Category Archives: DNA

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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Missing DNA evidence in Assange case

Embassy asylum ... Julian Assange. Photo: AP

LONDON: Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper has reported.

In a 100-page document shown to lawyers for the WikiLeaks founder, Swedish police made a case for the 41-year-old's extradition to Stockholm for questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom from a second woman, The Mail on Sunday reports.

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Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains in London's Ecuadorean embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the US, where the actions of his website are under investigation.

The Swedish police report said one woman, now age 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm. She said he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the newspaper said.

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No Assange DNA on torn condom - report

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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DNA evidence missing in Assange case

Artistic impression of the dynamics of DNA supercoils. A person manipulates a long DNA molecule. Loops in the DNA molecule are created by winding up the DNA. For the first time ever, the research by Van Loenhout, Grunt and Dekker revealed how these DNA loops dynamically move along the DNA strand.

If you take hold of a DNA molecule and twist it, this creates 'supercoils', which are a bit like those annoying loops and twists you get in earphone cables. Research carried out by TU Delft, The Netherlands, has found that in the DNA molecule these coils can make their way surprisingly quickly along the length of the DNA. This newly discovered 'hopping' mechanism - which takes places in a matter of milliseconds - could have important biological implications, because cells use the coils to bring specific pieces of DNA into contact with one another. The researchers from Cees Dekker's group at the Kavli Institute of Nanoscience in Delft will be publishing their results in Science this week.

Supercoiling

A DNA molecule in a cell is not simply a loose wire; it is completely wound up in a tangle of loops ('DNA supercoils'). These supercoils in a DNA molecule (see the illustration on the right) are similar to those annoying loops and twists you often get in earphone cables.

In living cells, the DNA supercoils form and unravel and move along the DNA molecule. They are vital to the regulation of DNA activity, in determining which genes are switched on or off for example. One of the ways in which cells use the supercoils is to bring pieces of DNA into contact with one another.

Dynamic

Static images of the DNA supercoils have been studied in detail in the past, but their dynamics remained unknown up till now. PhD student Marijn van Loenhout from the Kavli Institute of Nanoscience at Delft developed a new technique that enabled him to observe how the coils travel along a DNA molecule for the first time. The research was led by Professor Cees Dekker, head of the Bionanoscience Department.

The TU Delft team used magnetic tweezers to stretch out a small section of a DNA molecule and were then able to observe the movement of the DNA coils using fluorescence microscopy (see movies at the website). They succeeded in showing these movements in real time, at the level of the individual DNA molecule.

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Van Loenhout: "We have discovered that the coils can move slowly along the DNA via diffusion. But what we also saw - and this was totally unexpected - that they can 'hop' along relatively long distances (micrometres). In such a movement a loop disappears in one spot, while simultaneously another loop appears in another spot, much further away. This information enables us to test theories about the mechanics of DNA, testing how you tie a knot in DNA, as it were."

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Research: Hopping DNA supercoils

Among the many mysteries of human biology is why complex diseases such as diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease such as cancer or depression, while an identical twin remains perfectly healthy.

Now scientists have discovered a vital clue to unraveling these riddles.

The human genome is packed with at least 4 million gene switches that reside in bits of DNA that once were dismissed as junk but that turn out to play critical roles in controlling how cells, organs and other tissues behave.

The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.

The findings are the fruit of an immense federal project, involving 440 scientists from 32 labs around the world.

As they delved into the junk parts of the DNA that are not actual genes containing instructions for proteins they discovered it's not junk at all. At least 80 percent of it is active and needed.

The result is an annotated road map of much of this DNA, noting what it's doing and how.

It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

The findings have immediate applications for understanding how alterations in the nongene parts of DNA contribute to human diseases, which may in turn lead to new drugs.

They also can help explain how the environment can affect disease risk.

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DNA ‘junk' contains a treasure of information about disease

ScienceDaily (Sep. 13, 2012) Scientists at Karolinska Institutet in Sweden describe in a new study how so-called DNA origami can enhance the effect of certain cytostatics used in the treatment of cancer. With the aid of modern nanotechnology, scientists can target drugs direct to the tumour while leaving surrounding healthy tissue untouched.

The drug doxorubicin has long been used as a cytostatic (toxin) for cancer treatment but can cause serious adverse reactions such as myocardial disease and severe nausea. Because of this, scientists have been trying to find a means of delivering the drug to the morbid tumour cells without affecting healthy cells. A possible solution that many are pinning their hopes on is to use different types of nanoparticles as 'projectiles' primed with the active substance.

In the present study, which is published in the scientific journal ACS Nano, scientists at Karolinska Institutet show how DNA origami can be used as such a projectile (or carrier) of doxorubicin. DNA origami is a new technique for building nanostrucutres from DNA, the hereditary material found in the cell nucleus. Using this technique, researchers can produce highly complex nanostrucutres with surfaces to which complex patterns of proteins and many other molecules can easily be attached.

What the researchers did on this occasion was to package the doxorubicin in a DNA origami configuration designed in such a way that relaxed the degree of twist of the DNA double helix. This allowed the drug to be released more slowly and operate more effectively on the cancer cells at lower concentrations than is otherwise possible.

"When the DNA has a lower degree of twist, there's more room for the doxorubicin to become attached, which leads to its slower release," says group leader Dr Bjrn Hgberg. "Another advantage to using DNA origami is that we will quickly be able to develop the targeted protein system. This will enable us to deliver drugs in a way that is even more sparing of healthy cells."

The study has been financed with grants from several bodies, including the Swedish research Council, Vinnova (the Swedish governmental agency for innovation systems), the Royal Swedish Academy of Sciences, the Falk Foundation, the Jeansson foundations, Carl Bennet AB and the Axel and Eva Wallstrm Foundation.

Publication: 'A DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties', Yong-Xing Zhao, Alan Shaw, Xianghui Zeng, Erik Benson, Andreas M. Nystrm & Bjrn Hgberg, ACS Nano, online first 5 September 2012.

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Under-twisted DNA origami delivers cancer drugs to tumors

Lawrence Berkeley National Laboratory has made available for licensing a DNA extraction and isolation method that its inventors claim is more efficient, sensitive, and selective than current commercial DNA extraction kits.

In particular, the new technique may be especially valuable for downstream applications where the extraction of minute amounts of DNA plays a critical role, such as basic and applied biology research, forensics, biosecurity, and environmental testing, according to the technology's inventors.

"This is a general method to get DNA out from any kind of sample, but with higher sensitivity, we think, than current methods, and more versatility in terms of product models," Youn-Hi Woo, a staff scientist at Berkeley Lab and one of the method's inventors, told PCR Insider this week.

"It has a very broad field of use anywhere someone wants a very small amount of specific DNA from larger samples or a larger pool," she added.

According to the LBNL researchers, the most popular current commercial DNA extraction methods use detergents, paramagnetic particles, or membrane filters. Each of these methods works well for certain applications, but each also has drawbacks, such as non-specific DNA separation and contamination with salts or negatively charged polymers. In almost all cases, the various methods require that researchers perform extra time-consuming or laborious wash steps.

Furthermore, although paramagnetic particles eliminate many of the chemistry-related problems, they are difficult to employ using large sample volumes, meaning that researchers must first concentrate a sample down to microliter-scale volumes or less. This is particularly daunting with the larger-volume samples commonly found in environmental testing or forensics.

The new DNA extraction protocol, which the LBNL researchers described in a paper published earlier this year in Analytical Biochemistry, relies on the combination of the DNA-specific enzyme methyltransferase, or DNA Mtase, and so-called "click" chemistry, which has the ability to irreversibly couple two molecules under mild conditions.

More specifically, DNA in a complex sample is selectively labeled using MTaqI, an Mtase derived from Thermus aquaticus, and with alkynyl-SAM, a cofactor molecule that supplies methyl groups that the MTaqI transfers to the DNA when it recognizes short nucleotide sequences.

Then, the mixture is applied to an azide-modified click chemistry surface in the presence of copper ions, where the selected DNA molecules become covalently bound. Standard or vigorous washing steps wash away any contaminants, leaving behind only the desired DNA molecules bound to the modified surface.

"One strength of this technology is pulling out DNA by covalent bonds," Woo said. "This means it can't be pulled off easily. You can be pretty harsh in the washing steps to get rid of whatever the DNA was contaminated with. This gives you [more] freedom in what you do to purify your sample."

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LBNL Seeks Licensees for Highly Specific and Sensitive DNA Extraction Method

ENCODE (Image: Ed Yong)

The recent dustup over the ENCODE project and its confusing finding that 80% of DNA is functional surprises me greatly. What surprises me especially is that people are surprised by junk DNA. Unfortunately this time the scientists are also culpable since, while the publicity surrounding ENCODE has been a media disaster, the 80% claim originated in the scientific papers themselves. There is no doubt that the project itself which represents a triumph of teamwork, dogged pursuit, technological mastery and first-rate science has produced enormously useful data, and there is no doubt it will continue to do so. What is in doubt is how long it will take for the public damage to be repaired.

Theres a lot written about the various misleading statements about the project made by both scientists and journalists and I cannot add much to it. All I can do is to point to some excellent articles:Larry Moran has waged a longstanding effort to spread the true wisdom about junk DNA for years on his blog. Ed Yong exhaustively summarizes a long list of opinions, links and analysis. T. Ryan Gregory has some great posts dispelling the myth of the myth of junk DNA. And John Timmer has the best popular account of the matter. The biggest mistake on the part of the scientists was to define functional so loosely that it could mean pretty much all of DNA. The second big mistake was not in clarifying what functional means to the public.

But what I found astonishing was why its so hard for people to accept that much of DNA must indeed be junk. Even to someone like me who is not an expert, the existence of junk DNA appeared perfectly normal. I think that junk DNA shouldnt shock us at all if we accept the standard evolutionary picture.

The standard evolutionary picture tells us that evolution is messy, incomplete and inefficient. DNA consists of many kinds of sequences. Some sequences have a bonafide biological function in that they are transcribed and then translated into proteins that have a clear physiological role. Then there are sequences which are only transcribed into RNA which doesnt do anything. There are also sequences which are only bound by DNA-binding proteins (which was one of the definitions of functional the ENCODE scientists subscribed to). Finally, there are sequences which dont do anything at all. Many of these sequences consist of pseudogenes and transposons and are defective and dysfunctional genes from viruses and other genetic flotsam, inserted into our genome through our long, imperfect and promiscuous genetic history. If we can appreciate that evolution is a flawed, piecemeal, inefficient and patchwork process, we should not be surprised to find this diversity of sequences with varying degrees of function or with no function in our genome.

The reason why most of these useless pieces have not been weeded out is simply because there was no need to. We should remember that evolution does not work toward a best possible outcome, it can only do the best with what it already has. Its too much of a risk and too much work to get rid of all these defective and non-functional sequences if they arent a burden; the work of simply duplicating these sequences is much lesser than that of getting rid of them. Thus the sequences hung around in our long evolutionary history and got passed on. The fact that they may not serve any function at all would be perfectively consistent with a haphazard natural mechanism depending on chance and the tacking on of non-functionality to useful functions simply as extra baggage.

There are two other facts in my view which should make it very easy for us to accept the existence of junk DNA. Consider that the salamander genome is ten times the size of the human genome. Now this implies two possibilities; either salamanders have ten times functional DNA than we do, or that the main difference between us and salamanders is that they have much more junk DNA. Wouldnt the complexity of salamander anatomy of physiology be vastly different if they really had so much more functional DNA? On the contrary, wouldnt the relative simplicity of salamanders compared to humans be much more consistent with just varying degrees of junk DNA? Which explanation sounds more plausible?

The third reason for accepting the reality of junk DNA is to simply think about mutational load. Our genomes, as of other organisms, have undergone lots of mutations during evolution. What would be the consequences if 90% of our genome were really functional and had undergone mutations? How would we have survived and flourished with such a high mutation rate? On the other hand, its much simpler to understand our survival if we assume that most mutations that happen in our genome happen in junk DNA.

As a summary then, we should be surprised to find someone who says they are surprised by junk DNA. Even someone like me who is not an expert can think of three reasons to like junk DNA:

1. The understanding that evolution is an inherently messy and inefficient process that often produces junk. This junk may be retained if its not causing trouble.

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Three reasons to like junk DNA

Researchers show that DNA supercoils are dynamic structures that can hop long distances, a phenomenon that could affect gene regulation.

Scientists understanding of how long strings of DNA are packaged into tiny spaces just got a little more complicated. New research on single molecules of DNA show that supercoilssegments of extra-twisted loops of DNAcan moving by jumping along a DNA strand. The results, published today (September 13) in Science, give researchers new insights into DNA organization and point to a surprisingly speedy mechanism of gene regulation inside cells.

This is the first study that addresses the dynamics of DNA supercoils, said Ralf Seidel, who studies movement of molecular motor proteins along DNA at the University of Technology Dresden, but was not involved in the research. This supercoil hopping motion allows DNA strands to transmit supercoiling, bringing sites together in very fast manner.

DNA, being a double helix, is naturally twisted. In vivo, its packaged with proteins called histones that help condense the millions or billions of nucleotides into the small space of a cells nucleus. Constant interaction with proteins moving along the strand, like transcription factors that need to open the helix to read the DNA sequence, can affect both the double helixs twist, and the strands writhethe coiling of the strand around itself. These extra-twisted coils, called plectonemes or supercoils, form not unlike coils in phone cords. By bringing together distant segments of DNA, such as regulatory elements and the genes they control, supercoiling can affect expression.

In order to get a better sense of how supercoils behave, Cees Dekker at Delft University of Technology and his colleagues induced supercoils in single strands of DNA molecules, labeled with fluorescent dye. One end of the DNA was anchored to the side of a glass capillary tube and a magnetic bead was attached to the other end. This allowed the researchers to use miniscule magnets to twist the DNA and induce supercoils, and watch their movement using fluorescence microscopy.

Unexpectedly, the team found that supercoils move along DNA strands in one of two ways. Sometimes they slowly diffuse along the strand; other times, the supercoils hoppeddisappearing suddenly from one location while simultaneously appearing at a distant location further down the strand.

This is far more complicated than diffusion of supercoils down the DNAs length, said Prashant Purohit, who studies DNA behavior at the University of Pennsylvania, but was not involved in the study. The DNA is behaving non-locally, he noted. It shows that writhethe coiling of the DNA strandis a global, not local quantity [of the strand].

So far the intriguing phenomenon has only been observed on single strands of naked DNA, Seidel cautioned, so its unclear how supercoils might act in vivo, when the DNA is well-packaged and studded with proteins. It may be that such behavior is more important for DNA in prokaryotic cells, which have less packaged DNA than eukaryotic cells, noted Bryan Daniels, who models biological systems at the Wisconsin Institutes for Discovery at the University of Wisconsin-Madison.

The ionic environment of the cell is also likely to influence supercoiling behavior. DNA is more likely to condense in the presence of multivalent ions (3 or more positive charges), for example, than in an environment of singly-valent ions. And Dekker and his colleagues, who used singly-valent ions in their experiments, found that more supercoils formed at lower concentrations of ions.

Dekker and his team are now looking at how different DNA sequences and the presence of DNA-binding proteins can influence supercoil formation and motionthe first step toward understanding supercoil movement in vivo.

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DNA with a Twist

A London familys DNA could be the missing link in a centuries-long quest to find the remains of King Richard III.

A team of archeologists at the University of Leicester in England exhumed a skeleton believed to be Richards beneath one of the universitys parking lots Wednesday and are hoping DNA evidence from the London family will prove their suspicions true.

Richard was killed in 1485 during the Battle of Bosworth often cited as the deciding battle in the War of the Roses by Henry Tudor VII, father of the famed King Henry VIII.

Richards Machiavellian rise to power its believed he had his nephews murdered in order to seize the thrown and short two-year reign as king is chronicled in Shakespeares play Richard III.

In 2005, British historian John Ashdown-Hill traced Richards bloodline to Joy Ibsen, a retired journalist who moved to London, Ont., from England after the Second World War and raised a family.

Ashdown-Hill discovered Ibsen and Richard shared a maternal ancestor, Cecily Neville.

Though Ibsen died in 2008, she passed the gene on to her three children: Michael, who lives in the U..K; Jeff, who lives in Toronto; and Leslie on Vancouver Island.

Its pretty exciting, said Jeff, 49. I wasnt expecting the findings to be so concise ... Im hoping that if theres a proper funeral for him, well get invited and maybe get a chance to rub elbows with some royals.

The skeleton exhumed Wednesday was found in whats believed to be the choir of the lost Church of the Grey Friars, the same place historical records indicate Richard was buried. Initial examinations found trauma to the skull consistent with a battle injury and a barbed arrow through the skeletons upper back.

Especially telling is the spinal deformity found on the exhumed skeleton. Its believed Richard had severe scoliosis, a form of spinal curvature that caused his right shoulder to appear higher than the left, the same type of curvature found on the skeleton.

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DNA could help ID a king