Tuesday, July 17, 2012

Interview: Kat Graham Talks Her Music, Her Inspirations, And More ...

Kat Graham-RLE-000463.jpg

I got a chance to call in and have a candid interview with the fierce?Kat Graham! She talks about her experiences in the music industry, being on tour, plus her passions that her fans don't know about. Check out her insights after the jump!

Q: Would your music ever be featured on?The Vampire Diaries?

Kat Graham: I hope not. Unless "Kat Graham" visited?The Vampire Diaries.?I don't think Bonnie can sing my music. Not unless it's scoring music for the actual soundtrack, which I've done in the past. I'm not interested in singing?my?songs other than when I'm myself. Yea [laughs], I would rather not to be honest.

Q: I wanted to talk to you about your experience in the music industry since we all know how harsh the experience can be from the grind of trying to get a record deal, dealing with music execs, people wanting you to fit into a certain box, grueling rehearsals, or having "bad singing" days. How do you keep going? What do you tell yourself and how do you shut out the doubters?

KG: It's so interesting because, you know, I spent everyday since age 14 trying to make my music. There's not one day that goes by that I'm not listening to one of my songs or in rehearsal for one of my songs or dancing to one of my songs. And all I wanted when I was kid was to have a record deal. I wanted to be the first female, young teenager producer and It didn't happen. And when it finally did happen I was shelved because I was singed to Warner Bros. So that happened. And by the time I had such a bad taste in my mouth, when it was over and I had spent all my money to support my music, and did all my crappy music videos for my YouTube page or had bad management deals or whatever it was I was just kind of like "You know what? I just wanna make music, I'm not interested, I don't need to get singed. I just want to release my music and you know what, if it's meant to be, it will be." That's when I got singed to ?A& M Interscope Records, and it just all worked out. My experience with music, I'm not going to say extremely negative but it's definitely been a grind, it's been grimy, it hasn't been a pretty ?process. Its left me crying, you know, on the carpet in my tiny apartment with, like, no money. But it's been worth it, it's my passion, my dream, it's what I love to do. And I don't mind going broke for it. I love what I do. Now, it's all coming together and it's all worth it and it's really starting to happen now.?

Q: What's it like being on the road and getting to play your music for your fans??

KG: It's so incredible. I just want to live on the road. I can't understand artist that don't want to perform and like get on stage and do their songs for all their fans every night. If I'm not performing every night I get totally depressed. I know that sounds really weird but I hate sitting at home and not having a 1 a.m. performance now. It kills me. I love being on tour, I love being on the road. It's the most amazing feeling ever. I live for it; I love it.?

Q: Who are your inspirations on your style?

KG: My style is a little crazy. I'm always trying to, like, I think I'm toning it down, but then I always end up just doing my own thing. My biggest style inspirations come from the '90s. I'm really inspired by TLC, Janet Jackson, and designers like Jeremy Scott. I'm hugely inspired by Club Kids from New York back in the '90s. I'm inspired by the drag queen scene. Combat boots and the torn off jeans and a baggy shirt--I love that look. I love Kayne West, I'm really inspired by him a lot.?

Q: I know that you recently had a tour for your EP "Against The Wall." What was your favorite city and who was the loudest??

KG: The loudest was my favorite. Chicago was my favorite. I did this show at a local gay club called Roscoe's and I didn't know what to expect because I've done lots of gays clubs since I started performing. My biggest audience and my most loyal has been my gay fan base. But I definitely would have to say Roscoe's in Chicago was the most impressive. They knew all the songs, all the lyrics to my songs and they were singing them back to me so loud, I couldn't even hear myself in the monitors. It was just so piercingly loud that I actually started to cry because it was so beautiful to have that experience where the people knew my music. It was just the energy in it was like heartbreaking in the best way. It was the culmination of, you know, all the years that I spent struggling and having hope that it will all work out.?

Kat Graham-RLE-000460.jpg


Q: What are three passions that you have that your fans wouldn't know about?

KG: Let me ask my mom because she knows me.?To her mom in the background: "Name three passions that I have that fans wouldn't know about": Animals, art. I can be obsessive about art and artists. Like Renaissance artist, most particularly, Leonardo Da Vinci, and ,like, the history of things, knowing the background of that story behind it. Animals, art, and spirituality.?

Q: Musically speaking, what producers or other artists would you love to collaborate with??

KG: I would really love to collaborate with Gwen Stefani, and M.I.A.; artists that kind of make sense with me vocally. And in terms of style, I'm a very visual artist, I really love Pharell, I love people that really care about drums and I like beat-heavy. I'd love to work with Cee Lo. I don't know, there's a lot of them.?

Q: Can you describe your ideal day when you're not singing or acting??

KG: I'd have to say what I'm doing right now: having lunch with my mom, maybe going to yoga in the morning, you know, going to see a movie at night with my boyfriend, looking at different furniture. I just got a house, so I'm obsessed with decor?and art right now, finding cool pieces. Yeah, just shopping and hanging out with my mom. Very, very normal. But they?are?very rare the days, you know.?

You can watch the lastest episode of Kat's web series 'Road To' on Awesomeness TV now!

?

Source: http://www.starpulse.com/news/melissa_berne/2012/07/16/interview_with_kat_graham_about_her_mu

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Friday, July 6, 2012

India's Jindal Suspends Work at Bolivia Iron Ore Mine as Talks Falter

SANTA CRUZ, Bolivia--India's Jindal Steel & Power Ltd. (532286.BY) has suspended operations at its iron ore mine in Bolivia as last-ditch talks with the government to rescue the struggling project appear to have failed, according to Jindal executives in Bolivia.

Jindal's chief legal counsel in Bolivia, Jorge Gallardo, and other company managers said Wednesday that operations at the El Mutun mine were suspended and that negotiations had been stopped due to legal problems that made cancellation of the project "imminent."

In a statement, Jindal said it had "suspended its contractual obligations and informed the government of its intention to terminate the joint venture contract for El Mutun." Jindal executives said the company will leave Bolivia if the government doesn't signal its willingness to renegotiate the contract by July 8.

Mr. Gallardo said judicial charges levied by the authorities against Jindal executives as well as the Bolivian government's seizure of $36 million in cash guarantees posted by the Indian firm had generated conditions "unsuited to further negotiation or investment".

El Mutun is a vast iron ore deposit on Bolivia's border with Brazil which is estimated to contain 40 billion tons of ore.

In 2006, Jindal and Bolivian President Evo Morales signed a $2.1 billion contract to develop the mine and build a steel mill near the river port of Puerto Suarez.

But the ambitious project once showcased by Mr. Morales as an example of how his government and multinational companies could work as equal partners has been stalled for years.

The government accuses Jindal of violating the terms of the contract by not meeting its investment schedule. Jindal has blamed the government for failing to provide the gas and infrastructure necessary to move the project ahead.

Jindal began notifying Bolivian employees and contractors of plans to shut down the mine last month, pending last-minute negotiations with the government.

A chief engineer at the mine contacted by telephone also confirmed that operations "have been suspended."

Jindal wants the Morales administration to downsize the project due to the state's inability to provide the 10 million cubic meters of gas per day it needs for the steel works.

Bolivia's state oil and gas company YPFB said in April that it could only provide 2.5 million cubic meters of gas a day.

Jindal responded by proposing their investment be reduced.

Mining Minister Mario Virreira says that negotiations can't continue because Jindal's chief operating officer in Bolivia, Vikrant Gujral, can't be contacted.

Mr. Gujral is in India, according to Jindal executives, who say his return to Bolivia is being held up by legal charges filed against him and two other company officers, including Mr. Gallardo and Arvin Sharma, who is also India's honorary consul in Bolivia.

"The penal persecution initiated by a government prosecutor against our principal executives has not been withdrawn," Jindal said in its statement.

The Interior Ministry said the charges against the executives are related to "contract violations" and unwillingness to turn over company records for a government audit.

Write to Martin Arostegui at arostegui7@hotmail.com

Copyright ? 2012 Dow Jones Newswires

Source: http://feeds.foxbusiness.com/~r/foxbusiness/latest/~3/7WsxtiFGZsA/

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Source: http://news.yahoo.com/uganda-june-coffee-exports-drop-y-y-due-131659256--sector.html

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LA County voters to decide on condoms in porn films

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Source: http://news.yahoo.com/la-county-voters-decide-condoms-porn-films-053028581.html

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NASCAR not interested in mandatory cautions

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Source: http://news.yahoo.com/nascar-not-interested-mandatory-cautions-221455304--spt.html

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Christian On-line Dating - Find The Right One. | Travel, tours, hotels ...

Christian on-line relationship permits quite a lot of folks to have access to a database of Christian singles everywhere in the world. Christian on-line relationship service is meant to assist women and men meet other singles in a snug online environment. Christian online relationship service personals neighborhood is a source for creating relationships starting from companionship to friendship, romance to marriage.

Christian on-line relationship service is established to help folks construct profitable, lengthy-lasting relationships. Christian online dating service goals to help hundreds of thousands of people find the suitable partner for all times-lengthy love and happiness. Some Christian on-line dating service even gives features such as searches for bible study and prayer partners the world over, relying on which on-line Christian relationship service you accessed.

For those who need to be a part of Christian on-line courting, the following recommendations are given:

1. Post a Better Photograph ? Check out the pictures you?ve posted. Make sure that the photo you posted in Christian online dating websites depicts your finest self. With the help digital and disposable cameras it has turn into fast, simple, and low-cost to take a flattering photo.

2. Make Your Match Profile Answers Fascinating ? Your profile in Christian online relationship is an opportunity to express your self and stand out. Make sure that you are being authentic and interesting. In spite of everything, this is the page where your matches shall be deciding whether they want to get to know you.

3. Close Any Outdated Matches Who Aren?t Speaking ? If you have any open matches in Christian on-line relationship who have fallen silent, it?s good to officially shut communication with them. Not solely does it clear your display and assist you to prepare for brand new Christian online dating matches, it additionally provides a wake-up name to the opposite person who they?re falling behind. At all times use the closing reason ?Since you did not reply to my communication.?

4. Revisit Your Match Settings ? Many people set their Match Settings after they be a part of and neglect about them. As their life changes and their wants change, they do not take the time to replicate these modifications in their Match Settings. For example, many people determine after spending some time on that they would feel comfortable opening up their geographic vary a bit. They learn about how our communication system helps them focus on a couple of people who they are really occupied with meeting. So they really feel snug taking matches from across the country. So they should make crucial changes on their Christian online courting match settings.

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Related Posts:

Source: http://www.arbusinessplan.com/travel-and-dating/christian-on-line-dating-find-the-right-one/

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An Overview of Home Based Business Opportunities | OHLA BLOG

Sorry, Readability was unable to parse this page for content.

Source: http://www.blog.ohla.com/basicsuperintensivesummer/an-overview-of-home-based-business-opportunities

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Thursday, July 5, 2012

Three Kids Found, One Missing in California Child Abuse Case

Joseph Devenney/Getty Images(OAKLAND, Calif.) ? Three children associated with a couple and a babysitter arrested for abuse were recovered on Wednesday after a relative saw their names on the news and informed authorities she had been taking care of them, police said.? A fourth child, a 16-year-old girl, remains missing.

Oakland, Calif., police had been searching for the four children, who are associated with Reana Jackson, 20, and Aaron Tillman, 27, after the couple?s 3-year-old son was taken to the hospital while in the care of his babysitter, Szakyahha Safiyyah Williams, 24, for severe injuries caused by apparent abuse.

It was unclear how the other four children, who have different last names and are between the ages of 4 and 16 years old, are related to the couple.

Zaniyyah Nyema Johnson, 7; Antwan Alexander Johnson, 6; and Paradise Ghaimah-Medinah Mahasin, 4, who reportedly suffers from epilepsy, were all found in good physical condition in Patterson, Calif., police said in a statement.? They are in the custody of the Stanislaus County Sheriff?s Department.

The search for the children began on Monday after Jackson, Tillman and Williams were arrested in relation to the alleged abuse of Jackson?s unidentified 3-year-old son.

Police said Williams called on Monday and said the toddler was unresponsive and face down in a bathtub.? When paramedics arrived, the boy was clothed and dried.? He was taken to the hospital and revived by paramedics.

The boy?s injuries were indicative of abuse and left him in life-threatening condition, police said.

?Oakland police officers and investigators began an investigation due to the extent and nature of injuries and evidence of past physical abuse,? Oakland Police said in a statement.

Jackson, Tillman and Williams are being held at the Santa Rita Jail.? Williams faces charges of inflicting injuries on a child and assault.? Her bail has been set at $150,000, ABC News affiliate KGO reported.

Anyone with information regarding the whereabouts of 16-year-old Alyajah Marie Johnson is urged to contact the Oakland Police Department at 510-238-3641.

Copyright 2012 ABC News Radio

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Source: http://www.eastidahonews.com/2012/07/three-kids-found-one-missing-in-california-child-abuse-case/?utm_source=rss&utm_medium=rss&utm_campaign=three-kids-found-one-missing-in-california-child-abuse-case

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Medical Marijuana Use Sprouting In Israel

Moshe Rute smokes cannabis at the Hadarim nursing home in Kibutz Naan, Israel. In conjunction with Israel's Health Ministry, the Tikkun Olam company is distributing cannabis for medicinal purposes to more than 1,800 people in Israel. Enlarge Uriel Sinai/Getty Images

Moshe Rute smokes cannabis at the Hadarim nursing home in Kibutz Naan, Israel. In conjunction with Israel's Health Ministry, the Tikkun Olam company is distributing cannabis for medicinal purposes to more than 1,800 people in Israel.

Uriel Sinai/Getty Images

Moshe Rute smokes cannabis at the Hadarim nursing home in Kibutz Naan, Israel. In conjunction with Israel's Health Ministry, the Tikkun Olam company is distributing cannabis for medicinal purposes to more than 1,800 people in Israel.

Israel has become a world leader in the use of medical marijuana. More than 10,000 patients have received government licenses to consume the drug to treat ailments such as cancer and chronic pain.

But while the unorthodox treatment has gained acceptance in Israel, it still has its critics.

Susan Malkah breathes in the cloud of smoke from a plastic inhaler especially formulated for medical marijuana use. She has a number of serious ailments and is confined to a wheelchair.

"It's not like we're kids and we're getting high and going out and partying. You take it, you're by yourself usually, you just do it because you want to be in a better place. You don't want to sit and stew in the pain," says Malkah, who has been using cannabis for about two years. "It's natural, it helps, you don't have to fill your body full of chemicals. It's terrific."

More importantly, its use for medical purposes is legal in Israel. Malkah and other registered patients are being prescribed cannabis at the premier medical facility in a country known for its advanced medical care. That's because many of the head doctors at Jerusalem's Hadassah Medical Center are touting its use.

Dr. Reuven Or, director of the hospital's bone marrow transplantation department, says Israel was a pioneer in medical marijuana research and quickly saw and began to apply the benefits. Cannabis not only allows patients to regain their appetite, fight nausea and relax, but it's also proven to be an anti-inflammatory.

According to Or, medical marijuana use first began in the bone marrow transplant cancer ward.

"We started to use it as a routine treatment as part of all the other medications that we give. Slowly we enlarged the use to other cancer patients. We opened here a center that can help patients who are not hospitalized, from outpatients," Or says.

Eventually the Ministry of Health got on board, he says. Now, not only are cancer patients entitled to use medical marijuana, but people suffering from an entire list of other ailments including some psychological problems such as post-traumatic stress disorder are able to take advantage of its benefits.

One of the reasons it has been so widely accepted in Israel, Or says, is that cannabis use is mentioned in the Torah so the religious establishment doesn't object. His support of medical marijuana is purely scientific, however.

A worker tends to cannabis plants at a plantation in northern Israel. Researchers say they have developed marijuana that can be used to ease the symptoms of some ailments without getting patients high. Enlarge Baz Ratner/Reuters /Landov

A worker tends to cannabis plants at a plantation in northern Israel. Researchers say they have developed marijuana that can be used to ease the symptoms of some ailments without getting patients high.

Baz Ratner/Reuters /Landov

A worker tends to cannabis plants at a plantation in northern Israel. Researchers say they have developed marijuana that can be used to ease the symptoms of some ailments without getting patients high.

"We see many beneficial effects from the medical cannabis and therefore we are very open to use it," Or says.

In Israel, the Ministry of Health approves people for medical marijuana use with a recommendation from a doctor. After they get the license, the patient can either have it administered in a center, like the one at Hadassah Medical Center, or the drug can be given at home through one of about a dozen registered companies.

And its use has swelled in recent years. There were only a few hundred users in 2005, now there are more than 10,000 licensees. But not everyone is happy about that.

"People are waiting to see me now for six months," says Dr. Elyad Davidson, director of the pain relief unit in Haddassah. "I'm dealing so much with people who are waiting for the cannabis or on the cannabis list that it's not letting me treat the general population. So it's absurd in some ways."

Davidson says most patients who receive licenses are using cannabis to manage chronic pain. But he warns medical marijuana is not a miracle cure.

"We need more research and more knowledge [of] when to use cannabis for medical disorders and when not to use. We need to know that cannabis does have its problems, the public needs to know," he says.

Davidson says because it's a so-called "natural" drug that is grown and not fabricated in a lab, it's hard to control the quality of what a patient is getting and it's hard to know, as a doctor, how much a patient should be using.

He says there needs to be more oversight and regulation.

"I would like to see cannabis as like any of my other medications. It's a new class of medicine, for me that's good, I'm happy about that, but it needs to be dealt in all the aspects like any other medicine," he says.

But even medical warnings haven't stopped people from trying something that might alleviate the effects of their illness.

Back at the medical marijuana clinic, cancer patient Natalie Badwig is trying to incorporate medical marijuana into her life.

"Because of my weight loss, which has been quite drastic," Badwig says. "So the doctor suggested that I, you know, try cannabis and so I did."

She's hoping it will help her where nothing else has.

Source: http://feedproxy.google.com/~r/NprProgramsATC/~3/wvhxKplA7c0/medical-marijuana-use-sprouting-in-israel

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Monday, July 2, 2012

APA task force recommends treatment guidelines and position statements on transgender persons

APA task force recommends treatment guidelines and position statements on transgender persons [ Back to EurekAlert! ] Public release date: 2-Jul-2012
[ | E-mail | Share Share ]

Contact: Joan Robinson
joan.robinson@springer.com
49-622-148-78130
Springer

Report just published in Springer's Archives of Sexual Behavior

A report from the American Psychiatric Association (APA) Task Force on Treatment of Gender Identity Disorder (GID) recommends the development of clinical practice guidelines for psychiatrists caring for patients who are transgender. The report also encourages the development of position statements regarding the health care and civil rights of people who are gender variant or transitioning gender. The task force report is available online in Springer's journal Archives of Sexual Behavior.

The task force was charged with reviewing the scientific literature regarding gender identity disorder at different stages in a person's life. It examined the research and clinical evidence relating to treatment, and provided an opinion as to whether or not the APA should develop practice recommendations. The literature regarding treatment of gender dysphoria, or discomfort about one's own gender, in individuals with disorders of sex development was also assessed.

The report concluded that the quality of research evidence pertaining to most aspects of treatment for GID is not robust, but clinical consensus is sufficient to support the development of recommendations for the clinical management of GID in all age groups.

The task force also recommended that the APA create a separate mechanism for assessing the mental health needs of individuals with disorders of sex development, whether gender dysphoria is present or not.

In addition, the report recommended that the APA provide statements clarifying its positions on several issues. These include supporting the medical necessity of treatment for GID, defining the ethical issues regarding treatments for minors with GID or other manifestations of gender variance, and supporting the civil rights of persons who are gender variant, transgender, or transsexual.

The task force was formed to address concerns different from the diagnostic aspects of GID that were being considered as part of the next edition of the APA's Diagnostic and Statistical Manual of Mental Disorders (DSM). Although psychiatric diagnosis and treatment are linked, they are separate aspects of clinical mental health practice, and the DSM does not make recommendations for treatment. The APA first introduced GID as a diagnostic condition in the 1980 DSM, but has not taken any official position on treatment or other concerns of transgender persons.

Task Force Chair William Byne, M.D., Ph.D., said, "The American Medical Association has adopted a resolution supporting insurance coverage for medically necessary treatment for individuals diagnosed with GID. The task force report recommends the APA adopt a similar position, and issue other statements in support of the rights of gender variant persons."

###

The full task force report is available online at http://dx.doi.org/10.1007/s10508-012-9975-x.

Notes:
1. Byne, W., et al. (2012). Report of the American Psychiatric Association Task Force on Treatment of Gender Identity Disorder. Archives of Sexual Behavior; DOI 10.1007/s10508-012-9975-x
2. The task force report includes an appendix identifying health care policy and civil rights issues important to transgender persons and their treating clinicians, for use in specific policy development by the APA and other health care organizations.

The full-text report is also available to journalists on request.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


APA task force recommends treatment guidelines and position statements on transgender persons [ Back to EurekAlert! ] Public release date: 2-Jul-2012
[ | E-mail | Share Share ]

Contact: Joan Robinson
joan.robinson@springer.com
49-622-148-78130
Springer

Report just published in Springer's Archives of Sexual Behavior

A report from the American Psychiatric Association (APA) Task Force on Treatment of Gender Identity Disorder (GID) recommends the development of clinical practice guidelines for psychiatrists caring for patients who are transgender. The report also encourages the development of position statements regarding the health care and civil rights of people who are gender variant or transitioning gender. The task force report is available online in Springer's journal Archives of Sexual Behavior.

The task force was charged with reviewing the scientific literature regarding gender identity disorder at different stages in a person's life. It examined the research and clinical evidence relating to treatment, and provided an opinion as to whether or not the APA should develop practice recommendations. The literature regarding treatment of gender dysphoria, or discomfort about one's own gender, in individuals with disorders of sex development was also assessed.

The report concluded that the quality of research evidence pertaining to most aspects of treatment for GID is not robust, but clinical consensus is sufficient to support the development of recommendations for the clinical management of GID in all age groups.

The task force also recommended that the APA create a separate mechanism for assessing the mental health needs of individuals with disorders of sex development, whether gender dysphoria is present or not.

In addition, the report recommended that the APA provide statements clarifying its positions on several issues. These include supporting the medical necessity of treatment for GID, defining the ethical issues regarding treatments for minors with GID or other manifestations of gender variance, and supporting the civil rights of persons who are gender variant, transgender, or transsexual.

The task force was formed to address concerns different from the diagnostic aspects of GID that were being considered as part of the next edition of the APA's Diagnostic and Statistical Manual of Mental Disorders (DSM). Although psychiatric diagnosis and treatment are linked, they are separate aspects of clinical mental health practice, and the DSM does not make recommendations for treatment. The APA first introduced GID as a diagnostic condition in the 1980 DSM, but has not taken any official position on treatment or other concerns of transgender persons.

Task Force Chair William Byne, M.D., Ph.D., said, "The American Medical Association has adopted a resolution supporting insurance coverage for medically necessary treatment for individuals diagnosed with GID. The task force report recommends the APA adopt a similar position, and issue other statements in support of the rights of gender variant persons."

###

The full task force report is available online at http://dx.doi.org/10.1007/s10508-012-9975-x.

Notes:
1. Byne, W., et al. (2012). Report of the American Psychiatric Association Task Force on Treatment of Gender Identity Disorder. Archives of Sexual Behavior; DOI 10.1007/s10508-012-9975-x
2. The task force report includes an appendix identifying health care policy and civil rights issues important to transgender persons and their treating clinicians, for use in specific policy development by the APA and other health care organizations.

The full-text report is also available to journalists on request.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


Source: http://www.eurekalert.org/pub_releases/2012-07/s-atf070212.php

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An error-eliminating fix overcomes big problem in '3rd-gen' genome sequencing

ScienceDaily (July 1, 2012) ? A quantitative biologist at Cold Spring Harbor Laboratory (CSHL) and collaborators have published results of experiments that demonstrate the power of so-called single-molecule sequencing, which was recently introduced but whose use has so far been limited by technical issues.

The team, led by CSHL Assistant Professor Michael Schatz and Adam Phillippy and Sergey Koren of the National Biodefense Analysis and Countermeasures Center and the University of Maryland (UMD), has developed a software package that corrects a serious problem inherent in the newest sequencing technology: the fact that every fifth or sixth DNA "letter" it generates is incorrect. The high error rate is the flip side of the new method's chief virtue: it generates much longer genome "reads" than other technologies currently used, up to 100 times longer, and thus can provide a much more complete picture of genome structure than can be obtained with current, "2nd-gen" sequencing technology.

Using mathematical algorithms, Schatz and the team have preserved the great advantage of the "3rd-gen" method while all but eliminating its chief flaw. They have reduced the error rate from about 15% or greater to less than one-tenth of one percent. This mathematical "fix" -- which has been published in open-source code to the World Wide Web -- greatly increases the practical utility of 3rd-gen sequencing for the entire biomedical research community. The team demonstrates the breadth of potential applications of single-molecule sequencing by applying their fix to sequencing tasks ranging from the tiny bacteriophage virus at one end of the difficulty scale to the large and vastly more complex genome of the parrot, at the other. The parrot genome is more than a third the size of the human genome and is published online July 1 with the team's paper in Nature Biotechnology. The parrot sequence is "far superior to that of any previously sequenced bird genome," Schatz says.

To understand why it is better is to appreciate the advantages of 3rd-gen sequencing. The main advantage has to do with the average length of each "read" (i.e., genome segments read by a sequencer). The individual sequences are assembled into "contigs" -- shorthand for contiguous sequences -- much the way pieces in a jigsaw puzzle are assembled. In currently used 2nd-gen technology, the contigs are very small, and are massively redundant. A "consensus" version of each segment, representing the results of many layered reads, tends to be extremely accurate. But the small size of puzzle pieces prevents accurate assembly of certain genome portions, like those containing long repetitive sequences.

Obtaining superior versions of complete genomes was the objective that motivated Schatz and his collaborators, who also include HHMI Investigator Erich D. Jarvis of Duke University and CSHL Professor W. Richard McCombie, a sequencing pioneer, among others.

Combining the best of both generations

With single-molecule sequencing, the assembled contigs are much longer -- affording a much better picture of relatively larger genome segments, including those occupied by lengthy repeats. This is what Schatz and his team wanted to preserve, while at the same time boosting the error-free rate. They did so by effectively taking the best of both 2nd- and 3rd-gen technologies.

"We call our approach 'hybrid error correction,'" Schatz explains.

The team's major insight was to take advantage of the long-read data offered by a 3rd-gen machine like that used in their experiments, a Pacific Biosciences RS sequencer, and mixing in highly accurate short reads obtained from a separate 2nd-gen sequencer. The two data types were run through an open-source genome assembly program called Celera Assembler to generate a clean final assembly that has proven 99.9% error-free and composed of contigs whose median size is at least double that obtainable with 2nd-gen "short-read" sequencers. Contig sizes are expected to increase appreciably in subsequent iterations of the hybrid approach as single molecule long-read sequencing improves.

High-quality genome assemblies are especially important for genome annotation and comparative genome analyses. Many microbial genome analyses depend on finished genomes, but their cost is prohibitive using older technologies. High-quality analysis of the genomes of higher organisms depends upon continuous sequences that capture long stretches of DNA that spell out genes. Discoveries in recent years of spontaneously occurring structural changes in genomes called copy number variations -- such as those made by CSHL Professor Mike Wigler and his team in their research on schizophrenia and autism -- make clear the importance of being able to obtain clean and accurate pictures of the entire genomes of affected individuals.

With hybrid error correction, Schatz and his colleagues have "demonstrated that high error rates associated with long reads need not be a barrier to genome assembly," he summarizes. "High-error long reads can be efficiently assembled in combination with complementary short reads to produce assemblies not previously possible."

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The above story is reprinted from materials provided by Cold Spring Harbor Laboratory.

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


Journal Reference:

  1. Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis, Adam M Phillippy. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 2012; DOI: 10.1038/nbt.2280

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/~3/LW9lSUwlfYY/120701191609.htm

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