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Posts Tagged ‘DNA

DNA can provide your mugshot — Huh? Wha?

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Leaving a hair at a crime scene could one day be as damning as leaving a photograph of your face. Researchers have developed a computer program that can create a crude three-dimensional model of a face from a DNA sample.

Using genes to predict eye and hair colour is relatively easy. But the complex structure of the face makes it more valuable as a forensic tool — and more difficult to connect to genetic variation, says anthropologist Mark Shriver of Pennsylvania State University…who led the work…

Shriver and his colleagues took high-resolution images of the faces of 592 people of mixed European and West African ancestry living in the United States, Brazil and Cape Verde. They used these images to create 3D models, laying a grid of more than 7,000 data points on the surface of the digital face and determining by how much particular points on a given face varied from the average: whether the nose was flatter, for instance, or the cheekbones wider. They had volunteers rate the faces on a scale of masculinity and femininity, as well as on perceived ethnicity.

Next, the authors compared the volunteers’ genomes to identify points at which the DNA differed by a single base, called a single nucleotide polymorphism (SNP). To narrow down the search, they focused on genes thought to be involved in facial development, such as those that shape the head in early embryonic development, and those that are mutated in disorders associated with features such as cleft palate. Then, taking into account the person’s sex and ancestry, they calculated the statistical likelihood that a given SNP was involved in determining a particular facial feature.

This pinpointed 24 SNPs across 20 genes that were significantly associated with facial shape. A computer program the team developed using the data can turn a DNA sequence from an unknown individual into a predictive 3D facial model…Shriver says that the group is now trying to integrate more people and genes, and look at additional traits, such as hair texture and sex-specific differences…

At the moment, such genetic analyses are limited, imprecise. If you think scientists will leave it alone you don’t understand curiosity. If you think someone like the FBI or any other Alphabetoid snoop will leave it alone you don’t understand paranoia.

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Written by Ed Campbell

March 21, 2014 at 2:00 am

First bacteria to make the transition from humans to plants — and it’s named for Frank Zappa

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zappa christianity

What would you do if you discovered an odd strain of bacteria that exhibited unconventional behavior? Why, name it after Frank Zappa of course!…This is exactly what a team of Italian and Austrian researchers did when they found a bacterium that had apparently transitioned from causing acne in human skin to infecting the bark of grape vines.

“This is the first time it’s been found that a microorganism can switch from a human to a plant,” study author and self-professed Zappa fan Andrea Campisano, a microbiologist at the Edmund Mach Foundation in Italy, told the Los Angeles Times.

In addition to being a tribute to the late musician, the naming of P. acnes zappae is also a hat-tip to the Italian word for “hoe,” which is “zappa.”

Campisano is such a big fan of the experimental musician – he said he even has a quote from him prominently displayed on his lab computer screen: “If you end up with a boring miserable life because you listened to your mom, your dad, your teacher, your priest, or some guy on television … then you deserve it.”

Read the rest of this entry »

Written by Ed Campbell

February 20, 2014 at 8:00 pm

Geneticists producing atlas mixing genomes and events

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The Silk Road, land and sea

The rise and fall of empires, the march of armies, the flow of trade routes, the practice of slavery — all these events have led to a mixing of populations around the world. Such episodes have left a record in the human genome, but one that has so far been too complex to decipher on a global scale.

Now, geneticists applying new statistical approaches have taken a first shot at both identifying and dating the major population mixture events of the last 4,000 years, with the goal of providing a new source of information for historians.

Some of the hundred or so major mixing events they describe have plausible historical explanations, while many others remain to be accounted for. For instance, many populations of the southern Mediterranean and Middle East have segments of African origin in their genomes that were inserted at times between A.D. 650 and 1900, according to the geneticists’ calculations. This could reflect the activity of the Arab slave trade, which originated in the seventh century, and the absorption of slaves into their host populations…

Though all humans have the same set of genes, their genomes are studded with mutations, which are differences in the sequence of DNA units in the genome. These mutations occur in patterns because whole sets of mutations are passed down from parent to child and hence will be common in a particular population. Based on these patterns, geneticists can scan a person’s genome and assign the ancestry of each segment to a particular race or population.

The team led by Dr. Simon Myers has developed a statistical technique for identifying the chromosomal segments with particular precision. This enables them to perform a second feat, that of assigning a date to the one or more mixing events that have affected a population…

One of the most widespread events his group has detected is the injection of Mongol ancestry into populations within the Mongol empire, such as the Hazara of Afghanistan and the Uighur Turks of Central Asia. The event occurred 22 generations ago, according to genetic dating, which corresponds to the beginning of the 14th century, fitting well with the period of the Mongol empire.

In another example, the European colonization of America is recorded in the genomes of the Maya and Pima Indians. And Cambodian genomes mark the fall of the Khmer empire in the form of ancestral DNA from the invading Tai people…

Dr. Myers and Dr. Hellenthal said that they hoped historians would find their work useful, but that they had not collaborated with historians.

“In some sense we don’t want to talk to historians,” Dr. Falush said. “There’s a great virtue in being objective: You put the data in and get the history out. We do think this is a way of reconstructing history by just using DNA.”

Hopefully, this weekend, I intend to revisit a favorite topic – cross-pollination of research between varying scientific disciplines. Some universities, research facilities – even traditional engineering firms – have long held this practice to be especially beneficial. Here’s a unique contribution just waiting to be interpolated.

The group led by Myers, Hellenthal and Falush have provided a valuable service to every side of the study of history.

Written by Ed Campbell

February 16, 2014 at 8:00 am

DNA tests find living descendants of Uncle Ötzi

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A team of Austrian researchers have made a discovery that would put those genealogy websites to shame: they have located several living descendants of a 5,300-year-old human mummy.

The prehistoric individual, known as Ötzi the Iceman, was originally found frozen in the Alps back in 1991, according to Steve Nolan of the Daily Mail. The so-called ice mummy suffered from the oldest case of Lyme disease recorded to date, and was also lactose intolerant and predisposed to cardiovascular disease.

Now, forensic scientist Walther Parson and colleagues from the Institute of Legal Medicine at Innsbruck Medical University have identified 19 men who share a specific genetic mutation with Ötzi. These individuals were identified following an analysis of DNA samples from approximately 3,700 blood donors in the state of Tyrol, which is located in the western part of Austria.

“The discovery was made during a broader study into determining the origins of the people who now inhabit the Alpine regions. Along with their blood the donors were asked to provide their place of birth and family history,” said Matthew Day of The Telegraph.

To date, none of the men identified have been informed of their genetic link to Ötzi, Parson told Day. He added his research team is working with colleagues in Italy and Switzerland who are attempting to uncover the same genetic mutation in residents of those two nations…

“Painstaking research revealed what his last meals were, where he lived and that he was about 45 years old when he met his demise high on the mountain,” Day added. “The ice had also preserved his clothes and a quiver of arrows, giving scientists a unique insight into the lives and technology of people from thousands of years ago.”

Wonderful work. Modern genetic testing makes determinations possible which previous generations of researchers couldn’t begin to consider. Can’t wait for the next couple of chapters from Switzerland and Italy.

Maybe he was one of my own uncles? :)

Written by Ed Campbell

October 15, 2013 at 8:00 am

Ancient DNA unravels Europe’s genetic diversity

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Ancient DNA recovered from a time series of skeletons in Germany spanning 4,000 years of prehistory has been used to reconstruct the first detailed genetic history of modern-day Europeans.

The study…reveals dramatic population changes with waves of prehistoric migration, not only from the accepted path via the Near East, but also from Western and Eastern Europe.

The research was a collaboration between the Australian Centre for Ancient DNA…researchers from the University of Mainz, the State Heritage Museum in Halle, Germany, and National Geographic Society’s Genographic Project. The teams used mitochondrial DNA extracted from bone and teeth samples from 364 prehistoric human skeletons ‒ ten times more than previous ancient DNA studies.

“This is the largest and most detailed genetic time series of Europe yet created, allowing us to establish a complete genetic chronology,” says joint-lead author Dr Wolfgang Haak of ACAD. “Focussing on this small but highly important geographic region meant we could generate a gapless record, and directly observe genetic changes in ‘real-time’ from 7,500 to 3,500 years ago, from the earliest farmers to the early Bronze Age.”

“Our study shows that a simple mix of indigenous hunter-gatherers and the incoming Near Eastern farmers cannot explain the modern-day diversity alone,” says joint-lead author Guido Brandt, PhD candidate at the University of Mainz. “The genetic results are much more complex than that. Instead, we found that two particular cultures at the brink of the Bronze Age 4,200 years ago had a marked role in the formation of Central Europe’s genetic makeup.”

Professor Kurt Alt (University of Mainz) says: “What is intriguing is that the genetic signals can be directly compared with the changes in material culture seen in the archaeological record. It is fascinating to see genetic changes when certain cultures expanded vastly, clearly revealing interactions across very large distances.” These included migrations from both Western and Eastern Europe towards the end of the Stone Age…

Dr Haak says: “None of the dynamic changes we observed could have been inferred from modern-day genetic data alone, highlighting the potential power of combining ancient DNA studies with archaeology to reconstruct human evolutionary history.”

Fascinating stuff. Work which wouldn’t have been at all practical a decade or so back in time.

My personal pleasure was taking part in an early National Geographic DNA track of my patriarchal DNA from Africa through the steppes of Central Asia to Scotland – perfectly in line with the research of Gerhard Herm and his anthropological history of “The Celts”.

Capabilities are advanced enough that I may try an updated go-round with NatGeo.

Written by Ed Campbell

October 11, 2013 at 2:00 am

Saving the orange by altering its DNA

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Burning infected trees

The call Ricke Kress and every other citrus grower in Florida dreaded came while he was driving.

“It’s here” was all his grove manager needed to say to force him over to the side of the road.

The disease that sours oranges and leaves them half green, already ravaging citrus crops across the world, had reached the state’s storied groves. Mr. Kress, the president of Southern Gardens Citrus, in charge of two and a half million orange trees and a factory that squeezes juice for Tropicana and Florida’s Natural, sat in silence for several long moments…“O.K.,” he said finally on that fall day in 2005, “let’s make a plan.”

In the years that followed, he and the 8,000 other Florida growers who supply most of the nation’s orange juice poured everything they had into fighting the disease they call citrus greening.

To slow the spread of the bacterium that causes the scourge, they chopped down hundreds of thousands of infected trees and sprayed an expanding array of pesticides on the winged insect that carries it. But the contagion could not be contained.

They scoured Central Florida’s half-million acres of emerald groves and sent search parties around the world to find a naturally immune tree that could serve as a new progenitor for a crop that has thrived in the state since its arrival, it is said, with Ponce de León. But such a tree did not exist.

“In all of cultivated citrus, there is no evidence of immunity,” the plant pathologist heading a National Research Council task force on the disease said.

In all of citrus, but perhaps not in all of nature. With a precipitous decline in Florida’s harvest predicted within the decade, the only chance left to save it, Mr. Kress believed, was one that his industry and others had long avoided for fear of consumer rejection. They would have to alter the orange’s DNA — with a gene from a different species.

I would be remiss if I didn’t point out an excellent article on the battle to save Florida’s citrus crops. Though Monsanto represents genomic crop research about as much as Ted Nugent represents American rock music – we often see the worst of capitalist robber barons accepted on the Left as defining contemporary botanical science. And that just ain’t so.

There is no more justification on the Left than there is on the Right for opportunism. Admittedly, I don’t get upset over Republicans and conservatives letting themselves be overwhelmed by the bigotry of the Tea Party and other looney brigades. I can rationalize it away and say they deserve the diseases they catch from those they’re in bed with. But, the Left faces a comparable danger of anti-science, anti-intellectualism, Luddite behavior from that segment of environmentalism that treats the world as a religious temple rather than the sum of knowable processes.

From that first Earth Day I attended in Amherst, Mass, I have counted environmental activism as part of the responsibilities I accept as a concerned human being. That concern includes educated, material and scientific grounding for the positions I fight for.

A long, detailed and accurate article worth reading. Take the time.

Written by Ed Campbell

July 28, 2013 at 2:00 pm

You say tomato – I say comparative transcriptomics

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Brad Townsley/UC Davis

You say tomato, I say comparative transcriptomics. Researchers in the U.S., Europe and Japan have produced the first comparison of both the DNA sequences and which genes are active, or being transcribed, between the domestic tomato and its wild cousins.

The results give insight into the genetic changes involved in domestication and may help with future efforts to breed new traits into tomato or other crops, said Julin Maloof…senior author on the study.

For example, breeding new traits into tomatoes often involves crossing them with wild relatives. The new study shows that a large block of genes from one species of wild tomato is present in domestic tomato, and has widespread, unexpected effects across the whole genome…

Among other findings, genes associated with fruit color showed rapid evolution among domesticated, red-fruited tomatoes and green-fruited wild relatives. And S. pennellii, which lives in desert habitats, had accelerated evolution in genes related to drought tolerance, heat and salinity…

New technology is giving biologists the unprecedented ability to look at all the genes in an organism, not just a select handful. The researchers studied not just the plants’ DNA but also the messenger RNA being transcribed from different genes. RNA transcription is the process that transforms information in genes into action. If the DNA sequence is the list of parts for making a tomato plant, the messenger RNA transcripts are the step-by-step instructions…

“We could not have done a study like this ten years ago — certainly not on any kind of reasonable budget,” Maloof said. “It opens up a lot of new things we can do as plant scientists.”

Bravo! Like anyone who has Mediterranean genes – and cooking – in their life, I have an inordinate interest in tomatoes.

I grew up in a New England factory town with tomatoes in the backyard garden. I live in the high desert country of New Mexico with tomatoes in our courtyard garden. I cook with fresh, dried, canned and whatever kind of tomatoes I can get hold of any time of the year.

They’re all delicious and all good for me – as far as I’m concerned.

Written by Ed Campbell

July 3, 2013 at 8:00 pm

Thirdhand smoke causes DNA damage

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deathsmoke

A study led by researchers from Lawrence Berkeley National Laboratory has found for the first time that thirdhand smoke—the noxious residue that clings to virtually all surfaces long after the secondhand smoke from a cigarette has cleared out—causes significant genetic damage in human cells.

Furthermore, the study also found that chronic exposure is worse than acute exposure, with the chemical compounds in samples exposed to chronic thirdhand smoke existing in higher concentrations and causing more DNA damage than samples exposed to acute thirdhand smoke, suggesting that the residue becomes more harmful over time.

“This is the very first study to find that thirdhand smoke is mutagenic,” said Lara Gundel, a Berkeley Lab scientist and co-author of the study. “Tobacco-specific nitrosamines, some of the chemical compounds in thirdhand smoke, are among the most potent carcinogens there are. They stay on surfaces, and when those surfaces are clothing or carpets, the danger to children is especially serious…”

Thirdhand smoke is particularly insidious because it is extremely difficult to eradicate. Studies have found that it can still be detected in dust and surfaces of apartments more than two months after smokers moved out. Common cleaning methods such as vacuuming, wiping and ventilation have not proven effective in lowering nicotine contamination. “You can do some things to reduce the odors, but it’s very difficult to really clean it completely,” said Destaillats. “The best solution is to substitute materials, such as change the carpet, repaint.”

Now the new study suggests thirdhand smoke could become more harmful over time…The researchers found that the concentrations of more than half of the compounds studied were higher in the chronic samples than in the acute. They also found higher levels of DNA damage caused by the chronic samples…

Great. The more we learn about cigarette smoking the more we learn about how deadly the smoke and its residue is. I expect we’ll eventually learn that many modern diseases might be traceable back to generations of cigarette smoke clinging to the household infrastructure of modern life – and how it affected DNA.

A society which does comparatively little to end this national habit is measured by stupidity more so than ignorance.

Written by Ed Campbell

June 22, 2013 at 2:00 pm

SCOTUS says coppers taking DNA samples the same as fingerprinting and photographing

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Police may take DNA samples from people arrested in connection with serious crimes, the Supreme Court ruled on Monday in a 5-to-4 decision.

The federal government and 28 states authorize the practice, and law enforcement officials say it is a valuable tool for investigating unsolved crimes. But the court said the testing was justified by a different reason: to identify the suspect in custody.

“When officers make an arrest supported by probable cause to hold for a serious offense and they bring the suspect to the station to be detained in custody,” Justice Anthony M. Kennedy wrote for the majority, “taking and analyzing a cheek swab of the arrestee’s DNA is, like fingerprinting and photographing, a legitimate police booking procedure that is reasonable under the Fourth Amendment.”

Justice Antonin Scalia summarized his dissent from the bench…“Make no mistake about it: because of today’s decision, your DNA can be taken and entered into a national database if you are ever arrested, rightly or wrongly, and for whatever reason,” Justice Scalia said from the bench…

There’s a bit more blah, blah, blah from Scalia. He voices the paranoia already part of the DNA of jerkwater populists who can’t get their brains around the United States as a union, a whole nation, instead of a confederacy.

Monday’s ruling, Maryland v. King, No. 12-207, arose from the collection of DNA in 2009 from Alonzo Jay King Jr. after his arrest on assault charges in Wicomico County, Md. His DNA profile, obtained by swabbing his cheek, matched evidence from a 2003 rape case, and he was convicted of that crime…

Justice Kennedy wrote in the majority opinion that the “quick and painless” swabbing procedure was a search under the Fourth Amendment, meaning it had to be justified as reasonable under the circumstances. The search was reasonable, he said, given “the need for law enforcement officers in a safe and accurate way to process and identify the persons and possessions they must take into custody.”

Such identification, he said, “is no different than matching an arrestee’s face to a wanted poster of a previously unidentified suspect; or matching tattoos to known gang members to reveal a criminal affiliation; or matching the arrestee’s fingerprints to those recovered from a crime scene.”

An inevitable follow-on to this decision will be appeals and modifications to the law in the same vein as other nations ahead of the United States in considering and utilizing modern technology.

The UK high courts have ruled that DNA samples gathered as part of an arrest must be destroyed, the results expunged if the suspect is found not guilty of any offense at the time.

Written by Ed Campbell

June 3, 2013 at 2:00 pm

New DNA test can beef up dairy and meat quality

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A genomics technique developed at Cornell to improve corn can now be used to improve the quality of milk and meat…

A team led by Ikhide Imumorin, Cornell assistant professor of animal science, is the first to apply a new, inexpensive yet powerful genomics technique to cattle called genotyping-by-sequencing (GBS). The protocol contains only four basic steps from DNA to data, and Imumorin’s work demonstrated it generates enough markers to put cattle genomics on the fast track.

“Breeders are interested in cattle with traits such as high meat or milk quality, disease resistance and heat tolerance, but identifying the best animals means sorting through thousands of unique gene variants in the genome,” said Imumorin. “Until recently, the cost of genomics techniques has set too high a bar for breeders, and many cattle species, particularly those outside the United States and Europe found in Africa and Asia, were excluded from the genomics revolution.”

Using samples from 47 cattle from six breeds from the United States and Nigeria, Imumorin’s team used GBS to identify more than 50,000 genetic markers for genetic profiling…The team’s analysis showed the markers were preferentially located in or near the gene-rich regions in the arms of the chromosome, making them well sited for tagging genes in genetic studies. The researchers also demonstrated that the markers accurately detect the relationships among the breeds.

“GBS democratizes genetic profiling, and our work shows its usefulness in livestock,” said Imumorin. “While a genetic profile could run $70 to $150 per individual using commercially available methods, GBS brings the cost down to around $40 a sample or less. It’s a very exciting time.”

Imumorin predicts that GBS will be deployed by breeders and geneticists scanning herds for superior breeding stock. He cited the example of how selection of bulls for use in breeding programs will be streamlined through GBS-driven genome analysis around the world without the steep cost of commercial SNP chips, the standard tool based on gene variants discovered in European cattle breeds and made into off-the-shelf genotyping chips.

“For example, a bull can have genes for superior milk production, but the only way to test that is to evaluate milk production in his daughters,” said Imumorin. “A bull will be at least five years old before two generations of his offspring can be evaluated, and that’s a long time for breeders to take care of a bull that may not make the final cut. These techniques hasten the day when a bull’s value can be assessed using genetics on its day of birth more cheaply than we can do now.”

Bravo. Cost-savings and accelerated genetic development are always welcome in cattle-breeding.

Written by Ed Campbell

May 22, 2013 at 8:00 pm

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