Daily Archives: November 9, 2012

ScienceDaily (Nov. 8, 2012) DNA sequence data is an indispensable source of research information in biology. But not all data are reliable. Almost 10% of all fungal DNA sequences are, for example, incorrectly identified to species level. A international team of researchers, with it's core at the University of Gothenburg, Sweden, has therefore prepared a guide to assist the scientific community in the quality control process.

A new scientific study sees the researchers putting together a number of guidelines to help other researchers to ensure a high level of quality among their newly generated DNA sequences.

DNA sequences make it possible to study biological samples and environments at a level of detail that traditional tools, such as microscopes, cannot provide. It is, for example, possible to investigate what species are present in seemingly barren substrates such as soil and seawater. Such studies often reveal an astonishing and hitherto unimagined diversity, and biology has made major advances as the use of DNA-based methods has become more widespread.

But as with many other sources of information, DNA sequences vary in quality and reliability. Several studies have found considerable quality problems in existing DNA sequence databases.

To verify ones DNA Sequence dataset for basic quality and authenticity has thus become an important part of biological research.

"Many researchers perceive quality control as difficult," says Henrik Nilsson at the University of Gothenburg. "There are, quite simply, no guidelines that you can hand out to new or established researchers so that everyone is using the same approach. Which is why there are major differences in how, and to what extent, quality control is carried out in the research community."

Henrik Nilsson is the lead author of a new scientific article on DNA sequence quality which has been published in the open-access journal MycoKeys.

One complication is that the software that is available to carry out parts of the quality control is cumbersome and often requires considerable computer capacity. The research group feels that it is not appropriate to require all biologists to have access to and be able to use such complex computer systems.

This is why they have written an article describing how quality control can be carried out manually without any tools beyond an Internet browser.

The article features a number of principles and observations on DNA sequences at different quality stages. Although the guidelines focus on fungi, where DNA sequences have had a particularly significant impact as a research instrument, they are general and can be used for most genes and groups of organisms.

Continued here:
New guideline for DNA sequences could prevent erroneous data

By Tim Gideon

The partnership between Monster and Beats that began with the Monster Beats by Dr. Dre is no longer, and now both brands make their own exclusive headphone models. The most recent from Monster is the DNA On-Ear headphones ($229.95 direct), with a highly stylized look that can be customized with various skins. The sound signature would still fit well in the Beats lineup, with boosted bass and highs that make pop music sound exciting, but will likely turn off audiophiles seeking flat response. The fact that the DNA distorts on tracks with deep bass at maximum volume is not as much of an issue as the price. Recently, we've seen a few better-sounding options at lower prices.

Design The DNA has a futuristic look, with rounded, triangular earpieces and circular, supra-aural (on-ear) earpads. Available in a variety of color combinations, our review model was white, glossy plastic, with gray padding and gray, rubberized material on the underside of the headband. This material is soft, but doesn't exactly feel like an overstuffed pillow floating on your head. The earpads can also feel a bit uncomfortable over time. The fit is secure, but the slight discomfort is one of the first things I noticed after a few minutes of testing.

Monster includes two cables, one with inline controls and a microphone for mobile phone calls. That the cables are removable and replaceable adds significant value to the DNA's pricesince cables are often the culprit when headphones malfunction, you can simply replace the cable rather than look into repairs or replacing the whole thing.

Other than the two cables, the only other accessory is a black felt drawstring bag that has internal pockets and a carabiner attached. As mentioned earlier, the DNA is designed to be customized by the userthe skins cost an extra $29.95 each, and come in flashy varieties such as leopard print, peacock feathers, and a carbon fiber look. With or without the skins, the color schemes for the headphones are the aforementioned white/gray, black/chrome, blue/gray, blue/chrome, and white/teal.

Performance On songs that feature deep bass, the DNA often distorts at high volume levels. A song like The Knife's "Silent Shout" starts to get fuzzy when you approach maximum volume. Granted, this is a volume you shouldn't be listening at, but at this price, distortion shouldn't enter the equation. At moderate-to-high volumes, before distortion kicks in, the bass response is powerfuleven palpable, as the headphone frame vibrates noticeably with the beat. This gets less intense at even more moderate volumes, where the deep bass and highly sculpted high frequency responsetwo typical Monster traitswork far better together to create an exciting mix.

On classical tracks, like John Adams' "The Chairman Dances," the boosted bass response lends some heft to the lower register percussion and strings. It's not what most audiophiles are looking for, as the bass and highs are quite exaggerated, but it does add some crispness and resonance to the mix without going overboard.

Generally, however, the DNA is best suited for modern mixes in popular music. At moderate volumes, the kick drum loop in Jay-Z and Kanye West's "No Church in the Wild" has a crisp attack backed up by an impressive thump, while the deep bass synth hits pack plenty of low-end resonance without distortion coming into the equation. The vocals are never obscured by the low-end intensity.

On Radiohead's "Staircase," the bouncing, doubled guitar-and-bass line carries a nice low-frequency presence, never booming, but definitely the star of the mixexcept for Thom Yorke's vocals, which are crisp and sit above everything else, thanks to the DNA's mid-to-high boost.

If you're a fan of deep bass, the DNA is not a bad choiceyou just have to accept the distortion at high volumes. A better-sounding example of what Monster can do with boosted low-end is the more expensive, bulkier, and sturdier Monster Inspiration . It's not perfect, but it performs with more power than the DNA, and without distortion.

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Monster DNA On-Ear Headphones

Tennis umpire Lois Goodman's DNA is not on the coffee cup that authorities say she used to bludgeonher 80-year-old husband to death last April, one of her attorneys said Thursday. He cited preliminary DNA test results.

Defense attorney Robert Sheahen said an initial DNA test showed that although her DNA was not on the shattered coffee cup, Alan Goodman's DNA was. The information was among thousands of pages of discovery turned over by L.A. County prosecutors to Goodman's defense team. Sheahen said prosecutors after Goodman's arrest sought her DNA and tested her pants butfound her DNA only on the clothing and none from her husband.

Sheahen said the "DNA findings bolster our contention from the very beginning that this is a horrible accident."

Goodman has pleaded not guilty to the attack on her husband. She told police she came home and found her husband dead in bed. She said she believed he crawled there after falling down the stairs and falling on the coffee cup he was carrying.

Prosecutors have insisted that Goodman was a calculating killer who bludgeoned her husband with the coffee cup and then stabbed him when it shattered. They allege she left him to die and went off to a tennis match and to get a manicure as he bled to death.

Sources familar with the investigation said they believe that the large amount of blood from Alan Goodman may have washed away his wife's DNA on the cup.

Authoritiesbegan to investigate the death as a homicide a few days after Alan Goodman's death when a coroner's investigator at the funeral home noticed a deep wound in his head. An autopsy revealed shards of pottery in the wound. They allege that Goodman wielded the broken coffee cup like a knife.

A search warrant executed April 21 turned up blood throughout the home "inconsistent with accidental death," Det. Jeffrey Briscoe wrote. Stains on carpets, the refrigerator door, inside a linen closet and on the wall leading to the garage suggested "a mobile victim" who, police theorized, would have called for help.

Goodman's attorneys insist the investigation was "botched from start to finish."

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Tennis umpire's DNA not on the murder weapon, attorney says