Category Archives: Genome

D.R. Venema and Scot McKnight, Adam and the Genome, (Brazos, 2017).

On first blush the title of this book suggests an Indie rock band. But seriously, this is a very well researched book on genetics, and Biblical interpretation vis a vis the origins of human life, and whether or not Adam (and Eve) were historical persons. The genetics part of the book by D.R. Venema is a difficult read for those not familiar with genetics, even at the lay persons level, whereas, Scot McKnights half of the book (beginning at p. 93) is quite clear, but in some ways more problematic, from my point of view. Nonetheless, it is written with the sort of style and grace and honesty that we have come to expect in Scots books.

If we ask what prompted the book, all is made clearer by statements late in the study on pp. 172-73. The concern is about people losing their faith due to an encounter with science, particularly evolutionary theory, especially perhaps those who have come from more fundamentalist Protestant backgrounds. Scot deals regularly with such students and frames the matter this way: Here is what is vital for this book: [a] persons faith was challenged by his realization about evolution and he was forced to make a choice about whether the Bible or evolution was the truest description and understanding of the world. He chose science because the understanding of the Bible was in his view demonstrably wrong. Dennis and I are proposing another alternative: accepting the reality of genetic evidence supporting a theory of evolution along with an understanding of Adam and Eve that is more in turn with the historical context of Genesis.

In other words, the interpretation of the Word should be adjusted on the basis of the assumed fait accompli of science to demonstrate it has the facts on its side. Neither side of these assumptions, the science or the Biblical interpretation assumptions are without their problems. But I absolutely agree that we need to have a good discussion about this because science is one thing and pseudo-science that denies the geological and genetic evidence for an old earth and ancient human race needs to countered.

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Adam and the Genome Part One - Patheos (blog)

April 12, 2017 by Pat Bailey Richard Michelmore, director of the UC Davis Genome Center, and colleagues have released the first comprehensive genome assembly for lettuce and the huge Compositae plant family, which includes diverse plants ranging from the sunflower to star thistle. Credit: Gregory Urquiaga/UC Davis

Today (April 12), UC Davis researchers announced in Nature Communications that they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the huge Compositae plant family.

Garden lettuce, or Lactuca sativa, is the plant species that includes a salad bar's worth of lettuce types, ranging from iceberg to romaine. With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

Lettuce is a member of the huge Compositae family, which includes the good, the bad, and the ugly of the plant world, from the daisy and sunflower to ragweed and the dreaded star thistle.

The genome assemblya compilation of millions of DNA sequences into a useful genetic portraitprovides researchers with a valuable tool for exploring the Compositae family's many related plant species.

"This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants," said Sebastian Reyes-Chin-Wo, the lead author and a graduate student in the laboratory of plant geneticist Richard Michelmore.

"This is particularly significant because Compositae is the most successful family of flowering plants on earth in terms of the number of species and environments inhabited," said Richard Michelmore, who directs the UC Davis Genome Center.

Triplicate genes may explain success:

The researchers found that specific genes in the lettuce genome were consistent with certain physical traitslike the production of a rubber-containing milky sapthat have also been found in taxonomically distinct species, such as the rubber tree.

The study also provided evidence that somewhere during the evolution of lettuce about 45 million years ago, its genome was "triplicated." As a result, one-fourth of the genomeincluding about 30 percent of all of its identified genesnow appears in multiple related regions. Because such genomic duplications may give plant species an advantage in colonizing new environments, the ancient triplication event might, in part, explain the success of the Compositae plant family.

New technology yields more precise information:

Michelmore noted that this is the first reported genome assembly of a plant species resulting from use of a new technology that gives information about the physical proximity of the DNA sequences to which proteins are bound.

The new approach, developed by Dovetail Genomics, a company spun out from UC Santa Cruz, resulted in a more contiguous and accurate genome assembly, even though lettuce has one of the larger plant genomes sequenced to date, he said.

Explore further: Sequencing hundreds of nuclear genes in the sunflower family now possible

More information: Sebastian Reyes-Chin-Wo et al, Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce, Nature Communications (2017). DOI: 10.1038/ncomms14953

Journal reference: Nature Communications

Provided by: UC Davis

Advances in DNA sequencing technologies have enormous potential for the plant sciences. With genome-scale data sets obtained from these new technologies, researchers are able to greatly improve our understanding of evolutionary ...

As vegetable growers face a lack of skilled farm labor and higher production costs, they are searching for effective, lower-cost mechanical means of getting their products to market. In a study in the February 2016 issue ...

Researchers from the University of Bristol have uncovered one of the reasons for the evolutionary success of flowering plants.

Like most annuals, lettuce plants live out their lives in quiet, three-act dramas that follow the seasons. Seed dormancy gives way to germination; the young plant emerges and grows; and finally in the climax of flowering, ...

Prickly lettuce, a common weed that has long vexed farmers, has potential as a new cash crop providing raw material for rubber production, according to Washington State University scientists.

U.S. Department of Agriculture (USDA) scientists in California have developed 16 new lettuce breeding lines. Lettuce production in the United States is concentrated mostly in California and Arizona, where it is grown year-round. ...

Scientists at the University of California, Davis have discovered that DNA sequences thought to be essential for gene activity can be expendable. Sequences once called junk sometimes call the shots instead.

The hot springs of Yellowstone National Park may be extreme environments, but they are host to a diversity of microbes that could shed light on the evolution of life on Earth and, perhaps, what lurks on distant planets.

Breaks in DNA can wreak havoc in the body, giving rise to cancer and other health problems. Yet sometimes cells rupture their own DNA for a good reason.

How some industrial pollutants or abnormal levels of cellular metabolites contribute to diverse human diseases is now more clearly understood, based on a new study from the University of Wisconsin Carbone Cancer Center (UWCCC) ...

Cocaine, nicotine, capsaicin. These are just three familiar examples of the hundreds of thousands of small molecules (also called specialized or secondary metabolites) that plants use as chemical ammunition to protect themselves ...

A Florida Museum of Natural History study provides new insights into the complex, shared history between blood-sucking lice and the vitamin-producing bacterial sidekicks that enable them to parasitize mammals, including primates ...

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Gene salad: Lettuce genome assembly published - Phys.Org

The largest genome sample ever analyzed for a human epidemic reveals that the West Africa epidemic unfolded with small, overlapping outbreaks as the virus spread over short distances and that urban settings amplified the spread.

Meanwhile, another study harnessed different advanced scientific tools in the blood of a single sick patient to detail gene-level response during infection.

In a massive international collaboration, 93 scientists from 53 institutions in 16 countries contributed to the analysis of 1,610 Ebola virus genomes from the outbreak, composing 5% of all known cases. The team published its findings on Apr 12 in Nature.

Alongside the genome analysis, the researchers looked at 25 factors that could have contributed to the spread and duration of West Africa's outbreak.

Surprisingly few infected travelers sparked new outbreaks, and the ones that did mainly spread the disease short distances, sparing other countries in the regionGuinea-Bissau, Senegal, Mali, Cote d'Ivoire, and northern Guineafrom severe impact.

Gytis Dudas, PhD, with the Fred Hutchinson Cancer Research Center in Seattle, said in a press release from the institution, "We calculated that 3.6% of cases traveled, basically meaning that if you were able to focus on those mobile cases and reduce their mobility, you might have had a disproportionate effect on the epidemic."

Border closures appeared to have some impact on virus spread, but by the time the three hardest-hit countries closed their borders, travelers had already seeded outbreaks in each country. Dudas said in the later stages of the outbreak, a particularly mobile chain of infected people moved between Sierra Leone and Guinea.

Variables that didn't seem to have significant impacts on speeding or slowing the outbreak, in contrast, included shared languages, economic output, and climate.

The researchers said the information will help predict the future of Ebola outbreaks and help guide the response. They added that real-time sequencing and rapid data sharing doesn't replace boots-on-the-ground case finding and contact tracing, but in setting such as West Africa where resources are limited, such measures can help speed the response by telling responders where to place contact tracers, treatment beds, quarantine, and other infection control measures.

An unprecedented genetic analysis of blood samples taken daily after an Ebola patient was hospitalized revealed changes in antiviral and immune response at key points in disease progression, researchers reported Apr 12 in Science Translational Medicine.

The patient was admitted to the National Institutes of Health (NIH) Clinical Center isolation unit on day 7 of infection for a 26-day hospitalization.

He or she received supportive care, but no experimental treatments. The researchers' study goal was to explore how gene expression changes, including those linked to blood clotting problems and organ dysfunction, correlated with the patient's clinical condition.

A marked decline in antiviral responses correlated with virus clearance from white blood cells, and host responses shifted rapidly from gene activation in cell damage and inflammation toward those that promote cellular and organ repair. The shift came before the first signs of clinical improvement.

The investigators said that although the findings involve only a single patient, they might offer a clinical marker to tailor treatment or help guide the development of new treatments.

See also:

Apr 12 Nature study

Apr 12 Fred Hutchinson Cancer Research Center press release

Apr 12 Sci Transl Med case report

Apr 12 NIH press release

Read this article:
Huge genome study dissects Ebola outbreak's spread - CIDRAP

Science Daily

Sandy the dingo wins world's most interesting genome competition Science Daily 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 ...

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Sandy the dingo wins world's most interesting genome competition - Science Daily

For the first time in history, the U.S. Food and Drug Administration (FDA) has granted approval for direct-to-consumer (DTC) tests to be sold directly to consumers. Specifically, the FDA has authorized Silicon Valley-based genetic testing firm 23AndMe to market their Personal Genome Service Genetic Health Risk (GHR) tests for 10 diseases or conditions namely: Alpha-1 antitypsin deficiency, Celiac disease, factor XI deficiency, Gaucher disease type 1, G6PD, Parkinsons disease, early-onset primary dystonia, late-onset Alzheimers, hereditary hemochromatosis and hereditary thrombophilia.

To arrive at their decision, the FDA said they reviewed studies that showed how the procedures used by 23AndMe were able to correctly and consistently identify gene variants associated with the 10 conditions. They also looked into other peer-reviewed references that confirmed the links and therefore provided further support to backup 23AndMes data.

After being granted FDA approval on April 6, the company says the tests will be available to the public in April.

In anticipation of the debates and discussions that the FDAs decision might evoke, the agency made it clear that the disease risk tests are simply meant to provide genetic risk information but no more than that. This means that since there are several other factors that can raise or reduce a persons chances of becoming sick like lifestyle, diet and a persons environment the tests can only provide information on ones predisposition to develop a condition. Basically, the suggestion here is that the tests cannot be used to determine a persons overall health risks.

The information obtained from the DTC tests, however, can be used by individuals to reassess and possibly do some lifestyle adjustments, or maybe initiate consultations with a medical professional, especially if the information received is unfavorable.

Just imagine, through these $199.00 DTC tests, a person only has to do a simple saliva swab, send it to 23AndMe, then wait for around 6 8 weeks for an email from the company that will pretty much let him/her know if he/she has gene mutations that make him/her more susceptible to developing certain diseases.

Even in clinics and hospitals, lab test results cannot be taken at face value. Theres always a need for doctors to correlate the findings with their clinical assessment of the patient in order to come up with the correct diagnosis or a reasonable prognosis.

Interpretation of genetic information remains relatively difficult because the link between specific genes and certain medical conditions isnt always in black and white. If doctors find it difficult at times that they have to consult other experts to make an accurate assessment, what can be expected from people who have no medical background?

In the case of these DTC tests, if a person receives bad news about his/her disease risk, it might cause unnecessary stress and anxiety because the person will rely solely on that information, without the guidance of a medical practitioner who can put things in perspective.

Back in 2013, the FDA refused to authorize the DTC tests, citing a false positive result could lead to unnecessary treatments. Four years later, however, the tests were made possible via a new permit type from the FDA, including what the agency called special controls to assure the accuracy of tests.

Whether or not the public can handle the genetic data info properly remains to be seen.But for those who can, this may indeed prove helpful in the long run, especially if it manages to make people shift to healthier lifestyle choices because of the test results.

As 23andMe CEO and co-founder Anne Wojcicki said in a statement: This is an important moment for people who want to know their genetic health risks and be more proactive about their health. The FDA has embraced innovation and has empowered individuals by authorizing direct access to this information.

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FDA DNA-Test Clearance Opens Genome Floodgates - Wall Street Pit

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."

Read more:
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 ...

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