Category Archives: DNA

YUCAIPA >> Detectives finally got a break in a 16-year-old rape case thanks to DNA.

In July 2001, a woman reported she had been walking near California Street and Avenue E when four men pulled alongside her and forced her into their vehicle, according to a sheriffs news release. They drove her to a remote location and gang raped her, the news release said.

During the investigation DNA was collected as evidence and entered into the Combined DNA Index System database, but there wasnt a match at the time of the incident.

The case went cold. Then someone was arrested on an unrelated crime last November, bringing the case back to the surface, according to sheriffs officials.

Jose Angel Bueno, 47, of Riverside, was arrested for an unrelated crime. His DNA was taken by Riverside authorities and sent to the Department of Justice to be added into the national database.

Buenos sample came back as a match to the DNA collected from the unsolved 2001 rape case, officials said.

Detectives found Bueno in custody at West Valley Detention Center Wednesday on an unrelated case. They booked him for suspicion of rape and kidnapping with the intent to commit rape. Hes being held in lieu of $1 million bail.

Detectives believe there may be more victims that havent come forward.

Anyone with information is asked to call sheriffs detectives at 909-918-2305.

Go here to read the rest:
DNA links Riverside man to 2001 gang rape in Yucaipa, sheriff's ... - Redlands Daily Facts

An 'ignition key' revs up DNA shuffling to make antibodies ... Science Daily Rearranging the genome is a risky endeavor, and human cells reserve it for special occasions, like making egg and sperm cells. and more »

Original post:
An 'ignition key' revs up DNA shuffling to make antibodies ... - Science Daily

In the evolution of cancer, the most vicious circle may be that perpetrated by circular DNA, which is also known as extrachromosomal DNA (ecDNA). According to a new study, ecDNA is found in nearly half of all types of tumors, and it encodes multiple copies of driver oncogenes, or cancer-driving genes. Worse, driver oncogenes appear to be more harmful in ecDNA than in chromosomal DNA. Driver oncogenes in ecDNA contribute to tumor heterogeneity and drug resistance.

These new findings appeared February 8 in the journal Nature, in an article entitled, Extrachromosomal Oncogene Amplification Drives Tumour Evolution and Genetic Heterogeneity. The article indicates that ecDNA, once thought to be rare in tumor cells, is actually very common and seems to play a fundamental role in tumor evolution. The articles main pointthat ecDNA contributes to accelerated evolution in cancercould lead to new ways to prevent and treat many malignancies

The Nature paper is based on a study led by an interdisciplinary team led jointly by Paul Mischel, M.D., a member of the Ludwig Institute for Cancer Research, and Vineet Bafna, Ph.D., a professor at the University of California San Diego School of Medicine. The scientists analyzed cells from 17 different types of cancer to explore ecDNA. They also analyzed the structure and function of chromosomes of 2572 dividing cells during metaphase, and they developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis.

Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells, wrote the authors of the Nature paper. Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level.

Essentially, the researchers showed that ecDNA plays a far bigger role in the growth, diversity, and drug resistance of cancer cells than the same genes housed on chromosomes in such tumors.

Weve discovered something fundamental about how cancers diversify and evolve, said Mischel. This is an essential rethinking about what goes wrong with genes in cancer.

The Nature paper describes how the scientists performed whole-genome sequencing, structural modeling, and cytogenetics to detect, quantify, and analyze ecDNA. They found that ecDNA was present in about 40% of tumor cell lines, but was extremely rare in normal cells. And when the scientists looked specifically at patient-derived models of brain tumors, nearly 90% of these carried ecDNA. The researchers also found that oncogenes are more likely to occur on ecDNA than on chromosomes.

Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification, the authors added. We validated these predictions by quantitative analyses of cancer samples and verified their models predictions through experiments conducted on tumor samples from patients.

These studies revealed that tumors are more heterogeneous when oncogenes are amplified on ecDNA instead of on chromosomes, enabling them to more rapidly achieve and maintain high levels of cancer promoting genes.

Unlike chromosomes, ecDNA is parceled out randomly to daughter cells when a tumor cell divides. So, any given cell in a tumor might have no ecDNA in its nucleus, or it might be crammed with ecDNA. And the greater the variation in oncogene copy number, the greater the heterogeneity of cells in a tumor. It is this cellular diversity that makes tumors far more resistant to environmental challenges, most notably drug therapy.

The new work was inspired by a previous study led by Mischel and reported in Science in 2014. In that study, Mischel and colleagues revealed that ecDNA plays a central role in the drug resistance of certain brain tumors.

This finding came as a surprise because, for decades, cancer biologists had focused more on which genes promote cancer rather than where those genes are located. Genomic technologies too evolved along lines that favored this type of analysis. Although a few cancer biologists in the 1960s had described the presence of ecDNA in some tumor cells, they lacked the tools to quantify ecDNA, so the phenomenon had long been considered rare and inconsequential to the development of cancer.

It occurred to us after we made the observations published in 2014 that maybe ecDNA is a lot more common and consequential than anyone thought, explained Mischel. Understanding how tumor cells evolve and how they increase the copy number and variability of their drivers is likely to yield some pretty important clues about the fundamental biology of cancer and how we might be able to target it.

Mischel his team are now working to unearth the molecular mechanisms involved in the genesis and maintenance of ecDNA and exploring how ecDNA levels change in response to changes in the tumors internal environment.

Excerpt from:
Circular DNA Helps Cancer Roll with the Therapeutic Punches - Genetic Engineering & Biotechnology News

Are those DNA tests you take accurate? Do they work?

Chuck Ringwalt, wltx 11:35 PM. EST February 08, 2017

D.N.A. Deceit? Genetic Testing and Its Legitamacy (Photo: Ringwalt, Charles)

Columbia, SC (WLTX) - It's not unusual to want to learn more about yourself and after a few clicks online, you could be drowning in information. There are dozens of genetic tests offering the latest and greatest ways to answering your questions. You send them some salvia or a swab from your cheek and from that, they'll analyze your D.N.A., but sometimes the results you get back aren't definitive.

Richard Moody works at WLTX. He's adopted and said he doesn't have a desire to learn about his birth parents, but is interested in learning more about himself.

"Where did I originate? Where did our people, where did my people originate? And anything I could find out having to do for health reasons," Moody said.

Moody turned to genetic testing. He first used Ancestry D.N.A and about a year later used 23andMe

With some of his saliva packed and shipped, he waited for the results. What he got back provided some answers, but also raised some questions.

"Yeah. It would have been really cool if they were identical. Then I would have gone, 'Ah-Ha.' Now I go, 'Ehh,'" said Moody. Ancestry D.N.A estimated that his ancestry comprised mostly like those from Western Europe at 49 percent.

This included the countries of Belgium, France, Germany, Netherlands, Switzerland, Luxembourg, and Liechtenstein.

23&Me estimated that Richard is also European, but not primarily Western. These result said Moody was British and Irish at 53.5 percent and only 13.6 percent French and German.

"When you see something and you're going for information, it makes me a little uneasy just because they say two different things. From a broad perspective they say the same thing, but when you get granular, they go in opposite directions. 23&Me was a lot more granular," Moody said.

"It's good. It's fun information, but you do have to look at it as just that and not necessarily something to hang your hat on," Whitney Dobek said.

Dobek is a genetic counselor at the University of South Carolina's School of Medicine.

"These labs will take a sample from an individual, get the DNA information on those regions, see what the patterns are of variation and then they will compare that to their reference and what we know from the research and be able to use algorithms and determine what percentage ancestry you might be and how likely it is that you might have blue eyes," said Dobek.

Dobek admitted she's also taken 23andMe test andsaid these types of services run digitally. She said there is no one looking through a microscope, but millions of pieces of data being run through hard drives. "The testing itself is very computerized. It's done with this chip technology. That even our clinical genetic labs use and they're able to quickly pull down all of your variants out of your D.N.A and upload that into a computer and do the comparisons that way," she said. "The variation between the different labs has to do with the data that they are pulling from, so every lab has their own reference that they're looking at and depending on which lab you're pulling from, you're going to get slightly different answers because they're pulling from slightly different data and in addition to that they may be looking at slightly different variations within your D.N.A, so it's not necessarily that your ancestry isn't there. It just might be that that part of your D.N.A wasn't looked at."

And even though Moody said he has his reservations, he still very interested.

"You know, it's not one hundred percent correct, but it is it's absolutely noteworthy. It also says you're not likely to have cheek dimples. Well I don't, so it was right about that," he said.

( 2017 WLTX)

Go here to see the original:
DNA Deceit? Genetic Testing and It's Legitimacy - WLTX.com

DNA deceit? Are you putting your information in the wrong hands in order to learn more about your family history. News19's Chuck Ringwalt finds out.

Chuck Ringwalt, wltx 10:57 PM. EST February 08, 2017

D.N.A. (Photo: Ringwalt, Charles)

Columbia, SC (WLTX) - Companies like Ancestry D.N.A and 23andMe tout a more in-depth ancestry breakdown through analyzing your D.N.A for a relatively low cost. You get just that, but what else do they get in return?

"It kind of frightens me in a way because, you know, golly, just one little bit of saliva and they can tell a lot about me," Richard Moody said.

Moody works at WLTX and decided to have his D.N.A tested.

He said he didn't realize how much he was giving up when he sent out his saliva and checked the user agreement.

"Okay well now law enforcement can get it. Well, I haven't committed any crimes, however, what's the next thing that they're going to release and say, 'They can get it?' Is it a testing facility or whatever? That bothers me," he said.

Moody took two tests using Ancestry D.N.A and 23andMe. When you give your consent these companies have the authority to use and share your information for certain purposes like the service they provide, business improvements, advertising and research.

In certain cases they might be forced to hand over your information to the authorities if ever required by law. In an 2015 interview with CBS This Morning CEO of 23andMe Anne Wojcicki said they take your privacy seriously.

"We do everything we can to protect your privacy. And we've said under subpoenas, etc. We would do everything we can to fight those. Obviously you need to comply with law enforcement," she said.

According to 23andMe, the company has only receivedfour requests in the past 10 years and have been successful in their refusal to provide the data.

Consumer protection attorney Dave Maxfield said always read the fine print.

"You've given up a lot in exchange for something. Is it worth it? I mean you have to decide for yourself, but you have to decide as an informed consumer," he said.

Knowing what he does now, Moody said he would have paid more attention to the documents, but it wouldn't have stopped him from taking the tests.

"I would have still done it," he said.

This is part one of our story. Another aspect you may be concerned about is your results. Are they accurate? We had some questions about Moody's he took the two tests and ended up with two different sets of results. Tune in to News 19 at 11 p.m. for "D.N.A. Deceit? Genetic Testing and Its Legitimacy".

( 2017 WLTX)

Read the original post:
DNA Deceit? Genetic Testing and Privacy Concerns - WLTX.com

Snapshot flier(Photo: The Republic)

Phoenix police for the first timehave turned to technology that uses DNA samples to generate facial composites, in an effort to solve a 12-year-old caseinvolving a newborndiscarded in an airport trash can.

Detectives with the Phoenix PoliceCold Case Squadhave been searching for the mother of the baby girl since 2005, when the babywas found dead in a Sky Harbor International Airport trash bin. The cleaning crew found the newborn in a women's restroom with her umbilical cord still attached, police said.

Now, using the advanced technology, police have developed a computer-generated composite showing themost likely traits of a person who shares the DNA found at the crime scene.Something as simple as blood left at the crime scene can now be used to re-create what a person of interest may look like, police said on Wednesday.

Sandra Rodriguez, the original investigator on the case, said Wednesday the case has stuck with her ever since.

"It (the case) didn't go anywhere. There was just too much information and we just couldn't narrow it, or I couldn't narrow it down," Rodriguez said.

Rodriguez and several Phoenix cold-case detectives, who also met with the media on Wednesday,saidthey developed a profile on the mother that went into the national database but never received ahit on it. They since have exhausted their investigative possibilities and now areturning to the DNA technology to generate a composite, the first time the department has used the technology.

Parabon Snapshotis a DNAphenotyping, ancestry, and kinship analysis tool, according to the Police Department. By using DNA samples, the forensic DNA-analysisservicepredicts the physical appearance and ancestry of an unknown person.

The DNA phenotyping technology is able to create what looks like an avatar of a human based off what their DNA describes as being the most likely traits that they may possess. From freckles to eye color to which region of the world a person may have originated from, the technology is able to vividly suggest what a possible suspect may look like, though police stressed it is not considered a guarantee of a person's appearance.

The technology produces a report and composite profile based off the extracted DNA. However, DNA alone cannot provide weight or age information, said police, who added that a standardsample test costs $3,600.

With the help of the new composite depicting what the infant's mother may look like, police are seeking the public's help in finding any new leads in the case.

The Snapshot prediction results aredifferent from a sketch, where a victim will describe the features of a suspect to then be drawn out. Instead, Snapshot considers probabilities of certain traits and similar characteristics that a person of interest may possess based on their DNA, in this case shared by the mother and the newborn.

Cold-case detectives said they are unsure if they will use this technology on future cases.

Anyone with information about the case is asked to call Phoenix police at 602-262-6141 or Silent Witness at 480-948-6377 (WITNESS).

.

Read or Share this story: http://azc.cc/2k59VT8

See the article here:
Phoenix police use DNA composite to try to help solve 2005 cold case - AZCentral.com

Chanel Lewis is arraigned in Queens Criminal Court on Sunday, Feb. 5, 2017. Lewis was charged with murder in the strangulation death of Karina Vetrano, 30, as she jogged on a park trail near her Howard Beach home on Aug. 2, 2016. (Credit: Charles Eckert/Pool)

DNA recovered from the body of slain Howard Beach jogger Karina Vetrano was the best kind of genetic evidence for investigators to use to find her suspected killer, said a law enforcement official familiar with the case.

Crime scene detectives found nuclear DNA on Vetrano when her body was discovered the night of Aug. 2 in the weeds of Spring Creek Park in Queens, the official said.

After...

Optimum Online customers get unlimited digital access

There's more to the story! Subscribe now.

To continue reading, Newsday subscribers log in

To continue reading, Newsday subscribers log in or register

The best of Newsday every day in your inbox.

Read the original:
Police: Nuclear DNA led to suspect in Karina Vetrano killing - Newsday

DNA evidence connected an Interlochen man to a 2015 crash that severely injured a woman, according to charges filed this week.

Jeremy Allen Bower, 25, faces charges of operating with a suspended license causing serious injury and leaving the scene of a serious injury accident stemming from a July 1, 2015 crash on M-137 near Interlochen.

A driver told Grand Traverse County Sheriffs deputies that a Mercury Cougar swerved into his lane and crashed into him head-on, severely injuring one passenger.

The Mercury driver attempted to drive away and then fled on foot when his car would no longer drive. Deputies found a large amount of blood in the abandoned car which they sent to the state police crime lab to be sequenced.

Deputies later requested a DNA sample from Bower. The two DNA samples matched, according to the charges, which carry five years in prison.

Bower is also charged as a two-time habitual offender because he has a previous conviction for delivery of marijuana.

More:
DNA Match Links Man To Interlochen Crash - Traverse City Ticker

The Scientist

Non-Chromosomal DNA Drives Tumor Evolution | The Scientist ... The Scientist Researchers discover that short pieces of DNA harboring oncogenes are relatively widespread in cancer. and more »

Go here to see the original:
Non-Chromosomal DNA Drives Tumor Evolution | The Scientist ... - The Scientist

February 7, 2017 by Mark Derewicz Credit: CC0 Public Domain

Day in and day out, in our bodies, the DNA in cells is damaged for a variety of reasons, and thus intercellular DNA-repair systems are fundamental to the maintenance of life. Now scientists from the UNC School of Medicine have confirmed and clarified key molecular details of one of these repair systems, known as nucleotide excision repair.

Using an advanced sequencing technique to map and analyze DNA damage, the scientists demonstrated the functions in bacterial cells of two important excision repair proteins: Mfd and UvrD.

"The biochemical mechanisms of these proteins have been known for years from experiments involving purified protein and DNA, and that's very important, but in this new work we've clarified these proteins' roles in living cells," said co-senior author Christopher P. Selby, PhD, research assistant professor of biochemistry and biophysics at UNC.

"Ultimately, this better understanding of bacterial DNA repair could be useful toward the development of antibacterial drugs," said co-senior author Aziz Sancar, MD, PhD, the Sarah Graham Kenan Professor of Biochemistry and Biophysics at UNC.

The research publishes this week in the Proceedings of the National Academy of Sciences.

Sancar was awarded the 2015 Nobel Prize for Chemistry for his research in the 1980s and early 1990s on excision repair in bacteria and in human cells. This repair process, which also occurs in animal cells, fixes one of the most common forms of DNA damage: the bulky adduct, an unwanted chemical modification of DNA typically caused by a toxin or ultraviolet (UV) radiation.

To study excision repair in cells, Sancar, Selby and colleagues recently developed a new technique, XR-seq, which allows investigators to isolate and sequence the small lengths of adduct-damaged DNA that are snipped from the genome during the excision repair process. Knowing the sequences of these DNA snippets allows their locations in the genome to be mapped precisely. They used this method first in 2015 to generate a UV repair map of the human genome, and in 2016 they used the XR-seq method to generate the damage and repair maps of the anticancer cisplatin drug for the entire human genome. Now they have applied this method to answer some fundamental questions about damage repair in E. coli with the potential of developing novel antibiotic drugs.

The un-sticker: Mfd

In this study, which was also led by postdoctoral research associate Ogun Adebali, PhD, the researchers focused largely on Mfd, a protein known from prior work by Sancar and Selby to have a special - and mechanistically unusual - role in excision repair in bacteria.

"I think Mfd is the most interesting protein in E. coli," Selby said. Here's why: When the DNA of a bacterial gene is being transcribed into RNA, and the molecular machinery of transcription gets stuck at a bulky adduct, Mfd appears on the scene, recruits other repair proteins that snip away the damaged section of DNA, and "un-sticks" the transcription machinery so that it can resume its work. This Mfd-guided process is called transcription-coupled repair, and it accounts for a much higher rate of excision repair on strands of DNA that are being actively transcribed.

Using XR-seq to map UV-induced damage in E. coli bacteria cells, the researchers found clear evidence of transcription-coupled repair in normal cells, but not in cells that lack Mfd, thus confirming the protein's role in the process.

The unwinder: UvrD

In further experiments, the researchers defined the role of an accessory excision repair protein in E. coli - UvrD, which helps clear away each excised segment of damaged DNA.

In the absence of UvrD, the excised piece of DNA remains bound to the chromosomal DNA, making it hard for cellular waste-disposal enzymes to chop it up. At the same time, the repair proteins that excised the strand tend to remain stuck to it, and are thus kept from moving on to excise other bits of damaged DNA. UvrD's job is to unwind these damaged and discarded strands from chromosomal DNA, so that they can be disposed of quickly and the associated repair proteins can go on to catalyze additional rounds of repair.

Using XR-seq on UV-damaged E. coli cells, the UNC team confirmed that without UvrD, excised DNA fragments remain stuck to chromosomal DNA, survive much longer in cells, and - by holding onto excision repair proteins - slow down the overall rate of excision repair in cells.

In addition to clarifying the roles of Mfd and UvrD, the research generally heralds the use of the new XR-seq technique in mapping and studying excision repair processes.

"XR-seq provides a new type of sequence data, and in this work we've provided for the first time a genome-wide map of excision repair in a bacterium," said Adebali. "We think this map will be broadly useful to the scientific community."

The researchers now plan further studies using XR-seq in bacterial cells, as well as in human and other mammalian cells where the process of excision repair is less understood.

Explore further: Researchers create DNA repair map of the entire human genome

More information: Ogun Adebali et al, Genome-wide transcription-coupled repair inis mediated by the Mfd translocase, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1700230114

When the common chemotherapy drugs cisplatin or oxaliplatin hit cancer cells, they damage DNA so that the cells can't replicate. But the cells have ways to repair the DNA. The cancer drugs aren't as effective as patients ...

A key biochemical enables bacteria to repair otherwise fatal damage to their DNA, including that caused by antibiotics. That is the finding of a study led by researchers at NYU Langone Medical Center and published May 20 ...

(Medical Xpress)The results of two studies by two different teams studying the role that DNA repair plays in the production of mutation-prone sequencesprecursors to cancer, have been published in the journal Nature. ...

A recent study led by University of Kentucky researchers illuminates a new way that tobacco smoke may promote the development of lung cancer: inhibiting a DNA repair process called nucleotide excision repair (NER). The results ...

Researchers from the Institut Jacques Monod (CNRS/University of Paris Diderot), the Institute of Biology of the Ecole Normale Suprieure (ENS/CNRS/Inserm), and the University of Bristol, have described for the first time ...

If you have a soft spot for unsung heroes, you'll love a DNA repair protein called XPG. Scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) discovered that XPG plays a previously ...

Day in and day out, in our bodies, the DNA in cells is damaged for a variety of reasons, and thus intercellular DNA-repair systems are fundamental to the maintenance of life. Now scientists from the UNC School of Medicine ...

If you've ever been elbowed out of the way at the dinner table by older, stronger siblings, you'll identify with wolves competing with larger bears for food. A study by Utah State University ecologist Aimee Tallian and colleagues ...

Scientists have uncovered key processes in the healthy development of cells which line the human gut, furthering their understanding about the development of cancer.

While searching for a potential Achilles' heel in the insect responsible for spreading the bacterium that causes citrus greening disease, researchers have uncovered a protein that makes their bellies blue and may impact how ...

A study led by UC Santa Cruz researchers has found that drought dramatically increases the severity of West Nile virus epidemics in the United States, although populations affected by large outbreaks acquire immunity that ...

Few animals can match the humble hydra's resilience. The small, tentacled freshwater animals can be literally shredded into pieces and regrow into healthy animals. A study published February 7 in Cell Reports suggests that ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

See original here:
How life survives: Researchers confirm basic mechanism of DNA repair - Phys.Org