[Source Deb Daun, Bio5] - A novel therapeutic cancer vaccine developed by a research team at The University of Arizona Steele Children’s Research Center is advancing toward use in human clinical trials.
Dr. Emmanuel Katsanis, professor of pediatrics and a BIO5 member at the UA, and his research team developed the vaccine Chaperone Rich Cell Lysate, or CRCL, which utilizes proteins known as chaperone proteins. These special proteins are found inside cancer cells and are associated with the protein antigens unique to the individual’s cancer.
These antigens are needed for the immune system to identify the cancer to initiate an immune response to both destroy the existing tumor cells and boost the immune memory to protect against any recurrence of the tumor. However, in the individual with cancer, these tumor antigens are concealed from the immune system.
The CRCL vaccine employs a patented process that purifies the chaperone protein from the antigen, making the antigen again visible to the immune system. Previous therapeutic cancer vaccines have had disappointing results in the clinic, in part due to the difficulty in revealing these hidden tumor antigens; however, an additional problem is the sophisticated ability of tumor cells to avoid an immune response even when the tumor antigens have been revealed.
To overcome this tumor resistance, Katsanis has partnered with an Israeli biopharmaceutical company that has developed a cell therapy drug product called AlloStimTM – designed to provide the signals necessary to disable tumor immune avoidance mechanisms.
“We’re excited to see our research progress from the laboratory and move to human clinical trials, the combination of our technology to reveal hidden tumor antigens and the technology of Immunovative Therapies to disarm the tumor’s ability to avoid the immune response creates a powerful and unique combination that holds promise to overcome the past failures of cancer vaccines in the clinic,” Katsanis said.I
mmunovative Therapies, LTD, a cancer research-and-development company based in Israel, purchased an exclusive license to the chaperone protein patent held by the UA’s Steele Center. Immunovative Therapies is converting Katsanis’ chaperone protein technology to comply with Good Manufacturing Practices, required before beginning human clinical trials.
The new vaccine product, which combines CRCL and AlloStimTM, is named AlloVax and is designed to treat patients with newly diagnosed blood cancers like leukemia, lymphoma and multiple myeloma. When an individual develops a blood cancer, aggressive chemotherapy often can induce remission; unfortunately, because these treatments are unable to eliminate all of the microscopic cancer cells, the cancer frequently returns.
The returning cancers are deadly because they have developed a resistance to chemotherapy. AlloVax is designed to train the cancer patient’s immune system to identify and eliminate the cancer cells in the patient’s blood, keeping the patient in remission without the need for additional treatment.
Before an individual diagnosed with a blood cancer is treated with chemotherapy, a sample of the cancer is removed from his or her body. While receiving chemotherapy, the cancer sample is processed in the lab to extract the chaperone proteins.
Utilizing the UA’s patented process of purifying the chaperone proteins associated with the patient’s unique cancer antigens, the chaperone proteins then are mixed with Immunovative Therapies AlloStim cells. The mixture is injected into the patient’s skin.
Within the skin are specialized immune cells called dendritic cells, which then travel to the injection site and surround the chaperone proteins and unique cancer antigens that previously were hidden by the cancer cells. In the presence of danger signals released by AlloStim cells, these dendritic cells process the cancer antigens and are programmed by the AlloStim cells to understand that the cancer is a danger to the body.
The programmed dendritic cells containing the unique cancer antigens travel to the lymph node, where these programmed dendritic cells educate the patient’s T cells to destroy the cancer cells. These “educated killer T cells” will circulate in the body and continuously look for any cancer cells that might emerge. In the event of cancer recurrence, the T cells will destroy the cancer cells.
“AlloVax is truly a personalized and novel vaccine designed to train the immune system to destroy cancer cells,” Katsanis said. “It is designed to keep you in remission after you have been treated with chemotherapy and/or radiation. And now we are one step closer to treating patients with cancer.”
An animation of the process is available at: http://www.immunovative.co.il/flash/AlloVax/alloVax_presentation.php.
Thursday, May 29, 2008
Wednesday, May 28, 2008
UA Plant Scientists Develop New Cell-Sorting Technique
[Source: Deborah Daun, BIO5] - A new cell-sorting technique developed by UA plant scientists has the potential to enhance our understanding of how cells of all types work--or, in the case of diseases such as cancer, of how they fail to work.
Living organisms, including plants and animals, are made up of recognizable structures (which we call organs), that have specific functions--plant organs include leaves, roots, flowers, and fruit, for example, while animals have kidneys, livers, hearts, brains, and so-on. Each of these organs in turn is made up of a complex mix of different cell types, each having different functions. One of the challenges in understanding how organs function is the need to separate out these different cell types in order to analyze them. Other cell sorting methods often rely on using a machine that recognizes the differences in the optical properties of the different cell types. However it is difficult, and in some cases impossible, to separate the different cells within organs by this method.
Plant sciences professor and BIO5 member David Galbraith explains that instead of focusing on the cell as a whole, the technique his lab has developed focuses on cell nuclei. Other methods of teasing different cell types apart require that the cell remain intact--a challenge when working with plants that have rigid cell walls; and also when working with brain and other animal cells, which can be connected in intricate ways. "We thought it'd be a lot easier if we could take a razor and chop up the cells and then sort their nuclei," Galbraith says.
The nuclei of cells contain their genetic material--the "operating instructions" that regulate everything from how a saguaro stores water to how a human heart beats. For any given organism, the nucleus of every cell contains the same comprehensive set of instructions--but not every cell "reads" everything written there. Heart cells don't carry out the instructions for digesting food, for instance; a tree's leaves don't carry out the instructions for drawing water out of the soil. Yet even a single leaf is made up of many cells with many subtly different functions.
To develop their technique for separating such interconnected yet different cells, Galbraith and his graduate students focused on certain nutrient-transporting root cells in the small flowering plant Arabidopsis thaliana. They modified a green fluorescent protein (GFP) found in jellyfish by combining it with a protein that is found only in the nuclei of those root cells. They then arranged for this modified GFP to be produced only within specific cell types in the root, and as a result the GFP lit up only the nuclei within the cell types that the researchers were looking for. They were then able to take advantage of GFP's visible fluorescence to allow the cell sorter to rapidly sort and purify the fluorescent nuclei of that cell type, while leaving the nuclei of other cells behind. Galbraith and his students further showed that the sorted nuclei provided the same information about the state of the “operating instructions” as that obtained from separated cells.
"Isolating nuclei is a simple alternative to isolating the whole cell," Galbraith says, "one that lets people analyze a lot of cell types they weren't previously able to analyze." In other words, scientists now have one more tool for understanding how cells work--in plants and animals both.
"This is an interdisciplinary kind of technology," Galbraith says. "The BIO5 institute was an ideal place to develop this because it can now be applied not only to plants but also to animals and to biomedical problems."
While the individual research teams who make use of the new cell-sorting technique will decide what questions to tackle with it, Galbraith says this could potentially help us understand everything from how plants respond to environmental stresses and how to increase the yield of food crops, to how to treat diseases where the action of cells goes awry, as happens with cancer. "The more information we have, the more likely we are to be able to deal with problems," Galbraith says.
Living organisms, including plants and animals, are made up of recognizable structures (which we call organs), that have specific functions--plant organs include leaves, roots, flowers, and fruit, for example, while animals have kidneys, livers, hearts, brains, and so-on. Each of these organs in turn is made up of a complex mix of different cell types, each having different functions. One of the challenges in understanding how organs function is the need to separate out these different cell types in order to analyze them. Other cell sorting methods often rely on using a machine that recognizes the differences in the optical properties of the different cell types. However it is difficult, and in some cases impossible, to separate the different cells within organs by this method.
Plant sciences professor and BIO5 member David Galbraith explains that instead of focusing on the cell as a whole, the technique his lab has developed focuses on cell nuclei. Other methods of teasing different cell types apart require that the cell remain intact--a challenge when working with plants that have rigid cell walls; and also when working with brain and other animal cells, which can be connected in intricate ways. "We thought it'd be a lot easier if we could take a razor and chop up the cells and then sort their nuclei," Galbraith says.
The nuclei of cells contain their genetic material--the "operating instructions" that regulate everything from how a saguaro stores water to how a human heart beats. For any given organism, the nucleus of every cell contains the same comprehensive set of instructions--but not every cell "reads" everything written there. Heart cells don't carry out the instructions for digesting food, for instance; a tree's leaves don't carry out the instructions for drawing water out of the soil. Yet even a single leaf is made up of many cells with many subtly different functions.
To develop their technique for separating such interconnected yet different cells, Galbraith and his graduate students focused on certain nutrient-transporting root cells in the small flowering plant Arabidopsis thaliana. They modified a green fluorescent protein (GFP) found in jellyfish by combining it with a protein that is found only in the nuclei of those root cells. They then arranged for this modified GFP to be produced only within specific cell types in the root, and as a result the GFP lit up only the nuclei within the cell types that the researchers were looking for. They were then able to take advantage of GFP's visible fluorescence to allow the cell sorter to rapidly sort and purify the fluorescent nuclei of that cell type, while leaving the nuclei of other cells behind. Galbraith and his students further showed that the sorted nuclei provided the same information about the state of the “operating instructions” as that obtained from separated cells.
"Isolating nuclei is a simple alternative to isolating the whole cell," Galbraith says, "one that lets people analyze a lot of cell types they weren't previously able to analyze." In other words, scientists now have one more tool for understanding how cells work--in plants and animals both.
"This is an interdisciplinary kind of technology," Galbraith says. "The BIO5 institute was an ideal place to develop this because it can now be applied not only to plants but also to animals and to biomedical problems."
While the individual research teams who make use of the new cell-sorting technique will decide what questions to tackle with it, Galbraith says this could potentially help us understand everything from how plants respond to environmental stresses and how to increase the yield of food crops, to how to treat diseases where the action of cells goes awry, as happens with cancer. "The more information we have, the more likely we are to be able to deal with problems," Galbraith says.
Vertigo Can Be Treated Easily And Quickly
[Source: ScienceDaily] - A new guideline developed by the American Academy of Neurology found that the best treatment for vertigo is the easiest and quickest one. The guideline on benign paroxysmal positional vertigo (BPPV), an inner ear disorder that is a common cause of dizziness, is published in the May 27, 2008, issue of Neurology.
The disorder causes a feeling of spinning or whirling when the head is moved in certain ways, such as looking up or bending. The feeling lasts a short time but can be severe.
The guideline determined that in many cases the vertigo can be treated with simple maneuvers--a series of head and body movements performed by a doctor or therapist while the patient sits on a bed or table.
"The good news is that this type of vertigo is easily treated," said guideline author Terry D. Fife, MD, of the University of Arizona College of Medicine and Barrow Neurological Institute. Fife is also a Fellow of the American Academy of Neurology. "Instead of telling patients to 'wait it out' or having them take drugs, we can perform a safe and quick treatment that is immediate and effective."
Several maneuvers are in use for vertigo. The guideline found that canalith repositioning procedure, also called the Epley maneuver, is safe and effective for people of all ages. The Semont maneuver is possibly an effective treatment. To develop the guideline, the authors analyzed all available scientific studies on the topic.
The disorder is believed to be caused by loose calcium carbonate crystals that move in the sensing tubes of the inner ear. The maneuvers move the calcium crystals out of the sensing tube and into another inner chamber of the ear, from which they can be absorbed.
The guideline also evaluated whether restrictions on activity are needed after the maneuvers are performed. "There is no clear evidence to support these restrictions, which include sleeping upright and wearing a cervical collar," Fife said.
The guideline also reviewed whether patients can perform the maneuvers safely and effectively at home. "Having patients treat themselves using home exercises seems to pose little risk, but there is not sufficient evidence that this is as effective as maneuvers done by a doctor or therapist," Fife said.
Adapted from materials provided by American Academy of Neurology.
The disorder causes a feeling of spinning or whirling when the head is moved in certain ways, such as looking up or bending. The feeling lasts a short time but can be severe.
The guideline determined that in many cases the vertigo can be treated with simple maneuvers--a series of head and body movements performed by a doctor or therapist while the patient sits on a bed or table.
"The good news is that this type of vertigo is easily treated," said guideline author Terry D. Fife, MD, of the University of Arizona College of Medicine and Barrow Neurological Institute. Fife is also a Fellow of the American Academy of Neurology. "Instead of telling patients to 'wait it out' or having them take drugs, we can perform a safe and quick treatment that is immediate and effective."
Several maneuvers are in use for vertigo. The guideline found that canalith repositioning procedure, also called the Epley maneuver, is safe and effective for people of all ages. The Semont maneuver is possibly an effective treatment. To develop the guideline, the authors analyzed all available scientific studies on the topic.
The disorder is believed to be caused by loose calcium carbonate crystals that move in the sensing tubes of the inner ear. The maneuvers move the calcium crystals out of the sensing tube and into another inner chamber of the ear, from which they can be absorbed.
The guideline also evaluated whether restrictions on activity are needed after the maneuvers are performed. "There is no clear evidence to support these restrictions, which include sleeping upright and wearing a cervical collar," Fife said.
The guideline also reviewed whether patients can perform the maneuvers safely and effectively at home. "Having patients treat themselves using home exercises seems to pose little risk, but there is not sufficient evidence that this is as effective as maneuvers done by a doctor or therapist," Fife said.
Adapted from materials provided by American Academy of Neurology.
Tuesday, May 27, 2008
Consortium Supports UA Researcher's Non-Embryonic Stem Cell Research
[Source: Deborah Daun, BIO5] - A European consortium promoting non-embryonic stem cell research has chosen a UA professor's work on preventing vision loss as one of the first projects they will fund.
NovusSanguis (literally "new blood") launched this May and seeks to support research that uses both stem cells from umbilical cord blood and adult stem cells. UA College of Medicine professor and BIO5 member David Harris received a grant from the consortium to fund his research into using cord stem cells to regenerate damaged cornea cells. Harris' research is one of about 15 projects that NovusSanguis has initially committed to funding.
Harris has been studying umbilical cord stem cells since the 1990s, and was the first person in the world to "bank" cord blood for later use by families. He is currently scientific director of the Cord Blood Registry.
Stem cells are valuable because they are undifferentiated and can be induced to develop into many different types of specialized cells -- such as muscle cells, red blood cells, or brain cells. That flexibility makes them valuable in treating and developing treatments for a wide range of diseases, from heart disease and diabetes to leukemia and Parkinson's disease. Currently more than 75 diseases are treated with umbilical cord stem cells.
NovusSanguis was created by researchers at England's Newcastle University and France's Fondation Jérôme Lejeune. Two hundred international participants, including Dr. Harris, attended the launch of the consortium, which took place May 14 in Paris.
NovusSanguis (literally "new blood") launched this May and seeks to support research that uses both stem cells from umbilical cord blood and adult stem cells. UA College of Medicine professor and BIO5 member David Harris received a grant from the consortium to fund his research into using cord stem cells to regenerate damaged cornea cells. Harris' research is one of about 15 projects that NovusSanguis has initially committed to funding.
Harris has been studying umbilical cord stem cells since the 1990s, and was the first person in the world to "bank" cord blood for later use by families. He is currently scientific director of the Cord Blood Registry.
Stem cells are valuable because they are undifferentiated and can be induced to develop into many different types of specialized cells -- such as muscle cells, red blood cells, or brain cells. That flexibility makes them valuable in treating and developing treatments for a wide range of diseases, from heart disease and diabetes to leukemia and Parkinson's disease. Currently more than 75 diseases are treated with umbilical cord stem cells.
NovusSanguis was created by researchers at England's Newcastle University and France's Fondation Jérôme Lejeune. Two hundred international participants, including Dr. Harris, attended the launch of the consortium, which took place May 14 in Paris.
Ranking touts ASU's impact in ecology research
[Source: ASUNews] - ASU's research and publication efforts have landed the university at the sixth spot in Thomson Scientific’s U.S. University’s Top 10 for ecology and environmental sciences.
The rankings, developed for 21 subject areas, were derived from an examination of 9,200 publications (from 2001-2005) associated with the Thomson’s University Science Indicators database. The top scores were held by University of California, Santa Barbara; Stanford University; University of Wisconsin, Madison; Harvard University and University of Washington.
"This honor reflects the breadth of ASU in ecology and environmental sciences, spanning microbial to social groups, marine to landscape and urban; and, with recent hires, has become one of the very best in behavioral ecology," says Professor Rob Page, founding director of the School of Life Sciences.
Page believes it is ASU’s signature interdisciplinarity, as well as research excellence in these areas, that led to ASU being ranked. There is plenty of evidence to support this opinion. For example, the School of Life Sciences in the College of Liberal Arts and Sciences has 101 researchers, 250 graduate students, more than 832 publications since 2001, and topped ASU’s charts for research expenditures for academic units in 2007.
Life sciences researchers study a diverse array of subjects and systems, from philosophy of sciences to transmission of disease. While their academic homes are in the School of Life Sciences, many of these scientists are also leaders or collaborators in ASU’s research centers and institutes, including the Global Institute of Sustainability, Biodesign Institute at ASU, Center for Social Dynamics and Complexity, International Institute for Species Exploration, and Center for Biology and Society.
A recent example of the multi-faceted environmental sciences resources being created at ASU is the “ecoSERVICES ASU” group in the College of Liberal Arts and Sciences. Under the leadership of life sciences professors Ann Kinzig and Charles Perrings, this group “studies the causes and consequences of change in ecosystem services – the benefits that people derive from the biophysical environment – and analyzes biodiversity change in terms of its impacts on the things that people care about.” EcoSERVICES ASU hosts Diversitas, an international program that meshes with another international initiative around the science of biodiversity and ecosystem change, the International Mechanism for Scientific Expertise on Biodiversity (IMOSEB), supported by International Council for Science (ICSU) and United Nations Educational, Scientific and Cultural Organization (UNESCO).
The breadth of ASU’s expertise in ecology and environmental sciences creates a big footprint. Big enough to top the charts. It spans the boundaries of schools, centers, and institutes, and collaborative focus, running the gamut from urban to ant studies, environmental engineering, water resources, sustainability, nutrient cycling, and everything fish, fowl, microbial, and ecosystems in between.
Since 1966, ASU researchers have published more than 44,644 total publications; 31,858 articles in peer-reviewed journals, according to the Thomson’s “ISI Web of Knowledge” tool.
Interestingly, the top two highly cited papers at ASU to date are held by Sudhir Kumar, director of the Center for Evolutionary Functional Genomics and professor in the School of Life Sciences, for two publications in molecular evolutionary genetics. Thomson’s database tool is not inclusive of all publications and journals of significance, still it provides an indicator, in these 21 fields, of the impact of an institution’s research enterprise. Some of ISI’s highly cited researchers within the subject category include ASU professors Nancy Grimm, James Collins, James Elser, Jingle Wu, Michael Rosenberg, and Phil Hedrick, for his work in conservation genetics.
This national ranking illustrates the long standing success and impact of our life sciences research enterprise at ASU and arises directly as a result of attracting outstanding faculty in our ecological, evolutionary, and environmental sciences,” says Sid Bacon, dean of natural sciences in the College of Liberal Arts and Sciences.
Margaret Coulombe, margaret.coulombe@asu.edu
480-727-8934
School of Life Sciences
The rankings, developed for 21 subject areas, were derived from an examination of 9,200 publications (from 2001-2005) associated with the Thomson’s University Science Indicators database. The top scores were held by University of California, Santa Barbara; Stanford University; University of Wisconsin, Madison; Harvard University and University of Washington.
"This honor reflects the breadth of ASU in ecology and environmental sciences, spanning microbial to social groups, marine to landscape and urban; and, with recent hires, has become one of the very best in behavioral ecology," says Professor Rob Page, founding director of the School of Life Sciences.
Page believes it is ASU’s signature interdisciplinarity, as well as research excellence in these areas, that led to ASU being ranked. There is plenty of evidence to support this opinion. For example, the School of Life Sciences in the College of Liberal Arts and Sciences has 101 researchers, 250 graduate students, more than 832 publications since 2001, and topped ASU’s charts for research expenditures for academic units in 2007.
Life sciences researchers study a diverse array of subjects and systems, from philosophy of sciences to transmission of disease. While their academic homes are in the School of Life Sciences, many of these scientists are also leaders or collaborators in ASU’s research centers and institutes, including the Global Institute of Sustainability, Biodesign Institute at ASU, Center for Social Dynamics and Complexity, International Institute for Species Exploration, and Center for Biology and Society.
A recent example of the multi-faceted environmental sciences resources being created at ASU is the “ecoSERVICES ASU” group in the College of Liberal Arts and Sciences. Under the leadership of life sciences professors Ann Kinzig and Charles Perrings, this group “studies the causes and consequences of change in ecosystem services – the benefits that people derive from the biophysical environment – and analyzes biodiversity change in terms of its impacts on the things that people care about.” EcoSERVICES ASU hosts Diversitas, an international program that meshes with another international initiative around the science of biodiversity and ecosystem change, the International Mechanism for Scientific Expertise on Biodiversity (IMOSEB), supported by International Council for Science (ICSU) and United Nations Educational, Scientific and Cultural Organization (UNESCO).
The breadth of ASU’s expertise in ecology and environmental sciences creates a big footprint. Big enough to top the charts. It spans the boundaries of schools, centers, and institutes, and collaborative focus, running the gamut from urban to ant studies, environmental engineering, water resources, sustainability, nutrient cycling, and everything fish, fowl, microbial, and ecosystems in between.
Since 1966, ASU researchers have published more than 44,644 total publications; 31,858 articles in peer-reviewed journals, according to the Thomson’s “ISI Web of Knowledge” tool.
Interestingly, the top two highly cited papers at ASU to date are held by Sudhir Kumar, director of the Center for Evolutionary Functional Genomics and professor in the School of Life Sciences, for two publications in molecular evolutionary genetics. Thomson’s database tool is not inclusive of all publications and journals of significance, still it provides an indicator, in these 21 fields, of the impact of an institution’s research enterprise. Some of ISI’s highly cited researchers within the subject category include ASU professors Nancy Grimm, James Collins, James Elser, Jingle Wu, Michael Rosenberg, and Phil Hedrick, for his work in conservation genetics.
This national ranking illustrates the long standing success and impact of our life sciences research enterprise at ASU and arises directly as a result of attracting outstanding faculty in our ecological, evolutionary, and environmental sciences,” says Sid Bacon, dean of natural sciences in the College of Liberal Arts and Sciences.
Margaret Coulombe, margaret.coulombe@asu.edu
480-727-8934
School of Life Sciences
Thursday, May 22, 2008
Arizona lawmakers look to ban human-animal embryos
[Source: Mike Sunnucks ,Phoenix Business Journal] - Two Arizona members of the U.S. House of Representatives want to prohibit the creation of human-animal embryos and the use of the hybrid embryonic mix for medical and scientific research.
U.S. Reps. Rick Renzi and Trent Franks back a federal bill barring human-animal hybrids in the U.S. Renzi has already signed onto the measure and Franks will soon, said Franks spokeswoman Bethany Barker.
Human-animal hybrid embryos involve injecting human DNA into animal eggs, such as rabbits or cows. Scientists can then extract stem cells for research related to human diseases and serious maladies.
The U.S. prohibition comes on the heels of the British Parliament giving preliminary approval to the contentious research method.
Both British Prime Minister Gordon Brown and Conservative opposition leader David Cameron back the U.K. measure allowing for human-animal embryo hybrids to further medical research.
The British plan requires the man-animal embryos to be destroyed within two weeks. Chinese scientists have also conducted such embryonic research. The practice is banned in some other countries.
The Arizona Republican lawmakers back a U.S. ban put forward by U.S. Rep. Chris Smith, R-N.J. The proposed U.S. ban questions the ethics of meshing man and animal in the same embryo.
Renzi represents Flagstaff, Sedona and Casa Grande while Franks represents Glendale, Sun City, Peoria and Kingman.
U.S. Reps. Rick Renzi and Trent Franks back a federal bill barring human-animal hybrids in the U.S. Renzi has already signed onto the measure and Franks will soon, said Franks spokeswoman Bethany Barker.
Human-animal hybrid embryos involve injecting human DNA into animal eggs, such as rabbits or cows. Scientists can then extract stem cells for research related to human diseases and serious maladies.
The U.S. prohibition comes on the heels of the British Parliament giving preliminary approval to the contentious research method.
Both British Prime Minister Gordon Brown and Conservative opposition leader David Cameron back the U.K. measure allowing for human-animal embryo hybrids to further medical research.
The British plan requires the man-animal embryos to be destroyed within two weeks. Chinese scientists have also conducted such embryonic research. The practice is banned in some other countries.
The Arizona Republican lawmakers back a U.S. ban put forward by U.S. Rep. Chris Smith, R-N.J. The proposed U.S. ban questions the ethics of meshing man and animal in the same embryo.
Renzi represents Flagstaff, Sedona and Casa Grande while Franks represents Glendale, Sun City, Peoria and Kingman.
Monday, May 19, 2008
More Universities Hasten Bioinformatics Discoveries Using High-Performance SGI Solutions
[Source: PRNewswire-FirstCall/] - SGIC high-performance compute (HPC) systems have long been a fixture in universities throughout the world, speeding time to discovery across a wide range of disciplines.
SGI shared-memory servers can be found in university research facilities throughout the world, but a new trend is prompting universities to migrate from smaller systems that serve individual departments to larger clusters and shared-memory systems capable of meeting the needs of many departments and disciplines. This trend is saving IT administrators the cost and time of managing multiple small systems, and it offers a new generation of researchers the kind of HPC resources they need to tackle ever-larger bioinformatics problems.
Universities are choosing SGI systems to meet the demanding challenges of bioinformatics for several reasons.
The SGI server architecture offers the ability to scale compute power by adding processors as needed, without a forklift upgrade.
SGI systems meet the need for both shared memory and cluster computing environments to maximize application performance and enhance workflows.
Both shared memory and cluster capabilities can be combined to create a seamless, hybrid environment.
"Over the last several years, a number of universities have begun purchasing larger SGI Altix multiprocessor systems and have added IT departments to manage their use within the central data center," said Deepak Thakkar, Ph.D. higher education and research solutions manager, SGI. "Many researchers and departments then use grant monies and university matching funds to purchase processors on these large systems. Their purchased processors are always there for their needs, and occasionally, depending on the volume from other departments, IT managers can make more processors available to specific projects."
Recent examples of this trend include Michigan State University, Universite de Montreal, and the University of Arizona, all which are using SGI Altix systems for cutting edge bioinformatics research.
Michigan State University -- Gene Mutation Research
Michigan State University (MSU) has used an SGI(R) Altix(R) XE1300 cluster with 1,024 cores since September 2007. Evolutionary biologist Barry Williams, assistant professor, Zoology and Microbiology and Molecular Genomics, purchased 16 cores of the SGI Altix XE system to identify which forces of nature, such as natural selection or changes in population size, cause changes in DNA to accumulate over time, as well as those forces that prevent new mutations that arise in natural populations. When Williams sees mutations that seem to have some effect on genotype, he makes those mutations in many different strains of yeasts, and puts them in different environments to verify their potential effects. Williams works primarily with easily manipulated single-cell yeast microbes.
While he has done work on the university's existing SGI(R) Altix(R) 3700 HPC system at MSU, installed some two years ago, Williams considers the number of projects he can run in parallel on the new SGI Altix XE cluster as a boon to his research.
"It's not unusual for one analysis running on one processor to take several days to a week. We have 6,000 genes that make up the yeast genome that we want to analyze, and each one can take a day. Without the Altix cluster this just becomes impossible," said Williams, who also conducts artificial life research on the SGI system. "The artificial life evolves autonomous computer programs in silico -- we do this to make general predictions about the evolutionary process that we can next test in the yeasts. The beauty of artificial life research is that you can repeat the experiment of evolution with the exact same starting conditions and let evolution take place again and again. I have 16 processors on the systems, so at any one time I can run 16 completely different worlds in parallel. They all start at the same point; they all have the same genetic diversity; they all start with the same individuals and the same conditions, but simultaneously, 16 times, I can let them evolve for millions upon millions of generations."
Many other MSU departments including Nuclear Physics, Mathematics and Chemistry will also be harnessing the power of the SGI system (see separate release, April 29, 2008).
Universite de Montreal -- World's Largest Heart Simulation Model with 2 Billion Elements
In the quest to discover how the mechanisms of heart disease work, researchers at the Universite de Montreal (UdM) ran the largest mathematical simulation of a heart ever assembled -- a 2 billion element model -- on a high-performance SGI(R) Altix(R) 4700 system with 1.2TB of memory. (See separate release January 15, 2008) The SGI Altix is believed to be the largest shared memory computing system in Canada
Until recently, the largest heart models in the world had at most a few million elements.
Dr. Mark Potse and Dr Alain Vinet, both affiliated with the Research Center of Sacre-Coeur Hospital and the Biomedical Engineering department at UdM, began running 100 to 120 million-point models as part of their heart disease research. Potse and Vinet regularly use 60 of the 768 Intel(R) Itanium(R) 2 processors running on the SGI Altix which, as part of the Quebec Network for High-Performance Computing (RQCHP), is shared by many researchers from across Canada since it's unveiling in February 2007.
In October last year, Potse and Vinet had the opportunity to run their custom electrocardiography (ECG) code using the entire SGI Altix system with all 786 processors and all 1.2TB of shared memory. Originally written by them on an earlier SGI system and ported to the SGI Altix system's Linux(R) environment in 2003, the ECG code made the leap from 120 million points to 2 billion with ease.
"This was a test to see if the simulation works and to determine that, if we have a much bigger machine, our software will be able to run more efficiently," said Potse. "This capability is really for the future when we can use this size of machine on a regular basis, but with the Altix system we have made the heart model of the future today."
The new UdM model is up to 1,000 times more detailed than previous models, enabling new scientific discoveries that would never be possible via observation alone.
University of Arizona -- Maize Sequencing Research
The University Information Technology Services (UITS) at the University of Arizona (UA)) purchased two SGI Altix 4700 systems with a total of 1.2TB of memory over a year ago. Instead of departments purchasing processors before installation, the UA allows professors and researchers to add processors to the scalable SGI compute environment. The systems are a university-wide resource available to any department in need of HPC, which includes a number of ongoing and new bioinformatics projects.
Research Professor Cari Soderlund heads the Arizona Genomics Computational Laboratory (AGCoL) that is currently working on the computational aspects of sequencing 30,000 genes for maize. In order to determine the sequence of genes, subsequences of about 800 base pairs (bp) are generated. To reconstruct the original gene sequence, the sub sequences are analyzed to determine the overlapping sub-sequences. For the 700,000 sequences, the global shared memory of the SGI Altix system will accelerate data generation and analysis.
"As our lab is often processing large datasets, the speedup from the SGI Altix system should increase the turn-around time between the generation of biological data and computational analysis," said Soderlund, who recently began porting her project to the SGI Altix system. "It would also allow for more experimentation of parameters and algorithms for larger datasets."
"The Altix 4700 has been our workhorse for the past year and is used by researchers throughout campus, including life sciences," said Dr. Michael Bruck, Assistant Director of Research Computing at the UA's UITS, which coordinates central research computer resources on campus. "The Altix is meeting and exceeding our expectations."
SGI Altix systems empower research at many prestigious universities, including UC Riverside, Purdue University, Stony Brook University, University of Utah, Technische Universitat Dresden (TU Dresden), University of Sao Paulo and U.S. Air Force Academy.
"With many universities deploying both shared memory systems and clusters such as the SGI Altix servers and Altix XE clusters, we are now seeing jobs scheduled based upon the architecture that best suits their computing needs-an entirely seamless process for the researchers," added Thakkar. "SGI systems are being rapidly adopted not only for bioinformatics, but for all disciplines ranging from astronomy to zoology."
The fresh fish myth: fish farming in the desert
[Source: Ashli Woods, Inside Tucson Business] - Kevin Fitzsimmons’ passion for aquaculture is evident, right down to the blue fish swimming on his tan collared dress shirt.
The University of Arizona professor has devoted his career to correcting what he believes is a stigma placed on fish farms based on misconceptions that have been amplified by environmental groups.
"We can no more feed the world by hunting and gathering fish out of the ocean than we can by hunting and gathering on land. I mean if we were all out there hunting deer and buffalo we’d be in pretty bad shape," he said laughing at the notion.
Fish farming and aquaculture, the method of harvesting fish in farms for commercial sale, is quickly taking over the seafood market and replacing commercial fishermen. Though it has been practiced in Asia for hundreds of year, American aquaculturists have struggled to convince environmentalists, health experts, and the general public that farmed fish is equal in quality and health to wild fish.
Arizona alone is home to more than 30 fish farms that produce an average of 500,000 pounds of fish a year, according to the Arizona Aquaculture Association. Arizonan fish farms produce mainly catfish, tilapia and trout.
The United Nations Food and Agriculture Organization (UNFAO) estimates last year nearly 50 percent of fish consumed in the world was farm-raised, with the amount increasing each year.
Certain demographic trends have led to soaring numbers of seafood consumption in the United States in recent years, most importantly numerous studies suggesting the health benefits of fish. Fish are high in protein, low in fat, and full of Omega-3 fatty acids as well as polyunsaturated fatty acids, making them a staple in a diet-crazed society.
In an attempt to maximize the health benefits, consumers have been wary of farmed fish which many believe are inferior to wild fish.
Fitzsimmons explains: "Quality-wise there is very little difference. If anything the farmed fish typically is better quality because you schedule the harvest, you schedule the processing, you can have trucks there with ice, it’s much better. If you go take the fish out of a cage or a pond or a tank and take it right to the processing plant, that’s going to be better than someone who’s going to drag it under water for a couple of hours dead, bring it up on the boat then take it to shore and process it. I mean it’s several days old. You’re calling it fresh and it’s been dead for a long time."
He adds that although farmed fish have been shown to have less Omega-3s than wild fish, it is still the second-highest source. Farmers have improved the feed given to the fish to add more of the fatty acids, but increasing them more would further increase the cost by around 3 percent, an increase farmers try to avoid.
"All fish is healthy," Victor Banda, fishmonger at the 17th Street Market, said while showing off his selection of fish, a good portion of which is imported from fish farms from out of state. Dressed head to toe in a fisherman’s gray rubber gear and bathed in fishy cologne, he explains that even wild fish can contain pollutants depending on which waters they are taken from.
Not all fish sold at the 17th Street Market, or other markets around town, are brought in from the ocean by fishermen. In fact, at Banda’s market there is nearly the same amount of farmed fish as there are wild. You can’t beat the cost of farmed fish, Banda explains.
Rincon Market customers Eugenia Bas-Isaac and her husband Raymond Latchman buy their fish from fishmonger Yuri Rabayev, and don’t mind paying extra to buy fresh caught salmon.
"Farmed fish is yuck," she said while scrunching up her face like a child refusing to take cough medicine. "You can really taste the difference and it’s so much better for you."
However Rabayev believes "farming preserves the wild fish," and there is little difference in taste and quality.
Farming continues to be, in Fitzsimmon’s opinion, the only realistic and financially sustainable way to meet the increasing consumer need. UNFAO also estimates that an additional 40 tons of seafood will be needed by 2030 to meet consumer demand. This has the potential to be terribly detrimental to ocean life if farming is not implemented, Fitzsimmons said.
For Arizonan fish farmers, using the amount of water needed for farming would not be practical. However the idea is to combine two industries – aquaculture and agriculture – to increase profitability. In the desert especially, water is an expensive commodity making fish farming impractical. However, if fish farmers team-up to share water used for crop farming, both can increase profit.
Commercial fishing as an occupation is quickly being replaced by fish farms and fishing is becoming a sport rather than occupation. According to the American Sportsfishing Association, the sport of fishing created 14,729 jobs in Arizona in 2006 and brought $849,711,854 to the state in retail sales. The sport has taken over as a more lucrative business than the occupation.
"If you’re looking purely at the economics," Fitzsimmons said, "the sportsman will pay more to catch fish for entertainment than the commercial boat ever would."
Safe and cost-effective fish farms are replacing commercial fisheries. High costs to insure fishing boats and the fishermen they carry, coupled with high fuel costs and increased real estate on coast-line-producing high dock fees have left fishing companies unable to compete with fish farms.
"I feel bad for the shrimp guy in Louisiana who can’t go out and catch shrimp now in the morning and come back to the dock in New Orleans and sell them cheaper than some guy can go to Ecuador, build a farm, hatch out all the larvae, feed them for four months, process them and fly them to New Orleans," Fitzsimmons said. "If he can put them there cheaper than a fisherman can go out and catch them, then obviously there is something wrong with the economic model of fishing. You feel sad for them."
He added: "I had a grandfather who had a trunk company who sold trunks to cars and then they started building the trunks in the cars so he went out of business. Granted fish farming is no where near as romantic as going out to sea like these guys, but I guess that’s progress."
The University of Arizona professor has devoted his career to correcting what he believes is a stigma placed on fish farms based on misconceptions that have been amplified by environmental groups.
"We can no more feed the world by hunting and gathering fish out of the ocean than we can by hunting and gathering on land. I mean if we were all out there hunting deer and buffalo we’d be in pretty bad shape," he said laughing at the notion.
Fish farming and aquaculture, the method of harvesting fish in farms for commercial sale, is quickly taking over the seafood market and replacing commercial fishermen. Though it has been practiced in Asia for hundreds of year, American aquaculturists have struggled to convince environmentalists, health experts, and the general public that farmed fish is equal in quality and health to wild fish.
Arizona alone is home to more than 30 fish farms that produce an average of 500,000 pounds of fish a year, according to the Arizona Aquaculture Association. Arizonan fish farms produce mainly catfish, tilapia and trout.
The United Nations Food and Agriculture Organization (UNFAO) estimates last year nearly 50 percent of fish consumed in the world was farm-raised, with the amount increasing each year.
Certain demographic trends have led to soaring numbers of seafood consumption in the United States in recent years, most importantly numerous studies suggesting the health benefits of fish. Fish are high in protein, low in fat, and full of Omega-3 fatty acids as well as polyunsaturated fatty acids, making them a staple in a diet-crazed society.
In an attempt to maximize the health benefits, consumers have been wary of farmed fish which many believe are inferior to wild fish.
Fitzsimmons explains: "Quality-wise there is very little difference. If anything the farmed fish typically is better quality because you schedule the harvest, you schedule the processing, you can have trucks there with ice, it’s much better. If you go take the fish out of a cage or a pond or a tank and take it right to the processing plant, that’s going to be better than someone who’s going to drag it under water for a couple of hours dead, bring it up on the boat then take it to shore and process it. I mean it’s several days old. You’re calling it fresh and it’s been dead for a long time."
He adds that although farmed fish have been shown to have less Omega-3s than wild fish, it is still the second-highest source. Farmers have improved the feed given to the fish to add more of the fatty acids, but increasing them more would further increase the cost by around 3 percent, an increase farmers try to avoid.
"All fish is healthy," Victor Banda, fishmonger at the 17th Street Market, said while showing off his selection of fish, a good portion of which is imported from fish farms from out of state. Dressed head to toe in a fisherman’s gray rubber gear and bathed in fishy cologne, he explains that even wild fish can contain pollutants depending on which waters they are taken from.
Not all fish sold at the 17th Street Market, or other markets around town, are brought in from the ocean by fishermen. In fact, at Banda’s market there is nearly the same amount of farmed fish as there are wild. You can’t beat the cost of farmed fish, Banda explains.
Rincon Market customers Eugenia Bas-Isaac and her husband Raymond Latchman buy their fish from fishmonger Yuri Rabayev, and don’t mind paying extra to buy fresh caught salmon.
"Farmed fish is yuck," she said while scrunching up her face like a child refusing to take cough medicine. "You can really taste the difference and it’s so much better for you."
However Rabayev believes "farming preserves the wild fish," and there is little difference in taste and quality.
Farming continues to be, in Fitzsimmon’s opinion, the only realistic and financially sustainable way to meet the increasing consumer need. UNFAO also estimates that an additional 40 tons of seafood will be needed by 2030 to meet consumer demand. This has the potential to be terribly detrimental to ocean life if farming is not implemented, Fitzsimmons said.
For Arizonan fish farmers, using the amount of water needed for farming would not be practical. However the idea is to combine two industries – aquaculture and agriculture – to increase profitability. In the desert especially, water is an expensive commodity making fish farming impractical. However, if fish farmers team-up to share water used for crop farming, both can increase profit.
Commercial fishing as an occupation is quickly being replaced by fish farms and fishing is becoming a sport rather than occupation. According to the American Sportsfishing Association, the sport of fishing created 14,729 jobs in Arizona in 2006 and brought $849,711,854 to the state in retail sales. The sport has taken over as a more lucrative business than the occupation.
"If you’re looking purely at the economics," Fitzsimmons said, "the sportsman will pay more to catch fish for entertainment than the commercial boat ever would."
Safe and cost-effective fish farms are replacing commercial fisheries. High costs to insure fishing boats and the fishermen they carry, coupled with high fuel costs and increased real estate on coast-line-producing high dock fees have left fishing companies unable to compete with fish farms.
"I feel bad for the shrimp guy in Louisiana who can’t go out and catch shrimp now in the morning and come back to the dock in New Orleans and sell them cheaper than some guy can go to Ecuador, build a farm, hatch out all the larvae, feed them for four months, process them and fly them to New Orleans," Fitzsimmons said. "If he can put them there cheaper than a fisherman can go out and catch them, then obviously there is something wrong with the economic model of fishing. You feel sad for them."
He added: "I had a grandfather who had a trunk company who sold trunks to cars and then they started building the trunks in the cars so he went out of business. Granted fish farming is no where near as romantic as going out to sea like these guys, but I guess that’s progress."
UA Researchers Create a Leaner, Greener Computer Cluster
[Source: University of Arizona Communications] - A shared computer cluster at The University of Arizona is significantly reducing both the environmental impact and the energy costs of campus computing.
The computer cluster is cooled by chilled water instead of air conditioning. As a result the data center at the UA's University Information Technology Services, known as UITS, has been able to reduce its continuous air conditioning systems use from 50 tons to 30 tons – a 40 percent savings in air conditioning use, and one that also will extend the life of the air conditioning units in the data center.
A computer cluster isn't all that different from a desktop machine. It’s essentially a number of computers, often linked by local area networks, that work together as a more powerful single computer. Computer clusters already help run many University projects, and much of research in general.
The UA’s new computer cluster is shared by Arizona Research Labs, the BIO5 Institute, the ecology and evolutionary biology department and the astronomy department. It also allows the participating departments and programs to conserve resources by letting them "borrow" computing power from other departments and programs using the cluster during high-use times.
"We're sharing the computing power, so we can use it more efficiently," explains Nirav Merchant, director of biotechnology computing for Arizona Research Labs and a member of BIO5.
Traditionally each department or program would need enough power to cover its own high-volume times, even though at other times that power would go unused. Essentially, the researchers are taking advantage of one another's downtime. Merchant describes the arrangement as being akin to a sort of "computer condo" inhabited by the departments and programs. "There are parts of the condo residents have access to that are entirely their own, but there are also community resources everyone can benefit from," Merchant said.
Pooling resources and reducing the environmental impact of computing is crucial in an era where the amount of data to be analyzed increases daily – and where what researchers hope to learn from that data grows more complicated. "We're very conscious of the green aspect of computing," Merchant says, "especially as everything becomes bigger and faster and more complex."
A Child, a Bizarre Tumor and a Perilous Operation
[Source: KERIDWEN CORNELIUS, NYTimes.com] - Three-year-old Grace Webster perches on the operating table, tiny and cold, covered only by a diaper and her sandy-blond Raggedy Ann hair. Her blue eyes gaze warily at the monster-size machines sprouting tube tentacles that encircle her — machines that will guide surgeons four inches into her brain.
Grace had her first menstrual period at 14 months old. Her body is racked more than 10 times a day with seizures, some of them bizarrely mimicking laughter or rage.
The source of her suffering is a hypothalamic hamartoma, or H.H., a tumor on the hypothalamus that strikes only a few thousand people in the world. And while the tumor is not malignant, until five years ago it was considered incurable, even when baffled doctors could diagnose it. Surgery was risky and largely ineffective. Medication seldom helped. Many children were institutionalized.
Now, thanks to an innovative surgical procedure, scores of these children have been cured at two centers that specialize in the disease. One is in Melbourne, Australia; the other is the Barrow Neurological Institute here in Phoenix.
It is 8 a.m. on April 20, 2007, and on the operating table at Barrow a nurse and a neuroanesthesiologist are trying to coax the anesthesia mask onto Grace’s mouth.
She is having none of it. Her face turns bright pink and crinkles into a wail. One arm clutches her plush puppy; the other stretches toward the door as she calls for her mother, Erica.
Finally the mask is in place, and Grace’s belly billows rhythmically as the anesthesiologist pumps the vapors into her body. The nurses insert tubes into her mouth, arm, toes, back and urethra. (Now it is Grace who is sprouting tentacles.)
She is wheeled into the adjoining room to undergo a specialized M.R.I. It produces a high-definition image integrated with a tracking system that will guide the surgeons to the tumor. The doctors will take images of Grace’s brain throughout the surgery, pinpointing the location of structures. The scans will also reveal the exact size of the tumor.
“It’s a big, nasty one,” says the anesthesiologist, Dr. Steven Shedd. At 3.23 centimeters across, it is about the size of a Ping-Pong ball. It bulges out from the hypothalamus and fills much of the neighboring cavity.
The hypothalamus is one of the brain’s jacks of all trades. It maintains the body’s status quo, regulating temperature, blood pressure, fluid balance and digestion. It also controls appetite, aggression and embarrassment, accounting for the strange cluster of hamartoma symptoms.
When Grace had her first menstrual period, her mother rushed her to the pediatrician. Tests revealed that Grace’s reproductive organs had reached the developmental stage of a 12-year-old. She was given a diagnosis of hypothalamic hamartoma four days later. Soon, the Websters were told, Grace would experience “gelastic,” or laughing, seizures.
The seizures begin with a wide, crooked smile, like a string attached to her eye and the corner of her mouth has been tugged slightly. “That’s not her smile,” said Erica Webster, a business analyst, showing a home video of her daughter. Grace’s stare is unfocused, her giggle jerky and her breathing convulsed. Still, to the untrained eye, it looks like an adorable quirk, not the fingerprint of a massive tumor.
Between the ages of 4 and 10 — or earlier in severe cases like Grace’s — the character of the seizures morphs from Jekyll to Hyde. Fits of laughter become bursts of room-demolishing rage and intense, paralyzing fits.
“It’s like turning on a light switch and having somebody take over your child’s body,” Mrs. Webster said of the rage seizures. The first time, Grace was coloring contentedly, when — flick — she was screaming and hitting wildly. When her parents blocked her from smacking the furniture, she turned on herself, scratching her face and biting her arms.
Eventually, cognitive development goes from steady to sluggish to stagnant. The children often exhibit autism and social maladjustment. The personality that shone between seizures dims and disappears.
Faced with this dismal future, many parents like Erica and Perry Webster risk surgery to give their child a normal life. Mr. Webster, a civil designer, said they were reassured that “other H.H. kids have undergone the procedure and thrived.” But it will be a long day in the waiting room.
Back in the operating room, the mood is upbeat. Rock music is playing. The surgeon, Dr. Harold L. Rekate, a grandfatherly presence with kind eyes, is shaving Grace’s hair. There are nine doctors and nurses in the room, sheathing Grace with a linen closet’s worth of sterile blankets. By the time they’re finished, she is a mound of blue with nothing but a patch of scalp peeking through.
The first neurosurgeon to tackle the tumor is Dr. Scott D. Wait, youngish and TV-medical-drama handsome. “This is such a big tumor,” he says, “that for cases like these we bring in multiple surgeons.” Today, there will be three.
Dr. Wait slices into the scalp and peels back the skin to expose the skull. Before he drills, he touches the bone with a wand, a skewerlike navigational device that takes pictures of the brain. The squeal of the drill drowns out the music, which has taken a turn toward the elevatorish.
It’s 11:22. Dr. Wait maneuvers into a surgical chair and presses his face into a giant microscope. The magnified image pops up on a TV screen on the wall. A scalpel and tiny scissors move into view, gently slicing and clipping away the brain’s outer membranes. Underneath, purple veins rope and red arteries spider web around the flesh-colored convolutions of the brain.
11:55. The music is silenced. Dr. Wait delves slowly into the cleft between the two hemispheres, slicing through the corpus callosum — the bridge connecting them — into a membrane called the septum pallucidum.
Surgically, this is a road less traveled. In the past, surgeons took the shorter path from the underside of the brain, with little success. Many parents were told there was no hope.
Two of those parents were Lisa and Jon Soeby of Phoenix, whose 4-year-old son, CJ, had as many as 300 seizures a day. The Soebys discovered that an Australian neurosurgeon, Dr. Jeffrey Rosenfeld, had pioneered a different surgical route: he approached the hamartoma from the top, diving between the hemispheres so they separated like two halves of a book. At the book’s binding lay the tumor.
Since the doctors at Barrow would not perform the novel procedure, the Soebys flew to Melbourne. It was a success, and in 2003, Dr. Rosenfeld traveled to CJ’s hometown to teach his “transcallosal” approach to the neurosurgeons here. They now specialize in it, receiving hamartoma patients from around the world. Grace Webster, from Anderson, Calif., is patient No. 101.
12:20. Dr. Wait is navigating Grace’s third ventricle, a tiny basin of cerebrospinal fluid. There in the fluid convulses a pink, fatlike mass: the tumor.
Dr. Wait and Dr. Rekate consult the M.R.I. scans on the monitor. Green lines converge in a bull’s-eye on the hamartoma. Dr. Wait digs into the tumor, which bleeds; the suction tip wails and vacuums the blood.
“Let me play for a little while,” says Dr. Rekate, switching seats with Dr. Wait. He wields an ultrasonic surgical aspirator, an instrument that vibrates at 23,000 revolutions a second, simultaneously emulsifying, irrigating and sucking up the tumor.
1:26 p.m. A man strides in wearing a surgical cap with a piano-key pattern: Dr. Robert Spetzler, the director of the Barrow institute.
Dr. Rekate surrenders the chair. Dr. Spetzler, sinewy and intense, probes at the tumor with the aspirator. Twenty minutes creep by.
Dr. Rekate gasps. “Is that the basilar artery?”
It is the equivalent of a land mine, the main blood supplier to the back of the brain. As Dr. Spetzler swipes the aspirator around the vessel, he murmurs something like “I feel very uncomfortable here.”
Puddles of bloody fluid flood the cavity, but only from minuscule arteries. The topography of the heart monitor and vitals signs remains reassuringly mountainous.
Dr. Spetzler attacks the seemingly unending tumor from all sides. The tissues begin to look deceptively similar.
“This is where I trust what the wand is seeing,” Dr. Rekate says, “because it’s not so obvious inside.”
2:17. Dr. Spetzler rises. “I don’t think there’s any more,” he says. He exits unceremoniously, with a “Thank you” from Dr. Rekate.
When the door shuts, Dr. Wait shakes his head. “Holy cow,” he says, about Dr. Spetzler’s decision to run the aspirator over the basilar artery. “I don’t think I’ll ever do that.”
Dr. Wait begins to close Grace up and prepare her for another M.R.I. Dr. Rekate leaves. The rock music returns.
At 5 p.m., the results are revealed. “Wow, we got all of that thing out,” Dr. Wait says. But he adds, “I can’t guarantee she’ll never have another seizure.”
Once removed, a hypothalamic hamartoma will not grow back. But Grace’s fate remains to be seen. At Barrow, 90 percent of hamartoma patients emerge from transcallosal surgery with at least 90 percent fewer seizures, Dr. Rekate says, and 60 percent of those are seizure-free. Ten percent are not helped at all. Two patients have died.
The transcallosal approach is an old approach for tumors of the ventricle, but it is new for H.H., said Dr. George Jallo, a pediatric neurosurgeon at Johns Hopkins Hospital in Baltimore.
“The doctors at Barrow have refined the technique, and they’ve had great success,” Dr. Jallo said. But he added: “The verdict is still out. We need many more years following these children to see what the long-term effects are.”
A year after the operation, Grace still suffers from a form of diabetes and low thyroid function, but these conditions are improving. Thanks to physical and speech therapy, she is catching up in her development, growing more active and sociable.
She must continue to get Lupron injections every 28 days until she is 11, to stave off the precocious puberty. But most important, she no longer experiences the seizures that convulsed her with seeming rage or laughter.
Now when Grace laughs, it is not the tumor, but the lyrical giggle of a sassy, seizure-free 4-year-old.
Some experts see fatty microbes as ideal power source
[Source: Ryan Randazzo, The Arizona Republic] - The lowly cyanobacterium isn't much to look at, but the simple life form thought to have originally created the oxygen in Earth's atmosphere could be on the verge of making another dramatic impact on the planet: transforming the oil business.
Arizona State University researchers are exploring how one of Earth's smallest organisms may supplant its largest industry by growing bacteria to make diesel-engine fuel.
Energy company BP and Science Foundation Arizona partnered for the project.
Researchers are building "photobioreactors" to grow the bacteria, hoping to prove that the bacteria can be raised on a commercial scale, said Bruce Rittmann, director of the Center for Environmental Biotechnology at the ASU Biodesign Institute.
Bacteria have an advantage over other "biofuels" such as corn ethanol and soybean biodiesel, he said.
Not only do the bacteria contain a higher concentration of fats that can be burned for energy, but they grow faster than crops and can be continuously harvested.
"We have one (strain) with a high lipid content, and by promoting the right conditions, it can thrive and grow very fast," Rittmann said.
Instead of needing fertilizer, which is costly and requires energy to produce, researchers hope to feed the bacteria the carbon dioxide released from electric power plants.
That is an increasingly popular idea in the energy industry, where carbon-dioxide emissions are getting increased scrutiny for their contribution to global climate change.
Arizona Public Service Co. already has had some success "feeding" the carbon dioxide from a natural-gas power plant to algae for biodiesel, and plans to test at a coal-fired plant.
Researchers around the globe are investigating both bacteria and algae because they have high energy potential, require little space to grow and can thrive in marginal water.
The bacteria being tested at ASU are similar to the algae tested by researchers at APS and elsewhere because they both use photosynthesis to convert sunlight to energy, but Rittmann said the bacteria have advantages over algae.
"Algae and bacteria both accumulate a lot of lipids, but they do so for different reasons," he said. "When bacteria accumulate a lot of lipids, they do it when they are growing fast. That is ideal. Algae do the opposite, and produce high lipids when under stress, and are not growing very well."
Other Arizona projects are focusing on algae, including:
• XL Renewables Inc., which has a Casa Grande development center where officials hope to open a 40-acre algae production site in November. The company also offers algae-growing systems for sale.
• Scottsdale-based PetroSun Inc., a gas- and oil-drilling company, announced in February that it formed a joint venture with Gilbert-based Optimum Biofuels to build an algae biorefinery near Coolidge. PetroSun, a publicly traded penny stock, also has announced plans to open similar plants in Louisiana, Texas, Mexico and Central America.
• Amereco Biofuels Corp., which has a small biodiesel project in the far West Valley using recycled restaurant cooking oil, is researching various strains of algae for biodiesel.
Researchers close in on new melanoma gene
[Source: TGen] - Genome-wide study rapidly scans DNA for clues, narrows search
It has long been known that prolonged exposure to the suns harmful UV rays can lead to Melanoma, the deadliest form of skin cancer. An unanswered question, however, is why some people are more likely to develop melanoma than others. Despite years of research and clinical development, melanoma incidences continue to rise around the world. According to the National Cancer Institute, the percentage of people in the United States who develop melanoma each year has more than doubled in the past 30 years.
Results published today from a study led by researchers from The Translational Genomic Research Institute (TGen) in Phoenix, Arizona and The Queensland Institute of Medical Research (QIMR), Queensland, Australia, however, may yet change these statistics. The team is close to discovering a new gene that could help explain variation in melanoma risk.
In a report appearing in an Advance Online Publication (AOP) of the journal Nature Genetics, the researchers and their colleagues identify a region on chromosome 20 (20q11.22) that influences a person’s risk of developing melanoma.
According to Dr Kevin Brown, TGen Investigator and the paper's co-first author, compared to other genetic research focusing on familial (or inherited) cases of melanoma, this finding holds implications for the general population
"We're closing in on genetic variants which cause 16 percent of the population to be at nearly double the increased risk of developing the disease. In public health terms, this finding is highly significant," Dr. Brown said.
The researchers narrowed the gene location through a genome-wide association study - a first in melanoma research. Genome-wide studies involve rapidly scanning DNA of many people to find genetic variations associated with a particular disease. After identifying new genetic associations, researchers can use the information to develop better strategies to detect, treat and prevent the disease.
"The aim of our work is to identify and understand the genetic factors influencing melanoma so we can better predict risk estimates," said QIMR's Dr. Stuart MacGregor, co-first author on the study. "This in turn, means people will be better informed and can take the right precautions to avoid developing this increasingly common cancer."
How The Study Works
A genome-wide association study involves scanning the DNA from two sets of individuals: those with a particular disease (cases) and those of similar individuals without the disease (controls). The DNA of each sample then undergoes examination for strategically selected markers of genetic variation, called single nucleotide polymorphisms, or SNPs. If certain genetic variations are found to be significantly more frequent in people with the disease compared to people without disease, those variations are said to be "associated" with the disease. The associated genetic variations can serve as roadmaps to the region of the human genome where the disease-causing gene resides.
The study - whose data collection began 20 years ago - involved more than 4,000 Australian samples (2,019 cases and 2,105 controls) and was a joint project between Australian, American and European research groups.
About Melanoma
According to the National Cancer Institute's on-line booklet, What You Need to Know About Melanoma, melanoma is a form of cancer that begins in melanocytes (cells that make the pigment melanin). It may begin in a mole (skin melanoma), but can also begin in other pigmented tissues, such as in the eye or in the intestines.
Melanoma is the most serious type of cancer of the skin. Each year in the United States, more than 64,800 people learn they have melanoma and approximately 8,400 will die from the disease. The disease is particularly prevalent in the Southwest, particularly Arizona, where the incidence rate is double the national average and is becoming more common every year.
Funding
Funding for Dr. Browns lab was provided by Melanoma Research Foundation (MRF) Research Grant Program, whose purpose is to support promising medical research that will further the goal of developing an effective treatment and possible cure of malignant melanoma, while encouraging scientists and clinicians to join in this mission. The Foundation funds both junior and senior researchers. In both grant programs, emphasis will be placed on projects that explore innovative approaches to understanding melanoma and its treatment. Both basic and clinical research projects will be considered.
"Each year, we receive grant requests from some of the best and brightest melanoma researchers in the world," said Linda Pilkington, Executive Director, Melanoma Research Foundation. "The research conducted by scientists like Dr. Brown gives melanoma patients the hope they need and deserve - hopefully one day leading to a cure for this deadly disease."
About the Melanoma Research Foundation
The Melanoma Research Foundation (MRF) is the largest private, national organization devoted to melanoma in the United States. The Foundation is committed to the support of medical research in finding effective treatments and eventually a cure for melanoma. The Foundation also educates patients and physicians about prevention, diagnosis and treatment of melanoma, while acting as an advocate for the melanoma community to raise awareness of this disease and the need for a cure. The MRF Web site is the premiere source for melanoma information seekers. More information is available at www.melanoma.org.
Media Contacts:
TGen
Galen Perry
Phone: (602) 343-8423
E-mail: gperry@tgen.org
QIMR
Felipe Beltran, QIMR Media Relations Officer
Phone: (07) 3362 0291
E-mail: Felipe.Beltran@qimr.edu.au
MRF
Heather R. Huhman
Phone: (202) 742-5259
E-mail: Heather@JonesPA.com
It has long been known that prolonged exposure to the suns harmful UV rays can lead to Melanoma, the deadliest form of skin cancer. An unanswered question, however, is why some people are more likely to develop melanoma than others. Despite years of research and clinical development, melanoma incidences continue to rise around the world. According to the National Cancer Institute, the percentage of people in the United States who develop melanoma each year has more than doubled in the past 30 years.
Results published today from a study led by researchers from The Translational Genomic Research Institute (TGen) in Phoenix, Arizona and The Queensland Institute of Medical Research (QIMR), Queensland, Australia, however, may yet change these statistics. The team is close to discovering a new gene that could help explain variation in melanoma risk.
In a report appearing in an Advance Online Publication (AOP) of the journal Nature Genetics, the researchers and their colleagues identify a region on chromosome 20 (20q11.22) that influences a person’s risk of developing melanoma.
According to Dr Kevin Brown, TGen Investigator and the paper's co-first author, compared to other genetic research focusing on familial (or inherited) cases of melanoma, this finding holds implications for the general population
"We're closing in on genetic variants which cause 16 percent of the population to be at nearly double the increased risk of developing the disease. In public health terms, this finding is highly significant," Dr. Brown said.
The researchers narrowed the gene location through a genome-wide association study - a first in melanoma research. Genome-wide studies involve rapidly scanning DNA of many people to find genetic variations associated with a particular disease. After identifying new genetic associations, researchers can use the information to develop better strategies to detect, treat and prevent the disease.
"The aim of our work is to identify and understand the genetic factors influencing melanoma so we can better predict risk estimates," said QIMR's Dr. Stuart MacGregor, co-first author on the study. "This in turn, means people will be better informed and can take the right precautions to avoid developing this increasingly common cancer."
How The Study Works
A genome-wide association study involves scanning the DNA from two sets of individuals: those with a particular disease (cases) and those of similar individuals without the disease (controls). The DNA of each sample then undergoes examination for strategically selected markers of genetic variation, called single nucleotide polymorphisms, or SNPs. If certain genetic variations are found to be significantly more frequent in people with the disease compared to people without disease, those variations are said to be "associated" with the disease. The associated genetic variations can serve as roadmaps to the region of the human genome where the disease-causing gene resides.
The study - whose data collection began 20 years ago - involved more than 4,000 Australian samples (2,019 cases and 2,105 controls) and was a joint project between Australian, American and European research groups.
About Melanoma
According to the National Cancer Institute's on-line booklet, What You Need to Know About Melanoma, melanoma is a form of cancer that begins in melanocytes (cells that make the pigment melanin). It may begin in a mole (skin melanoma), but can also begin in other pigmented tissues, such as in the eye or in the intestines.
Melanoma is the most serious type of cancer of the skin. Each year in the United States, more than 64,800 people learn they have melanoma and approximately 8,400 will die from the disease. The disease is particularly prevalent in the Southwest, particularly Arizona, where the incidence rate is double the national average and is becoming more common every year.
Funding
Funding for Dr. Browns lab was provided by Melanoma Research Foundation (MRF) Research Grant Program, whose purpose is to support promising medical research that will further the goal of developing an effective treatment and possible cure of malignant melanoma, while encouraging scientists and clinicians to join in this mission. The Foundation funds both junior and senior researchers. In both grant programs, emphasis will be placed on projects that explore innovative approaches to understanding melanoma and its treatment. Both basic and clinical research projects will be considered.
"Each year, we receive grant requests from some of the best and brightest melanoma researchers in the world," said Linda Pilkington, Executive Director, Melanoma Research Foundation. "The research conducted by scientists like Dr. Brown gives melanoma patients the hope they need and deserve - hopefully one day leading to a cure for this deadly disease."
About the Melanoma Research Foundation
The Melanoma Research Foundation (MRF) is the largest private, national organization devoted to melanoma in the United States. The Foundation is committed to the support of medical research in finding effective treatments and eventually a cure for melanoma. The Foundation also educates patients and physicians about prevention, diagnosis and treatment of melanoma, while acting as an advocate for the melanoma community to raise awareness of this disease and the need for a cure. The MRF Web site is the premiere source for melanoma information seekers. More information is available at www.melanoma.org.
Media Contacts:
TGen
Galen Perry
Phone: (602) 343-8423
E-mail: gperry@tgen.org
QIMR
Felipe Beltran, QIMR Media Relations Officer
Phone: (07) 3362 0291
E-mail: Felipe.Beltran@qimr.edu.au
MRF
Heather R. Huhman
Phone: (202) 742-5259
E-mail: Heather@JonesPA.com
Friday, May 16, 2008
UA oncologist receives $1M endowed chair
[Source: FAYANA RICHARDS, Tucson Citizen] - A University of Arizona professor of medicine was awarded the $1 million John Norton Endowed Chair for Prostate Cancer Research at the Arizona Cancer Center.
The gift was made to the UA Foundation.
The chair will go to oncologist Dr. Frederick "Rick" Ahmann, professor of medicine and surgery.
"Virtually no other oncologist in the U.S. has devoted his or her career to preventing and treating prostate cancer more than Dr. Rick Ahmann," said Dr. David S. Alberts, director for Arizona Cancer Center, in a press release.
Alberts, who appointed Ahmann to the chair position, said that "there is no more deserving physician scientist to receive a named prostate cancer chair."
The new chair position hits close to home for John Norton and his family.
Norton, a 17-year prostate cancer survivor, said he was referred to Ahmann by his Phoenix physician.
"We are on the threshold of new and better ways to treat prostate cancer," said Norton in a news release. "We must financially support people with the qualities and abilities of Dr. Ahmann."
Donors John and Doris Norton have participated in various philanthropic efforts including the donation of $4 million to UA's College of Agriculture.
The gift was made to the UA Foundation.
The chair will go to oncologist Dr. Frederick "Rick" Ahmann, professor of medicine and surgery.
"Virtually no other oncologist in the U.S. has devoted his or her career to preventing and treating prostate cancer more than Dr. Rick Ahmann," said Dr. David S. Alberts, director for Arizona Cancer Center, in a press release.
Alberts, who appointed Ahmann to the chair position, said that "there is no more deserving physician scientist to receive a named prostate cancer chair."
The new chair position hits close to home for John Norton and his family.
Norton, a 17-year prostate cancer survivor, said he was referred to Ahmann by his Phoenix physician.
"We are on the threshold of new and better ways to treat prostate cancer," said Norton in a news release. "We must financially support people with the qualities and abilities of Dr. Ahmann."
Donors John and Doris Norton have participated in various philanthropic efforts including the donation of $4 million to UA's College of Agriculture.
New Study Links Fate Of Personal Care Products To Environmental Pollution And Human Health Concerns
[Source: ScienceDaily] - Parental concerns in maintaining germ-free homes for their children have led to an ever-increasing demand and the rapid adoption of anti-bacterial soaps and cleaning agents. But the active ingredients of those antiseptic soaps now have come under scrutiny by the EPA and FDA, due to both environmental and human health concerns.
Two closely related antimicrobials, triclosan and triclocarban, are at the center of the debacle. Whereas triclosan (TCS) has long captured the attention of toxicologists due to its structural resemblance to dioxin (the Times Beach and Love Canal poison), triclocarban (TCC) has ski-rocketed in 2004 from an unknown and presumably harmless consumer product additive to one of today's top ten pharmaceuticals and personal care products most frequently found in the environment and in U.S. drinking water resources.
Now, Biodesign Institute at Arizona State Univesity researcher Rolf Halden and co-workers, in a feat of environmental detective work, have traced back the active ingredients of soaps -- used as long ago as the 1960s -- to their current location, the shallow sediments of New York City's Jamaica Bay and the Chesapeake Bay, the nation's largest estuary.
"Our group has shown that antimicrobial ingredients used a half a century ago, by our parents and grandparents, are still present today at parts-per-million concentrations in estuarine sediments underlying the brackish waters into which New York City and Baltimore discharge their treated domestic wastewater," said Halden, a new member of the institute's Center for Environmental Biotechnology. "This extreme environmental persistence by itself is a concern, and it is only amplified by recent studies that show both triclosan and triclocarban to function as endocrine disruptors in mammalian cell cultures and in animal models."
Aiding in his team's research was another type of contamination: the radioactive fallout from nuclear testing conducted in the second half of the last century. Using the known deposition history and half-lives of two radioactive isotopes, cesium-137 and beryllium-7, Halden and his collaborators Steven Chillrud, Jerry Ritchie and Richard Bopp were able to assign the approximate time at which sediments observed to contain antimicrobial residues had been deposited in the two East Coast locations.
By analyzing vertical cores of sediment deposited over time in the two sampling locations on the East Coast, they showed that TCC, and to a lesser extent, TCS, can persist in estuary sediments. TCC was shown to be present at parts per million levels, which could represent unhealthy levels for aquatic life, especially the bottom feeders that are important to commercial fishing industries like shellfish and crabs.
In the Chesapeake Bay samples, the group noticed a significant drop in TCC levels that corresponded to a technology upgrade in the nearby wastewater treatment plant back in 1978. However, earlier work by the team had shown that enhanced removal of TCC and TCS in wastewater treatment plants leads to accumulation of the problematic antimicrobial substances in municipal sludge that often is applied on agricultural land for disposal. Lead author Todd Miller concludes that "little is actually degraded during wastewater treatment and more information is needed regarding the long term consequences these chemicals may have on environmentally beneficial microorganisms."
Along the way of studying the deposition history of antimicrobials in sediments, the team also discovered a new pathway for the breakdown of antimicrobial additives of consumer products. Deep in the muddy sediments of the Chesapeake Bay, they found evidence for the activity of anaerobic microorganisms that assist in the decontamination of their habitat by pulling chlorine atoms one by one off the carbon backbone of triclocarban, presumably while obtaining energy for their metabolism in the process. "This is good news," said Halden, "but unfortunately the process does not occur in all locations and furthermore it is quite slow. If we continue to use persistent antimicrobial compounds at the current rate, we are outpacing nature's ability to decompose these problematic compounds."
While combining bioenergy production and pollutant destruction has its own appeal, Halden sees a simpler solution to combating the pollution his team discovered: limit the use of antimicrobial personal care products to situations where they improve public health and save lives.
"The irony is that these compounds have no measurable benefit over the use of regular soap and water for hand washing; the contact time simply is too short." Unfortunately this cannot be said for the bottom-dwelling organisms in the sampling locations on the East Coast. "Here," Halden concludes, "the affected organisms are experiencing multi-generational, life-time exposures to our chemical follies."
Halden is planning to continue his research on persistent antimicrobials by studying their body burden and associated health effects in susceptible populations including mothers and their babies.
The work was funded in part by the Johns Hopkins Center for a Livable Future and the National Institute of Environmental Health Sciences.
Two closely related antimicrobials, triclosan and triclocarban, are at the center of the debacle. Whereas triclosan (TCS) has long captured the attention of toxicologists due to its structural resemblance to dioxin (the Times Beach and Love Canal poison), triclocarban (TCC) has ski-rocketed in 2004 from an unknown and presumably harmless consumer product additive to one of today's top ten pharmaceuticals and personal care products most frequently found in the environment and in U.S. drinking water resources.
Now, Biodesign Institute at Arizona State Univesity researcher Rolf Halden and co-workers, in a feat of environmental detective work, have traced back the active ingredients of soaps -- used as long ago as the 1960s -- to their current location, the shallow sediments of New York City's Jamaica Bay and the Chesapeake Bay, the nation's largest estuary.
"Our group has shown that antimicrobial ingredients used a half a century ago, by our parents and grandparents, are still present today at parts-per-million concentrations in estuarine sediments underlying the brackish waters into which New York City and Baltimore discharge their treated domestic wastewater," said Halden, a new member of the institute's Center for Environmental Biotechnology. "This extreme environmental persistence by itself is a concern, and it is only amplified by recent studies that show both triclosan and triclocarban to function as endocrine disruptors in mammalian cell cultures and in animal models."
Aiding in his team's research was another type of contamination: the radioactive fallout from nuclear testing conducted in the second half of the last century. Using the known deposition history and half-lives of two radioactive isotopes, cesium-137 and beryllium-7, Halden and his collaborators Steven Chillrud, Jerry Ritchie and Richard Bopp were able to assign the approximate time at which sediments observed to contain antimicrobial residues had been deposited in the two East Coast locations.
By analyzing vertical cores of sediment deposited over time in the two sampling locations on the East Coast, they showed that TCC, and to a lesser extent, TCS, can persist in estuary sediments. TCC was shown to be present at parts per million levels, which could represent unhealthy levels for aquatic life, especially the bottom feeders that are important to commercial fishing industries like shellfish and crabs.
In the Chesapeake Bay samples, the group noticed a significant drop in TCC levels that corresponded to a technology upgrade in the nearby wastewater treatment plant back in 1978. However, earlier work by the team had shown that enhanced removal of TCC and TCS in wastewater treatment plants leads to accumulation of the problematic antimicrobial substances in municipal sludge that often is applied on agricultural land for disposal. Lead author Todd Miller concludes that "little is actually degraded during wastewater treatment and more information is needed regarding the long term consequences these chemicals may have on environmentally beneficial microorganisms."
Along the way of studying the deposition history of antimicrobials in sediments, the team also discovered a new pathway for the breakdown of antimicrobial additives of consumer products. Deep in the muddy sediments of the Chesapeake Bay, they found evidence for the activity of anaerobic microorganisms that assist in the decontamination of their habitat by pulling chlorine atoms one by one off the carbon backbone of triclocarban, presumably while obtaining energy for their metabolism in the process. "This is good news," said Halden, "but unfortunately the process does not occur in all locations and furthermore it is quite slow. If we continue to use persistent antimicrobial compounds at the current rate, we are outpacing nature's ability to decompose these problematic compounds."
While combining bioenergy production and pollutant destruction has its own appeal, Halden sees a simpler solution to combating the pollution his team discovered: limit the use of antimicrobial personal care products to situations where they improve public health and save lives.
"The irony is that these compounds have no measurable benefit over the use of regular soap and water for hand washing; the contact time simply is too short." Unfortunately this cannot be said for the bottom-dwelling organisms in the sampling locations on the East Coast. "Here," Halden concludes, "the affected organisms are experiencing multi-generational, life-time exposures to our chemical follies."
Halden is planning to continue his research on persistent antimicrobials by studying their body burden and associated health effects in susceptible populations including mothers and their babies.
The work was funded in part by the Johns Hopkins Center for a Livable Future and the National Institute of Environmental Health Sciences.
Friday, May 9, 2008
Researchers make nano-scale DNA research tool
[Reuter]) - U.S. researchers have made a very small research tool that may one day help scientists probe the activity of genes and proteins in a single cell, they said on Thursday, opening the door to a new realm of genetic research.
The tool is designed to do the work of current gene chip systems used to examine thousands of genes at the same time for mutations or to uncover clues to disease.
But it is made on the nano-scale -- which involves objects tens of thousands of times smaller than the width of a human hair.
"We have made little chips that are like the gene chips but instead of being lab scale they are molecular scale," said Stuart Lindsay, a physics professor and researcher at Arizona State University's Biodesign Institute.
"They have the potential to be used all the way down into analyzing single cells," said Lindsay, whose research appears in the journal Science.
Current gene chips analyze entire batches of cells. This technology would allow for much more refined analysis that could detect genetic changes from one cell to another, for instance.
The work, led by Hao Yan of the institute's Center for Single Molecule Biophysics, draws on a type of nanotechnology known as DNA origami, a method of folding a single long strand of DNA into a complex structure that is bound by short synthetic staples.
The nano probes assemble themselves in a water soluble solution and can be made at very low cost, Lindsay said.
"You end with 10,000 billion items in the test tube," he said.
On the surface of each DNA probe is a dangling single strand of DNA that can bind to the target ribonucleic acid or RNA, the chemical messengers of genes.
Lindsay said the new system is one of the first practical applications of structural DNA nanotechnology, which uses the properties of DNA to create different nanostructures.
"I think there is huge potential to come from nanotechnology," Lindsay said in a telephone interview. "This array is our first baby step in that direction."
(Editing by Maggie Fox and Mohammad Zargham)
The tool is designed to do the work of current gene chip systems used to examine thousands of genes at the same time for mutations or to uncover clues to disease.
But it is made on the nano-scale -- which involves objects tens of thousands of times smaller than the width of a human hair.
"We have made little chips that are like the gene chips but instead of being lab scale they are molecular scale," said Stuart Lindsay, a physics professor and researcher at Arizona State University's Biodesign Institute.
"They have the potential to be used all the way down into analyzing single cells," said Lindsay, whose research appears in the journal Science.
Current gene chips analyze entire batches of cells. This technology would allow for much more refined analysis that could detect genetic changes from one cell to another, for instance.
The work, led by Hao Yan of the institute's Center for Single Molecule Biophysics, draws on a type of nanotechnology known as DNA origami, a method of folding a single long strand of DNA into a complex structure that is bound by short synthetic staples.
The nano probes assemble themselves in a water soluble solution and can be made at very low cost, Lindsay said.
"You end with 10,000 billion items in the test tube," he said.
On the surface of each DNA probe is a dangling single strand of DNA that can bind to the target ribonucleic acid or RNA, the chemical messengers of genes.
Lindsay said the new system is one of the first practical applications of structural DNA nanotechnology, which uses the properties of DNA to create different nanostructures.
"I think there is huge potential to come from nanotechnology," Lindsay said in a telephone interview. "This array is our first baby step in that direction."
(Editing by Maggie Fox and Mohammad Zargham)
Study debunks heart attack-male baldness link
[Source: Reuters Health] A new study of more than 5,000 men calls into question the idea that baldness can signal a greater risk of heart disease.
Dr. Eyal Shahar of the University of Arizona in Tucson and colleagues found little difference in the heart attack risk between men with full heads of hair and their balding peers. Hair loss also wasn't related to thickening of the lining of the carotid arteries, the main vessels that supply blood to the brain. An increase in the lining of these arteries, known as carotid intimal-medial thickness, is a warning sign of atherosclerosis.
Some have suggested that baldness in men is related to increased levels of the hormone androgen, and that this hormone may also play a role in the development of coronary atherosclerosis, or "hardening of the arteries" within the heart, Shahar and his team note in their report, published in the American Journal of Epidemiology.
One previous study found that vertex baldness, or loss of hair at the top of the head, was strongly linked to heart attack risk; in fact, the balder men were on top, the greater was their risk.
To further investigate the issue, the researchers looked at 5,056 men 52 to 75 years old, 767 of whom had suffered a heart attack previously. About one third had little or no hair loss, while 13 percent had frontal baldness only, and 54 percent had vertex baldness.
Men going bald at the front of their heads were 28 percent more likely to have had a heart attack, while mild vertex baldness was tied to a 2 percent greater risk of heart attack,
However, the relationship didn't get stronger with baldness severity; men with moderate vertex baldness were 40 percent more likely to have had a heart attack, while risk was increased by 18 percent for men with severe vertex baldness.
There was no relationship between any type of baldness and carotid intimal-medial thickness.
If the types of baldness seen in the current study are indeed due to high androgen levels, Shahar and his colleagues note, it's likely that the hormone does not increase heart attack or atherosclerosis risk.
They conclude: "The results of this study suggest that male pattern baldness is not a surrogate measure of an important risk factor" for heart attacks or for atherosclerosis without symptoms.
SOURCE: American Journal of Epidemiology, May 15, 2008
Dr. Eyal Shahar of the University of Arizona in Tucson and colleagues found little difference in the heart attack risk between men with full heads of hair and their balding peers. Hair loss also wasn't related to thickening of the lining of the carotid arteries, the main vessels that supply blood to the brain. An increase in the lining of these arteries, known as carotid intimal-medial thickness, is a warning sign of atherosclerosis.
Some have suggested that baldness in men is related to increased levels of the hormone androgen, and that this hormone may also play a role in the development of coronary atherosclerosis, or "hardening of the arteries" within the heart, Shahar and his team note in their report, published in the American Journal of Epidemiology.
One previous study found that vertex baldness, or loss of hair at the top of the head, was strongly linked to heart attack risk; in fact, the balder men were on top, the greater was their risk.
To further investigate the issue, the researchers looked at 5,056 men 52 to 75 years old, 767 of whom had suffered a heart attack previously. About one third had little or no hair loss, while 13 percent had frontal baldness only, and 54 percent had vertex baldness.
Men going bald at the front of their heads were 28 percent more likely to have had a heart attack, while mild vertex baldness was tied to a 2 percent greater risk of heart attack,
However, the relationship didn't get stronger with baldness severity; men with moderate vertex baldness were 40 percent more likely to have had a heart attack, while risk was increased by 18 percent for men with severe vertex baldness.
There was no relationship between any type of baldness and carotid intimal-medial thickness.
If the types of baldness seen in the current study are indeed due to high androgen levels, Shahar and his colleagues note, it's likely that the hormone does not increase heart attack or atherosclerosis risk.
They conclude: "The results of this study suggest that male pattern baldness is not a surrogate measure of an important risk factor" for heart attacks or for atherosclerosis without symptoms.
SOURCE: American Journal of Epidemiology, May 15, 2008
Genetics Confirm Oral Traditions Of Druze In Israel
[Source: ScienceDaily] - DNA analysis of residents of Druze villages in Israel suggests these ancient religious communities offer a genetic snapshot of the Near East as it was several thousands of years ago.
The Druze harbor a remarkable diversity of mitochondrial DNA types or lineages that appear to have separated from each other many thousands of years ago, according to a new study by multinational team, led by researchers at the Technion-Israel Institute of Technology Rappaport School of Medicine.
But instead of dispersing throughout the world after their separation, the full range of lineages can still be found within the small, tightly knit Druze population.
Technion researcher Karl Skorecki noted that the findings are consistent with Druze oral tradition suggesting the adherents came from diverse ancestral lineages "stretching back tens of thousands of years." The Druze represent a "genetic sanctuary" or "living relic" that provides a glimpse of the genetic diversity of the Near East in antiquity, the researchers write in the May 7th issue of the journal PLoS ONE.
But there is a modern twist to their story: the diversity of Druze mitochondrial DNA, which is the part of the genome that is passed on strictly through the maternal line, offers a unique opportunity for researchers to study whether people in different mitochondrial DNA lineages are predisposed to different kinds of diseases.
Skorecki points to metabolic syndrome, the combination of insulin resistance, high cholesterol, abdominal obesity and other factors, as one such disease. Mitochondria are the energy factories within cells, so one might expect that differences in mitochondrial DNA might be linked to different predispositions to energy-related diseases such as metabolic syndrome, he explained.
With the Druze, "you can look at 150 kinds of mitochondrial DNA within one group with a similar environment, and be able to see the specific contribution of these variations" to disease, Skorecki said.
Dan Mishmar, a genetics researcher at Ben-Gurion University who was not involved with the study, said there is another "great advantage" to studying the link between disease and mitochondrial DNA variation in a group like the Druze. Although the Druze have great variety in their mitochondrial genome, the rest of their genome inherited from both paternal and maternal lines has grown less diverse as a result of thousands of years of intermarriage.
That means that researchers searching for genetic mutations linked to disease would have an easier time discerning whether these mutations are limited to the mitochondrial genome, which could help researchers design specific, targeted therapies, Mishmar explained.
The findings also guide the approach to screen for genetic disease among the Druze. Instead of scanning for disease-linked genes associated with an entire population--as is the case with Ashkenazi Jews, for example-it may make sense to screen within smaller groups. "Since they are comprised of so many distinct lineages, genetic disease may vary from clan to clan and village to village," Skorecki explained.
The researchers, including Druze co-authors Fuad Basis of the Rambam Medical Center and former Technion student Yarin Hadid, took genetic samples from 311 Druze households in 20 villages in Israel. They soon discovered an unusually high frequency of a mitochondrial DNA haplogroup-a distinct collection of genetic markers - called haplogroup X - among the Druze. Haplogroup X is found at low frequencies throughout the world, and is not confined to a specific geographical region as are most other mitochondrial DNA haplogroups.
Even more unusual, the Druze villages contained a striking range of variations on the X haplogroup. Together, the high frequency and high diversity of the X haplogroup "suggest that this population provides a glimpse into the past genetic landscape of the Near East, at a time when the X haplogroup was more prevalent," the researchers note.
How did the Druze become a genetic sanctuary in the Near East? The religious minority has lived for centuries in remote, mountainous regions, and unlike other monotheistic religions, the group has not sought converts since shortly after the "Dawa" or "revelation" of the religion in 1017 C.E. These factors, along with other cultural and political practices, may have kept the Druze a people apart for thousands of years, according to Skorecki and colleagues.
Skorecki is best-known for his 1997 discovery of genetic evidence indicating that the majority of modern-day Jewish priests (Kohanim) are descendants of a single common male ancestor, consistent with the Biblical high priest, Aaron. He also led an international team of researchers who, in 2006, found that some 3.5 million or 40 percent of Ashkenazi Jews are descended from just four "founding mothers," who lived in Europe 1,000 years ago.
Researchers from the Rambam Health Care Campus, Haifa, Israel, Washington University in St. Louis, Missouri, the University of Arizona in Tucson, Arizona and the Weizmann Institute of Science in Rehovot, Israel also contributed to the PLoS ONE study.
The Druze harbor a remarkable diversity of mitochondrial DNA types or lineages that appear to have separated from each other many thousands of years ago, according to a new study by multinational team, led by researchers at the Technion-Israel Institute of Technology Rappaport School of Medicine.
But instead of dispersing throughout the world after their separation, the full range of lineages can still be found within the small, tightly knit Druze population.
Technion researcher Karl Skorecki noted that the findings are consistent with Druze oral tradition suggesting the adherents came from diverse ancestral lineages "stretching back tens of thousands of years." The Druze represent a "genetic sanctuary" or "living relic" that provides a glimpse of the genetic diversity of the Near East in antiquity, the researchers write in the May 7th issue of the journal PLoS ONE.
But there is a modern twist to their story: the diversity of Druze mitochondrial DNA, which is the part of the genome that is passed on strictly through the maternal line, offers a unique opportunity for researchers to study whether people in different mitochondrial DNA lineages are predisposed to different kinds of diseases.
Skorecki points to metabolic syndrome, the combination of insulin resistance, high cholesterol, abdominal obesity and other factors, as one such disease. Mitochondria are the energy factories within cells, so one might expect that differences in mitochondrial DNA might be linked to different predispositions to energy-related diseases such as metabolic syndrome, he explained.
With the Druze, "you can look at 150 kinds of mitochondrial DNA within one group with a similar environment, and be able to see the specific contribution of these variations" to disease, Skorecki said.
Dan Mishmar, a genetics researcher at Ben-Gurion University who was not involved with the study, said there is another "great advantage" to studying the link between disease and mitochondrial DNA variation in a group like the Druze. Although the Druze have great variety in their mitochondrial genome, the rest of their genome inherited from both paternal and maternal lines has grown less diverse as a result of thousands of years of intermarriage.
That means that researchers searching for genetic mutations linked to disease would have an easier time discerning whether these mutations are limited to the mitochondrial genome, which could help researchers design specific, targeted therapies, Mishmar explained.
The findings also guide the approach to screen for genetic disease among the Druze. Instead of scanning for disease-linked genes associated with an entire population--as is the case with Ashkenazi Jews, for example-it may make sense to screen within smaller groups. "Since they are comprised of so many distinct lineages, genetic disease may vary from clan to clan and village to village," Skorecki explained.
The researchers, including Druze co-authors Fuad Basis of the Rambam Medical Center and former Technion student Yarin Hadid, took genetic samples from 311 Druze households in 20 villages in Israel. They soon discovered an unusually high frequency of a mitochondrial DNA haplogroup-a distinct collection of genetic markers - called haplogroup X - among the Druze. Haplogroup X is found at low frequencies throughout the world, and is not confined to a specific geographical region as are most other mitochondrial DNA haplogroups.
Even more unusual, the Druze villages contained a striking range of variations on the X haplogroup. Together, the high frequency and high diversity of the X haplogroup "suggest that this population provides a glimpse into the past genetic landscape of the Near East, at a time when the X haplogroup was more prevalent," the researchers note.
How did the Druze become a genetic sanctuary in the Near East? The religious minority has lived for centuries in remote, mountainous regions, and unlike other monotheistic religions, the group has not sought converts since shortly after the "Dawa" or "revelation" of the religion in 1017 C.E. These factors, along with other cultural and political practices, may have kept the Druze a people apart for thousands of years, according to Skorecki and colleagues.
Skorecki is best-known for his 1997 discovery of genetic evidence indicating that the majority of modern-day Jewish priests (Kohanim) are descendants of a single common male ancestor, consistent with the Biblical high priest, Aaron. He also led an international team of researchers who, in 2006, found that some 3.5 million or 40 percent of Ashkenazi Jews are descended from just four "founding mothers," who lived in Europe 1,000 years ago.
Researchers from the Rambam Health Care Campus, Haifa, Israel, Washington University in St. Louis, Missouri, the University of Arizona in Tucson, Arizona and the Weizmann Institute of Science in Rehovot, Israel also contributed to the PLoS ONE study.
Wednesday, May 7, 2008
SGI Breakthrough Technology Empowers Genome Center Research Around the World
[Source: www.SunHerald.com ] - As scientists seek to accelerate sequencing genomes of varied arrays of organisms from fish parasites to cancer cells in an effort to determine causes and cures of diseases that plague mankind, breakthrough technology from SGI (Nasdaq: SGIC) is powering research in genome centers around the world. Leading institutions, including the Translational Genomics Research Institute in Phoenix, Ariz., the Malaysia Genome Institute in Selangor and the China National Human Genome Center in Shanghai, have turned to SGI(R) high-performance computing and storage solutions to create an optimal workflow for faster time to discovery.
"Exciting combinations of SGI technology enable bioscientists to achieve genome query results faster," said Deepak Thakkar, Ph.D., Higher Education and Research Segment Manager, SGI. "International genome centers, each with unique computational needs and demands, have turned to SGI for their high performance compute, scalable storage and acceleration technology needs. Whether using an SGI cluster to run many iterations of a search or handling massive data sets on our powerful servers, bioscientists rely on SGI delivering faster time to insight."
The Translational Genomics Research Institute
Discovering the differences and changes within the genome that trigger disease is a priority for The Translational Genomics Research Institute (TGen). TGen deploys technology from SGI to more quickly and efficiently analyze molecular profile data sets in their search for cancer cures. In use for a year (see separate release December 5, 2007) and purchased through a National Institute of Health (NIH) grant, the SGI(R) Altix(R) 4700 system is assisting TGen researchers in understanding the genomic variation -- a process which requires comparison searches of enormous data sets -- that can be rapidly used for diagnosis and treatment of disease in a manner tailored to individual patients.
Since implementing the SGI system, TGen has observed significant performance gains in analyzing large gene expression datasets on the SGI Altix system.
"On SGI's Altix machines, we have used MPI parallel programming libraries and Intel's icc compiler to parallelize and optimize code, respectively," said TGen Scientific Programmer Waibhav Tembe, Ph.D., who has been actively involved in developing and benchmarking several tools on the SGI Altix systems. "Benchmarks run on Melanoma gene expression dataset consisting of about 8,000 genes from several dozens of samples showed that the analysis time was reduced time of completion from seven days to seven hours and generated several statistically significant gene groups identified that are being investigated further by the life scientists and computational biologists. We are very optimistic that such speed improvements will be critical in expediting translational research and help scientists explore a larger solution space by analyzing larger datasets in the future."
TGen's in-house code harnesses the compute power of the SGI Altix system's global shared memory to search for variations as minute as a change on one protein, trying to determine what effect that has across the entire spectrum of what is being observed.
"The success of TGen scientists to date has come at the sacrifice of time," said Dr. Edward Suh, CIO of TGen. "The 64-bit SGI computing instrument optimizes TGen researchers' ability to meet their data analysis needs efficiently, fostering timely and effective discovery for improved human health."
Malaysia Genome Institute
The Malaysia Genome Institute (MGI) is a network-based organization with international ties carrying out discovery research on tropical bioresources through projects in genome sequencing, comparative and functional genomics, and structural biology. Several major research projects are currently underway at MGI. For example, the Microbial Genomics Research for Gene and Natural Product Discovery project is focusing on two model organisms, Burkholderia pseudomallei, a locally important soil pathogen and Eimeria tenella, a local avian protozoan. The project will harness the SGI solution to dissect the organisms' genomes to gain new insights on virulence, antibiotic resistance, host specificity and infectivity.
Installed in July, 2007, MGI uses a hybrid computing solution that consists of SGI(R) Altix(R) XE 1200 clusters, an SGI(R) Altix(R) 4700 shared memory server and an SGI(R) InfiniteStorage CXFS(TM) SAN shared filesystem, which makes the entire workflow transparent to the user regardless of software employed, or stage of the process at which scientists are performing. (See separate release Feb. 20, 2008)
"Bioinformatics brings together an avalanche of systematic biological data with the analytic theory and practical tools of mathematics and computer science," said Mohd Noor Mat Isa, Laboratory Manager, Malaysia Genome Institute. "SGI delivers flexible computing with a hybrid architecture that integrates high-throughput, high-performance and FPGA-based solutions for all of our bioinformatics applications -- a solution that seamlessly runs applications in the environment best suited for optimal performance."
China National Human Genome Center
Schistosoma japonicum or blood fluke -- one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans -- has evolved for thousands of years. In the past few years the Schistosoma japonicum has been found in some lakes and rivers in the east and south China area. To study the parasite evolution, improve disease diagnosis in the very early stages, and develop more effective drugs to treat disease, bioscientists at the China National Human Genome Center (CHGC) in Shanghai are using a combination of SGI(R) RASC(TM) (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n (Basic Local Alignment Search Tool for nucleotides) software developed by Mitrionics, and the SGI(R) Altix(R) server platform.
CHGC implemented blood fluke genomics sequencing using the SGI RASC Appliance for Bioinformatics and SGI InfiniteStorage 350 storage solution (See separate release July 24, 2007). CHGC bioscientists achieve fast query times with the SGI InfiniteStorage 350, which ensures the data generated by the CHGC research, reaching hundreds of gigabytes in size, is both protected and available to maximize analysis.
"Shortened time to results is critical to our success. With the blood fluke genome research, we have 300 million base pairs to study, and have 6-7 times more calculations in each step. The large shared memory and ease-of-use with SGI RASC and SGI server and storage systems enables our scientists to focus on achieving results faster and not spending valuable time on computer science," said Dr. Zhou, Deputy Director of Bioinformatics Department, CHGC.
The Mitrion accelerated BLAST-n running on the SGI RASC Appliance for Bioinformatics runs large queries up to 19 times faster than a single-core cluster powered by AMD Opteron 8820 SE processors, and production runs of thousands of smaller queries by up to 60 times faster.
"Exciting combinations of SGI technology enable bioscientists to achieve genome query results faster," said Deepak Thakkar, Ph.D., Higher Education and Research Segment Manager, SGI. "International genome centers, each with unique computational needs and demands, have turned to SGI for their high performance compute, scalable storage and acceleration technology needs. Whether using an SGI cluster to run many iterations of a search or handling massive data sets on our powerful servers, bioscientists rely on SGI delivering faster time to insight."
The Translational Genomics Research Institute
Discovering the differences and changes within the genome that trigger disease is a priority for The Translational Genomics Research Institute (TGen). TGen deploys technology from SGI to more quickly and efficiently analyze molecular profile data sets in their search for cancer cures. In use for a year (see separate release December 5, 2007) and purchased through a National Institute of Health (NIH) grant, the SGI(R) Altix(R) 4700 system is assisting TGen researchers in understanding the genomic variation -- a process which requires comparison searches of enormous data sets -- that can be rapidly used for diagnosis and treatment of disease in a manner tailored to individual patients.
Since implementing the SGI system, TGen has observed significant performance gains in analyzing large gene expression datasets on the SGI Altix system.
"On SGI's Altix machines, we have used MPI parallel programming libraries and Intel's icc compiler to parallelize and optimize code, respectively," said TGen Scientific Programmer Waibhav Tembe, Ph.D., who has been actively involved in developing and benchmarking several tools on the SGI Altix systems. "Benchmarks run on Melanoma gene expression dataset consisting of about 8,000 genes from several dozens of samples showed that the analysis time was reduced time of completion from seven days to seven hours and generated several statistically significant gene groups identified that are being investigated further by the life scientists and computational biologists. We are very optimistic that such speed improvements will be critical in expediting translational research and help scientists explore a larger solution space by analyzing larger datasets in the future."
TGen's in-house code harnesses the compute power of the SGI Altix system's global shared memory to search for variations as minute as a change on one protein, trying to determine what effect that has across the entire spectrum of what is being observed.
"The success of TGen scientists to date has come at the sacrifice of time," said Dr. Edward Suh, CIO of TGen. "The 64-bit SGI computing instrument optimizes TGen researchers' ability to meet their data analysis needs efficiently, fostering timely and effective discovery for improved human health."
Malaysia Genome Institute
The Malaysia Genome Institute (MGI) is a network-based organization with international ties carrying out discovery research on tropical bioresources through projects in genome sequencing, comparative and functional genomics, and structural biology. Several major research projects are currently underway at MGI. For example, the Microbial Genomics Research for Gene and Natural Product Discovery project is focusing on two model organisms, Burkholderia pseudomallei, a locally important soil pathogen and Eimeria tenella, a local avian protozoan. The project will harness the SGI solution to dissect the organisms' genomes to gain new insights on virulence, antibiotic resistance, host specificity and infectivity.
Installed in July, 2007, MGI uses a hybrid computing solution that consists of SGI(R) Altix(R) XE 1200 clusters, an SGI(R) Altix(R) 4700 shared memory server and an SGI(R) InfiniteStorage CXFS(TM) SAN shared filesystem, which makes the entire workflow transparent to the user regardless of software employed, or stage of the process at which scientists are performing. (See separate release Feb. 20, 2008)
"Bioinformatics brings together an avalanche of systematic biological data with the analytic theory and practical tools of mathematics and computer science," said Mohd Noor Mat Isa, Laboratory Manager, Malaysia Genome Institute. "SGI delivers flexible computing with a hybrid architecture that integrates high-throughput, high-performance and FPGA-based solutions for all of our bioinformatics applications -- a solution that seamlessly runs applications in the environment best suited for optimal performance."
China National Human Genome Center
Schistosoma japonicum or blood fluke -- one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans -- has evolved for thousands of years. In the past few years the Schistosoma japonicum has been found in some lakes and rivers in the east and south China area. To study the parasite evolution, improve disease diagnosis in the very early stages, and develop more effective drugs to treat disease, bioscientists at the China National Human Genome Center (CHGC) in Shanghai are using a combination of SGI(R) RASC(TM) (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n (Basic Local Alignment Search Tool for nucleotides) software developed by Mitrionics, and the SGI(R) Altix(R) server platform.
CHGC implemented blood fluke genomics sequencing using the SGI RASC Appliance for Bioinformatics and SGI InfiniteStorage 350 storage solution (See separate release July 24, 2007). CHGC bioscientists achieve fast query times with the SGI InfiniteStorage 350, which ensures the data generated by the CHGC research, reaching hundreds of gigabytes in size, is both protected and available to maximize analysis.
"Shortened time to results is critical to our success. With the blood fluke genome research, we have 300 million base pairs to study, and have 6-7 times more calculations in each step. The large shared memory and ease-of-use with SGI RASC and SGI server and storage systems enables our scientists to focus on achieving results faster and not spending valuable time on computer science," said Dr. Zhou, Deputy Director of Bioinformatics Department, CHGC.
The Mitrion accelerated BLAST-n running on the SGI RASC Appliance for Bioinformatics runs large queries up to 19 times faster than a single-core cluster powered by AMD Opteron 8820 SE processors, and production runs of thousands of smaller queries by up to 60 times faster.
Tuesday, May 6, 2008
Scientists present Alzheimer's research update at confab
[Source: www.yourwestvalley.com ] -Sun Health Research Institute and its partners in the Arizona Alzheimer’s Consortium will have a free conference for the public to learn about progress in the fight against Alzheimer’s disease from 8 a.m. to 5 p.m. May 30 at the Renaissance Glendale Hotel & Spa, 9495 W. Coyotes Blvd.
The 10th annual event will feature presentations by leading physicians, researchers and scientists. Speakers include Joseph Rogers, Ph.D., president of Sun Health Research Institute, and Dr. Marwan Sabbagh, director of the Cleo Roberts Center for Clinical Research at Sun Health Research Institute.
A free buffet breakfast and lunch will be provided. Seating is limited, and registration is required by visiting www.azalz.org or by calling 602-239-6901.
The morning program features a community awareness forum, "Facing Alzheimer’s Together," with a focus on:
• Advances in diagnosing Alzheimer’s disease.
• Providing emotional support for caregivers.
• Physician and caregiver panel discussion with audience question-and-answer session.
The afternoon program is structured as a scientific forum, and morning session attendees are welcome to say for the afternoon session, featuring:
• Keynote speaker.
• Poster presentations.
• "Data blitz" presentations.
Alzheimer’s disease is the seventh-leading cause of death in the U.S., afflicting one in 10 people older than 65.
Treatments are available that improve the quality of life for some people with Alzheimer’s. Investigative treatments are being studied in clinical trials, and scientists have discovered several genes associated with the disease.
In addition, techniques are available to help people caring for a loved one with the disease.
The 10th annual event will feature presentations by leading physicians, researchers and scientists. Speakers include Joseph Rogers, Ph.D., president of Sun Health Research Institute, and Dr. Marwan Sabbagh, director of the Cleo Roberts Center for Clinical Research at Sun Health Research Institute.
A free buffet breakfast and lunch will be provided. Seating is limited, and registration is required by visiting www.azalz.org or by calling 602-239-6901.
The morning program features a community awareness forum, "Facing Alzheimer’s Together," with a focus on:
• Advances in diagnosing Alzheimer’s disease.
• Providing emotional support for caregivers.
• Physician and caregiver panel discussion with audience question-and-answer session.
The afternoon program is structured as a scientific forum, and morning session attendees are welcome to say for the afternoon session, featuring:
• Keynote speaker.
• Poster presentations.
• "Data blitz" presentations.
Alzheimer’s disease is the seventh-leading cause of death in the U.S., afflicting one in 10 people older than 65.
Treatments are available that improve the quality of life for some people with Alzheimer’s. Investigative treatments are being studied in clinical trials, and scientists have discovered several genes associated with the disease.
In addition, techniques are available to help people caring for a loved one with the disease.
Nationwide Biotech Crop Maps Suggested for Monitoring Environmental Impacts
[Source: Pat Bailey, UC Davis News Service] - A team of biologists, including a UC Davis plant scientist, is proposing that maps be created showing where all of the billion-plus acres of genetically engineered crops have been grown in the United States.
The comprehensive biotech mapping system, modeled after one now in use in Arizona, would permit much-needed studies of the positive or negative environmental impacts of genetically engineered crops, the researchers suggest in a Policy Forum piece published in the April 25 issue of the journal Science.
"Such maps would enable scientists to better analyze the effects of genetically modified crops on wildlife, water quality, insect pests and beneficial insects," said UC Davis Professor Paul Gepts, an expert on the evolutionary processes that have shaped the evolution of crop plants.
In Arizona, farmers routinely share maps of biotech cotton fields with scientists at the University of Arizona, enabling detailed analyses of the effects of this technology. That information is collected and stored in such a way that the privacy of the farmers is protected.
The U.S. Department of Agriculture already is collecting data at the individual farm level, but that information is only made available to researchers at the scale of entire states. In this forum piece, the authors maintain that such information needs to be made available at the county and township level in order to be useful in analyzing the impacts of biotech crops.
Lead author on this paper is Michelle Marvier of Santa Clara University. The other authors, in addition to Gepts, are Peter Kareiva of Santa Clara University and The Nature Conservancy, Norman Elstrand of UC Riverside, Yves Carrière and Bruce Tabashnik of the University of Arizona, Emma Rosi-Marshall of Loyola University Chicago, and L. LaReesa Wolfenbarger of the University of Nebraska at Omaha.
The comprehensive biotech mapping system, modeled after one now in use in Arizona, would permit much-needed studies of the positive or negative environmental impacts of genetically engineered crops, the researchers suggest in a Policy Forum piece published in the April 25 issue of the journal Science.
"Such maps would enable scientists to better analyze the effects of genetically modified crops on wildlife, water quality, insect pests and beneficial insects," said UC Davis Professor Paul Gepts, an expert on the evolutionary processes that have shaped the evolution of crop plants.
In Arizona, farmers routinely share maps of biotech cotton fields with scientists at the University of Arizona, enabling detailed analyses of the effects of this technology. That information is collected and stored in such a way that the privacy of the farmers is protected.
The U.S. Department of Agriculture already is collecting data at the individual farm level, but that information is only made available to researchers at the scale of entire states. In this forum piece, the authors maintain that such information needs to be made available at the county and township level in order to be useful in analyzing the impacts of biotech crops.
Lead author on this paper is Michelle Marvier of Santa Clara University. The other authors, in addition to Gepts, are Peter Kareiva of Santa Clara University and The Nature Conservancy, Norman Elstrand of UC Riverside, Yves Carrière and Bruce Tabashnik of the University of Arizona, Emma Rosi-Marshall of Loyola University Chicago, and L. LaReesa Wolfenbarger of the University of Nebraska at Omaha.
Fed tech research group boss visits UA, seeks ideas
[Source: BLAKE MORLOCK, Tucson Citizen] - The director of the federal agency designing planes that fly continuously for five years, plus low-cost titanium solar cells that would be efficient enough to power every house in Tucson and biofuel for jets was in town Friday. He's hoping to entice local brainpower to find the idea that could change the world.
Oh, yeah. And these are the folks who invented the Internet.
Tony Tether, director of the Defense Advanced Research Projects Agency, spoke to researchers and business leaders at the University of Arizona's BIO5 Institute about the kind of cutting edge work his people do.
DARPA funds research in the private sector and on college campuses while directing projects of its own.
All that work - from prosthetics to unmanned aerial vehicles launched from ballistic missiles - starts with a "what-if?" he said, adding DARPA is ready to tackle research that may not pan out.
"We thrive on your ideas," Tether said
Tether, along with Rear Adm. Jay Cohen, undersecretary of Homeland Security for science and technology, were invited to speak here by U.S. Rep. Gabrielle Giffords, D-Ariz., and the Southern Arizona Leadership Council.
BIO5 Director Vicki Chandler called DARPA a great conduit to grants for UA researchers.
Also, DARPA expects researchers to take risks.
"The world doesn't truly move forward without someone taking a risk," Chandler said.
Oh, yeah. And these are the folks who invented the Internet.
Tony Tether, director of the Defense Advanced Research Projects Agency, spoke to researchers and business leaders at the University of Arizona's BIO5 Institute about the kind of cutting edge work his people do.
DARPA funds research in the private sector and on college campuses while directing projects of its own.
All that work - from prosthetics to unmanned aerial vehicles launched from ballistic missiles - starts with a "what-if?" he said, adding DARPA is ready to tackle research that may not pan out.
"We thrive on your ideas," Tether said
Tether, along with Rear Adm. Jay Cohen, undersecretary of Homeland Security for science and technology, were invited to speak here by U.S. Rep. Gabrielle Giffords, D-Ariz., and the Southern Arizona Leadership Council.
BIO5 Director Vicki Chandler called DARPA a great conduit to grants for UA researchers.
Also, DARPA expects researchers to take risks.
"The world doesn't truly move forward without someone taking a risk," Chandler said.
Expert to present deep-sea research
[Source: The Arizona Republic] - John Delaney, a professor at the University of Washington School of Oceanography, will discuss how scientists and engineers are working to unlock deep-sea mysteries during a free public program at 6:30 p.m. Monday at Tempe Center for the Arts, 700 W. Rio Salado Parkway.
"The ocean depths are the last unexplored frontier on Earth," and a better understanding of that frontier "would revolutionize the ways humans can perceive and eventually manage their world," Delaney said. He is involved in the National Science Foundation's $335 million Ocean Observatories Initiative program to develop new technologies designed to probe the ocean depths.
Arizona State University researchers will be helping with research at the Center for Ecogenomics, which is based at ASU's Biodesign Institute and directed by Deirdre Meldrum, dean of the university's Ira A. Fulton School of Engineering.
Delaney and Meldrum are collaborating on studying ecosystems in the region of the Pacific Ocean that overlies the Juan de Fuca tectonic plate off the U.S. Northwest.
Meldrum's center at ASU is developing sensors to measure biological, chemical and physical aspects of the sea-floor environs at the microbial level. The sensors will provide real-time data and measurements to researchers on land via the Web.
"When this new system is connected to the Internet, it will allow scientists anywhere in the world to interact with the oceans," Delaney said.
"Such developing technologies allow us to design and perform entirely new types of studies as if we were actually in the ocean," Meldrum sa. "Now we can literally conduct oceanographic research from the desert, and make ASU a leader in this kind of remote environmental science."
For more information on the National Science Foundation Ocean Observatories Initiative, go to www.ooi.washington.edu.
"The ocean depths are the last unexplored frontier on Earth," and a better understanding of that frontier "would revolutionize the ways humans can perceive and eventually manage their world," Delaney said. He is involved in the National Science Foundation's $335 million Ocean Observatories Initiative program to develop new technologies designed to probe the ocean depths.
Arizona State University researchers will be helping with research at the Center for Ecogenomics, which is based at ASU's Biodesign Institute and directed by Deirdre Meldrum, dean of the university's Ira A. Fulton School of Engineering.
Delaney and Meldrum are collaborating on studying ecosystems in the region of the Pacific Ocean that overlies the Juan de Fuca tectonic plate off the U.S. Northwest.
Meldrum's center at ASU is developing sensors to measure biological, chemical and physical aspects of the sea-floor environs at the microbial level. The sensors will provide real-time data and measurements to researchers on land via the Web.
"When this new system is connected to the Internet, it will allow scientists anywhere in the world to interact with the oceans," Delaney said.
"Such developing technologies allow us to design and perform entirely new types of studies as if we were actually in the ocean," Meldrum sa. "Now we can literally conduct oceanographic research from the desert, and make ASU a leader in this kind of remote environmental science."
For more information on the National Science Foundation Ocean Observatories Initiative, go to www.ooi.washington.edu.
Friday, May 2, 2008
How Birds Navigate: Research Team Is First To Model Photochemical Compass
Source: ScienceDaily] - It has long been known that birds and many other animals including turtles, salamanders and lobsters, use the Earth's magnetic field to navigate, but the nature of their global positioning systems (GPS) has not been completely understood.
One school of thought hypothesizes that birds use magnetically-sensitive chemical reactions initiated by light (called chemical magnetoreception) to orient themselves, but no chemical reaction in the laboratory, until now, has been shown to respond to magnetic fields as weak as the Earth's.
Scientists from Arizona State University and the University of Oxford, whose work appears in the April 30 advanced online publication of the journal Nature, have synthesized and studied a sophisticated molecule that, under illumination, is sensitive to both the magnitude and the direction of magnetic fields as tiny as the Earth's, which is, on average, one-twenty thousandth as strong as a refrigerator magnet.
ASU's Devens Gust, professor of chemistry and biochemistry in the College of Liberal Arts and Sciences, states that "although the chemical magnetoreception mechanism for avian magnetic navigation has been discussed by many investigators, our research provides the first proof that this mechanism can actually function with magnetic fields as small as those of the Earth."
Gust, who also is a faculty researcher in the Center for Bioenergy and Photosynthesis at ASU, says "the design, synthesis and a few initial magnetic field effect studies were done at ASU in the context of artificial photosynthetic solar energy conversion. The Oxford group, led by Peter Hore, professor of chemistry, realized that these effects might be relevant to chemical magnetoreception, constructed the extremely sensitive apparatus needed to observe the phenomena, and carried out the appropriate experiments."
Ten years ago, a National Science Foundation-sponsored research team at Arizona State led by Gust, Thomas Moore and Ana Moore, professors of chemistry and biochemistry, synthesized a molecular "triad" and demonstrated that when the triad was exposed to light, it formed a short-lived, high-energy charge-separated species whose lifetime was influenced by magnetic fields.
The special molecules were originally synthesized as artificial photosynthetic reaction centers, being developed as chemical solar energy conversion systems. They were inspired by the way plants harvest sunlight, and had nothing whatsoever to do with bird navigation.
A related triad molecule was recently synthesized by Paul Liddell, assistant research professional working with Gust and the Moores, and studied by Hore and coworkers at the University of Oxford. The British researchers used lasers that sent out pulses of light lasting only one-thousand millionth's of a second to investigate the molecular properties. A major problem was to completely shield their experiments from the Earth's magnetic field.
The wonder molecule comprises three units (a carotene-porphyrin-fullerene triad). When excited by light, the triad molecule forms a charge-separated state with the negative charge on the soccer-ball-like fullerene (or buckyball) portion and the positive charge on the rod-like carotene portion. The lifetime of the charge-separated species before it returns to the normal state is sensitive to the magnitude and direction of a weak magnetic field, similar to that of the Earth. The triad molecule, in its charge separated state, could be thought of as having little bar magnets at either end -- so far apart that they interact with each other only weakly.
Gust and Liddell were joined in this research by Kiminori Maeda, Kevin Henbest and Christiane Timmel of the University of Oxford's inorganic chemistry laboratory and Filippo Cintolesi, Ilya Kuprov, Christopher Rodgers and Hore of Oxford's physical chemistry laboratory.
"These results provide a clear proof of principle that the magnetic compass sense of migratory birds is based on a magnetically-sensitive chemical reaction whose product yields and/or rate depend on the orientations of the molecules involved with respect to the geomagnetic field," adds Hore.
Gust also notes that understanding animal navigation systems is of great ecological importance because weak, man-made magnetic fields are produced by many widely-used technologies, such as power lines and communications equipment. In fact, this also allows for a diagnostic test of the magnetoreceptor mechanism, he says. Research has shown that both broadband radio noise (0.1-10.0 MHz) and constant frequency (7MHz) signals disrupted magnetic orientation in European robins.
"Of course," Gust adds, "this research does not prove that birds actually use this mechanism, only that they could. But, there is a large body of research on birds that is consistent with the magnetoreception idea."
The international research team is busily designing new molecules and experiments to further prove their case. This work has demonstrated that the ingenious chemical magnetoreception concept is indeed feasible. It certainly provides some insight into the structure and dynamic design features needed for a molecular interpretation of how the birds go about keeping their appointments in strange places across the world.
Adapted from materials provided by Arizona State University.
New cooling device helps treat babies
[Source: Ken Alltucker, The Arizona Republic] - Timing is everything for newborn Macie Chloe Reynolds.
A persistent doctor, loving parents and a life-changing technology certainly help, too.
This week, Macie became the first newborn at an Arizona hospital to be treated with the "cool-cap" machine, a new device that aims to help otherwise healthy, full-term infants recover from traumatic deliveries.
Macie appeared healthy and in good spirits Thursday following 72 hours of cool-cap machine treatments. And her parents were cautiously optimistic that their nine-pound, six-ounce baby girl would be the first of many Arizona infants to benefit from the new technology now available at Phoenix Children's Hospital.
"There is a light at the end of the tunnel," said Kevin Reynolds, Macie's father. "We just don't know how long the tunnel is."
Phoenix Children's Hospital is the first Arizona hospital to use the Olympic Cool-Cap device. The machine is used on newborns, such as Macie, that face complications due to a lack of oxygen during birth, a condition known as hypoxic-ischemic encephalopathy. The condition can devastate babies and their families, causing such disabilities as dyslexia, cerebral palsy and even death. The cool-cap machine works to lower the infant's brain temperature to help counteract complications.
The whirlwind week for the Reynolds' took an unexpected turn Monday morning as mother Tarin had to undergo an emergency cesarean section due to complications with her pregnancy at Banner Gateway Hospital in Gilbert. Her placenta had separated before the baby was born, cutting off the baby girl's oxygen.
Macie was delivered shortly before 7 a.m. but she was not out of the woods. She was flown via medical helicopter from Banner Gateway to Phoenix Children's Hospital for treatment. Phoenix Children's had installed the cool-cap machine just last week.
"Before, if the baby had a brain injury at birth, there would be nothing we could do," said Dr. Cristina Carballo. "This is such an incredible thing to be able to do."
Carballo had learned about the cool-cap system from clinical trials that showed the device was safe and effective. It is the only Food and Drug Administration-approved device designed to aid infant brain injuries caused by a lack of oxygen. After learning about the device's potential impact, Carballo prodded the hospital's administration to purchase the device and related equipment.
Natus Medical, the San Carlos, Calif.-based company that sells the Oympic Cool Cap, gained FDA approval in February to sell the device in the United States. It's now used in fewer than 200 Level 3 neonatal intensive care units in the United States, company executives said.
Phoenix Children's is the only hospital in Arizona with the device, though a spokesman for Banner Children's hospital at Banner Desert in Mesa expects the hospital will soon consider purchasing the cool-cap system.
The device works by keeping the infant's brain cool while the rest of the body remains about three degrees below normal body temperature. It includes a helmet-like shell that is placed over the baby's head, and tubes circulate cold water through the cap for a cooling effect.
The overall system, which retails for about $75,000, includes a cooling unit, a control unit, temperature probes and the water-filled cap.
The condition hypoxic-ischemic encephalopathy, or HIE, occurs in an estimated two to four times out of every 1,000 births. The FDA estimates that the cool-cap device could annually help 5,000 to 9,000 babies in the United States. It should help at least five to six babies each year in the Phoenix area, Carballo estimates.
As Macie arrived at Phoenix Children's Monday morning, Kevin Reynolds said he experienced a swirl of emotions. His wife was still at Banner, following the difficult birth, and his daughter would become the first baby to undergo the cool-cap treatment in Arizona.
"I was overcome by the fact that I didn't know what was going to happen," said Reynolds, a Gilbert resident and high school Spanish teacher.
Time is critical in births, such as Macie's. The infant must be treated by the cool-cap within six hours of birth, and typical newborn procedures, such as putting the baby under a heat lamp, must be avoided.
Macie was put on the system within the required time and remained on the machine until just before noon Thursday. Her body temperature was gradually elevated to normal levels within four hours.
Macie will stay at Phoenix Children's for observation. Her mother, Tarin, arrived at her baby's side Wednesday.
Despite the stressful period, the Reynolds' said they look forward to soon returning home with their baby girl.
"You are going to do everything you possibly can do to help your child," Reynolds said.
Reach the reporter at ken.alltucker@arizonarepublic.com or (602)444-8285.
A persistent doctor, loving parents and a life-changing technology certainly help, too.
This week, Macie became the first newborn at an Arizona hospital to be treated with the "cool-cap" machine, a new device that aims to help otherwise healthy, full-term infants recover from traumatic deliveries.
Macie appeared healthy and in good spirits Thursday following 72 hours of cool-cap machine treatments. And her parents were cautiously optimistic that their nine-pound, six-ounce baby girl would be the first of many Arizona infants to benefit from the new technology now available at Phoenix Children's Hospital.
"There is a light at the end of the tunnel," said Kevin Reynolds, Macie's father. "We just don't know how long the tunnel is."
Phoenix Children's Hospital is the first Arizona hospital to use the Olympic Cool-Cap device. The machine is used on newborns, such as Macie, that face complications due to a lack of oxygen during birth, a condition known as hypoxic-ischemic encephalopathy. The condition can devastate babies and their families, causing such disabilities as dyslexia, cerebral palsy and even death. The cool-cap machine works to lower the infant's brain temperature to help counteract complications.
The whirlwind week for the Reynolds' took an unexpected turn Monday morning as mother Tarin had to undergo an emergency cesarean section due to complications with her pregnancy at Banner Gateway Hospital in Gilbert. Her placenta had separated before the baby was born, cutting off the baby girl's oxygen.
Macie was delivered shortly before 7 a.m. but she was not out of the woods. She was flown via medical helicopter from Banner Gateway to Phoenix Children's Hospital for treatment. Phoenix Children's had installed the cool-cap machine just last week.
"Before, if the baby had a brain injury at birth, there would be nothing we could do," said Dr. Cristina Carballo. "This is such an incredible thing to be able to do."
Carballo had learned about the cool-cap system from clinical trials that showed the device was safe and effective. It is the only Food and Drug Administration-approved device designed to aid infant brain injuries caused by a lack of oxygen. After learning about the device's potential impact, Carballo prodded the hospital's administration to purchase the device and related equipment.
Natus Medical, the San Carlos, Calif.-based company that sells the Oympic Cool Cap, gained FDA approval in February to sell the device in the United States. It's now used in fewer than 200 Level 3 neonatal intensive care units in the United States, company executives said.
Phoenix Children's is the only hospital in Arizona with the device, though a spokesman for Banner Children's hospital at Banner Desert in Mesa expects the hospital will soon consider purchasing the cool-cap system.
The device works by keeping the infant's brain cool while the rest of the body remains about three degrees below normal body temperature. It includes a helmet-like shell that is placed over the baby's head, and tubes circulate cold water through the cap for a cooling effect.
The overall system, which retails for about $75,000, includes a cooling unit, a control unit, temperature probes and the water-filled cap.
The condition hypoxic-ischemic encephalopathy, or HIE, occurs in an estimated two to four times out of every 1,000 births. The FDA estimates that the cool-cap device could annually help 5,000 to 9,000 babies in the United States. It should help at least five to six babies each year in the Phoenix area, Carballo estimates.
As Macie arrived at Phoenix Children's Monday morning, Kevin Reynolds said he experienced a swirl of emotions. His wife was still at Banner, following the difficult birth, and his daughter would become the first baby to undergo the cool-cap treatment in Arizona.
"I was overcome by the fact that I didn't know what was going to happen," said Reynolds, a Gilbert resident and high school Spanish teacher.
Time is critical in births, such as Macie's. The infant must be treated by the cool-cap within six hours of birth, and typical newborn procedures, such as putting the baby under a heat lamp, must be avoided.
Macie was put on the system within the required time and remained on the machine until just before noon Thursday. Her body temperature was gradually elevated to normal levels within four hours.
Macie will stay at Phoenix Children's for observation. Her mother, Tarin, arrived at her baby's side Wednesday.
Despite the stressful period, the Reynolds' said they look forward to soon returning home with their baby girl.
"You are going to do everything you possibly can do to help your child," Reynolds said.
Reach the reporter at ken.alltucker@arizonarepublic.com or (602)444-8285.
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