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Posts Tagged ‘genomics’

The initial draft of the genome is already complete and has been put online for other researchers to access in hopes that biologists and geneticists can unravel the mystery behind the naked mole rat’s unique hardiness. For instance, naked mole rats live to be about 30 (common rats live to about age four) and they do so in harsh underground environments where oxygen is scarce.

They also show resistance to a number of diseases, namely cancer. There have been no recorded naked mole rat deaths attributed to cancer in the decades of study devoted to the creatures, and that makes its genome a rich hunting ground for researchers trying to pinpoint the genetic hallmarks of cancer--or the mechanisms for cancer resistance.

But that’s not the only unique and interesting quirk that researchers would like to explore in the naked mole rat’s genome. Previous research has shown that they feel no pain in their skin and that they are surprisingly resistant to strokes (they are already imbued with a low metabolic rate that allows them to live on less oxygen, but this physical trait could go beyond simple metabolism).

In other words the naked mole rat, while not completely indestructible (although acid doesn’t seem to burn them, so there’s another superhero-like quality they possess), are survivors from whom we can hopefully learn a few genetic tricks. This genome blueprint is a start. If it turns out that naked mole rats are genetically predisposed to stop speeding bullets, you’ll read about it here.

[BBC]

DFTD is pretty nasty stuff and has only emerged as a killer of Tasmanian devils in the last fifteen years, but the effects have been widespread and disastrous. The disease disfigures the victim, which usually dies form starvation or suffocation due to massive facial tumors that impede its ability to get by in the wild. Worse, the disease is easily communicable, spreading through biting, mating, even simple touching.

The scheme hatched by scientists involves keeping a population of Tasmanian devils in zoos and other facilities where they won’t be in contact with wild Tasmanian devils--and therefore will be quarantined from the disease. Once DFTD has run its course, the captive populations could be reintroduced into the wild and allowed to repopulate their native island.

But researchers didn’t want to simply grab a sample of devils at random--that could inadvertently limit further the already limited genetic diversity of the overall devil population, possibly with adverse effects. So the team took two devils--one from the extreme northwest and another from the far reaches of the southeast to represent geographic diversity--and sequenced their genomes.

From that genetic analysis the researchers created a model that represents the range of genetic diversity currently on the island, and helps them determine which specimens should be selected for captivity based on the objective of maintaining complete genetic diversity should the wild population collapse completely. Further, they sampled the genetic makeup of genomes secured from museum samples of devil specimens dating back more than two centuries to see how much genetic diversity has changed since humans first arrived on Tasmania (somewhat surprisingly, the change over the last century been minimal).

The idea isn’t just to preserve the species in captivity, but to preserve it with the exact degree of genetic diversity it has in the wild now--in other words, to manipulate nature while keeping it on its natural genetic course as much as possible. If the plan works, it could be extended to other endangered species as well.

Genome Wowser--the name is derived from the Genome Browser Website set up by UCSC in 2000, but with additional “wow”--is kind of like a Google Maps for the genome. You can search for a specific gene by entering its name in the search box, or you can simply browse for points of interest. Annotations added by researchers serve as guideposts, offering insight into genes’ particular known or supposed expressions.

There’s also information embedded about epigenetics--how genes are modified by chemical processes, and all of that information is updated regularly. Factor in the upcoming versions that will include more than three dozen other species--including cats, dogs, chimpanzees, and 11 species of fruit flies--and Genome Wowser is a pretty powerful tool for geneticists and the scientifically curious alike. Try doing all of that on Kindle.

Entomologists are submitting suggestions for 5,000 insects and other arthropods whose genomes should be sequenced, in a hunt for vulnerable regions that can be targeted with pesticides. The five-year 5000 Insect and Other Arthropod Genome Initiative, otherwise known as the i5K Initiative, will target insects that are known to be important to worldwide agriculture, food safety and medicine, among other impacts.

The study will examine insects that serve as disease transmitters and close relatives that do not, so researchers can compare genes that make some insects disease vectors and others benign. Certain species of mosquito, for instance, carry diseases like malaria or yellow fever, while other species do not, and understanding the genomic difference could help fight the disease-carrying types.

Pinpointing the genes that cause susceptibility to pesticides could actually help beneficial insects, like bees, while eradicating harmful ones from farm fields. Geneticists could mine data for specific detoxification genes found in certain insects, said Kevin J. Hackett, a national program leader at the USDA Agricultural Research Service, in an interview in the magazine American Entomologist.

“If we know about those genes from one insect to another, we can use that information to actually kill the insects," he said. “Or if you take beneficial insects like honey bees, which do not have as many detoxifying genes and are more susceptible to chemicals, that kind of information could be used to help protect bees.”

The project is feasible now because the costs of genetic sequencing have fallen sharply in recent years. As researchers begin sequencing genomes, they will be available on several public domain databases, entomologists said.

Do you know a lot about bugs, or the troubles they cause? Click here to nominate a species for sequencing.

[via BBC]

Horner has spent a career digging up some of the best-preserved biological artifacts leftover from the dinosaurs’ tenure on this planet, but in none of them, not even the soft tissues like preserved blood vessels, could he or his team find intact DNA--the kind you need to clone a dinosaur a la Jurassic Park. So he and some colleagues are looking for dino-era DNA in dinosaurs’ descendants: modern birds.

Chickens, Horner says, have the keys to building a dinosaur etched into their genomes. Things like teeth, claws, and tails are still expressed in embryonic chickens, but are all turned off at some point during embryonic development by genes that evolution has made ubiquitous in modern birds. By turning these genes off, we’ve already engineered chickens expressing teeth, and by turning off still more we might resurrect more of the dinosaur’s prehistoric traits, no mosquito mining necessary.

Horner tells the story better than we do, hear him explain it in the video below.

[TED]

OK, maybe it’s not that monumental; new genomes are sequenced all the time. But this one is special — cacao is no ordinary plant. Who cares about the corn genome when you can study chocolate instead?

The genome sequence, which enters the public domain today, is the result of a partnership among a few unlikely bedfellows: Mars Inc., maker of M&Ms, Milky Way bars and other treats; the U.S. Department of Agriculture’s Agricultural Research Service; and IBM. The trio hopes international agricultural researchers will immediately start refining the sequence. As with any gene mapping project, decoding the complete genome will take some time.

In a twist, the New York Times reports that a competing team, led by Mars rival Hershey, is also working on its own genome sequence. That team won't discuss its findings until they are published in a scientific journal, however.

The Mars team's preliminary results will be available via the Cacao Genome Database, to ensure that the data remains perpetually patent-free. The Times quotes Hershey's team saying they will also make their sequence available, but won't restrict patents.

Mars hopes its $10 million investment will pay off eventually, said Howard-Yana Shapiro, the firm’s global staff officer of plant science and research.

“Although it may not benefit the bottom line in the short term, in the long run, it will ensure mutually beneficial results for the company, cocoa farmers and tree crop production in key regions of the world,” he said.

Genome sequencing takes plant breeding and cultivation to a new level. Armed with information about a plant’s genetic code, scientists can more easily search for genes that produce desirable traits for boosting yields and disease resistance. And, of course, ensuring genetically engineered chocolatey awesomeness.

Juan Carlos Motamayor, senior cacao scientist at Mars, said breeders have been studying cacao genes for about 20 years. The genome sequence will help researchers determine specific links among genes, genetic markers and certain traits, he said. Despite its importance to 6.5 million farmers worldwide, cacao is considered an "orphan crop" because it is not as well studied as corn, rice or soy.

“We needed to narrow down the location of the genes, or narrow down the correlation between markers and traits, so we could do a market-specific selection more efficiently,” Motamayor said.

Fungal resistance is a key issue in cocoa production, for instance — fungal diseases have cost the cocoa industry $700 million a year for the past 15 years. Brazil was the world’s second largest cocoa country, producing over 400,000 tons per year, until a fungus infected almost all of its crops. Now, 70 percent of the world’s cocoa comes from Africa, and Ivory Coast is the world’s biggest producer.

Researchers want to guard against further losses (if not chocolate hoarders) by identifying genes that confer disease resistance. It would also be nice to know which genes control traits like yield and flavor.

IBM researchers used the Blue Gene supercomputer to analyze the genome, and advances in the mapping process allowed researchers to finish their work three years ahead of schedule.

While a sustainable supply of chocolate might be less crucial than, say, corn, let’s be honest — it’s a bit more exciting. Thanks, science!

Over the weekend, the New London Chamber Choir offered three performances of "Allele," a 20-minute, 40-part choral work in which the members sing their own genetic codes. The chorus of "A C T G" rises to a haunting, oddly textured crescendo; listen here.

Composer Michael Zev Gordon worked with Dr. Andrew Morley, who has been testing the genes of 250 musicians and 250 non-musicians to see if a certain gene determines musical ability.

Morley, who has sung in a choir and composed music, realized musical notes look a bit like genetic sequences. He consulted with Gordon, who viewed the genetic code as raw material that could be translated into notes, according to the BBC.

Gordon decided to assign a note to each of the four bases that make up DNA. He describes his work in a Guardian guest column published last month. He mapped a segment of a chosen polymorphism according to the "do-re-mi" scale, and added a rhythm.

"I arrived, to my surprise, at something that sounded quite like plainsong: it became the initial gesture of the piece," he writes.

The piece begins with a single voice singing a rhythm, and then more voices join in to convey the biological idea of replication and reproduction, BBC explains. At the climax, each of the 40 singers is singing part of his or her own genetic code.

The differences are subtle enough to sound harmonious -- a fitting metaphor for the genetic similarities we all share.

[via PhysOrg, BBC, Oxford Times]