Daily Archives: February 20, 2013

Feb. 20, 2013 DNA, just like hair, has a tendency to become knotted, thus it may be useful to disentangle it. Unfortunately, it is not possible to "actively" choose at random (or better, in one solution) the filaments with the desired features, and this is why scientists adopt "passive" solutions like, for instance, having the DNA pass through nano-pores or nano-channels.

"Channels and filaments have physical features we may exploit to selectively let a type of molecule pass through" explains Micheletti. "You can have more or less entangled filaments and featuring knots of different types. In our study we have considered a specific DNA filament model and examined its behavior within a nano-channel. We have observed that by varying the channel's width it is possible to drastically change the quantity and complexity of the knots formed by the DNA."

The nano-channels may therefore be a tool with a double function: on one side they are used to understand the "knotting pattern" of a DNA fragment, on the other they may be used to select entangled filaments in the desired manner. The sectors employing DNA, mainly in sequencing, require an increasing number of new techniques to select the DNA filaments according to their characteristics, such as length, shape as well as entanglement.

"Experimental physicists will be, in the first instance, interested is such technique to obtain knot-free DNA," explains Micheletti referring to the usefulness of the methodology (that for now has been studied through simulation). "We should not forget that such method may also help us better understand, for instance, the functioning of topoisomerases, enzymes that have a very important role in cell metabolism." Such enzymes play a key role in an organism: they maintain the DNA stretched out when the cell is not undergoing the cell division process.

"We are used to envisage chromosomes in their typical rod shaped appearance, the one preceding mitosis, that is to say cell reproduction," adds Micheletti. "However, usually the DNA is a sort of indistinct bundle that fills up the cell's nucleus. The topoisomerases maintain the disentangled filaments with the lowest possible rate of knotting, and do so by snipping and reattaching the little pieces of genetic material." Only on the "disentangled" filament all those transcription processes which are fundamental to the survival of an organism can actually function. "The functioning of such enzymes may be better grasped if, before having them perform, we already know to what extent the molecule was entangled in the first place, and our methodology may be useful to this purpose." concludes Micheletti.

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The above story is reprinted from materials provided by Sissa Medialab, via AlphaGalileo.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Nano-channel disentangles knotted DNA

An assault took place in Maryland in 2009. Alonzo Jay King was identified by photographs and fingerprints at the scene, and as a result he was arrested and charged with the crime.

While he was being booked for his arrest for assault, under a Maryland statute that allowed the police to take DNA from all people arrested for violent crimes, Kings cheek was swabbed to take a DNA sample even though the police had enough evidence to charge him with the assault.

When the DNA sample was entered in Marylands DNA database, it matched the DNA taken from an unsolved rape that happened back in 2003.

King was convicted of second-degree assault for the case for which he was originally arrested; he was also convicted of the 2003 rape based on the DNA evidence and was sentenced to life in prison without the possibility of parole.

King appealed the rape conviction because he says that taking the DNA sample was a search and seizure for which the state should have obtained a warrant. The Fourth Amendment to the U.S. Constitution states:

The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.

Because the state didnt get the warrant, King argues, it violated his Fourth Amendment right against unreasonable searches and seizures.

The Maryland law that requires the taking of a DNA sample at arrest is, according to King, unconstitutional, and so his rape conviction should be thrown out.

The Maryland Court of Appeals, which heard the case, balanced Kings expectation of privacy from warrantless, suspicionless searches against the states right to collect evidence of violent crimes.

But since, according to the court, the authorities investigating the case for which King was arrestedthe assaulthad enough photographic and fingerprint evidence of the crime, they sided with King, stating: Although we have recognized (and no one can reasonably deny) that solving cold cases is a legitimate government interest, a warrantless, suspicionless search can not be upheld by a generalized interest in solving crimes. As a result, the court threw out Kings conviction.

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Do police need a warrant to get your DNA?

SANTA CLARA, Calif.--(BUSINESS WIRE)--

Agilent Technologies Inc. (NYSE:A) today launched the Genomic DNA ScreenTape, a prepackaged consumables device that works with the companys 2200 TapeStation instrument to determine the quantity, size and quality of genomic DNA in less than two minutes per sample, using only one microliter of material.

The automated 2200 TapeStation and new Agilent Genomic DNA ScreenTape address an important bottleneck and revolutionize the currently subjective quality assessment of genomic DNA, said Dr. Donna McDade Walker, product manager for microfluidics at Agilent. Within minutes of testing their genomic DNA samples, researchers can be confident that their starting materials are of the highest quality. This introduction demonstrates our commitment to expanding the range of automated sample QC tools for next-generation sequencing and workflows for array comparative genome hybridization.

The quality of genomic data depends on the quality of the starting material. Therefore, it is imperative to determine whether samples contain a sufficient quantity of intact, high-quality genomic DNA before committing time, money and resources to a genomics experiment. The standard, manual method for assessing the quality of genomic DNA samples is laborious, can take several hours to complete and is prone to mistakes.

For more information about the new Agilent Genomic DNA ScreenTape, visit http://www.agilent.com/genomics/QCgDNA.

About Agilent Technologies

Agilent Technologies Inc. (NYSE:A) is the worlds premier measurement company and a technology leader in chemical analysis, life sciences, diagnostics, electronics and communications. The companys 20,500 employees serve customers in more than 100 countries. Agilent had revenues of $6.9 billion in fiscal 2012. Information about Agilent is available at http://www.agilent.com.

NOTE TO EDITORS: Further technology, corporate citizenship and executive news is available at http://www.agilent.com/go/news.

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TRADE NEWS: Agilent Technologies Launches Genomic DNA ScreenTape

TRAVERSE CITY, Mich. (AP) Live Asian carp don't necessarily have to be present for their DNA to turn up in the environment, according to a government study released Wednesday that could intensify the debate over how to prevent the aggressive, hungry invaders from reaching the Great Lakes and other vulnerable waters.

DNA is found in excrement, slime and scales from live fish. But the report by three federal agencies identifies six other possible means through which genetic fingerprints from bighead and silver carp could find their way into locations such as the Chicago waterway system and western Lake Erie, where it has been detected in dozens of samples taken in recent years.

Those potential pathways include storm sewers, fisheries sampling gear, fish-eating birds, dead fish carcasses, barges and sediments, the U.S. Army Corps of Engineers said in a statement accompanying the report. It said carp DNA attached to any of those sources could remain for days before disintegrating.

Scientists with the corps, the U.S. Fish and Wildlife Service and the U.S. Geological Survey are conducting a three-year study designed to answer questions raised by the repeated discovery of Asian carp DNA in rivers and canals in the Chicago area including locations beyond an electric barrier intended to block the carp's northward march toward Lake Michigan. Their DNA also has been found in the Mississippi River beyond Minneapolis.

"The purpose ... is to improve the understanding and interpretation of Asian carp environmental DNA results, so we can refine and make this relatively young monitoring tool the most effective to detect live Asian carp presence," said Kelly Baerwaldt, an Army corps fisheries biologist and Asian carp program manager. Additional reports are planned as the study continues.

Bighead and silver carp escaped into the Mississippi River from sewage treatment ponds and fish farms in the Deep South decades ago and have migrated northward, invading numerous tributary rivers. The filter feeders gobble massive volumes of plankton microscopic plants and animals crucial to aquatic food webs.

Scientists say if allowed to infest the Great Lakes, the carp eventually could crowd out native species, endangering the region's $7 billion fishing industry. Silver carp, which spring from the water when startled and have collided jarringly with boaters, pose a threat to tourism.

Some state and local officials in the Great Lakes region want structures placed in the Chicago waterways to seal off Lake Michigan from the Mississippi watershed. Business and government leaders in Chicago say that would devastate shipping in the area, and some have questioned whether the DNA findings are sufficient evidence that the carp have evaded the electric barrier.

Just one live carp has been found beyond the barrier network, which is in a canal 37 miles southwest of the city.

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Study: Asian carp DNA may not signal live fish