Tagged: DNA

Row over cow settled by DNA tests


The cow in question

A woman in the southern Indian state of Kerala is set to win a court battle to keep a cow after DNA tests proved it belongs to her, her lawyer says…The woman, TS Sashilekha, had been accused by her neighbour Geetha of stealing the animal.

The acrimonious dispute even saw the cow in question appear in court.

It is thought to be the first time an ownership battle over an animal has been decided by DNA tests in India, where Hindus consider cows to be holy.

The legal battle between the two women began last year when Geetha claimed that a cow in her herd was the mother of the disputed animal…But DNA tests ordered by the court did not match, meaning that Sashilekha will get to keep the cow.

…N Chandra Babu, lawyer for Sashilekha, told the BBC, “It is a rare case and possibly the first of its kind in history. Perhaps this is the first time a DNA test was held on a cow to find out its real owner.”

After the disputed cow was produced in court, Sashilekha was allowed to keep it in her possession – but only after paying 45,000 rupees in securities.

I understand why the court would ask the eventual victor to provide security presumably covering the value of the cow. Hopefully, returned without charges. Another good reason why she is suing the accuser for costs and compensation.

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Human-Chicken Interactions project gets off the ground


Modern chickens are descended primarily from the red junglefowl

The meat and eggs of domestic chickens are a source of protein for billions. Yet how and when the birds were domesticated remains a mystery. The answers to these questions could reveal a wealth of information about the genetics of domestication, as well as human behaviour, and how we can improve our husbandry of the birds.

In a bid to learn more about the chicken and its lineage, the UK government is funding a £1.94-million (US$3.3-million) effort to determine how the chicken went from being a wild fowl roaming the jungles of southeast Asia several thousand years ago to one of the world’s most abundant domesticated animals. The Cultural and Scientific Perceptions of Human–Chicken Interactions project — ‘Chicken Coop’ for short — will examine human history from the perspective of the fowl…

But no domestic animal has been moulded and remoulded by humans as extensively as chickens, says Greger Larson, an evolutionary geneticist. The animals have been bred for eating, egg-laying and fighting. And in the case of one particularly vocal breed, the creatures have even been strapped to the masts of Polynesian boats to act as foghorns. “Chickens are polymaths,” he says…

Because…mutations are so common in contemporary chickens, Larson’s team and others assumed that humans influenced these traits through selective breeding early in the course of domestication. But DNA from chickens recovered at archaeological sites across Europe, spanning the period from around 280 bc to ad 1800, has turned that idea on its head. In an analysis published last month, Larson’s team reported that none of 25 ancient chickens would have had yellow legs, and that just 8 out of 44 birds carried two copies of the TSHR variant…universal in modern breeds. So even 200 years ago, chickens may have been very different from those we know today.

With the help of other Chicken Coop members, Larson is also trying to get to grips with the wider evolutionary forces that shaped modern chickens. He hopes to determine why, for instance, chickens have not been wiped out by disease. This might have been expected because their very rapid selection — much of which has taken place since 1900 — should have led to inbreeding and, by whittling down immune genes, a reduced ability to respond to infections.

I love chicken almost as much as I love pork. I wasn’t raised with any religious or philosophical beliefs that inhibit the consumption of animal protein. So, no problem there. :)

Until modern science comes up with a sound reason to avoid healthfully-raised specimens of foods my progenitors used to catch in the wild – and eat – I will continue to do the same. Though restricting my hunt to the aisles of markets of all types, from chain stores to local farmers.

Dating and DNA affirm Paleoamerican-Native American connection


Click to enlargeDaniel Riordan Araujo

Eastern Asia, Western Asia, Japan, Beringia and even Europe have all been suggested origination points for the earliest humans to enter the Americas because of apparent differences in cranial form between today’s Native Americans and the earliest known Paleoamerican skeletons. Now an international team of researchers has identified a nearly complete Paleoamerican skeleton with Native American DNA that dates close to the time that people first entered the New World…

The skeleton of a teenage girl was found in Hoyo Negro, a deeply submerged chamber in the Sac Actun cave system in the eastern Yucatan Peninsula, Mexico. Alberto Nava Blank and a team of science divers discovered the skeleton along with many extinct animal remains deep inside this inundated cave in 2007. The divers named the girl Naia…

Kennett and Brendan J. Culleton, postdoctoral fellow in anthropology, Penn State, were originally asked to directly date the skeleton. After traditional and well accepted direct-dating methods failed because the bones were mineralized from long emersion in warm salty water within this limestone cave system, they worked closely with colleagues to build a geochronological framework for Naia using a unique combination of techniques to constrain the age of the skeleton to the end of the ice age.

To build the case for a late Pleistocene age they collaborated with Yemane Asmerom and Victor Polyak from the University of New Mexico using global sea level rise data to determine when the cave system, which at the time Naia and the extinct animals entered was dry, filled with water. The site where Naia lies is now 130 feet below sea level and sea level rise would have raised the groundwater level in the cave system and submerged everything between 9,700 and 10,200 years ago. So initial estimates of the latest that animals and humans could have walked into the cave system was 9,700 years ago.

At the same time, the researchers experimented with uranium thorium dating the skeleton directly. Asmerom and Polyak tried to directly date Naia’s teeth using this method, but that also did not work well.

The bones were found deep below today’s ground surface in a collapsed chamber connected to the surface via a web of now flooded tunnels that Naia once walked along to fall to her untimely death. Because the caves are limestone, mineral deposits continued to form while the cave was largely dry. Working with Patricia Beddows, Northwestern University, Chatters noticed accumulations of calcium carbonate — tiny rosettes of calcite deposited by water dripping off the cave roof — which could be accurately dated using the uranium thorium method. Because these drip water deposits formed on top of Naia’s bones, their date must occur after she fell in the cave. The oldest one dated so far is 12,000 years old.

Naia’s tooth enamel was also radiocarbon dated to 12,900 years ago by Kennett’s lab…

Morphologically, Naia does not look like a contemporary Native American, but mitochondrial DNA testing — maternally inherited DNA — carried out by Brian Kemp, Washington State University, and his collaborators shows that she has a D1 haplotype. This is consistent with the hypothesis that her ancestors’ origins were in Beringia, a now partially submerged landmass including parts of Siberia, Alaska and the Yukon. Early humans moved into this area from elsewhere in Asia and remained there for quite some time. During that time they developed a unique haplotype that persists today in Native Americans. Genetically, Paleoamericans have similar attributes as modern Native Americans even if their morphology appears different.

There is so much more that can be determined about paleolithic finds with the aid of modern chemistry and the tools grounded in DNA. Has to make paleontologists a heck of a lot happier about the focus and improved accuracy they can bring to their studies.

Lifetime science students like me really appreciate the difference between sound hypothesis and certified measurement. Even if the increments are centuries. :)

DNA can provide your mugshot — Huh? Wha?

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.

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

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.”

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Geneticists producing atlas mixing genomes and events


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.

DNA tests find living descendants of Uncle Ötzi

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? :)

Ancient DNA unravels Europe’s genetic diversity

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.

Saving the orange by altering its DNA


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.

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.