Daily Archives: September 19, 2012

3Qs: New clues to unlocking the genome

Posted: September 19, 2012 at 1:14 pm

Veronica Godoy-Carters research focuses on the genetic mechanisms guiding specialized DNA polymerases, a type of cellular machine important in DNA replication when cells are under stress. Credit: iStockphoto.

Last week, Nature Magazine, Genome Research and Genome Biology published 30 papers on breakthrough research that will change the face of genetics. After nearly a decade of searching, the Encyclopedia of DNA Elements (ENCODE) Consortium has assigned biochemical functions to 80 percent of the genome. Previously considered "junk," the development adds significant insight into the importance of the noncoding regions of DNA. We asked Veronica Godoy-Carter, assistant professor of biology, toexplain.

What is noncoding DNA and why has it been called "junk"?

The genetic material present in all living organisms is DNA. It is understood that "coding" DNA can be "read" by the cellular machinery, as we read a page in a book, mostly as proteins (e.g., your hair and nails are made up of proteins). However, there are sections of the DNA in metazoans (e.g., humans) and in some unicellular organisms known to have no readable code, that is, noncoding DNA.The word "junk" was used in the 14th century to denote an old or inferior rope. Today it is used to characterize useless articles or those of little value. Thus, when researchers started to decipher the linearsequenceof the DNA, it became obvious that a large fraction of it is noncoding. Therefore, the word "junk" was used to describe such noncodingregions.

We've known for a while that noncoding DNA actually has very important physiological functions. How does this new research change or add to that understanding?

ENCODE has shown that, contrary to previous views, most of the sequences of the human genome are not useless. Though it was previously known than noncoding regions were important for regulation, this project has demonstrated that noncoding sequences serve as a roadmap for regulatory DNA binding proteins that effect expression of coding regions. Previous to this large-scale analysis, no one knew about the extent of regulatory regions that existed in "junk" DNA, now referred to as "dark matter." For example, there are many sites that are specifically chemically modified, permitting inhibition or induction of the DNA coding regions. Remarkably, the regulation of expression does not only occur in coding regions that are adjacent to regulatory elements, as previously thought. In some cases, regulation is long range and seems to occur only when the regulatory elements are near coding regions in the three-dimensional space!

How will this new understanding of noncoding DNA change the face of genetic research?

The long-range regulation of coding regions in the DNA is such an exciting finding because it will permit us to start understanding the effect of known changes in the DNA sequence (i.e., mutations) between, say, healthy and cancer tissues. As it turns out, many mutations associated with disease are in noncoding regions, whichpreviously made little sense. Nowit will be possible to map mutations on this roadmap andimportantlyit will be possible to understand how mutations far away in the linear DNA change the regulatory landscape ofcells.

Journal reference: Nature Genome Research Genome Biology

Provided by Northeastern University

The rest is here:
3Qs: New clues to unlocking the genome

Posted in Genome | Comments Off on 3Qs: New clues to unlocking the genome

Research and Markets: US Personalized Cancer Genome Sequencing Market

Posted: at 1:14 pm

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/5ckx7v/us_personalized) has announced the addition of the "US Personalized Cancer Genome Sequencing Market" report to their offering.

The US personalized cancer Whole-Genome Sequencing market is primarily classified into targeted genome sequencing and Whole-Genome Sequencing. Our report entitled US Personalized Cancer Genome Sequencing Market takes into account the Whole-Genome Sequencing services, i.e. one of the most attractive sectors due to its inherent capability of high revenue generation and efficiency in terms of personalized treatment. The US, which is the frontrunner in the provision of such high-end service, is on the focus by market players because of favorable demographics and rising awareness among the industry participants.

In order to properly analyze the virtues and significance of the US personalized cancer Whole-Genome Sequencing market, our report has effectively studied the current and future status of cancer in the whole country as well as states. In view of the fact that cancer affects some age groups in a significant manner, we have also investigated the age wise statistics of the disease. To get proper insight into the market, an in-depth analysis into the high-income group population is provided so that players can have a clear picture about their potential customer base and market to be tapped.

An in-depth study of the regulatory environment governing the US personalized cancer Whole-Genome Sequencing market has also been provided. It has been found that regulations related to personalized cancer sequencing are primarily governed with the accreditation of the laboratories performing the sequencing services and analysis and also the usage of FDA approved tests for conducting these tests. Further we have also discussed the various constraints faced by the industry players with suitable suggestions for overcoming them.

Companies Mentioned:

- Illumina

- Complete Genomics

- Beckman Coulter Genomics

- Expression Analysis

Continue reading here:
Research and Markets: US Personalized Cancer Genome Sequencing Market

Posted in Genome | Comments Off on Research and Markets: US Personalized Cancer Genome Sequencing Market

Press Release

Posted: at 1:14 pm

Research and MarketsPosted on:19 Sep 12

Research and Markets (http://www.researchandmarkets.com/research/t8mv4n/global_psoriasis) has announced the addition of the "Global Psoriasis Drug Pipeline Capsule - 2012 Update" report to their offering.

Fore Pharma's latest report 'Global Psoriasis Drug Pipeline Capsule - 2012 Update' provides most up-to-date information on key Research and Development activities (R&D) in the global Psoriasis market. It covers active Psoriasis pipeline molecules in various stages of clinical trials, preclinical research, and drug discovery.

This report helps executives track competitors pipeline molecules. The information presented in this report can be used for identifying partners, evaluating opportunities, formulating business development strategies, executing in-licensing and out-licensing deals.

The report provides information on pipeline molecules by company and mechanism of action across the R&D stages. It also provides information on pipeline molecules developed in leading geographies (North America and Europe). Licensing activities are thoroughly captured in this report.

Key Topics Covered:

1. Psoriasis - Disease Overview

2. Psoriasis Pipeline Overview

3. Psoriasis Phase 3 Clinical Trial Pipeline Insights

4. Psoriasis Phase 2 Clinical Trial Pipeline Insights

Read more:
Press Release

Posted in Psoriasis | Comments Off on Press Release

'US administration has put blame where it belongs'

Posted: at 1:14 pm

In an interview with DW, Eva Galperin from the Electronic Frontier Foundation, argues that Google's 'pro-active' approach to the censorship of the controversial "Innocence of Muslims" video sets a dangerous precedent.

DW: Do you think the "Innocence of Muslims" video should be banned by Google?

Eva Galperin: I most certainly do not think that the video should be banned, either in the United States or in Egypt and in Libya were Google chose to ban it in spite of the fact that they acknowledged that it was consistent with their terms of service and they had not received any court orders.

Do you believe in free speech at any cost?

I believe in free speech within the limits of US law, which is not completely unadulterated free speech. And furthermore, I do acknowledge that Google does have to obey the law in countries where it receives a valid court order, such as countries where it has offices and is therefore under that country's jurisdiction. I do think that's one of the reasons why Google needs to be extremely circumspect about where they have their offices, because if they want to maintain their devotion to freedom of expression, they need to understand that when they move into other countries where freedom of expression is not as strongly supported, they may have to make these kinds of compromises when they receive court orders in countries like India and possibly Malaysia.

Some critics are calling for a concrete, transnational system of internet governance. Would you approve of such an idea?

Free speech, but not at any cost: Eva Galperin

Worldwide internet governance is highly problematic. Partially because of the clashes between various countries right to autonomy and their right to decide what kind of content is allowed in each country. But also because the US frequently uses these kinds of worldwide treaties or agreements in order to push through its own intellectual property agenda which can often lead to widespread censorship, which we are very concerned about, which we saw with ACTA [Anti-Counterfeiting Trade Agreement], and also what you saw domestically in the United States their attempt to pass SOPA [Stop Online Piracy Act].

Do you think Obama's condemnation of the video can be read as an attack on free speech?

No I don't. I think that the White House has been fairly clear in its support of freedom of speech, while at the same time condemning the violence. There is nothing about condemning the violence that necessitates the censorship of this video. I think that by condemning the violence without calling for the censorship of this video, the White House is making it clear that they are putting the blame where it belongs - on the perpetrators of the violence.

Continued here:
'US administration has put blame where it belongs'

Posted in Censorship | Comments Off on 'US administration has put blame where it belongs'

Time to reset boundaries of free speech

Posted: at 10:15 am

By STEVEN KURLANDER | Florida Voices Published: September 19, 2012 Updated: September 19, 2012 - 12:00 AM

Consider the famous axiom about free speech handed down by the renowned American jurist, Oliver Wendell Holmes: "The most stringent protection of free speech would not protect a man in falsely shouting fire in a theatre and causing a panic."

So what about a trailer for a movie that depicts the Prophet Muhammad as a philandering fraud who sanctioned rape and child sexual abuse?

Muslims consider any representation of the Prophet Mohammed insulting and blasphemous. And for disrespecting the Prophet over the years, Americans and other westerners have suffered violence, even death.

Given the known consequences, it's time to ban garbage that mocks the God of a billion people and purposefully incites the worst religious passions. It's time the Supreme Court reconsidered whether such fiery speech should indeed be protected.

Because of the blasphemous film, enraged Muslims have rioted in several Arab countries and last week killed U.S. Ambassador Christopher Stevens and three staffers at the American consulate in Benghazi, Libya.

Violence against Americans and other westerners triggered by anti-Islamic rhetoric, books, cartoons and now movies is nothing new in this post-9/11 world. In March, a number of Allied troops in Afghanistan were killed after our troops mistakenly burned several copies of the Quran.

This time it's the trailer for a movie called "Innocence of Muslims," a film produced by Nakoula Basseley Nakoula, a 55-year-old Coptic Christian immigrant from Egypt.

The video, which depicts a mock trial of the Prophet Mohammed, has been widely circulated on YouTube and promoted by Gainesville pastor Terry Jones, who has gained notoriety for planning Quran-burning events.

The most recent judicial standard on free speech was set by the Supreme Court in 1969. Called the "imminent lawless action" test, it balances First Amendment rights with the intent of a speaker to incite an imminent and likely violation of the law.

Read the rest here:
Time to reset boundaries of free speech

Posted in Free Speech | Comments Off on Time to reset boundaries of free speech

Photos: Space Station's Expedition 33 Mission

Posted: at 6:14 am

Space Triathlon Runner Sunita Williams

NASA astronaut Sunita Williams completed a triathlon from space Sept. 16, 2012, using an orbital treadmill to complete the running portion, a stationary bicycle for the biking leg, and a resistance machine to simulate swimming.

NASA astronaut Sunita Williams (front left) takes command of the International Space Station from cosmonaut Gennady Padalka (front right) during a ceremony marking the start of the Expedition 33 increment aboard the space station on Sept. 15, 2012.

NASA astronaut Sunita Williams, Expedition 32 flight engineer and commander of the International Space Station's Expedition 33 crew, poses for a photo with her spacesuit ahead of an Aug. 30, 2012, spacewalk.

The International Space Station's Expedition 33 crew. From left: NASA astronaut Sunita Williams, Russian cosmonaut Yuri Malenchenko, Japannese astronaut Akihiko Hoshide, Russian cosmonauts Evgeny Tarelkin and Oleg Novitskiy and NASA astronaut Kevin Ford.

The Expedition 33 patch depicts the International Space Station (ISS) orbiting around the Earth, and into the future. Image released December 2011.

The Soyuz TMA-05M rocket launches from the Baikonur Cosmodrome in Kazakhstan on July 15, 2012. Crewmembers for Expeditions 32 & 33 were flying to the International Space Station.

The Soyuz TMA-05M rocket launches from the Baikonur Cosmodrome in Kazakhstan on July 15, 2012.

Expedition 32/33 crew members leave building 254 following their suited up for launch July 15, 2012 at the Baikonur Cosmodrome in Kazakhstan.

The grid structure at the upper side of each Aquatic Habitat, an aquarium for the International Space Station, captures air in each grid, while preventing water from escaping. Air will be injected with special syringe by the crew prior to the start of an investigation in 2012.

The rest is here:
Photos: Space Station's Expedition 33 Mission

Posted in Space Station | Comments Off on Photos: Space Station's Expedition 33 Mission

Genetic test predicts risk for Autism

Posted: at 6:14 am

Professor Stan Skafidas, Director, Centre for Neural Engineering, University of Melbourne

A team of Australian researchers, led by The University of Melbourne has developed a genetic test that is able to predict the risk of developing Autism Spectrum Disorder, ASD.

Lead researcher Stan Skafidas, Director of the Centre for Neural Engineering and Professor of Electrical and Electronic Engineering at the University of Melbourne, said the test could be used to assess the risk for developing the disorder.

This test could assist in the early detection of the condition in babies and children and help in the early management of those who become diagnosed, he said.

It would be particularly relevant for families who have a history of Autism or related conditions such as Aspergers Syndrome, he said.

Autism affects around one in 150 births and is characterised by abnormal social interaction, impaired communication and repetitive behaviours.

The test correctly predicted ASD with more than 70 per cent accuracy in people of central European descent. Ongoing validation tests are continuing including the development of accurate testing for other ethnic groups.

Clinical neuropsychologist, Dr Renee Testa from the University of Melbourne and Monash University, said the test would allow clinicians to provide early interventions that may reduce behavioural and cognitive difficulties that children and adults with ASD experience.

Early identification of risk means we can provide interventions to improve overall functioning for those affected, including families, she said.

A genetic cause has been long sought with many genes implicated in the condition, but no single gene has been adequate for determining risk.

Originally posted here:
Genetic test predicts risk for Autism

Posted in Genetic Engineering | Comments Off on Genetic test predicts risk for Autism

Assessment of HPV DNA Alone Insufficient to Identify HPV-Driven Head and Neck Cancers

Posted: at 6:14 am

ScienceDaily (Sep. 18, 2012) Human papillomavirus (HPV) DNA positivity alone, particularly when assessed using polymerase chain reaction methods, is a poor biomarker for HPV-driven head and neck cancers, according to two studies published in Cancer Research, a journal of the American Association for Cancer Research. These studies identified alternative potential markers including viral load, viral gene expression and the evaluation of HPV DNA in combination with certain HPV assays.

Prior research has established that HPV is a cause of some head and neck cancers, including oropharyngeal cancer, and that patients with HPV-associated disease tend to have a better clinical outcome. Consequently, the proper assessment of the clinical status of individual tumors has become a goal of clinicians treating this disease because HPV at the tumor site does not indicate causal involvement in the cancer.

In the first study, Dana Holzinger, Ph.D., of the division of genome modifications and carcinogenesis at the German Cancer Research Center in Heidelberg, Germany, and colleagues analyzed the potential of direct and indirect HPV markers to identify patients with HPV-driven tumors.

They analyzed 199 oropharyngeal squamous cell carcinoma specimens for HPV DNA, viral load, RNA expression patterns seen in cervical carcinomas and the p16 protein, which is associated with tumor suppression.

Results indicated that the cervical cancer RNA expression pattern and viral load were associated with the lowest risk for death from oropharyngeal cancer. In contrast, a weaker association was found for samples that were HPV DNA-positive or that expressed the p16 protein.

"We showed that high viral load and a cancer-specific pattern of viral gene expression are most suited to identify patients with HPV-driven tumors among patients with oropharyngeal cancer," Holzinger said. "Viral expression pattern is a completely new marker in this field and viral load has hardly been analyzed before."

In a second study, researchers evaluated several biomarkers individually and in combination for overall survival among head and neck cancers including polymerase chain reaction-based and serological HPV DNA testing, and p16 immunohistochemistry.

They found that the expression of two oncoproteins, E6 and E7, was associated with improved survival in oropharyngeal disease. In addition, HPV DNA positivity or p16 expression combined with E6 and E7 expression were also associated with enhanced survival. However, neither HPV DNA positivity nor expression of p16 alone yielded a similar result.

"Assessment of HPV DNA using polymerase chain reaction methods as a biomarker in individual head and neck cancers is a poor predictor of outcome and is also poorly associated with antibody response indicative of exposure and/or infection by HPV," said study author Karl T. Kelsey, M.D., professor in the department of epidemiology and the department of pathology and laboratory medicine at Brown University in Providence, R.I. "We may not be diagnosing these tumors as accurately and precisely as we need to for adjusting treatments."

The next step in this research is further validating the findings of these two studies using head-to-head comparisons and developing assays for direct clinical application of the markers.

See the article here:
Assessment of HPV DNA Alone Insufficient to Identify HPV-Driven Head and Neck Cancers

Posted in DNA | Comments Off on Assessment of HPV DNA Alone Insufficient to Identify HPV-Driven Head and Neck Cancers

Expansion of criminal DNA collection proposed

Posted: at 6:14 am

MADISON Anyone arrested for a felony offense and all adults convicted of misdemeanor crimes would be required to provide a DNA sample to law enforcement under a proposal from the state Department of Justice.

Adults arrested for certain misdemeanor crimes such as fourth-degree sexual assault and prostitution also would have to provide DNA samples, which would be entered into a national database used to match DNA evidence collected at crime scenes to suspects.

Currently, state law allows DNA to be collected only from adults and juveniles convicted of felonies, with about 12,000 samples obtained each year.

Brian OKeefe, administrator for the DOJs Division of Law Enforcement Services, said the expected addition of about 68,000 DNA samples a year at least initially under the proposed expansion would help law enforcement solve more cases more quickly and get criminals off the street.

The number of new samples would eventually drop, he said, because DNA profiles of those reoffending would not have to be added to the system.

But Chris Ahmuty of the ACLU of Wisconsin, said, It seems like theyve gone for the nuclear option when it comes to DNA on arrest.

Casting such a wide net raises concerns about cost, management and privacy and turns the presumption of innocence on its head, Ahmuty said. He added that the DOJ proposal is more encompassing and costly than previous legislative proposals.

OKeefe said the proposed expansion of DNA collection would begin in October 2014 and cost about $7 million in its first two years.

To cover those costs including the addition of 26 full-time positions DOJ is asking that everyone convicted of a felony be required to pay a $250 surcharge, and that everyone convicted of a misdemeanor pay a $150 surcharge.

Currently, a DNA surcharge for people convicted of felonies is often waived by a judge.

Read more:
Expansion of criminal DNA collection proposed

Posted in DNA | Comments Off on Expansion of criminal DNA collection proposed

FBI eager to embrace mobile 'Rapid DNA' testing

Posted: at 6:14 am

It's been the FBI's dream for years -- to do near-instant DNA analysis using mobile equipment in the field -- and now "Rapid DNA" gear is finally here.

The idea is that you simply drop into the system a cotton swab with a person's saliva, for example, and the "Rapid DNA" machine spits out the type of DNA data that's needed to pin down identity. Now that such equipment exists, the FBI is pushing to get it into the hands of law enforcement agencies as soon as possible. [Also see: "FBI building system that blows away fingerprinting"]

"DNA has emerged as the gold standard in forensics analysis," Steven Martinez, executive assistant director of the science and technology branch at the FBI, said in his keynote address to attendees of the Biometric Consortium Conference in Tampa on Tuesday.

RELATED: Biometrics scares people

Though the genetic information contained in an individual's DNA, which is in all human cells, has been used since the late 1980s to solve crime cases, analysis of DNA has remained frustratingly slow because DNA had to be sent to special labs to be analyzed. New "Rapid DNA" devices are now ready to be evaluated and the FBI has received two basic types.

One is called the RapidHIT, which is made by IntegenX, a Pleasanton, Calif.-based company whose CEO Stevan Jovanovich was in the exhibit hall to explain how the Rapid DNA device can spit out an individual's DNA data within 90 minutes.

Another company, NetBio, is also believed to have delivered its Rapid DNA-type equipment to the FBI, Jovanovich says, and the National Institute of Standards and Technology (NIST) is expected to play an important role in helping certify systems and processes for how these boxes will be used by the FBI and local police stations to collect DNA data on suspects.

Jovanovich notes that the networked IntegenX RapidHIT box, which is based on a hardened version of Windows and measures about 27-by-24-by-16 inches, costs about $245,000. RapidHIT boxes are already in use with intelligence agencies, says Jovanovich, who adds he's not at liberty to say which ones or what they're doing with them.

The FBI, which is believed to have upwards of 10 million DNA records on individuals already stored in databases, anticipates a significant expansion of DNA collection by means of Rapid DNA equipment.

The FBI has been known for pioneering a massive collection of fingerprint images and an online matching system that can be accessed remotely to help local law enforcement, as well as the Department of Defense and other law-enforcement agencies, nail down the identities of criminals and terrorists. Today, Dr. Alice Isenberg, chief of the biometrics analysis section at the FBI laboratory, explained in her presentation how the FBI hopes to expand the national DNA database used to investigate crime for DNA matches online as well.

Read more from the original source:
FBI eager to embrace mobile 'Rapid DNA' testing

Posted in DNA | Comments Off on FBI eager to embrace mobile 'Rapid DNA' testing