Category Archives: Transhuman News

AnAustralian"gift to science" has been named the winner of a global competition.

Sandy thepurebred desert dingo beat four international finalists to take first place in the World's Most Interesting Genome Competition.

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Sandy the purebred desert dingo beat four international finalists to take first place in the World's Most Interesting Genome Competition. Vision: UNSW

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Sandy the purebred desert dingo beat four international finalists to take first place in the World's Most Interesting Genome Competition. Vision: UNSW

The win will give Australian scientists the opportunity to decode her DNAand test a hypothesis raised by Charles Darwin almost 150 years ago.

The public determined the winner of the annual competition.Sandy edged out a TemplePitvipersnake, a solar-powered sea slug, an explosive bombardier beetleand a pink pigeon to claim 41 per cent of votes. Up for grabs was thePacific BiosciencesSMRTGrant, whichenables sequencing of thecomplete genome of an important animal or plant.

The proposal to study Sandy's DNAwas led by Professor Bill Ballard from the University of NSW, with Professor Claire Wade of the University of Sydney, Dr Richard Melvin of UNSW, Dr RobertZammitof the Vineyard Veterinary Hospital and Dr AndreMinocheof the Garvan Institute of Medical Research also part of the project.

The sequencing will be carriedout at the Universityof Arizona.

"We are thrilled that our bid to have Sandy's DNA sequenced captured the public's imagination," Professor Ballard, from UNSW'sSchool of Biotechnology andBiomolecularSciences, said.

Professor Ballard has previously saidDarwintheorisedthat there are two stepsto the process of domestication:unconscious selection, as a result of non-intentional human influences, and artificial selection, through deliberate human activities such as breeding.

Sequencing Sandy's DNA will allow scientists to examine the changes in genesassociated with the process of domestication.

"Sandy is truly agift to science," Professor Ballard said. "As a rare, wild-born pure dingo, she provides a unique case study. Pure dingoes are intermediate between wild wolves and domestic dogs, with a range of non-domesticated traits. So sequencing Sandy's genome will help pinpoint some of the genes for temperament and behaviour that underlie the transition from wild animals to perfect pets."

Professor Ballard added that "learning more about dingo genetics will help efforts to conserve these wonderful Australian animals, through the development of improved tests for dingo purity".

Sandy and her siblings, Eggie and Didi, were three weeks old when they were found motherless near the Strzelecki Trackin central Australia in2014 by Barry and Lyn Eggleton, who raised the pups themselves.

Purebred desert dingoes are increasingly rare in Australia as the native animalsinterbreed with wild and domesticdogs andare targeted as pests by landholders.

Scientists at the UNSW'sRamaciotti Centre for Genomics haveworked on the genomes of other important native species including the koala, the Tasmanian devil, the wombat, the platypus, the Queensland fruit fly and the Wollemi Pine.

"We're very proud of UNSW's history of contribution to genomics and we are delighted that Sandy's genome will now be sequenced as the prize for winning this competition," UNSW molecular biologist and Deputy Vice-Chancellor (Education), Professor Merlin Crossley, said.

"Australia has so many interesting animals to sequence and the results enhance our understanding of evolution and biology and help improve agriculture and pest management."

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Sandy the desert dingo wins The World's Most Interesting Genome Competition - The Sydney Morning Herald

April 13, 2017 This is Sandy Maliki, a pure desert dingo and winner of the World's Most Interesting Genome competition. The UNSW-led proposal to have Sandy's DNA decoded beat four other finalists for the Pacific Biosciences SMRT Grant, which provides cutting-edge sequencing of the complete genome of a particularly fascinating plant or animal. Credit: Barry Eggleton/Pure Dingo

A wild-born, pure Australian desert dingo called Sandy Maliki has taken out first place in the World's Most Interesting Genome competition.The UNSW-led proposal to have Sandy's DNA decoded was one of five finalists for the Pacific Biosciences SMRT Grant, which provides cutting-edge sequencing of the complete genome of a particularly fascinating plant or animal.

The public determined the winner, with two-year old Sandy securing 41 per cent of the international community votes, closely followed by a Temple Pitviper snake, then a solar-powered sea slug, an explosive bombardier beetle, and a pink pigeon.

"We are thrilled that our bid to have Sandy's DNA sequenced captured the public's imagination," says project leader, Professor Bill Ballard of the UNSW School of Biotechnology and Biomolecular Sciences.

"Sandy is truly a gift to science. As a rare, wild-born pure dingo, she provides a unique case study. Pure dingoes are intermediate between wild wolves and domestic dogs, with a range of non-domesticated traits. So sequencing Sandy's genome will help pinpoint some of the genes for temperament and behaviour that underlie the transition from wild animals to perfect pets.

"As well, learning more about dingo genetics will help efforts to conserve these wonderful Australian animals, through the development of improved tests for dingo purity," Professor Ballard says.

Sandy and her sister and brother were discovered as three-week old pups in the Australian desert near the Strzelecki Track in 2014 by NSW animal lovers, Barry and Lyn Eggleton, who have hand-reared them ever since. The pups were close to death and their parents could not be found.

The dingo sequencing project will be the first to test Charles' Darwin's 1868 theory that the process of domestication can be divided into two steps: unconscious selection as a result of non-intentional human influences; and artificial selection as a result of breeding by humans for desired traits.

"This project will reveal the DNA changes between wolves and dingoes (unconscious selection) and dingoes and dogs (artificial selection)," says Professor Ballard.

A key aim of the annual international PacBio competition, which attracted more than 200 entries this year, is to raise public awareness of science and how genomic research can benefit society. Sandy's team, which set up a DancingwithDingoes Facebook page, enlisted the support of a wide variety of people around the world, including animal conservationists and fans of wolves, dingoes and dogs.

"We also engaged with staff and students at UNSW, by bringing two pure alpine dingoes from the Bargo Dingo Sanctuary onto campus for everyone to meet," says Professor Ballard.

The cutting edge PacBio technology allows DNA to be sequenced in long sections containing tens of thousands of bases, rather than in shorter sections of a few hundred bases, as with existing techniques. This can reveal important rearrangements in the genome that affect gene expression.

The sequencing will be carried out at the University of Arizona, with initial analysis by Computomics in Germany.

The Australian team behind the Sandy project also includes Professor Claire Wade of the University of Sydney, Dr Richard Melvin of UNSW, Dr Robert Zammit of the Vineyard Veterinary Hospital and Dr Andre Minoche of the Garvan Institute of Medical Research.

UNSW has a strong reputation in genomics research, with scientists at the university's Ramaciotti Centre for Genomics having worked on the genomes of a variety of other important native creatures, including the koala, the Tasmanian devil, the wombat, the platypus, the Queensland fruit fly and the Wollemi Pine.

"We're very proud of UNSW's history of contribution to genomics and we are delighted that Sandy's genome will now be sequenced as the prize for winning this competition," says UNSW molecular biologist and Deputy Vice-Chancellor (Education) Professor Merlin Crossley.

"Australia has so many interesting animals to sequence and the results enhance our understanding of evolution and biology and help improve agriculture and pest management".

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For more information about Sandy Maliki and her siblings, Eggie Warrigal and Didi Mirigung, see their Pure Dingo Facebook page.

Dingoes were introduced to Australia about 5000 years ago. It is widely accepted they were not domesticated by Indigenous Australians. Pure dingoes are becoming increasingly rare as the native animals interbreed with wild dogs and domestic dogs, and are targeted as pests by landowners.

Explore further: Dingo a distinct species, study says

(Phys.org) The dingo has been classified as a distinct Australian animal following research that sheds new light on its defining physical characteristics.

Australia's largest predator, the dingo, is resistant to one of the main threats to its survival as a specieschanges to skull shape brought about by cross breeding (hybridisation) with dogs, research shows.

(PhysOrg.com) -- Australia's native dog the dingo may have arrived here much earlier and by quite a different route than previously thought, a new study has found.

(PhysOrg.com) -- Studies in the past have shown that wolves are smarter than domesticated dogs when it comes to solving spatial problems, and now new research has shown that dingoes also solve the problems well.

The proud owner of dingo 'Kimba', James Bornstein, is part of the new wave of Australian exotic pet lovers whose unconventional companions are growing in popularity.

Marle and Digger may be small and cute puppies, but make no mistake, warns their handler Matt Williams: these 18-week-old dingoes are wild animals that would never make suitable pets.

People's ability to make random choices or mimic a random process, such as coming up with hypothetical results for a series of coin flips, peaks around age 25, according to a study published in PLOS Computational Biology.

Imagine that the way flies and butterflies drink nectar and other fluids can be imitated for use in medicine, potentially to deliver life-saving drugs to the bodyand also how this method can save their own lives in times ...

A team of scientists from the Broad Institute of MIT and Harvard, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering & Science at MIT, and the Wyss Institute for Biologically Inspired ...

The bacterial flagellum is one of nature's smallest motors, rotating at up to 60,000 revolutions per minute. To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting ...

Hunting is a major threat to wildlife particularly in tropical regions, but a systematic, large-scale estimate of hunting-induced declines of animal numbers has been lacking. A study published in Science on April 14 fills ...

There are many processes that take place in cells that are essential for life. Two of these, transcription and translation, allow the genetic information stored in DNA to be deciphered into the proteins that form all living ...

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Sandy the dingo wins world's most interesting genome competition - Phys.Org

A new method lets researchers quicklyscreen the non-coding DNA of the human genome for links to diseases that are driven by changes in gene regulation.

The technique could revolutionize modern medicines understanding of the genetically inherited risks of developing heart disease, diabetes, cancer, neurological disorders, and others, and lead to new treatments.

As reported in Nature Biotechnology, the new technique relies on the gene-hacking system called CRISPR/Cas9. Originally discovered as a natural antiviral defense mechanism in bacteria, the system recognizes and homes in on the genetic code of previous intruders and then chops up their DNA. In the past several years, researchers have harnessed this biologic system to precisely cut and paste DNA sequences in living organisms.

With the new tool, Gersbach and his colleagues are exploring the 98 percent of our genetic code often referred to as the dark matter of the genome.

The technique is already producing results, identifying previously known genetic regulatory elements while also spotting a few new ones. The results also show it can be used to turn genes either on or off, which is superior to other tools for studying biology that only turn genes off. Different cell types also produced differentbut partially overlappingresults, highlighting the biological complexity in gene regulation and disease that can be interrogated with this technology.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:How scientists explore our genomes dark matter

For more background on the Genetic Literacy Project, read GLP on Wikipedia

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Keys to heart disease, diabetes, cancer may be in genome's 'dark matter' - Genetic Literacy Project

New lettuce genome assembly offers clues to success of huge plant ... Science Daily A treasure-trove of genetic information has been unlocked about lettuce and related plants, completing the first reported comprehensive genome assembly for ... and more »

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New lettuce genome assembly offers clues to success of huge plant ... - Science Daily

April 11, 2017 A depiction of a part of a simulated DNA molecule within a nanochannel. The green beads are an unknotted portion of the molecule and the orange beads are a knot. Credit: Jain and Dorfman

While DNA sequencing provides precise, nucleotide-by-nucleotide genomic information, genome mapping provides a bigger-picture perspective of sequenced DNA that can provide valuable structural information. Like mapping roads to depict a city's structural information without needing to detail each home or business, genome mapping can be a powerful tool for understanding variations of large pieces of rearranged or altered DNA.

More technically, genome mapping is used to obtain large-scale genomic information with a resolution of around 2000 base pairs (bp), as opposed to the single-base resolution of sequencing. Genome mapping complements DNA sequencing, offering insight into huge, intact molecules between 150,000 and 1 million bp in length. Obtaining measurements of such large segments is not without its challenges, but new research into the physics of nanochannel mapping published this week in the journal Biomicrofluidics, may help overcome a (literal) knot in the process and advance genome mapping technology.

A team of researchers from the University of Minnesota partnered with BioNano Genomics, a company commercializing genome mapping in nanochannels, to understand the basic physics that underlies the mapping, and use that understanding to improve the technology. BioNano Genomics maps genomes by encoding DNA with sequence-specific, fluorescent labels before injecting it into nanochannels that cause the molecule to stretch out. The structural mapping information is read from the stretched DNA.

DNA knots, however, would put a kink in this method as the molecular tangle could be read incorrectly as a structural variation in the genome sequence. To better understand these nanoknots, the group uses computer simulations to model nanochannel configurations of DNA and compares the predictions to measurement-based characterizations.

"We looked at the probability that the DNA would form a knot inside the channel and predicted the size of the knots," said Kevin Dorfman, a member of the research team and lead author of the work. "This is important in mapping because knots could be incorrectly characterized as changes in DNA sequence structure when, in fact, they are just rearrangements of the DNA within the channel."

This line of research posed several challenges. The probability of forming knots is very low, and the molecules used in genome mapping are very large, requiring the team to come up with a computational pipeline capable of simulating this system at both the resolution of the knots as well as the DNA segment as a whole.

"Previous work on DNA knotting in these types of nanochannels looked at molecules that were almost an order of magnitude smaller than the ones in our study," Dorfman said. Another challenge the team faced was handling the terabytes of data from the millions of DNA chains that were generated to get meaningful statistics.

The goal of this research was to see whether or not the model's predictions of knotting were consistent with bright spots observed during experiments that could be knots on the DNA molecule.

"We found that experimental results are not consistent with equilibrium statistical mechanics, meaning that the knots in the experiments may not actually be knotswhile the way the data were processed in the experiments suggests many potential knotting events, we cannot definitively identify these events as knots," Dorfman said.

To address the discrepancy between experiments and simulations, the group will have to return to experiments, collecting dynamic data from the movement of the knots.

"The dynamic information can give us very important insights about the structure of the DNA in the channel, and potentially allow us to tell if the knots are, indeed, knots," Dorfman said.

Since knot formation is very rare, acquiring huge data sets, screening them to locate possibly knotted DNA, then analyzing those DNA molecules in detail is necessary.

The work did reveal, however, that these knots are not an intrinsic problem in genome mapping. If knot formation was frequent, this would make the processing of genome mapping data much more challenging. If the apparent knots in the experiments come from some other sources, then they can be removed by changing other parts of the experimental protocol.

Explore further: Improving accuracy in genomic mapping with time-series data

More information: "Simulations of knotting of DNA during genome mapping," Biomicrofluidics (2017). DOI: 10.1063/1.4979605

If you already have the sequenced map of an organism's genome but want to look for structural oddities in a sample, you can check the genomic barcodea series of distances between known, targeted sitesby cutting a DNA ...

Anyone who has been on a sail boat knows that tying a knot is the best way to secure a rope to a hook and prevent slippage. Similarly, knots in sewing threads prevent them slipping through two pieces of fabric. How, then, ...

Many of the processes essential to life involve proteins - long molecules which 'fold' into three-dimensional shapes allowing them to perform their biological role.

Nanotechnologies require a detailed knowledge of the molecular state. For instance, it is useful to know when and how a generic polymer, a long chain of polymers (chain of beads), knots. The study of molecular entanglement ...

Protein factors are responsible for organizing chromosomes inside the nucleus in three dimensions (3D), forming a shape like a gift bow, with proteins aggregating as the central 'knot' holding the ribbon-like loops of DNA ...

Scientists at The University of Manchester have produced the most tightly knotted physical structure ever known - a scientific achievement which has the potential to create a new generation of advanced materials.

People's ability to make random choices or mimic a random process, such as coming up with hypothetical results for a series of coin flips, peaks around age 25, according to a study published in PLOS Computational Biology.

Imagine that the way flies and butterflies drink nectar and other fluids can be imitated for use in medicine, potentially to deliver life-saving drugs to the bodyand also how this method can save their own lives in times ...

A team of scientists from the Broad Institute of MIT and Harvard, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering & Science at MIT, and the Wyss Institute for Biologically Inspired ...

The bacterial flagellum is one of nature's smallest motors, rotating at up to 60,000 revolutions per minute. To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting ...

Hunting is a major threat to wildlife particularly in tropical regions, but a systematic, large-scale estimate of hunting-induced declines of animal numbers has been lacking. A study published in Science on April 14 fills ...

There are many processes that take place in cells that are essential for life. Two of these, transcription and translation, allow the genetic information stored in DNA to be deciphered into the proteins that form all living ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

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What's a knotand what's notin genomic mapping - Phys.org - Phys.Org