Friday, November 8, 2013

Hope builds for a drug that might shut down a variety of cancers

Hope builds for a drug that might shut down a variety of cancers


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7-Nov-2013



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Contact: Sarah Smith
sas2072@med.cornell.edu
646-317-7401
Weill Cornell Medical College



Cancer cells 'go to sleep' when crucial set of molecules is targeted




NEW YORK (November 7, 2013) -- The most frequently mutated gene across all types of cancers is a gene called p53. Unfortunately it has been difficult to directly target this gene with drugs. Now a multi-institutional research team, led by Dr. Lewis Cantley and investigators at Weill Cornell Medical College, has identified a family of enzymes they say is crucial for the growth of cancers that have genetic aberrations in p53. Targeting these enzymes with novel agents might prevent the growth of p53 mutant cancers, thereby benefiting a broad spectrum of cancer patients, including those with breast, ovarian, lung, colorectal and brain tumors.


In the Nov. 7 issue of Cell, investigators pinpoint two cellular enzymes -- Type 2 phosphatidylinositol-5-phosphate 4-kinases α and β (Type 2 PIP kinases) -- as essential for cancer growth when cells have lost p53, the powerful tumor-suppressor gene long dubbed the "guardian of the genome." More than half of all cancers lose this gene, allowing these cancers to grow at will.


The researchers discovered that the Type 2 PIP kinases are not critical for the growth of normal cells but become essential for cell growth when p53 is lost due to mutations or deletions. The scientists showed, in animal and lab studies of human cancer cells, that targeting these molecules effectively shuts down the growth of p53 mutant cancers.


Although the studies were conducted in human breast cancer cells, the researchers believe Type 2 PIP kinase inhibitors could block the growth of cancers with a mutated or missing p53 gene.


"The fact that one can delete the Type 2 PIP kinases in normal human cells or in mice with essentially no effect on cell survival suggests that inhibitors of these enzymes should have little toxicity," says Dr. Cantley, the study's senior author and director of the Cancer Center at Weill Cornell Medical College and NewYork-Presbyterian Hospital.


Dr. Cantley is already leading an effort to develop drugs to shut down these kinases. "Well-designed Type 2 PIP kinase inhibitors may turn the tide on p53 mutant cancer," he says.


A Crucial Link


Dr. Cantley is known for his discovery of the PI 3-kinase oncogene, and pioneering work in teasing apart how the gene contributes to cancer. PI 3-kinases (PI3K) have been linked to a wide variety of cellular functions, including cell growth and proliferation, and most cancers activate PI3K by one or more mechanisms. Dr. Cantley's discovery led to promising avenues for the development of personalized cancer therapies.


Activity of PI3K is in some cases linked to Type 2 PIP kinases, so in this study, Dr. Cantley sought to understand the function of these enzymes. Because the researchers knew that a subset of breast cancers over-express these molecules, investigators looked at their role in HER2-positive breast cancers, which typically are more aggressive tumors.


The researchers, including those from Harvard Medical School, Beth Israel Deaconess Medical Center and other institutions, discovered that the enzymes are silent in cells that have healthy p53. One critical role of p53 is to "rescue" cells that are producing excess reactive oxygen species (ROS), which are byproducts of cells that are growing too rapidly. The oxidative stress produced by ROS can damage cell structures, so p53 attempts to reduce ROS in affected cells. "If, however, ROS levels exceed the capacity of p53s to rescue it, then p53 takes on a second function, which is to kill the cell," Dr. Cantley says.


"That is why cancers often disable p53. If p53 is mutated or gone, then the cell keeps on growing at a very high rate," he says. "And then ROS begins to damage genes, making the cancer even more aggressive."


The Type 2 PIP kinases are the backup rescue system to p53. But they only reduce ROS enough to keep the cells from dying. (Too much ROS will also kill a cell.)


What this means is that cancer cells become "absolutely dependent on these kinases to be able to grow," Dr. Cantley says.


Taking Advantage of "Synthetic Lethality"


But there is a big and important hitch in this scenario, he adds. If the Type 2 PIP kinases are inhibited, and if p53 is deactivated, the cancer cell essentially "goes to sleep," he says. "It just stops dividing and growing. This is called synthetic lethality: You can get by without one gene or another, but if you lose both of them nothing can grow."


Shutting down these enzymes, as the researchers did in their experiments, puts cancer cells to sleep but has no effect on healthy cells. "A normal cell doesn't need Type 2 PIP kinases at all, so inhibitors of these enzymes should not be toxic to humans," Dr. Cantley says.


Because it is not possible to replace p53 proteins or the gene in cells that have lost it (many attempts have been made), deactivating Type 2 PIP kinases is the next-best thing, he adds. "This would likely be a very powerful advance in the treatment of many cancers."


###


This work was supported by NIH grant R01 GM041890 and by a Stand Up to Cancer Dream Team Translational Research Grant, a Program of the Entertainment Industry Foundation (SU2C-AACR-DT0209).


Co-authors include first author Dr. Brooke M. Emerling, Gary Bellinger and Rayman Choo-Wing from Weill Cornell Medical College; Dr. George Poulogiannis, Kazumi S. Tsukazawa, Hye-Seok Shim, and Dr. Gina M. DeNicola from Harvard Medical School; Dr. Gerburg M. Wulf, Dr. John M. Asara, Xin Yuan, and Dr. Andrea Bullock from Beth Israel Deaconess Medical School; Dr. Jonathan B. Hurov from Agios Pharmaceuticals; Dr. Eric L. Bell from the Massachusetts Institute of Technology; Dr. Katja A. Lamia from The Scripps Research Institute; Dr. Lucia E. Rameh from Boston University School of Medicine; Dr. Atsuo T. Sasaki from the University of Cincinnati College of Medicine; Dr. Jiaxi Song, Dr. Victoria Brown, and Dr. Sabina Signoretti from Dr. Dana-Farber Cancer Institute.


Weill Cornell Medical College

Weill Cornell Medical College, Cornell University's medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside, aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and education, Weill Cornell has a strong presence in places such as Qatar, Tanzania, Haiti, Brazil, Austria and Turkey. Through the historic Weill Cornell Medical College in Qatar, the Medical College is the first in the U.S. to offer its M.D. degree overseas. Weill Cornell is the birthplace of many medical advances including the development of the Pap test for cervical cancer, the synthesis of penicillin, the first successful embryo-biopsy pregnancy and birth in the U.S., the first clinical trial of gene therapy for Parkinson's disease, and most recently, the world's first successful use of deep brain stimulation to treat a minimally conscious brain-injured patient. Weill Cornell Medical College is affiliated with NewYork-Presbyterian Hospital, where its faculty provides comprehensive patient care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center. The Medical College is also affiliated with Houston Methodist. For more information, visit weill.cornell.edu.



Office of External Affairs

Weill Cornell Medical College

tel: 646.317.7401

email: pr@med.cornell.edu

Follow WCMC on Twitter and Facebook



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Hope builds for a drug that might shut down a variety of cancers


[ Back to EurekAlert! ]

PUBLIC RELEASE DATE:

7-Nov-2013



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Contact: Sarah Smith
sas2072@med.cornell.edu
646-317-7401
Weill Cornell Medical College



Cancer cells 'go to sleep' when crucial set of molecules is targeted




NEW YORK (November 7, 2013) -- The most frequently mutated gene across all types of cancers is a gene called p53. Unfortunately it has been difficult to directly target this gene with drugs. Now a multi-institutional research team, led by Dr. Lewis Cantley and investigators at Weill Cornell Medical College, has identified a family of enzymes they say is crucial for the growth of cancers that have genetic aberrations in p53. Targeting these enzymes with novel agents might prevent the growth of p53 mutant cancers, thereby benefiting a broad spectrum of cancer patients, including those with breast, ovarian, lung, colorectal and brain tumors.


In the Nov. 7 issue of Cell, investigators pinpoint two cellular enzymes -- Type 2 phosphatidylinositol-5-phosphate 4-kinases α and β (Type 2 PIP kinases) -- as essential for cancer growth when cells have lost p53, the powerful tumor-suppressor gene long dubbed the "guardian of the genome." More than half of all cancers lose this gene, allowing these cancers to grow at will.


The researchers discovered that the Type 2 PIP kinases are not critical for the growth of normal cells but become essential for cell growth when p53 is lost due to mutations or deletions. The scientists showed, in animal and lab studies of human cancer cells, that targeting these molecules effectively shuts down the growth of p53 mutant cancers.


Although the studies were conducted in human breast cancer cells, the researchers believe Type 2 PIP kinase inhibitors could block the growth of cancers with a mutated or missing p53 gene.


"The fact that one can delete the Type 2 PIP kinases in normal human cells or in mice with essentially no effect on cell survival suggests that inhibitors of these enzymes should have little toxicity," says Dr. Cantley, the study's senior author and director of the Cancer Center at Weill Cornell Medical College and NewYork-Presbyterian Hospital.


Dr. Cantley is already leading an effort to develop drugs to shut down these kinases. "Well-designed Type 2 PIP kinase inhibitors may turn the tide on p53 mutant cancer," he says.


A Crucial Link


Dr. Cantley is known for his discovery of the PI 3-kinase oncogene, and pioneering work in teasing apart how the gene contributes to cancer. PI 3-kinases (PI3K) have been linked to a wide variety of cellular functions, including cell growth and proliferation, and most cancers activate PI3K by one or more mechanisms. Dr. Cantley's discovery led to promising avenues for the development of personalized cancer therapies.


Activity of PI3K is in some cases linked to Type 2 PIP kinases, so in this study, Dr. Cantley sought to understand the function of these enzymes. Because the researchers knew that a subset of breast cancers over-express these molecules, investigators looked at their role in HER2-positive breast cancers, which typically are more aggressive tumors.


The researchers, including those from Harvard Medical School, Beth Israel Deaconess Medical Center and other institutions, discovered that the enzymes are silent in cells that have healthy p53. One critical role of p53 is to "rescue" cells that are producing excess reactive oxygen species (ROS), which are byproducts of cells that are growing too rapidly. The oxidative stress produced by ROS can damage cell structures, so p53 attempts to reduce ROS in affected cells. "If, however, ROS levels exceed the capacity of p53s to rescue it, then p53 takes on a second function, which is to kill the cell," Dr. Cantley says.


"That is why cancers often disable p53. If p53 is mutated or gone, then the cell keeps on growing at a very high rate," he says. "And then ROS begins to damage genes, making the cancer even more aggressive."


The Type 2 PIP kinases are the backup rescue system to p53. But they only reduce ROS enough to keep the cells from dying. (Too much ROS will also kill a cell.)


What this means is that cancer cells become "absolutely dependent on these kinases to be able to grow," Dr. Cantley says.


Taking Advantage of "Synthetic Lethality"


But there is a big and important hitch in this scenario, he adds. If the Type 2 PIP kinases are inhibited, and if p53 is deactivated, the cancer cell essentially "goes to sleep," he says. "It just stops dividing and growing. This is called synthetic lethality: You can get by without one gene or another, but if you lose both of them nothing can grow."


Shutting down these enzymes, as the researchers did in their experiments, puts cancer cells to sleep but has no effect on healthy cells. "A normal cell doesn't need Type 2 PIP kinases at all, so inhibitors of these enzymes should not be toxic to humans," Dr. Cantley says.


Because it is not possible to replace p53 proteins or the gene in cells that have lost it (many attempts have been made), deactivating Type 2 PIP kinases is the next-best thing, he adds. "This would likely be a very powerful advance in the treatment of many cancers."


###


This work was supported by NIH grant R01 GM041890 and by a Stand Up to Cancer Dream Team Translational Research Grant, a Program of the Entertainment Industry Foundation (SU2C-AACR-DT0209).


Co-authors include first author Dr. Brooke M. Emerling, Gary Bellinger and Rayman Choo-Wing from Weill Cornell Medical College; Dr. George Poulogiannis, Kazumi S. Tsukazawa, Hye-Seok Shim, and Dr. Gina M. DeNicola from Harvard Medical School; Dr. Gerburg M. Wulf, Dr. John M. Asara, Xin Yuan, and Dr. Andrea Bullock from Beth Israel Deaconess Medical School; Dr. Jonathan B. Hurov from Agios Pharmaceuticals; Dr. Eric L. Bell from the Massachusetts Institute of Technology; Dr. Katja A. Lamia from The Scripps Research Institute; Dr. Lucia E. Rameh from Boston University School of Medicine; Dr. Atsuo T. Sasaki from the University of Cincinnati College of Medicine; Dr. Jiaxi Song, Dr. Victoria Brown, and Dr. Sabina Signoretti from Dr. Dana-Farber Cancer Institute.


Weill Cornell Medical College

Weill Cornell Medical College, Cornell University's medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside, aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and education, Weill Cornell has a strong presence in places such as Qatar, Tanzania, Haiti, Brazil, Austria and Turkey. Through the historic Weill Cornell Medical College in Qatar, the Medical College is the first in the U.S. to offer its M.D. degree overseas. Weill Cornell is the birthplace of many medical advances including the development of the Pap test for cervical cancer, the synthesis of penicillin, the first successful embryo-biopsy pregnancy and birth in the U.S., the first clinical trial of gene therapy for Parkinson's disease, and most recently, the world's first successful use of deep brain stimulation to treat a minimally conscious brain-injured patient. Weill Cornell Medical College is affiliated with NewYork-Presbyterian Hospital, where its faculty provides comprehensive patient care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center. The Medical College is also affiliated with Houston Methodist. For more information, visit weill.cornell.edu.



Office of External Affairs

Weill Cornell Medical College

tel: 646.317.7401

email: pr@med.cornell.edu

Follow WCMC on Twitter and Facebook



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Source: http://www.eurekalert.org/pub_releases/2013-11/wcmc-hbf110713.php
Similar Articles: Austin Mahone   government shutdown   Geno Smith   Cloudy With A Chance Of Meatballs 2   Dumb and Dumber 2  

Amy Tan tells sweeping tale in new book


"The Valley of Amazement" (Ecco), by Amy Tan

The prolific and award-winning Amy Tan has delivered yet another sweeping tale of mothers and daughters that spans continents and generations. "The Valley of Amazement" begins in Shanghai in the early 1800s where she introduces readers to Lucia Minturn, who owns a high-end courtesan house, and her daughter, Violet, who grows up there among the women and their customers.

Through choice — or perhaps by accident — Violet ends up abandoned in Shanghai while her mother sets sail for San Francisco. Left with few options, Violet reinvents herself as a wealthy and much sought-after half-white, half-Chinese courtesan.

As she learns and later plies her trade, Tan brings to life a world with which few are familiar. And it's fascinating. Her descriptions of the countryside, of the houses, of the lifestyle and the customers are well-drawn and multi-layered. Her characters are brought to life as three-dimensional, complicated people.

The only distraction from the near-perfect pacing is the occasional overwrought language — particularly when it comes to sex and intimacy: "We conjoined and separated, conjoined and separated, so that we could have the joy of looking into each other's eyes before falling into each other again."

Then again, the language may sound awkward only to modern ears.

Readers also may find themselves wondering throughout "The Valley of Amazement" whether they hadn't already read this book. It covers no new ground and offers no surprises, but in Tan's skilled hands that doesn't detract from the joy of reading it.

___

Online:

http://www.amytanauthor.com/

Source: http://news.yahoo.com/amy-tan-tells-sweeping-tale-book-193351984.html
Category: jonbenet ramsey   melissa mccarthy   Tony Gonzalez   Jordan Linn Graham   Linda Ronstadt  

Pioneer's $299 DDJ-SB controller lets you spin records on the cheap (video)


Pioneer's allinone $299 DJ controller lets anyone dabble in spinning records


You might have the ambition and desire to be the next Deadmau5, but the price of some DJ controllers aren't exactly wallet-friendly. Thankfully there are plenty of affordable options out there, and one of them has just arrived from Pioneer. Dubbed the DDJ-SB, it claims similar basic features and operability with DDJ-SX that debuted last year, but at almost half the cost. A 2-channel controller, the DDJ-SB uses the popular Serato DJ Intro software and touts two decks with large jog wheels for easy scratching, a "filter fade" function for smoother transitions, multiple performance pads and a USB interface so you can hook it up easily to your computer. Sure, you'll still need some knowhow to fully make use of it, but at only $299 each, you could invest your savings on a few DJ lessons. Head past the break for a video of the DDJ-SB in action.



Source: http://www.engadget.com/2013/11/07/pioneer-ddj-sb/?ncid=rss_truncated
Tags: jimi hendrix   Miss World 2013   adam levine   Kaepernick   sunday night football  

Thursday, November 7, 2013

Dartmouth researcher finds novel genetic patterns that make us rethink biology and individuality

Dartmouth researcher finds novel genetic patterns that make us rethink biology and individuality


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7-Nov-2013



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Contact: Derik Hertel
derik.hertel@dartmouth.edu
603-650-1203
The Geisel School of Medicine at Dartmouth






Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth's Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the restresulting in several different genotypes in one individualand second, some of the same genetic mutations occur in unrelated people. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams' surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought. His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.1


Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or "somatic" mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.


"We are in reality diverse beings in that a single person is genetically not a single entityto be philosophical in ways I do not yet understandwhat does it mean to be a person if we are variable within?" says Williams, the study's senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. "What makes you a person? Is it your memory? Your genes?" He continues, "We have always thought, 'your genome is your genome.' The data suggest that it is not completely true."


In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. "This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences." says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.


Having multiple genotypes from mutations within one's own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and childor twinsexchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body).2 Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that "proved" that she was unrelated to two of her three biological sons.3


Williams says that, although this was a small study, "there is a lot more going on than we thought, and the results are, in some ways, astoundingly weird."


Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA)a part of DNA that is only inherited from the mother.4 Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjectsonly detected in three body tissuesare "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model . a decidedly non-random process that results in particular mutations, but only in specific tissues."


If our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations "match" among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.


Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, "This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age." Amos, who is also a Professor of Community and Family Medicine at Geisel, says, "To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages." Williams concurs, saying, "Clearly these do accumulate with age, but how and why is unknownand needs to be determined."


As more and better data become available from high-throughput genetic analyses and high-powered computers, researchers are identifying an increasing number of medical conditions that result from somatic mutations, including neurological, hematological, and immune-related disorders. Williams and colleagues are conducting further research to examine how diseases, other than cancer or even benign conditions, may result from somatic changes.5 Williams, Moore and Amos will employ iQBS's Discovery supercomputer for next-generation sequencing to process subjects' DNA data.6 Future analyses will include large, whole-genome sequencing of the data for the two individuals studied in the current report.


Williams explains, "We know that cancer is caused by mutations that cause a tumor. But in this work, we chose to study mutations in people without any cancer. Knowing how we accumulate mutations may make it easier to separate genetic signals that may cause cancer from those that accumulate normally without affecting disease. It may also allow us to see that many changes that we thought caused cancer do not in many situations, if we find the same mutations in normal tissues."


Just as our bodies' immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, "Most genetic changes don't cause disease, and if they did, we'd be in big trouble. Fortunately, it appears our systems filter a lot of that out."


Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, "The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility."


###


1 Williams, Scott, et al., Recurrent tissue-specific mtDNA mutations are common in humans. http://www.plosgenetics.org/doi/pgen.1003929.


2 Strain L, Dean JC, Hamilton MP, Bonthron D. A true hermaphrodite chimera resulting from embryo amalgamation after in vitro fertilization. N Engl J Med 1998;(338):166-9/


3 Norton AT and Zehner O. Project MUSE: Today's Research, Tomorrow's Inspiration. http://www.academia.edu/202539/Which_Half_Is_Mommy_Tetragametic_Chimerism_and_Trans-Subjectivity.


4 The Bradshaw Foundation [online learning resource with main areas of focus on archaeology, anthropology and genetic research]: Mitochondrial DNA: The EVE Gene. http://www.bradshawfoundation.com/journey/eve.htm.


5 Li, Chun and Williams, Scott M. Human somatic variation: It's not just for cancer anymore. Current Genetic Medicine Reporter (In Press).


6 Discovery iQBS website. http://iqbs.org/resources/discovery-supercomputer/.




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Dartmouth researcher finds novel genetic patterns that make us rethink biology and individuality


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PUBLIC RELEASE DATE:

7-Nov-2013



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Contact: Derik Hertel
derik.hertel@dartmouth.edu
603-650-1203
The Geisel School of Medicine at Dartmouth






Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth's Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the restresulting in several different genotypes in one individualand second, some of the same genetic mutations occur in unrelated people. We think of each person's DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams' surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought. His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal on November 7, 2013.1


Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or "somatic" mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.


"We are in reality diverse beings in that a single person is genetically not a single entityto be philosophical in ways I do not yet understandwhat does it mean to be a person if we are variable within?" says Williams, the study's senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. "What makes you a person? Is it your memory? Your genes?" He continues, "We have always thought, 'your genome is your genome.' The data suggest that it is not completely true."


In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. "This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences." says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.


Having multiple genotypes from mutations within one's own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and childor twinsexchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body).2 Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that "proved" that she was unrelated to two of her three biological sons.3


Williams says that, although this was a small study, "there is a lot more going on than we thought, and the results are, in some ways, astoundingly weird."


Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA)a part of DNA that is only inherited from the mother.4 Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjectsonly detected in three body tissuesare "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model . a decidedly non-random process that results in particular mutations, but only in specific tissues."


If our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations "match" among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.


Christopher Amos, PhD, Director of the Center for Genomic Medicine and Associate Director for Population Sciences at the Cancer Center, says, "This paper identifies mutations that develop in multiple tissues, and provides novel insights that are relevant to aging. Mutations are noticed in several tissues in common across individuals, and the aging process is the most likely contributor. The theory would be that selected mutations confer a selective advantage to mitochondria, and these accumulate as we age." Amos, who is also a Professor of Community and Family Medicine at Geisel, says, "To confirm whether aging is to blame, we would need to study tissues from multiple individuals at different ages." Williams concurs, saying, "Clearly these do accumulate with age, but how and why is unknownand needs to be determined."


As more and better data become available from high-throughput genetic analyses and high-powered computers, researchers are identifying an increasing number of medical conditions that result from somatic mutations, including neurological, hematological, and immune-related disorders. Williams and colleagues are conducting further research to examine how diseases, other than cancer or even benign conditions, may result from somatic changes.5 Williams, Moore and Amos will employ iQBS's Discovery supercomputer for next-generation sequencing to process subjects' DNA data.6 Future analyses will include large, whole-genome sequencing of the data for the two individuals studied in the current report.


Williams explains, "We know that cancer is caused by mutations that cause a tumor. But in this work, we chose to study mutations in people without any cancer. Knowing how we accumulate mutations may make it easier to separate genetic signals that may cause cancer from those that accumulate normally without affecting disease. It may also allow us to see that many changes that we thought caused cancer do not in many situations, if we find the same mutations in normal tissues."


Just as our bodies' immune systems have evolved to fight disease, interestingly, they can also stave off the effects of some genetic mutations. Williams states that, "Most genetic changes don't cause disease, and if they did, we'd be in big trouble. Fortunately, it appears our systems filter a lot of that out."


Mark Israel, MD, Director of Norris Cotton Cancer Center and Professor of Pediatrics and Genetics at Geisel, says, "The fact that somatic mutation occurs in mitochondrial DNA apparently non-randomly provides a new working hypothesis for the rest of the genome. If this non-randomness is general, it may affect cancer risks in ways we could not have previously predicted. This can have real impact in understanding and changing disease susceptibility."


###


1 Williams, Scott, et al., Recurrent tissue-specific mtDNA mutations are common in humans. http://www.plosgenetics.org/doi/pgen.1003929.


2 Strain L, Dean JC, Hamilton MP, Bonthron D. A true hermaphrodite chimera resulting from embryo amalgamation after in vitro fertilization. N Engl J Med 1998;(338):166-9/


3 Norton AT and Zehner O. Project MUSE: Today's Research, Tomorrow's Inspiration. http://www.academia.edu/202539/Which_Half_Is_Mommy_Tetragametic_Chimerism_and_Trans-Subjectivity.


4 The Bradshaw Foundation [online learning resource with main areas of focus on archaeology, anthropology and genetic research]: Mitochondrial DNA: The EVE Gene. http://www.bradshawfoundation.com/journey/eve.htm.


5 Li, Chun and Williams, Scott M. Human somatic variation: It's not just for cancer anymore. Current Genetic Medicine Reporter (In Press).


6 Discovery iQBS website. http://iqbs.org/resources/discovery-supercomputer/.




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Source: http://www.eurekalert.org/pub_releases/2013-11/tgso-drf110713.php
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Roy Choi's Tacos Channel LA And The Immigrant Experience





Chef Roy Choi was named Food and Wine Magazine's Best New Chef in 2010.



Bobby Fisher/Courtesy of Harper Collins


Chef Roy Choi was named Food and Wine Magazine's Best New Chef in 2010.


Bobby Fisher/Courtesy of Harper Collins


Roy Choi is a chef who's celebrated for food that isn't fancy. He's one of the founders of the food truck movement, where instead of hot dogs or ice cream, more unusual, gourmet dishes are prepared and sold. His Kogi trucks specialize in tacos filled with Korean barbecue.


Choi was born in South Korea in 1970 and moved to Los Angeles with his parents at the age of 2. His parents owned a Korean restaurant near Anaheim for a few years when he was a child. He tells Fresh Air's Terry Gross that his mother had some serious cooking talent.


"She had flavor in her fingertips," he says. "She had this connection and this innate ability to capture flavor in the moment and people felt it. Because our lives were so based around food, when someone is good at food, everyone notices and it's a big deal."





Customers line up at one of Roy Choi's Kogi BBQ food trucks near the campus of UCLA.



Matt Sayles/AP


Customers line up at one of Roy Choi's Kogi BBQ food trucks near the campus of UCLA.


Matt Sayles/AP


Choi's new book, L.A. Son: My Life, My City, My Food, is part memoir, part cookbook.



Interview Highlights


On what Korean tacos represent for him


The Korean taco was a phenomenon. ... It just came out of us, we didn't really think about it. The flavor, in a way, didn't exist before, but it was a mash up of everything we had gone through in our lives.


It became a voice for a certain part of Los Angeles and a certain part of immigration and a certain part of life that wasn't really out there in the universe. We all knew it and we all grew up with it, and it was all around us, but the taco kind of pulled it together. It was like a lint roller; it just put everything onto one thing. And then when you ate it, it all of a sudden made sense.


As I was putting it together, it was all of the pieces of my life coming together. It was almost like an avalanche. So it was growing up; it was being around low-riding; it was growing up in Korea, the immigration, being around the American school system; all the snack food and junk food that I've eaten; all of the tacos that I've eaten. It was all of these things. Then I really wanted to make it feel like Los Angeles, so I felt like it had to be just like a street taco in L.A.



On his Hawaiian restaurant, A-Frame, which is housed in an old IHOP


It's my love for the Hawaiian Islands, but it's not a tiki restaurant: It's really taking the feeling of "aloha." So we put people together, it's all communal seating, so strangers get to sit together. ... You eat everything with your hands and it's like a backyard barbecue.


... I wasn't always the most professional looking/acting dude in the world, so I'd go into restaurants, get treated not that well, kind of like crap. So what happened was I thought, "OK, if I ever make a restaurant, as soon as anyone opens that door, no matter where you're from, I want you to feel like we've been waiting for you."


On his rice bowl restaurant, Chego


That's a real personal place. ... A lot of Asian-Americans, growing up, we kind of live double lives. We had our refrigerators at home and the way we ate at home, and then we went to school and we couldn't really show that food because it was real stinky and stuff like that.


When you're going through that whole puberty/teenage angst ... you don't want to show that. Chego was my vision to show that food, to open the refrigerator, to show it to the world, and then make these rice bowls that were under $10. So it was also a platform to create great, delicious, healthy fast food that's affordable.


On growing up in Orange County and the cultural differences between his family and his friends


I was doomed because everyone had peroxide in their hair and they were coming from ski trips on Mammoth Mountain and snorkeling trips in the Cayman Islands, listening to Depeche Mode and The Cure, and I had never seen anything like that before. It wasn't really my rhythm.



A lot of Asian-Americans, growing up, we kind of live double lives. We had our refrigerators at home and the way we ate at home, and then we went to school and we couldn't really show that food because it was real stinky ...



I did the best I could. I was doomed because there weren't that many Asians and girls weren't really feeling me, but I was also doomed because if we get down to the food, the food was different for me too. I was embarrassed to show the food [we were eating] because everywhere I went, it was so different. Youngsters are mean to each other sometimes so I'd bring friends over and they'd look at my food and they'd be like, "Ew, what is that?"


... When you bring a bunch of rich friends from Orange Country over to your house and your whole house is surrounded by dead salted fish, it was tough.


... I loved it at the time. When I say the word "embarrassed" it's not that I was embarrassed and that I tried to shy away from it or that I tried to put it into the dirt and hope that it never came out again; it's just I didn't have the language to really stick up for it at that time.



On his addictions


Gambling hit me at like 22, 21. And it was three years of the darkest time of my life, but it started out just all fireworks and pom-poms, you know?


It was an amazing ride for the first year, I mean tens of thousands of dollars in shoeboxes ... just ballin' crazy. ... And then I started losing. And when you start losing in gambling, then you start chasing it. ... I lost all my friends; I lost all my family; I stole from my family ... sold everything I had.


... I'm addicted to feeding people right now. It's a good thing. I don't know how long this is gonna last right now, so I'm living it up and really focusing and putting everything I got into it. I'm putting my back into it.



Source: http://www.npr.org/2013/11/07/243527051/roy-chois-tacos-channel-la-and-the-immigrant-experience?ft=1&f=1032
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