those differences had potential effects in traits ranging from height to likelihood of contracting lupus. “It really spans the whole spectrum of human genes,” says McCoy.
The researchers were also able to compare how strongly or weakly the human and Neanderthal genes were expressed in different body parts.
Interestingly, McCoy says, they found that Neanderthal genes in the brains and testes of the people tested were expressed more weakly than genes in other areas. The reason for this is likely unequal evolution: As humans continued to evolve away from Neanderthals, McCoy says, it’s likely that those body parts have evolved faster than others. Thus, they diverged further from the Neanderthal genes, and are less likely to be expressed by cells there.
For Vanderbilt University geneticist Tony Capra, who was not involved in this study, the reduced gene expression in the testes may be a sign of how mutations from Neanderthals might have reduced the fertility of early human-Neanderthal hybrids. “It further illustrates that Neanderthal DNA that remains in modern humans has the potential to influence diverse traits,” says Capra, who has done work scanning electronic medical recordsto look for the effects of Neanderthal DNA on our health.
“This is a very comprehensive study of the impact of Neanderthal introgression on gene expression in modern humans,” adds Fernando Racimo, a researcher at New York Genome Center who also wasn’t involved in the study. Racimo says he would like to see research into other cases of human hybridization, specificallyancient Denovisans and Australian aboriginals, whose genes live on in the inhabitants of Australias Melanesian islands.
McCoy says studying the genetic legacies of Melanesian people is on his wish list, but that will have to wait until RNA samples are collected. “I mooch off of other people’s data,” he jokes.
The technique used in this study could be applied within the human species too, McCoy adds. Comparing allele expression in different areas of the body and among different people could help scientists pin down more of the intricacies of gene expression, he says. But even by just probingthe role of Neanderthal DNA in our genomes, we can still better understand how our disparate genes work together to make us.
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How Ancient Neanderthal DNA Still Influences Our Genes Today – Smithsonian
Posted: at 5:54 pm
Police believe this man killed Liberty German and Abigail Williams on Feb. 13. German took this photo from her phone before the two were forced to a remote area along Deer Creek, where the girls were killed.(Photo: Provided)
DELPHI, Ind. Carroll County SheriffTobe Leazenby clarified his on-air comments from aFriday interviewduring a Fox59 report,notinghe didn’t intendto confirm or denythat investigators collected DNA evidence in thedouble homicide investigation ofAbby Williams and Liberty German.
The TV station’s report said investigators acquired DNA evidence critical to the investigation of the case. However, Leazenby said he was speaking about physicalevidence in general and not about DNA evidence in particular.
“We can’t say that we have evidence or that we don’t,”Leazenby said. “At this point all facets of physical evidence are being considered.”
Williams and German disappeared Feb. 13 while hiking the historic trails near the Monon High Bridge. Family members reported the girls missing when they failed to return to their pick-up point.
Volunteer searchers found the girls’ bodies about 12:15 p.m. Feb. 14. They were about 50 feet north of Deer Creek about a half-mile east of the bridge, police said.
Police released a grainy photo of a man walking the trails about the same time as German and Williams and days later said the man was a suspected in the killings. Investigators announced this week that the photo was taken by German, who also recorded the voice of the man suspected of killing the girls.
Other than the photo and the audio recording, police have released very little of the evidence they have collected.
Police said Feb. 15 that the manner of death was homicide, based on the autopsy that day. But they refused to discuss the cause of death or the injuries the girls endured based on the autopsy.
Leazenby said the department is expediting the analysis of all physical evidence, fairly common in a case such as this. WhileLeazenby said he can’t speak to specifically what evidence was acquired at the scene, every crime scene has physical evidence.
“There is an old rule in our business that any time there is an exchange involvinghumans there is take and leave. You take something and you leave something … whether it’s hair shed, skin or even a gum wrapper.”
Leazenby said he felt the need to clarify the Fox59 report because “we don’t want to have mass confusion.”
A reward fund set up for information leading to an arrest topped $50,000 on Thursday.
By early afternoon Friday, police have received more than 5,000 tips in the last 11 days, Leazenby said. Investigators are following up on these tips.
Email tips now outnumber phone tips by 2 to 1,he said.
Tips may be phoned in at844-459-5786 or emailed firstname.lastname@example.org. Tipsters may remain anonymous.
Call J&C reporter Emma Ea Ambrose at 765-431-1192. Follow her on Twitter: @emma_ea_ambrose.
J&C breaking news reporter Ron Wilkins can be reached at 765-420-5231; follow on Twitter@RonWilkins2
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Sheriff clarifies reports of DNA evidence – Journal and Courier
Posted: at 5:54 pm
February 24, 2017 by Whitney Clavin A protein called DNA primase (tan) begins to replicate DNA when an iron-sulfur cluster within it is oxidized, or loses an electron (blue and purple). Once this primase has made an RNA primer, a protein signaling partner, presumably DNA polymerase alpha (blue), sends an electron fromits reduced cluster, which has an extra electron (yellow and red). The electron travels through the DNA/RNA helix to primase, which comes off the DNA.Thiselectron transfer signalsthe next steps in replication. Credit: Caltech
In the early 1990s, Jacqueline Barton, the John G. Kirkwood and Arthur A. Noyes Professor of Chemistry at Caltech, discovered an unexpected property of DNAthat it can act like an electrical wire to transfer electrons quickly across long distances. Later, she and her colleagues showed that cells take advantage of this trait to help locate and repair potentially harmful mutations to DNA.
Now, Barton’s lab has shown that this wire-like property of DNA is also involved in a different critical cellular function: replicating DNA. When cells divide and replicate themselves in our bodiesfor example in the brain, heart, bone marrow, and fingernailsthe double-stranded helix of DNA is copied. DNA also copies itself in reproductive cells that are passed on to progeny.
The new Caltech-led study, based on work by graduate student Elizabeth O’Brien in collaboration with Walter Chazin’s group at Vanderbilt University, shows that a key protein required for replicating DNA depends on electrons traveling through DNA.
“Nature is the best chemist and knows exactly how to take advantage of DNA electron-transport chemistry,” says Barton, who is also the Norman Davidson Leadership Chair of Caltech’s Division of Chemistry and Chemical Engineering.
“The electron transfer process in DNA occurs very quickly,” says O’Brien, lead author of the study, appearing in the February 24 issue of Science. “It makes sense that the cell would utilize this quick-acting pathway to regulate DNA replication, which necessarily is a very rapid process.”
The researchers found their first clue that DNA replication might involve the transport of electrons through the double helix by taking a closer look at the proteins involved. Two of the main players in DNA replication, critical at the start of the process, are the proteins DNA primase and DNA polymerase alpha. DNA primase typically binds to single-stranded, uncoiled DNA to begin the replication process. It creates a “primer” made of RNA to help DNA polymerase alpha start its job of copying the single strand of DNA to create a new segment of double-helical DNA.
DNA primase and DNA polymerase alpha molecules both contain iron-sulfur clusters. Barton and her colleagues previously discovered that these metal clusters are crucial for DNA electron transport in DNA repair. In DNA repair, specific proteins send electrons down the double helix to other DNA-bound repair proteins as a way to “test the line,” so to speak, and make sure there are no mutations in the DNA. If there are mutations, the line is essentially broken, alerting the cell that mutations are in need of repair. The iron-sulfur clusters in the DNA repair proteins are responsible for donating and accepting traveling electrons.
Barton and her group wanted to know if the iron-sulfur clusters were doing something similar in the DNA-replication proteins.
“We knew the iron-sulfur clusters must be doing something in the DNA-replication proteins, otherwise why would they be there? Iron can damage the DNA, so nature would not have wanted the iron there were it not for a good reason,” says Barton.
Through a series of tests in which mutations were introduced into the DNA primase protein, the researchers showed that this protein needs to be in an oxidized statewhich means it has lost electronsto bind tightly to DNA and participate in DNA electron transport. When the protein is reducedmeaning it has gained electronsit does not bind tightly to DNA.
“The electronic state of the iron-sulfur cluster in DNA primase acts like an on/off switch to initiate DNA replication,” says O’Brien.
What’s more, the researchers demonstrated that electron transport through DNA plays a role in signaling DNA primase to leave the DNA strand. (Though DNA primase must bind to single-stranded DNA to kick off replication, the process cannot begin in earnest until the protein pops back off the strand).
The scientists propose that the DNA polymerase alpha protein, which sits on the double helix strand, sends electrons down the strand to DNA primase. DNA primase accepts the electrons, becomes reduced, and lets go of the DNA. This donation and acceptance of electrons is done with the help of the iron-sulfur clusters.
“You have to get the DNA primase off the DNA quicklythat really starts the whole replication process,” says Barton. “It’s a hand off of electrons from one cluster to the other through the DNA double helix.”
Many proteins involved in DNA reactions also contain iron-sulfur clusters and may also play roles in DNA electron transport chemistry, Barton says. What began as a fundamental question 25 years ago about whether DNA could support migration of electrons continues to lead to new questions about the chemical workings of cells. “That’s the wonder of basic research,” she says. “You start with one question and the answer leads you to new questions and new areas.”
Explore further: Structure of key DNA replication protein solved
More information: Elizabeth O’Brien et al. The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport, Science (2017). DOI: 10.1126/science.aag1789
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Electrons use DNA like a wire for signaling DNA replication – Phys.org – Phys.Org
DNA evidence discovered at scene where two Indiana teens were found murdered now top priority – kfor.com
Posted: at 5:54 pm
DELPHI, Ind. – Investigators say they discovered DNA evidence at the crime scene where two Indiana teenagers were found murdered last week.
That evidence now has top priority for processing by investigators, Fox 59 reports.
Its a strong lead, in a case where authorities have been clamoring for any clue about the suspect who murdered 13-year-old Abby Williams and 14-year-old Libby German.
In an attempt to identify the possible murder suspect, investigators previously released a grainy suspect photo, a chilling audio of a man’s voice saying “down the hill,” and now a DNA sample.
Photos of the man police want to speak with.
We asked for a fast-track as far as that piece information, said Carroll County Sheriff Tobe Leazenby. “So I cant go into specifics because of the ongoing [investigation].
Police havent said specifically what kind of evidence they recovered
Investigators believe the girls met the suspect in a chance encounter or the person knew they were going to be there. Liberty German’s decision to make a recording provided police with their best information.
The bodies were discovered along the edge of Deer Creek in Delphi which is about a half-mile away from the Monon High Bridge, an abandoned rail bridge over Deer Creekthat was the last place the two girls were seen. They were supposed to meet with family members later Monday evening, but when the teens didnt show up, their families called police.
Officials are asking anyonewho may have taken pictures in the area or was just on the trail to contact authoritiesimmediately.
Anyone with information about this case is encouraged to call the Delphi Homicide Investigation Tip Line at (844) 459-5786. Information can also be reported by calling the Indiana State Police at (800) 382-7537, or the Carroll County Sheriffs Department at (765) 564-2413. Information can also be emailed to Abbyandlibbytip@cacoshrf.com.Information can be reported anonymously
The Indiana State Police, the FBI, and the Carroll County Sheriffs Department have announced a reward ofup to $41,000 in the case, depending upon the value of the information provided.
New tool to map RNA-DNA interactions could help researchers translate gene sequences into functions – Phys.Org
Posted: at 5:54 pm
February 24, 2017 Artistic rendering of RNA-DNA interactions. A 3-D structure of tightly coiled DNA is depicted as the body of a dragon in Chinese myth. Interacting RNAs are depicted as hairs, whiskers and claws, which are essential for the dragon to function. Credit: Victor O. Leshyk
Bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that’s capable of providing a full account of all the RNA molecules that interact with a segment of DNA, as well as the locations of all these interactionsin just a single experiment.
RNA molecules can attach to particular DNA sequences to help control how much protein these particular genes produce within a given time, and within a given cell. And by knowing what genes produce these regulatory RNAs, researchers can start to identify new functions and instructions encoded in the genome.
“Most of the human genome sequence is now known, but we still don’t know what most of these sequences mean,” said Sheng Zhong, bioengineering professor at the UC San Diego Jacobs School of Engineering and the study’s lead author. “To better understand the functions of the genome, it would be useful to have the entire catalog of all the RNA molecules that interact with DNA, and what sequences they interact with. We’ve developed a tool that can give us that information.”
Zhong and his team published their findings in the Feb. issue of Current Biology.
Existing methods to study RNA-DNA interactions are only capable of analyzing one RNA molecule at a time, making it impossible to analyze an entire set of RNA-DNA interactions involving hundreds of RNA molecules.
“It could take years to analyze all these interactions,” said Tri Nguyen, a bioengineering Ph.D. student at UC San Diego and a co-first author of the study.
Using MARGI, an entire set of RNA-DNA interactions could be analyzed in a single experiment that takes one to two weeks.
The MARGI technique starts out with a mixture containing DNA that’s been cut into short pieces and RNA. In this mixture, a subset of RNA molecules are interacting with particular DNA pieces. A specially designed linker is then added to connect the interacting RNA-DNA pairs. Linked RNA-DNA pairs are selectively fished out, then converted into chimeric sequences that can all be read at once using high-throughput sequencing.
Zhong and his team tested the method’s accuracy by seeing if it produced false positive results. First, the researchers mixed RNA and DNA from both fruit fly and human cells, creating both “true” RNA-DNA pairs, meaning they’re either fully human or fully fruit fly, and “false” RNA-DNA pairs, meaning they’re half human and half fruit flythese are the ones that shouldn’t be detected. The team then screened the entire mixture using MARGI. The method detected a large set of true RNA-DNA interactions, but it also detected approximately 2 percent of the false ones.
“This method is not perfect, but it’s an important step toward creating a full functional annotation of the genome,” said co-first author Bharat Sridhar, a visiting bioengineering researcher in Zhong’s group.
Explore further: Size matters… and structure too: New tool predicts the interaction of proteins with long non-coding RNAs
More information: Bharat Sridhar et al, Systematic Mapping of RNA-Chromatin Interactions InVivo, Current Biology (2017). DOI: 10.1016/j.cub.2017.01.011
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Posted: February 23, 2017 at 12:48 pm
Authorities said Thursday that they have DNA and are seeking a person of interest in the baffling murder of Vanessa Marcotte in the Central Massachusetts town of Princeton.
Worcester District Attorney Joseph D. Early Jr. said at a press conference that, based on witness statements and information extracted from the DNA, investigators are looking for a Hispanic or Latino male in his thirties who may have been in the area where Marcotte was killed on Aug. 7. He asked for the publics help in finding the person.
Early described the person of interest as having light to medium brown skin, an athletic build, and a shaved head or short hair. He said the person would possibly have had scratches on his face, neck, arms, hands, and upper body around the time of the murder.
Early would not say where the DNA was recovered, but added, We feel this DNA is from our person of interest.
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He cautioned people not to confront the man, if they think they know who he is. They should call authorities instead.
I could only ask for your prayers, said John Marcotte. Thats all we want: justice.
Marcotte, 27, who lived in New York, was visiting her mother on Sunday, Aug. 7, when she went for an afternoon run. When she didnt return, her family called police, who found her body in the woods off Brooks Station Road, about a half-mile from her mothers home.
Police believe the attack happened between 1 p.m. when Marcotte left her mothers house and 4 p.m. Her body was found at 8:20 p.m.
Police revealed in November that they were looking for a dark SUV seen in the area. On Thursday, Early reiterated that detail.
Early said anyone with information fitting the decription of the person of interest should contact authorities at 508-453-7589, an anonymous tip line.
We want to do everything we can to find this killer, he said.
The rest is here:
Officials announce break in Marcotte murder case – The Boston Globe
Posted: at 12:48 pm
DNA evidence proves a maternal dynasty existed in North America 1200 years ago
An ancient North American dynasty ruling parts of the what is now the southwestern US 1,200 years ago used to only pass its power to elites born from powerful women, according to new DNA evidence. In a paper published in the journal Nature …
New DNA Evidence Just Gave Us Unprecedented Insight Into the Mysterious Chaco Civilisation
Ancient DNA Yields Unprecedented Insights into Mysterious Chaco Civilization
DNA suggest Chaco culture passed on power via mom
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DNA evidence proves a maternal dynasty existed in North America 1200 years ago – Quartz