Posts Tagged ‘DNA’
New DNA test can beef up dairy and meat quality
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.
Mediterranean wasp spiders spreading to northern Europe
Temperature tolerance is key to the spread of wasp spiders into northern Europe, according to scientists.
Since the 1930s the distinctive spiders have expanded their range from the Mediterranean coast to Norway…Researchers in Germany traced the population boom to breeding between the native European spiders and an isolated colony living near the Black Sea.
Molecular Ecology reports the genetic mixing resulted in generations rapidly adapting to living in colder climates.
Wasp spiders (Argiope bruennichi) are commonly named for their bright, striped abdomens and were recently recorded by the Woodland Trust in Usk, south Wales for the first time.
The first official records of this conspicuous species in the UK were made in the 1920s.
Henrik Krehenwinkel from the Max Planck Institute for Evolutionary Biology, Germany, analysed the DNA of spiders caught across their current range, and museum specimens to understand more about their evolutionary history.
Piecing together the genetic puzzle, he found that the spiders diverged after the last ice age: part of the population stayed on the Mediterranean while a colony headed east to Central Asia.
While these eastern populations adapted to live in climates as diverse as the tropical south of Japan and cold south-eastern Siberia, the spiders in the Mediterranean remained limited to warm areas.
But, according to the research, rising temperatures across the continent in the last century allowed the Mediterranean spiders to join up and breed with a previously isolated Black Sea population…
He theorised that the novel combination of genes resulted in new physical characteristics that helped spiders to survive in different environments.
Mr Krehenwinkel described the hatchlings as “highly dispersive”, commenting that they can cover huge distances via a method known as “ballooning”: riding the breeze on a special parachute made of gossamer silk threads.
“By aerial dispersal, little spiders can cover distances of several hundred kilometres,” he told BBC Nature.
Cripes. One of my favorite signs of spring really making it to our tough dry terrain and altitude is the silk from balloon spiders being captured by our East-facing fence. Generally blown there by a warming West wind.
I wonder if our balloon spiders are distant kin of the wasp spider?
Tagging criminals by shooting them with a DNA gun
Imagine that you’re a police officer in the midst of a riot. While you may be able to apprehend the offenders closest to you, you can see plenty of other looters and vandals who you’re just not able to get to at the moment. Well, that’s where SelectaDNA’s High Velocity DNA Tagging System would come into the picture. At the heart of the system is a gun that shoots non-lethal pellets, which contain uniquely-coded synthetic DNA.
The idea is that when things have calmed down a bit, the police can set about rounding up the wrong-doers who they couldn’t nab when the riot was in full swing. In order to do so, they’d use one of SelectaDNA’s portable microscopes/readers to check suspects for the telltale DNA.
Each case of non-toxic pellets has a DNA code that’s specific to that batch, although all 14 pellets within the case share that same code – this means that the code could be used to tie a suspect to a certain event, but it couldn’t be used to single that one person out from all the other DNA-tagged suspects…
The gun itself is available in pistol or rifle form, both of which are powered by CO2 cartridges. The pistol can squeeze off 20 shots per 12-gram cartridge, while the rifle’s capacity is higher. Both guns allow users to hit targets from a range of 30 to 40 meters (98 to 131 feet).
The company also makes a grease, gel and spray containing the synthetic DNA, for marking belongings against theft or for tagging attackers.
On one hand, this surely is a beneficial use of science – aiding coppers to pinpoint evildoers, especially those in gang scrums.
On the other hand, I can’t help but think of making life easier for those government ideologues who’d like this system as second choice to the lack of RFID tags implanted at birth. 
Leicester scientists print out the human genome in 130 volumes
An exhibition on genomics – the study of genetic material which is driving major medical research innovations – has opened at Leicester’s New Walk Museum.
Inside DNA: A Genomic Revolution offers people the chance to learn more about genome research and have a say in the future policy of the science…
The University of Leicester’s Department of Genetics has printed out an entire human genome – amounting to 130 volumes of some 300 pages – which is going on display at the museum.
The work has been done by the Genetics Education Networking for Innovation and Excellence (Genie), based at the university.
Genie spokesman Dr Cas Kramer said: “Genie’s outreach programme has enabled us to develop workshops to further enhance the Inside DNA exhibit and we are very much looking forward to working with the museum over the next six months.”
Clare Matterson, from the Wellcome Trust, which funds the exhibition, said: “Over a decade since the first human genome was published, scientists are starting to get to grips with what the information in our DNA means for health and disease.
“Inside DNA is more relevant than ever, giving people a chance to explore issues raised by this research.”
Bravo!
Man wrongly charged with rape after DNA evidence tray re-used!
A man wrongly accused and charged with raping a woman was the “innocent victim” of an avoidable mistake, the forensics watchdog said today.
Adam Scott was arrested and held in custody for months after a plastic tray containing a sample of his DNA was re-used in the analysis of a swab from a rape victim in Manchester by private firm LGC Forensics.
Forensic science regulator Andrew Rennison said Mr Scott, from Devon, was an “innocent victim of avoidable contamination“.
It also emerged that the same error happened at least once before, on October 12 last year, the report added.
“The contamination was the result of human error by a technician who failed to follow basic procedures for the disposal of plastic trays used as part of a validated DNA extraction process,” he said…
“These errors were compounded by the failure at LGC to consider the possibility of contamination despite concerns expressed by the investigating officer about the reliability of the DNA profile.”
He went on: “It is unlikely that the case against Mr Scott would ever have proceeded to trial and, in the absence of any further evidence, the case would probably have been discontinued.
“However, this is of little comfort to Mr Scott who was charged on October 23 2011 and remanded in custody on this case until it was withdrawn on March 7 2012…”
LGC said it “deeply regrets the incident of contamination”, blah, blah, blah.
Results from the best science in the world still must run the gauntlet of human beings who may or may not be capable of maintaining legitimate standards. The procedures for checking quality in this case were as useless as the test.
Wi-fi and the Web inspire “Bi-fi” for bioengineering
The internet has revolutionized global communications and now researchers at Stanford University are looking to provide a similar boost to bioengineering with a new process dubbed “Bi-Fi.” The technology uses an innocuous virus called M13 to increase the complexity and amount of information that can be sent from cell to cell. The researchers say the Bi-Fi could help bioengineers create complex, multicellular communities that work together to carry out important biological functions.
Cells naturally use chemicals to communicate with the chemical signals typically acting as both the message and the messenger. However, this method of communication is extremely limited in terms of complexity and bandwidth.
“If your network connection is based on sugar then your messages are limited to ‘more sugar,’ ‘less sugar,’ or ‘no sugar’” explains Drew Endy, PhD, an assistant professor of bioengineering. By separating the messenger and the message, Endy and Monica Ortiz, a doctoral candidate in bioengineering, have been able to greatly increase the amount of data that can be transmitted.
They chose the virus M13 to act as the messenger because when it infects bacteria, it doesn’t kill its host but makes itself at home indiscriminately sending out DNA strands that it reproduces within its host. The engineers are able to control these strands of DNA, so custom DNA messages can be wrapped within proteins produced by M13 and sent out to infect other cells. Once they arrive in a new host, they release the packaged DNA message…
Using DNA to store the message means that it can contain any sort of genetic instruction. M13 is known to have packaged DNA strands containing as many as 40,000 base pairs, which is far in excess of the majority of genetic messages of interest in bioengineering that range from several hundred to many thousand base pairs…
The researchers believe that their Bi-Fi biological internet could lead to the development of biosynthetic factories consisting of huge masses of microbes collaborating to produce complex fuels, pharmaceuticals and other useful chemicals. Even more exciting, the researchers say that with improvements, the technology could one day be used in more complex three-dimensional programming of cellular systems, such as the regeneration of tissue of organs.
Looks like one of those qualitative processes that could be as scary as useful. Why, oh why, does my poor brain switch into sci-fi plots starring Milla Jovovich?
The positive side no doubt is where the research bucks will go. I hope.
Space sugar may lead to planetary prebiotic chemistry — and evolution to DNA and beyond
Using the latest-generation Atacama Large Millimeter Array (ALMA), which is an advanced system of 64 radio-telescope antennas in northern Chile, scientists at the European Southern Observatory have discovered a simple form of sugar orbiting a small binary star. Known as 16293-2422, that star is only 400 light-years away, and has about the same mass as the Sun. The finding could shed light on how the building blocks of life can originate spontaneously in deep space, even without a planet to support them.
The molecule found was glycolaldehyde (C2H4O2), not dissimilar to the table sugar (C12H22O11) we’re familiar with, and one of the building blocks of DNA and RNA. Glycolaldehyde has been found inside distant cloud dust as early as in 2000 but, crucially, this marks the first time that scientists have detected it in the right place and at the right time for life to blossom in its vicinity…
Most chemical reactions on Earth occur in liquid water, but in interstellar space the complex molecules appear to form on the surface of tiny dust particles. Smaller molecules such as water, formaldehyde, methane, ammonia, carbon dioxide or methanol coat the surfaces and interiors of the grains in the dust clouds. Then, when a shock wave hits the dust, it provides the energy to assemble more complex molecules (such as sugars) from the simpler ones and then free them from the dust grains.
One of the open questions on the origins of life on Earth is the mystery of how, based on our ample fossil record, life seems to have originated very shortly after the right conditions arose on our planet. This finding might help explain why, as there is mounting evidence now that prebiotic chemistry – the formation of the molecular building blocks necessary for the creation of life – occurs in interstellar clouds long before those clouds collapse to form a new planetary system.
Cripes! Another fascinating area of study – incorporating astrophysics, astrochemistry, prebiotic chemistry and leading to organic life and evolution.
It boggles the mind.
Scientists build anew on remains of junk DNA theory
The genetic “control panel” of the human body that regulates the activity of our 23,000 genes has been revealed for the first time in a scientific tour de force that could revolutionise the understanding and treatment of hundreds of diseases.
Scientists have once and for all swept away any notion of “junk DNA” by showing that that the vast majority of the human genome does after all have a vital function by regulating the genes that build and maintain the body.
Junk DNA was a term coined 40 years ago to describe the part of the genome that does not contain any genes, the individual instructions for making the body’s vital proteins. Now, this vast genetic landscape could hold hidden clues to eradicating human disease, scientists said.
Hundreds of researchers from 32 institutes around the world collaborated on the immense effort to decipher the hidden messages within the 98 per cent of the human genome without any genes and was thought, therefore, to have no function.
They have concluded in a series of 30 research papers published simultaneously today, in Nature, Science and other journals, that this so-called junk DNA is in fact an elaborate patchwork of regulatory sequences that act as a huge operating system for controlling the genome…
“We see that 80 per cent of the genome is actively doing something. We found that a much bigger part of the genome – a surprising amount in fact – is involved in controlling when and where proteins are produced,” Dr. Ewen Birney said.
Defects in this part of the genome could be responsible for a range of illnesses, from diabetes and Crohn’s disease to disorders of the immune system, such as lupus. Knowing about them could lead to a fundamental reappraisal of what goes wrong in scores of difficult conditons, said John Stamatoyannopoulous of Washington University in Seattle, another leader of the consortium.
Bravo! As happens so often, study and experimentation pries away prominence of a small body of knowledge only to open the door to new studies magnitudes larger and broader. Gonna need more molecular biologists, gang.
DNA tests if you’re using stolen wood, helps curb illegal logging
Unlike the Crime Scene Investigators from the popular TV series, these detectives are hired to look for evidence of rogue wood from stores increasingly worried about being duped by a global trade in illegal timber now worth billions.
They take wood samples into their lab and put them through DNA tests that can pinpoint the species and origin of a piece of timber. They also track timber and timber products from forest to shop to ensure clients’ shipments are legal.
“This is like CSI meets save the planet,” says Jonathan Geach, executive director of Double Helix Tracking Technologies, the Singapore company that has developed and commercialized DNA testing for wood, the only firm in the world to do so…
The money earned from a trade that Interpol estimates at up to $30 billion annually is untaxed and often run by organized gangs to fund crime and conflict. The logging increases global warming with heightened carbon emissions, and landslides through loss of watersheds. It causes loss of livelihoods in forest communities and dents global timber prices.
Until now, the battle against trade in illegal timber has been waged with regulations and preventive measures, and has not met with much success. Now it is increasingly focused on using the criminal justice system and law enforcement techniques.
Retailers such as Kingfisher, Marks & Spencer and Australian timber wholesaler Simmonds Lumber are either already using the technology or looking to add it to their existing timber sourcing practices…
As new U.S. laws started to bite over the past two years, and with tougher laws set for Europe in 2013, the number of clients is growing, says Kevin Hill, DoubleHelix’s founder.
Within two years, the aim is to license Lowe’s DNA extraction technique to accredited laboratories globally, as the $150 billion timber industry comes under increasing pressure to stamp out illegal wood.
As much as I hate the phrase, this is a true win-win situation for consumers and sellers alike. Contractors and end users will have verified questions like sustainability. Lumbering interests and mills will profit from sales with guaranteed quality, legality.
RTFA for many details about the economics and science. Interesting stuff.
The 1st, 2nd, and 3rd nations – and may be too complex to enjoy
By now you’ve probably read about the paper which reports that there seem to have been three waves of humans migrating into the New World prior to the arrival of Europeans. A major aspect of this result is that it does not emerge out of a vacuum, but rather comes close to settling an old question in linguistics…
The late Joseph Greenberg generated a series of audacious phylogenies of languages of the world. Greenberg’s attempts received mixed reviews. It seems that there is little controversy about some of his classifications of African languages, but linguists of American native dialects rejected his division of the languages of the New World into three broad families, Eskimo-Aleut, Na-Dene, and Amerind…The linguistic trichotomy also lent itself to a narrative of three migrations…
Despite all this drama, the scientific isn’t too hard to understand. Aside from the nifty statistics one problem is that many of these native groups have European and African admixture, but there are workarounds to that (e.g., just pull out genomic segments which are indigenous, and use those)…
On a big picture note this puts the lie to the idea that before agriculture hunter-gatherer societies were subject purely to differentiation in situ. The Eskimo-Aleut and Na-Dene erupted into a settled landscape, and dispossessed the indigenous groups of their lands…The First Americans “struck back” in this case, shoving aside the pioneers of northern living who had likely originated more recently from the margins of eastern Asia. Of course, the Eskimo-Aleut and related peoples were not First Americans only, rather, it was the old (First American) and new (Asian) ganging up upon the not so old or new (Asian).
At which point I will leave it up to more diligent readers to wander through this article – and/or the slightly deeper stuff – to sort it out to your own satisfaction.
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