Tagged: DNA

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.

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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.

Thirdhand smoke causes DNA damage

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.

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

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.

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

Balloon spiders

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.