Category Archives: DNA

BBC News

Ancestry.com denies exploiting users' DNA - BBC News BBC News A leading genealogy service, Ancestry.com, has denied exploiting users' DNA following criticism of its terms and conditions. The US company's DNA testing ... and more »

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A family tree can reveal a lot, especially if it belongs to a microscopic troublemaker with a knack for genetic shape-shifting.

DNA sleuthing can outline the route an emerging pathogen might take once it makes landfall in the Americas and encounters a wholly unprotected population. Its a modern take on old-fashioned public health surveillance strategies that focused on the exhaustive collection and analysis of samples from the field. Now theyve been bolstered by rapid genome sequencing and the result can be a picture of an epidemic rendered in exquisite detail, and in near-real time.

For those trying to anticipate the shape of the next pandemic of human disease, the resulting road map could be invaluable.

Three independent research groups demonstrated the promise of such an approach by creating a family tree of the Zika virus, the latest scourge to hit the Americas. Their work was published Wednesday in the journal Nature.

The family tree reveals that the virus may have made landfall in Brazil sometime in late 2013 or early 2014, probably arriving from a group of Pacific islands then in the grips of an outbreak.

Upon finding ideal conditions in northeastern Brazil including dense human populations and hordes of the Aedes egyptii mosquitoes that spread the virus Zika circulated widely throughout the country for more than a year before its presence was first detected in mid-2015, one of the studies found. By then, physicians had begun to take note of a sharp rise in births of babies with unusually small heads the first of 2,366 babies with Zika-related microcephaly eventually born in Brazil by the end of 2016.

But the Zika virus didnt stay put. By late 2014, it had broken out of Brazil and was circulating in the Caribbean, following a well-worn path of human migrants. As 2015 dawned, the same strain was also tearing through the populations of Honduras and Colombia.

Brazils final direct export of Zika was to Puerto Rico, where it began to circulate widely in 2015.

From there, a second study led by researchers from the Scripps Research Institute in La Jolla suggests that the island nations of the Caribbean became the springboard for Zikas onward travel.

The Caribbean strain jumped northwest, across the Tropic of Cancer, via Zika-infected mosquitoes and people who were traveling aboard cruise ships and planes mainly bound for Miami.

Like tinder that didnt catch immediately, Florida withstood at least four and perhaps as many as 40 small but unsustained ignitions of the Zika virus in 2015. A few local infections would take place, but the density of mosquitoes or humans was too low for an outbreak to pick up steam.

But these repeated sparks eventually ignited a fire. By the early days of 2016, Zika was spreading in Florida. Public health officials would eventually confirm 256 cases of local infection in 2016, all but 15 of them in Miami-Dade County.

It had taken a year, give or take, for the sustained spread of Zika to be detected in Brazil, Honduras and the Caribbean. But U.S. public health authorities were quick to determine that the virus was spreading in Puerto Rico and Florida: in both places, only a few months separated the start of Zikas circulation and the detection of that event.

The three research groups painstakingly collected mosquitoes and human viral samples from across 11 countries and territories. The teams subjected those samples to genetic analysis sometimes right on the spot using field versions of genome sequencers described in a study in Nature Protocols.

Altogether, the researchers analyzed the full or partial genomes of 183 Zika samples. One of them was the earliest known Zika sample collected in the Americas.

Like all viruses, as Zika spread from person to person and from country to country, its genetic blueprint changed in small but discernible ways. The RNA in each sample steadily picked up mutations over time as it gained exposure to new people and the viruses they hosted. (In fact, in a study published last week in Nature, researchers identified a much earlier mutation in the South Pacific version of the Zika virus that appears to have contributed to its rapid spread through the Americas.)

The result of the 183 genetic analyses is a sprawling family tree of Zika viruses all related, but each just a tiny bit different from its predecessors or its progeny.

By carefully recording the dates and locations of the Zika samples collected between 2013 and 2016, the three research teams in effect show when and where Zika virus began circulating in a given country or territory. They looked at mutations in the genetic fine print of the samples and lined them up end to end, allowing them to refine the dates, pedigrees and origins of each.

The family tree allowed them to trace Zikas path as it traveled through the Americas. It provides evidence for the potent effect that international travel, migration and mosquito-control efforts can exert over the spread of a virus.

It also serves as a test bed for tracking the progress of future disease-causing viruses as they encounter dense populations with no resistance to them.

In a comment published alongside the three papers, University of Arizona evolutionary biologist Michael Worobey wrote that the new studies collectively set a new standard for what can be achieved by studying disease outbreaks in tantalizingly close to real time, using rapidly-obtained genome sequences.

But its future, he added, is hardly assured.

Such work is possible mostly through the sustained efforts of a fairly small number of scientists supported by modest grants from a few enlightened funders, Worobey writes. Systematic pathogen surveillance is within our grasp, but is still undervalued and underfunded relative to the magnitude of the threat.

melissa.healy@latimes.com

@LATMelissaHealy

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What the DNA of the Zika virus tells scientists about its rapid spread - Los Angeles Times

FOX40

What Do At-Home DNA Tests Really Tell Us? FOX40 So, he took all three DNA tests, and we sent them off in the mail. My Heritage asked for Eman to take a swab of his cheeks, while both Ancestry DNA and 23 and Me asked him to fill a test tube with saliva. It took more than six weeks to get all the ...

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What Do At-Home DNA Tests Really Tell Us? - FOX40

May 25, 2017 The drawing is a facial reconstruction of the sample Chan. Credit: The authors of the reconstructions are Serrulla y Sann, and the original source is: Serrulla, F., and Sann, M. (2017). Forensic anthropological report of Elba. Cadernos do Laboratorio Xeolxico de Laxe 39, 35-72.

In human history, the transition from hunting and gathering to farming is a significant one. As such, hunter-gatherers and farmers are usually thought about as two entirely different sets of people. But researchers reporting new ancient DNA evidence in Current Biology on May 25 show that in the area we now recognize as Romania, at least, hunter-gatherers and farmers were living side by side, intermixing with each other, and having children.

"We expected some level of mixing between farmers and hunter-gatherers, given the archaeological evidence for contact among these communities," says Michael Hofreiter of University of Potsdam in Germany. "However, we were fascinated by the high levels of integration between the two communities as reconstructed from our ancient DNA data."

The findings add evidence to a longstanding debate about how the Neolithic transition, when people gave up hunting and gathering for farming, actually occurred, the researchers say. In those debates, the question has often been about whether the movement of people or the movement of ideas drove the transition.

Earlier evidence suggested that the Neolithic transition in Western Europe occurred mostly through the movement of people, whereas cultural diffusion played a larger role to the east, in Latvia and Ukraine. The researchers in the new study were interested in Romania because it lies between these two areas, presenting some of the most compelling archaeological evidence for contact between incoming farmers and local hunter-gatherers.

Indeed, the new findings show that the relationship between hunter-gatherers and farmers in the Danube basin can be more nuanced and complex. The movement of people and the spread of culture aren't mutually exclusive ideas, the researchers say, "but merely the ends of a continuum."

The researchers came to this conclusion after recovering four ancient human genomes from Romania spanning a time transect between 8.8 thousand and 5.4 thousand years ago. The researchers also analyzed two Mesolithic (hunter-gatherer) genomes from Spain to provide further context.

The DNA revealed that the Romanian genomes from thousands of years ago had significant ancestry from Western hunter-gatherers. However, they also had a lesser but still sizeable contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. An analysis of the bones also showed they ate a varied diet, with a combination of terrestrial and aquatic sources.

"Our study shows that such contacts between hunter-gatherers and farmers went beyond the exchange of food and artefacts," Hofreiter says. "As data from different regions accumulate, we see a gradient across Europe, with increasing mixing of hunter-gatherers and farmers as we go east and north. Whilst we still do not know the drivers of this gradient, we can speculate that, as farmers encountered more challenging climatic conditions, they started interacting more with local hunter-gatherers. These increased contacts, which are also evident in the archaeological record, led to genetic mixing, implying a high level of integration between very different people."

The findings are a reminder that the relationships within and among people in different places and at different times aren't simple. It's often said that farmers moved in and outcompeted hunter-gatherers with little interaction between the two. But the truth is surely much richer and more varied than that. In some places, as the new evidence shows, incoming farmers and local hunter-gatherers interacted and mixed to a great extent. They lived together, despite large cultural differences.

Understanding the reasons for why the interactions between these different people led to such varied outcomes, Hofreiter says, is the next big step. The researchers say they now hope to use ancient DNA evidence to add more chapters to the story as they explore the Neolithic transition as it occurred in other parts of the world, outside of Europe.

Explore further: European hunter-gatherers owned pigs as early as 4600BC

More information: Current Biology, Gonzalez-Fortes and Jones et al.: "Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin" http://www.cell.com/current-biology/fulltext/S0960-9822(17)30559-6 , DOI: 10.1016/j.cub.2017.05.023

Journal reference: Current Biology

Provided by: Cell Press

European hunter-gatherers acquired domesticated pigs from nearby farmers as early as 4600BC, according to new evidence.

New research indicates that Baltic hunter-gatherers were not swamped by migrations of early agriculturalists from the Middle East, as was the case for the rest of central and western Europe. Instead, these people probably ...

Hunter-gatherers and immigrant farmers lived side-by-side for more than 2,000 years in Central Europe, before the hunter-gatherer communities died out or were absorbed into the farming population.

An international team led by researchers at Uppsala University and Stockholm University reports a breakthrough on understanding the demographic history of Stone-Age humans. A genomic analysis of eleven Stone-Age human remains ...

The beginnings of agriculture changed human history and has fascinated scientists for centuries.

Hunter-gatherers had almost no malocclusion and dental crowding, and the condition first became common among the world's earliest farmers some 12,000 years ago in Southwest Asia, according to findings published today in the ...

In human history, the transition from hunting and gathering to farming is a significant one. As such, hunter-gatherers and farmers are usually thought about as two entirely different sets of people. But researchers reporting ...

A new species of a fossil pliosaur (large predatory marine reptile from the 'age of dinosaur') has been found in Russia and profoundly change how we understand the evolution of the group, says an international team of scientists.

People using smartphones are more likely to make rational and unemotional decisions compared to PC users when presented with a moral dilemma on their device, according to a new study from City, University of London.

Middle Stone Age humans in the Porc-Epic cave likely used ochre over at least 4,500 years, according to a study published May 24, 2017 in the open-access journal PLOS ONE by Daniela Rosso from the University of Barcelona, ...

(Phys.org)A trio of researchers with Columbia University has conducted a series of experiments regarding how much effort people are willing to exert in fact-checking news stories. In their paper published in Proceedings ...

(Phys.org)The study of ancient civilizations, particularly those that did not leave extensive writing in the archaeological record, is reliant on the evidence of other kinds of material artifacts. And one of the keys to ...

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REYNOSA, Mex. Mexican authorities are taking newsteps to give the families of thousands of missing people some closure.

Thousands of people have gone missing due to conflicts between cartels and the government.

The state of Tamaulipas is creating a DNA database in an effort to identify unknown remains.

Families from all over Tamaulipas flocked the Reynosa General Hospital this week. None of them wanted to show their faces on camera.

One woman, who we will call Delores, told CHANNEL 5 NEWS her daughter was kidnapped by armed men from her Reynosa home.

I came to give a DNA sample here to find my daughter. Shes been missing for seven years, she said.

Delores said her daughter has four children of her own. One of them is a U.S. citizen.

The mother said she went to the hospital in hopes of giving her DNA sample to aid authorities in her daughters search.

Im living in anguish and anxiety, because I dont know what happened to her or why it happened to her, she said.

The Tamaulipas government said their efforts will spread in cities all over the state.

DNA from families of missing people will go into the database and be cross-referenced with DNA of human remains found in mass graves.

Human rights activist Eddie Canales said it was about time the government took action.

Twenty-three thousand people died in conflicts in Mexico last year. 2016. Its not recognized enough in this country, he said.

Canales said he also works all over the Rio Grande Valley trying to find migrants who go missing while crossing the border illegally.

Canales said hes helped organize DNA collection drives in Houston. He said DNA databases are the most effective way for families to find their missing loved ones.

However, he wasnt aware of the Tamaulipas campaign until we told him about it.

I will make efforts to reach out to those groups and see how we can collaborate and assist in whatever manner, he said.

The DNA collection will continue in Tamaulipas on Friday.

Anyone with family missing in Mexico can visit one of the eight locations in seven cities across the state.

The drive will be happening Friday from 9 a.m. to 5 p.m. in all the following cities:

You can call 01 (834) 31-861-50 for more details.

If you believe a family member went missing on the U.S. side of the border, there will be a DNA collection in Houston on June 10.

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Tamaulipas Creating DNA Database to Identify Unknown Remains - KRGV

Investopedia

Microsoft Expects DNA Data Storage to Be Operational By 2020 (MSFT) Investopedia believes that its data center will contain a fully functional DNA storage system by the end of the decade, representing a potentially massive breakthrough in the tech industry battle to meet surging global demand for space-effective information storage ... Microsoft Has a Plan to Add DNA Data Storage to Its CloudMIT Technology Review Microsoft Reportedly Wants to Use DNA for Cloud Data StorageGizmodo Microsoft working on DNA-based data storageBetaNews The Stack -Computer Business Review -ITProPortal all 13 news articles »

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Microsoft Expects DNA Data Storage to Be Operational By 2020 (MSFT) - Investopedia

A song made from DNA is unlikely to top the charts but converting DNA sequences into musical notes could lead to identifying mutations that would be otherwise missed. A recently published article in BMC Bioinformatics looks at six different algorithms that can convert DNA into musical notes and highlights the ability of sonification to discover specific DNA properties

Danielle Talbot 22 May 2017

DNA-MUSIC (Abhijit Bhaduri, Flickr CC)

Genomics researchers are all too used to seeing DNA sequences represented as long lists of A, T, C and Gs but could there be a better way to analyze this data? The recently published article by Dr Mark Temple of Western Sydney University suggests that representing DNA as musical notes could aid us in identifying stop and start codons and even help us to spot mutations that otherwise could prove much more difficult to find.

Sound has been used in the past to help aid analysis; even as far back as 1948, Alan Turings computer used different sounds to help indicate the progress of software to the user. As the amount of available genomic data increases, researchers are increasingly seeking new ways to analyze and seek out unique features. Using sound to identify these features in the same way that Turings machine used sound to identify progress could provide a novel way of processing these large data sets.

DNA representation (Andy Leppard, Flickr CC)

Dr Temple developed six separate sonification algorithms that could each parse a DNA sequence and convert it into a musical score. Some of the algorithms worked by treating each nucleotide as an individual note, while others used di- or tri-nucleotide groups, the protein sequence itself, or the codon reading frames. The resulting musical notation can then be played in the same way as any conventional music.

Listen track eight

Listen track twelve

This approach is particularly useful as it can highlight start and stop codons by using them to turn the music on or off, making those points in the DNA sequence abundantly clear. And this could be just the beginning of sound-based DNA analysis. As further research is carried out in this area, software could be developed that uses different sounds to represent features like binding sites, restriction endonucleases sites and SNPs. Todays DNA sequence browsers may use conventional analysis tools but perhaps we will soon see sonification algorithms like these included as well.

So while we may not see a DNA-based song topping iTunes, DNA sonification may open new avenues in DNA sequence analysis for researchers around the globe.

View the latest posts on the BMC Series blog homepage

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Sounding out the properties of DNA - BMC Blogs Network (blog)

BAKERSFIELD, CALIF - When it comes to the Jessica Martinez case, as well as numerous other cases, we're often told that evidence can be tested today that could potentially crack the case wide open. But what exactly does that mean? The science behind DNA testing is extremely complex, but we wanted to understand what new developments there are in 2017 that could help find justice for Jessica.

We found The Kern Regional Crime Lab is using new technology that could potentially help solve the Jessica Martinez case, as well as other cold cases, where decades have gone by without answers.

After someone is murdered, officials preserve physical evidence at the crime lab, where technicians test for the presence of DNA. If there is- then they look for what they call "locations", in order to develop a DNA profile. In the last two months, technicians in the lab have started using a new method.

"We were basically looking at 16 different locations in the DNA, where as with the global filer kit, we're looking at a total of 24 locations. So basically we're adding those additional locations for comparison", says DNA technical lead, Garett Sugimoto.

Sugimoto explains that having more locations to examine in the DNA, it gives them more information about the DNA to then compare against suspects. Having 24 locations, instead of 16, can make a big difference, Sugimoto says.

"I think the simplest way to explain it is if you think about a fingerprint, and if you had a fingerprint previously where you had 16 different points for comparison, well now you've just enhanced that fingerprint and now you have 24, and so it's just more points of identification, or more points for comparison", says Sugimoto.

In the Jessica Martinez case, DNA was recovered from the child's shoe. It hasn't been revealed what kind of DNA, but it hasn't matched anyone in CODIS, the nationwide DNA database, or to the primary suspect, Christopher Lightsey.

But the District Attorney's Crime Lab isn't giving up. Officials with the DA's office say some of the evidence in the case are being reexamined.

"Just the technology itself and where we are now with DNA testing, we could potentially test items from back in the early 2000's, when we wouldn't have considered them good items for DNA analysis. So I think we're looking at more items such as potential touch DNA samples and we're testing those more often, so the new kit can help test those kinds of samples", says Sugimoto.

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New DNA technology that could help solve the 27-year-old murder - Kern Golden Empire

Science Daily

Traffic-related air pollution linked to DNA damage in children Science Daily The study adds to previous evidence that air pollution causes oxidative stress, which can damage lipids, proteins, and DNA. Research has suggested that children may have different telomere shortening regulation than adults, which might make them more ...

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Traffic-related air pollution linked to DNA damage in children - Science Daily

Idaho Statesman

Boise State gets federal grant for post-conviction DNA testing, but not on Idaho cases Idaho Statesman The Idaho Innocence Project will benefit from a $630,000 U.S. Department of Justice grant to test DNA in possible wrongful-conviction cases. But none of the money can be used on Idaho cases, and the grant had to be given to Boise State University. Why?

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Boise State gets federal grant for post-conviction DNA testing, but not on Idaho cases - Idaho Statesman