[Source: ScienceDaily ] - Researchers at Barrow Neurological Institute at St. Joseph's Hospital and Medical Center recently participated in a pilot study with the Montreal Neurological Institute that suggests a certain type of MRI scanning can detect when a patient is failing brain tumor treatment before symptoms appear. The results of the study pave the way for a proactive treatment approach.
The study followed patients with recurring malignant brain tumors who were receiving chemotherapy. Patients received scans through an imaging device called MR spectroscopy to identify metabolic changes.
The scanning technique suggested that the use of metabolic imaging identifies chemical changes earlier than structural imaging such as a conventional MRI and CT scans. This approach allowed researchers to determine if the tumors were responding to treatment early by assessing metabolic changes in a brain tumor, which are easy to detect and appear before structural changes or symptoms. The result may give patients more time to try another treatment.
"The study has shown for the first time that metabolic response to brain tumor treatment can be detected earlier and faster by metabolic imaging instead of through structural imaging or assessment of the neurological status of a patient," says Mark C. Preul, M.D., Newsome Chair of Neurosurgery Research at St. Joseph's.
The imaging can be done often, poses no radiation hazard and is non-invasive.
"Frequent use of this type of imaging may be a useful tool to follow a patient's response to chemotherapy for malignant brain tumors," says Dr. Preul. "It gives us the ability to identify treatment failure early and more time to alter a patient's treatment plan before the disease progresses."
As a result of the pilot study, Barrow researchers are planning to conduct a second study that will use imaging in the same way to monitor the effects of brain tumor treatment. They are also developing imaging modalities that will show how brain tumors change their shape and metabolism with treatment.
Sunday, August 31, 2008
America's Most Endangered Foods
[Source: Allison Van Dusen, Forbes.com] - Walk the aisles of any grocery store in America and it may seem like the average shopper has access to a wide range of foods. Spend a minute talking to someone knowledgeable about endangered foods, however, and you realize you're only seeing a glimpse of what was once an extremely diverse bounty.
Sure, the average grocery store may carry six or seven different types of apples, some of them grown in America, but a century ago, Americans grew and ate more than 15,000 named varieties. Today you'd probably be lucky if you could find the trees representing the 1,500 kinds remaining in North America, according to Gary Paul Nabhan, editor of Renewing America's Food Traditions. The book lists some of the more than 1,000 food species and varieties once savored by Americans, but are now on the verge of disappearing from the landscape altogether.
In Depth: America's Most Endangered Foods
By displaying these food histories, printing pictures of them in their natural glory and sharing accompanying recipes from early American cooks--Mashpee Wampanoag quahog chowder anyone?--Nabhan hopes to encourage a concept known as eater-based conservation.
"This is not about taking the rarest animal and eating it," says Nabhan, director of the Center for Sustainable Environments at Northern Arizona University. "We're reminding people of the deep historical connections--that some of these foods that are endangered once fed hundreds of thousands of people. We want that to be a motivating force for eaters to be more selective of their choices."
Nabhan's list is organized by regional foodsheds, areas so named by the Renewing America's Food Traditions' collaborative to highlight foods--such as gumbo--that are somewhat iconic.
The effort was founded by seven organizations, including Slow Food USA, American Livestock Breeds Conservancy and Chefs Collaborative, which came together in 2004 to help conserve, restore and celebrate North America's unique food traditions. Nabhan compiled his list by working with collaborative members and talking to farmers, fishermen, foragers, herders, chefs, food historians and folklorists about what foods they've seen dramatically decline over the past few decades.
Among other findings, some of the endangered foods on their way to recovery include the Mission olive, silver fox rabbit and standard varieties of turkeys or heritage turkeys. The desert plum and Carolina northern flying squirrel are still considered too endangered to be eaten.
What Happened
When people hear about endangered foods, they often assume the cause has something to do with the way a fruit or vegetable tastes. But experts say it's more likely the result of changes in the way the country farms and transports goods. For instance, the sweet and flavorful black sphinx date, a new variety that emerged in Arizona in the 1920s, fell out of favor in part because its delicate skin caused it to spoil during long shipments. Traditional food varieties also can be contaminated by cross pollination with genetically modified crops, changing their taste and character. Disease, over-harvesting and climate changes can take a toll over time.
So do people. The spike in the world's population after World War II and the industrialization of agriculture, enabling the mass production of food, helped shape what kinds of livestock we eat, says Chuck Bassett, executive director of the American Livestock Breeds Conservancy. Prior to the war, small farmers raised multipurpose cattle for milk, beef and ability to work. After the war, there was a shift toward farming animals that maximized only one characteristic--one reason behind the popularity of the Holstein, the highest-producing dairy cow. On the other side of the coin, Pineywoods cattle, among the oldest breeds of cattle in the U.S. and one used for dairy as well as beef, were used less and steadily replaced by English and European cattle. Today, Pineywoods cows are considered critically endangered by Nabhan's group.
"When animals lose their jobs, they can become endangered," says Marjie Bender, research and technical program director for the American Livestock Breeds Conservancy.
Diversified Diet, Full Flavors
Many Americans who shop at farmers markets and go to great lengths to eat locally grown foods and diversify their diets likely are already aware of the move to renew interest in the country's endangered foods. But they're greatly outnumbered by those who are unaware of the situation--and who couldn't afford these types of foods anyway. Because of this, they're missing out on something important: flavor.
"You're losing a lot of pleasure in your diet," says Barry Glassner, author of The Gospel of Food. "As in so many other aspects of life, variety truly is the spice of life."
Are you interested in endangered foods? Or is the mainstream selection enough for you? Weigh in. Add your thoughts in the Reader Comments section below.
If you want to wake up your taste buds and help endangered foods make a comeback, your first step should be to look around your foodshed and seek out the rare foods in the recovery process that grow closest to home, Nabhan says. The idea is not to create national demand for these foods, whose producers likely couldn't handle it. Instead, it's to create a local interest that helps the farmers, producers and breeders maintain diversity and possibly, in the process, teach people a little bit of history.
And while some of the foods, such as the Tennessee Fainting Goat, may sound strange or funny, Nabhan hopes people will get over that and remember how these foods were once important to, and even celebrated by, communities.
"The real point," Nabhan says, "is that the textures, flavors and stories behind these foods can really enrich our lives and those of our families."
Sure, the average grocery store may carry six or seven different types of apples, some of them grown in America, but a century ago, Americans grew and ate more than 15,000 named varieties. Today you'd probably be lucky if you could find the trees representing the 1,500 kinds remaining in North America, according to Gary Paul Nabhan, editor of Renewing America's Food Traditions. The book lists some of the more than 1,000 food species and varieties once savored by Americans, but are now on the verge of disappearing from the landscape altogether.
In Depth: America's Most Endangered Foods
By displaying these food histories, printing pictures of them in their natural glory and sharing accompanying recipes from early American cooks--Mashpee Wampanoag quahog chowder anyone?--Nabhan hopes to encourage a concept known as eater-based conservation.
"This is not about taking the rarest animal and eating it," says Nabhan, director of the Center for Sustainable Environments at Northern Arizona University. "We're reminding people of the deep historical connections--that some of these foods that are endangered once fed hundreds of thousands of people. We want that to be a motivating force for eaters to be more selective of their choices."
Nabhan's list is organized by regional foodsheds, areas so named by the Renewing America's Food Traditions' collaborative to highlight foods--such as gumbo--that are somewhat iconic.
The effort was founded by seven organizations, including Slow Food USA, American Livestock Breeds Conservancy and Chefs Collaborative, which came together in 2004 to help conserve, restore and celebrate North America's unique food traditions. Nabhan compiled his list by working with collaborative members and talking to farmers, fishermen, foragers, herders, chefs, food historians and folklorists about what foods they've seen dramatically decline over the past few decades.
Among other findings, some of the endangered foods on their way to recovery include the Mission olive, silver fox rabbit and standard varieties of turkeys or heritage turkeys. The desert plum and Carolina northern flying squirrel are still considered too endangered to be eaten.
What Happened
When people hear about endangered foods, they often assume the cause has something to do with the way a fruit or vegetable tastes. But experts say it's more likely the result of changes in the way the country farms and transports goods. For instance, the sweet and flavorful black sphinx date, a new variety that emerged in Arizona in the 1920s, fell out of favor in part because its delicate skin caused it to spoil during long shipments. Traditional food varieties also can be contaminated by cross pollination with genetically modified crops, changing their taste and character. Disease, over-harvesting and climate changes can take a toll over time.
So do people. The spike in the world's population after World War II and the industrialization of agriculture, enabling the mass production of food, helped shape what kinds of livestock we eat, says Chuck Bassett, executive director of the American Livestock Breeds Conservancy. Prior to the war, small farmers raised multipurpose cattle for milk, beef and ability to work. After the war, there was a shift toward farming animals that maximized only one characteristic--one reason behind the popularity of the Holstein, the highest-producing dairy cow. On the other side of the coin, Pineywoods cattle, among the oldest breeds of cattle in the U.S. and one used for dairy as well as beef, were used less and steadily replaced by English and European cattle. Today, Pineywoods cows are considered critically endangered by Nabhan's group.
"When animals lose their jobs, they can become endangered," says Marjie Bender, research and technical program director for the American Livestock Breeds Conservancy.
Diversified Diet, Full Flavors
Many Americans who shop at farmers markets and go to great lengths to eat locally grown foods and diversify their diets likely are already aware of the move to renew interest in the country's endangered foods. But they're greatly outnumbered by those who are unaware of the situation--and who couldn't afford these types of foods anyway. Because of this, they're missing out on something important: flavor.
"You're losing a lot of pleasure in your diet," says Barry Glassner, author of The Gospel of Food. "As in so many other aspects of life, variety truly is the spice of life."
Are you interested in endangered foods? Or is the mainstream selection enough for you? Weigh in. Add your thoughts in the Reader Comments section below.
If you want to wake up your taste buds and help endangered foods make a comeback, your first step should be to look around your foodshed and seek out the rare foods in the recovery process that grow closest to home, Nabhan says. The idea is not to create national demand for these foods, whose producers likely couldn't handle it. Instead, it's to create a local interest that helps the farmers, producers and breeders maintain diversity and possibly, in the process, teach people a little bit of history.
And while some of the foods, such as the Tennessee Fainting Goat, may sound strange or funny, Nabhan hopes people will get over that and remember how these foods were once important to, and even celebrated by, communities.
"The real point," Nabhan says, "is that the textures, flavors and stories behind these foods can really enrich our lives and those of our families."
Canon links with UA, looks to tech park
[Source: Jack Gillum, Arizona Daily Star] - Imaging giant Canon USA Inc. is negotiating a lease to establish a research-and-development center at the University of Arizona Science and Technology Park, UA officials said.
The center would be home to research under a new collaboration between Canon, a global maker of computer and digital-imaging equipment; and the UA's College of Optical Sciences. The deal also comes with a $3 million research grant for the university.
It also would add another major high-tech tenant to the tech park at 9000 S. Rita Road. The park already is home to IBM Corp., Raytheon Missile Systems and General Dynamics.
"It's a huge deal," said Bob Breault, chairman of Breault Research. Four decades ago, "the hope was that we'd get a Kodak or a Canon to set up shop in Tucson. Now we do."
Few details were available this week, but Canon will be focusing its research on digital photography and medical imaging, said Gary Esham, associate dean of the Optical Sciences College.
The agreement, he said, "brings in dollars to do collaborative work" with the university and faculty. Esham said Canon will initially employ seven people at the park.
The work will include collaborations between Canon and UA faculty members on early-stage development of optics and imaging technologies. It's that faculty connection, Esham said, that made Canon seek out the UA, not the other way around.
"The fact is that this is a research effort, and that is usually the front end of anything that's going on," said Suzanne Gerdes, co-chair of the Arizona Optics Industry Association, an optics trade group. "It's nice to be recognized that the research capabilities are here."
The Canon announcement was discussed at an Arizona Board of Regents meeting earlier this month in Flagstaff. UA Vice Provost for Research Leslie P. Tolbert, who discussed the plan in Flagstaff, called the prospect of the imaging company coming "very exciting" for the UA and for Tucson.
A Canon spokeswoman said the company was not yet ready to release details of the program.
UA tech park spokeswoman Molly Gilbert confirmed that the park is in negotiations with Canon but said a lease has not been finalized.
● Contact reporter Jack Gillum at 573-4178 or at jgillum@azstarnet.com
The center would be home to research under a new collaboration between Canon, a global maker of computer and digital-imaging equipment; and the UA's College of Optical Sciences. The deal also comes with a $3 million research grant for the university.
It also would add another major high-tech tenant to the tech park at 9000 S. Rita Road. The park already is home to IBM Corp., Raytheon Missile Systems and General Dynamics.
"It's a huge deal," said Bob Breault, chairman of Breault Research. Four decades ago, "the hope was that we'd get a Kodak or a Canon to set up shop in Tucson. Now we do."
Few details were available this week, but Canon will be focusing its research on digital photography and medical imaging, said Gary Esham, associate dean of the Optical Sciences College.
The agreement, he said, "brings in dollars to do collaborative work" with the university and faculty. Esham said Canon will initially employ seven people at the park.
The work will include collaborations between Canon and UA faculty members on early-stage development of optics and imaging technologies. It's that faculty connection, Esham said, that made Canon seek out the UA, not the other way around.
"The fact is that this is a research effort, and that is usually the front end of anything that's going on," said Suzanne Gerdes, co-chair of the Arizona Optics Industry Association, an optics trade group. "It's nice to be recognized that the research capabilities are here."
The Canon announcement was discussed at an Arizona Board of Regents meeting earlier this month in Flagstaff. UA Vice Provost for Research Leslie P. Tolbert, who discussed the plan in Flagstaff, called the prospect of the imaging company coming "very exciting" for the UA and for Tucson.
A Canon spokeswoman said the company was not yet ready to release details of the program.
UA tech park spokeswoman Molly Gilbert confirmed that the park is in negotiations with Canon but said a lease has not been finalized.
● Contact reporter Jack Gillum at 573-4178 or at jgillum@azstarnet.com
Biotech firms plant roots in Tucson area to lure top talent
[Source: Ken Alltucker, The Arizona Republic] - A key goal among Phoenix bioscience interests is to create a cluster of research companies that offer high-wage jobs and discover important breakthroughs.
That idea is that a critical mass of companies located near one another would draw batches of smart, talented workers who seek out those employers for challenging and lucrative careers. Such an achievement would spur the type of wealth and innovation that could drive the region's economy.
But some biotech observers believe such a cluster may be emerging in Arizona, just 90 miles south of the Valley in the growing southern Arizona bedroom community of Oro Valley.
The freshest evidence of that is Ventana Medical Systems' recent purchase of a 17-acre site next to its existing campus. About six months after Swiss drug giant Roche plunked down $3.4 billion to purchase Ventana, the company acquired a large chunk with an eye toward a major expansion of its tissue-diagnostics business.
Ventana isn't the only company that has planted its biotech roots in the Tucson suburb. French drugmaker sanofi-aventis is building a new research lab in the same technology park where Ventana is headquartered, and the small-but-growing tech firm Integrated Biomolecule Corp. also is expanding its workforce.
All companies have ties to the University of Arizona, and all the companies have big growth plans.
"This is a good model of what you want to happen in Phoenix and Flagstaff," Walt Plosila, a senior adviser to Ohio-based Battelle Technology Partnership Practice, said of the emerging Oro Valley cluster.
Science Foundation Arizona President and Chief Executive Officer William Harris also has taken note. The foundation's charge is to improve the state's science and technology initiatives through strategic investments in companies and education.
"It shows how you can diversify the economy," Harris said.
Similar efforts are under way to foster such bioscience growth in the Phoenix area.
The state of Arizona and city of Phoenix has invested tens of millions on a downtown biomedical hub anchored by the Translational Genomics Research Institute and a new medical school. And Arizona State University's five-year-old Biodesign Institute is beginning to churn out companies in research areas as alternative energy.
But Plosila and others believe that the Phoenix-area's growing biotech scene has not reached a critical mass of private bioscience companies yet that rivals such clusters as San Diego, San Francisco or Boston.
Phoenix and Flagstaff have made some biotech niches, particularly in medical-device manufacturing. The keys to attracting more research jobs and company clusters are sustained, targeted investment to nurture good ideas and attract private capital.
"It is sort of the entrepreneurial hotbed of Arizona in terms of research and development," Plosila said of Oro Valley.
University of Arizona roots
Ventana, in particular, shows the potential for one idea to have a major impact on the community, Harris said.
Dr. Thomas Grogan, a UA pathology professor, started the company in the mid-1980s over his frustration with the accuracy of cancer tests. He developed his own testing methods, arranged findings and built a company that went public in 1996 until its purchase by Roche this year.
"It's the genius of one person who created an idea that has been purchased by Roche and has created a lot of wealth," Harris said.
Today, Ventana employs about 900. About 600 research and development, executive, administrative and manufacturing positions are at the company's headquarters, and the company has 165 positions it plans to fill, spokeswoman Alana Bolton said.
The company has not laid out detailed plans for its expansion other than to say Roche's global business and international ties are expected to generate more jobs in Oro Valley.
"We will be the hub and center for tissue-based diagnostics for cancer," Bolton said. "We will grow and get bigger."
Among the major pharmaceutical companies, Roche has been the most aggressive in pursuing the personalized drugs based on a person's genetic makeup.
"The reason why Roche bought Ventana is because they recognize personalized medicine will only come from having the expertise that Ventana has," said Ray Woosley, president and chief executive officer of the Tucson-based Critical Path Institute, a non-profit group that works with federal regulators and biotech companies to speed the approval process for pharmaceuticals and medical devices.
On the heels of its Ventana acquisition, Roche is seeking to further bolster its biotech business with an attempt to purchase South San Francisco-based Genentech. Genentech has rebuffed Roche's initial offer of $89 per share but has appointed a special committee that will consider subsequent offers.
Roche largely plans to keep Ventana's operations and culture in tact. One sign of that is that Ventana CEO Christopher Gleeson has retained his position. Bolton declined to say how many people left the company after the merger.
More expansion
Sanofi-aventis is another pharmaceutical company that is investing millions in Oro Valley. The drugmaker is building a $60 million research lab slated to open in June. The company now employs 60 chemists, biologists and other staff. The new facility has the capacity for 108 workers, but the company has no firm timeline on when those positions will be filled, spokeswoman Janet Metz said.
Sanofi-aventis has recruited scientists from UA as well as attracted talent from out of state. "They (Oro Valley) seem to be building the new biotech hub, and that's where we wanted to be," Metz said.
Robert Green has seen the growth of Oro Valley's biotech sector since relocating his company to the town in 2004. His company, Integrated Biomolecule Corp., provides services such as analytical testing and product development for pharmaceutical companies.
"It was a town that clearly said they would like us to be here and like us to help build a biotech cluster," said Green, who founded the company in his garage and later worked from UA's science and technology park before locating to Oro Valley.
He said Oro Valley has a wide range of housing prices and quality schools, two factors that help draw employees.
"For years, we were an outpost in Oro Valley with clients out of state," Green said. "Now that is switching. We have a lot of support with companies in the state. All of this clustering activity contributes to that."
Representatives of the region's main economic development group, Tucson Regional Economic Opportunities, said years of investment in UA is beginning to pay off for Southern Arizona.
TREO counts more 100 biotech companies employing more than 2,000 non-hospital workers in the Tucson-Oro valley region.
"The investment in the university system is paying huge economic dividends for us now," said David Welsh, TREO's senior vice president for strategic partnerships.
Oro Valley Mayor Paul Loomis said large employers such as Ventana benefit the town more than just economically. The company supports a half marathon and cultural groups such as the Greater Oro Valley Arts Council.
"They are the flagship of our biotech community," Loomis said.
That idea is that a critical mass of companies located near one another would draw batches of smart, talented workers who seek out those employers for challenging and lucrative careers. Such an achievement would spur the type of wealth and innovation that could drive the region's economy.
But some biotech observers believe such a cluster may be emerging in Arizona, just 90 miles south of the Valley in the growing southern Arizona bedroom community of Oro Valley.
The freshest evidence of that is Ventana Medical Systems' recent purchase of a 17-acre site next to its existing campus. About six months after Swiss drug giant Roche plunked down $3.4 billion to purchase Ventana, the company acquired a large chunk with an eye toward a major expansion of its tissue-diagnostics business.
Ventana isn't the only company that has planted its biotech roots in the Tucson suburb. French drugmaker sanofi-aventis is building a new research lab in the same technology park where Ventana is headquartered, and the small-but-growing tech firm Integrated Biomolecule Corp. also is expanding its workforce.
All companies have ties to the University of Arizona, and all the companies have big growth plans.
"This is a good model of what you want to happen in Phoenix and Flagstaff," Walt Plosila, a senior adviser to Ohio-based Battelle Technology Partnership Practice, said of the emerging Oro Valley cluster.
Science Foundation Arizona President and Chief Executive Officer William Harris also has taken note. The foundation's charge is to improve the state's science and technology initiatives through strategic investments in companies and education.
"It shows how you can diversify the economy," Harris said.
Similar efforts are under way to foster such bioscience growth in the Phoenix area.
The state of Arizona and city of Phoenix has invested tens of millions on a downtown biomedical hub anchored by the Translational Genomics Research Institute and a new medical school. And Arizona State University's five-year-old Biodesign Institute is beginning to churn out companies in research areas as alternative energy.
But Plosila and others believe that the Phoenix-area's growing biotech scene has not reached a critical mass of private bioscience companies yet that rivals such clusters as San Diego, San Francisco or Boston.
Phoenix and Flagstaff have made some biotech niches, particularly in medical-device manufacturing. The keys to attracting more research jobs and company clusters are sustained, targeted investment to nurture good ideas and attract private capital.
"It is sort of the entrepreneurial hotbed of Arizona in terms of research and development," Plosila said of Oro Valley.
University of Arizona roots
Ventana, in particular, shows the potential for one idea to have a major impact on the community, Harris said.
Dr. Thomas Grogan, a UA pathology professor, started the company in the mid-1980s over his frustration with the accuracy of cancer tests. He developed his own testing methods, arranged findings and built a company that went public in 1996 until its purchase by Roche this year.
"It's the genius of one person who created an idea that has been purchased by Roche and has created a lot of wealth," Harris said.
Today, Ventana employs about 900. About 600 research and development, executive, administrative and manufacturing positions are at the company's headquarters, and the company has 165 positions it plans to fill, spokeswoman Alana Bolton said.
The company has not laid out detailed plans for its expansion other than to say Roche's global business and international ties are expected to generate more jobs in Oro Valley.
"We will be the hub and center for tissue-based diagnostics for cancer," Bolton said. "We will grow and get bigger."
Among the major pharmaceutical companies, Roche has been the most aggressive in pursuing the personalized drugs based on a person's genetic makeup.
"The reason why Roche bought Ventana is because they recognize personalized medicine will only come from having the expertise that Ventana has," said Ray Woosley, president and chief executive officer of the Tucson-based Critical Path Institute, a non-profit group that works with federal regulators and biotech companies to speed the approval process for pharmaceuticals and medical devices.
On the heels of its Ventana acquisition, Roche is seeking to further bolster its biotech business with an attempt to purchase South San Francisco-based Genentech. Genentech has rebuffed Roche's initial offer of $89 per share but has appointed a special committee that will consider subsequent offers.
Roche largely plans to keep Ventana's operations and culture in tact. One sign of that is that Ventana CEO Christopher Gleeson has retained his position. Bolton declined to say how many people left the company after the merger.
More expansion
Sanofi-aventis is another pharmaceutical company that is investing millions in Oro Valley. The drugmaker is building a $60 million research lab slated to open in June. The company now employs 60 chemists, biologists and other staff. The new facility has the capacity for 108 workers, but the company has no firm timeline on when those positions will be filled, spokeswoman Janet Metz said.
Sanofi-aventis has recruited scientists from UA as well as attracted talent from out of state. "They (Oro Valley) seem to be building the new biotech hub, and that's where we wanted to be," Metz said.
Robert Green has seen the growth of Oro Valley's biotech sector since relocating his company to the town in 2004. His company, Integrated Biomolecule Corp., provides services such as analytical testing and product development for pharmaceutical companies.
"It was a town that clearly said they would like us to be here and like us to help build a biotech cluster," said Green, who founded the company in his garage and later worked from UA's science and technology park before locating to Oro Valley.
He said Oro Valley has a wide range of housing prices and quality schools, two factors that help draw employees.
"For years, we were an outpost in Oro Valley with clients out of state," Green said. "Now that is switching. We have a lot of support with companies in the state. All of this clustering activity contributes to that."
Representatives of the region's main economic development group, Tucson Regional Economic Opportunities, said years of investment in UA is beginning to pay off for Southern Arizona.
TREO counts more 100 biotech companies employing more than 2,000 non-hospital workers in the Tucson-Oro valley region.
"The investment in the university system is paying huge economic dividends for us now," said David Welsh, TREO's senior vice president for strategic partnerships.
Oro Valley Mayor Paul Loomis said large employers such as Ventana benefit the town more than just economically. The company supports a half marathon and cultural groups such as the Greater Oro Valley Arts Council.
"They are the flagship of our biotech community," Loomis said.
Friday, August 29, 2008
Forensic Breakthrough Stirs NIH to Close GWAS Data from Public View
[GenomeWeb News] – Large amounts of aggregate human DNA data that the National Institutes of Health and other groups made open to researchers around the world is being locked up from public view due to privacy concerns that arose this week when a new forensic DNA method was announced that could conceivably leave people vulnerable to identification.
Until now, there was little concern that information from large public databases of information from genome-wide association studies could be used to identify singular individuals out of the thousands who gave samples.
But a study released this week by the Translational Genomics Research Institute and the University of California, Los Angeles, which is aimed at helping crime solvers identify one person from among many potentially contaminated DNA samples at a crime scene, spurred NIH to close down their publicly available GWAS databases.
NIH said today that on Aug. 25 it removed aggregate statistics files of individual GWAS studies, including the Database of Genotypes and Phenotypes (dbGaP), run by the National Center for Biotechnology Information, and the Caner Genetic Markers of Susceptibility database, run by the National Cancer Institute.
That data is still available for use by researchers who apply for access to the data and agree to protect its confidentiality using the same approach they do for individual-level study data.
NIH also confirmed that other groups, including the Wellcome Trust Case Control Consortium, and the Broad Institute of MIT and Harvard, that have been hosting such public datasets, also have removed the aggregate data from public availability.
The TGen and UCLA research shows that it’s possible to use an algorithm and Affymetrix or Illumina microarrays “to find an individual of interest in a mixture of hundreds or even thousands of people’s DNA,” as was reported earlier today in GenomeWeb Daily News. Among the potential real-world applications, the researchers noted that this technique holds particular promise for forensics investigations, since it opens the door to analyzing contaminated DNA samples or sampling a large crime scene area.
“Similarly, it might provide closure to families of victims of mass disaster if individual DNA profiles could be identified from mixed samples,” Kathy Hudson, director of the Genetics and Public Policy Center at Johns Hopkins University, said today in an e-mail to GenomeWeb Daily News. “Those are both two great contributions of genome science to society,” Hudson added.
This method also could potentially be used to identify individuals from a GWAS-style aggregate database, although, TGen researcher David Craig told GWDN today, it is unlikely any information could have been compromised so far.
To dig out one specific profile from within a set, the inquirer would need to have a “highly dense genomic profile” of at least 10,000 specific genetic variations from an individual. That profile of single nucleotide polymorphisms then would be compared against the dataset to measure its uniqueness.
However complex, NIH admitted that this new analytical tool goes beyond prior expectations, which held that individual profiles would need to be compared one against another to confirm a match, and that it is now possible to detect a single profile even in pooled data.
When Craig alerted NIH to the methods that TGen and UCLA were developing, NIH tested it out and then began fashioning its policy response and then notified the Broad Institute and the Wellcome Trust about the vulnerability. Craig noted that he worked with NIH in advance of the release of this study, and that they were preparing for how to handle their public databases.
“We knew the implications, and we worked with [NIH] for a while,” Craig said. NIH “took all of this very seriously, even though it really sounds kind of farfetched,” he explained. “They went down a very pre-emptive path.”
NIH and other groups conducting GWA studies know that one of the core ethical components of their work, and a critical element of convincing people to participate in these studies, is offering the closest guarantee possible that their personal medical and genomic information will not be compromised. As genomics researchers launch major pushes to try to recruit new people to join GWA studies, they will want assurances that no one will pinpoint them and misuse their information in unethical or harmful ways.
GPPC’s Kathy Hudson described one of the ethical concerns in her e-mail: “So, the unlikely but concerning scenario is that law enforcement has a DNA sample from a crime scene, searches an NIH database, finds a match and gets a subpoena to identify what researcher provided the cohort data.
“While a fairly remote concern, and there are some protections even against subpoena, NIH did the right thing in acting to protect research participants,” she wrote.
NIH said today that it is “unaware that [this technique] has been used to compromise any information within NIH GWAS datasets,” and added that the genomics tools required are “not commonly used outside of the research community.”
Further, NIH said, “even if an individual’s SNP profile was found within a pooled dataset, all that would be learned is that this profile was contained in the dataset and, thus, it could then be associated with the characteristics of that dataset (e.g., disease or control population).”
That is not a concern because the NIH’s GWAS databases do not contain names or other such identifiable information about participants.
“The confidence level in the system is very high,” said Laura Rodriguez, who is acting director of the National Human Genome Research Institute’s Office of Policy Communications and Education.
Under a new policy adopted earlier this year, which now will cover the aggregate data from GWA studies, “Access is granted for a specific research purpose, for a specific data set, for a specific period of time.”
When the news came up that this new method was possible, Rodriguez said, NIH wanted to respond very prudently. “Our goal is to protect confidentiality of the data, and that’s why we took the cautious step,” she said.
Rodriguez expects that in the long run this new research will not steer individuals away from participating in GWA studies, and she said that NIH expects to continue to provide access to this data, if through a more secure process.
She added that NIH is still considering how it will handle these types of databases in the future, and she admitted “this issue is broader than dbGaP now,” and that NIH is “aware of the bigger picture. She also admits that they were taken by surprise.
“People really didn’t think this could be true,” she said.
Until now, there was little concern that information from large public databases of information from genome-wide association studies could be used to identify singular individuals out of the thousands who gave samples.
But a study released this week by the Translational Genomics Research Institute and the University of California, Los Angeles, which is aimed at helping crime solvers identify one person from among many potentially contaminated DNA samples at a crime scene, spurred NIH to close down their publicly available GWAS databases.
NIH said today that on Aug. 25 it removed aggregate statistics files of individual GWAS studies, including the Database of Genotypes and Phenotypes (dbGaP), run by the National Center for Biotechnology Information, and the Caner Genetic Markers of Susceptibility database, run by the National Cancer Institute.
That data is still available for use by researchers who apply for access to the data and agree to protect its confidentiality using the same approach they do for individual-level study data.
NIH also confirmed that other groups, including the Wellcome Trust Case Control Consortium, and the Broad Institute of MIT and Harvard, that have been hosting such public datasets, also have removed the aggregate data from public availability.
The TGen and UCLA research shows that it’s possible to use an algorithm and Affymetrix or Illumina microarrays “to find an individual of interest in a mixture of hundreds or even thousands of people’s DNA,” as was reported earlier today in GenomeWeb Daily News. Among the potential real-world applications, the researchers noted that this technique holds particular promise for forensics investigations, since it opens the door to analyzing contaminated DNA samples or sampling a large crime scene area.
“Similarly, it might provide closure to families of victims of mass disaster if individual DNA profiles could be identified from mixed samples,” Kathy Hudson, director of the Genetics and Public Policy Center at Johns Hopkins University, said today in an e-mail to GenomeWeb Daily News. “Those are both two great contributions of genome science to society,” Hudson added.
This method also could potentially be used to identify individuals from a GWAS-style aggregate database, although, TGen researcher David Craig told GWDN today, it is unlikely any information could have been compromised so far.
To dig out one specific profile from within a set, the inquirer would need to have a “highly dense genomic profile” of at least 10,000 specific genetic variations from an individual. That profile of single nucleotide polymorphisms then would be compared against the dataset to measure its uniqueness.
However complex, NIH admitted that this new analytical tool goes beyond prior expectations, which held that individual profiles would need to be compared one against another to confirm a match, and that it is now possible to detect a single profile even in pooled data.
When Craig alerted NIH to the methods that TGen and UCLA were developing, NIH tested it out and then began fashioning its policy response and then notified the Broad Institute and the Wellcome Trust about the vulnerability. Craig noted that he worked with NIH in advance of the release of this study, and that they were preparing for how to handle their public databases.
“We knew the implications, and we worked with [NIH] for a while,” Craig said. NIH “took all of this very seriously, even though it really sounds kind of farfetched,” he explained. “They went down a very pre-emptive path.”
NIH and other groups conducting GWA studies know that one of the core ethical components of their work, and a critical element of convincing people to participate in these studies, is offering the closest guarantee possible that their personal medical and genomic information will not be compromised. As genomics researchers launch major pushes to try to recruit new people to join GWA studies, they will want assurances that no one will pinpoint them and misuse their information in unethical or harmful ways.
GPPC’s Kathy Hudson described one of the ethical concerns in her e-mail: “So, the unlikely but concerning scenario is that law enforcement has a DNA sample from a crime scene, searches an NIH database, finds a match and gets a subpoena to identify what researcher provided the cohort data.
“While a fairly remote concern, and there are some protections even against subpoena, NIH did the right thing in acting to protect research participants,” she wrote.
NIH said today that it is “unaware that [this technique] has been used to compromise any information within NIH GWAS datasets,” and added that the genomics tools required are “not commonly used outside of the research community.”
Further, NIH said, “even if an individual’s SNP profile was found within a pooled dataset, all that would be learned is that this profile was contained in the dataset and, thus, it could then be associated with the characteristics of that dataset (e.g., disease or control population).”
That is not a concern because the NIH’s GWAS databases do not contain names or other such identifiable information about participants.
“The confidence level in the system is very high,” said Laura Rodriguez, who is acting director of the National Human Genome Research Institute’s Office of Policy Communications and Education.
Under a new policy adopted earlier this year, which now will cover the aggregate data from GWA studies, “Access is granted for a specific research purpose, for a specific data set, for a specific period of time.”
When the news came up that this new method was possible, Rodriguez said, NIH wanted to respond very prudently. “Our goal is to protect confidentiality of the data, and that’s why we took the cautious step,” she said.
Rodriguez expects that in the long run this new research will not steer individuals away from participating in GWA studies, and she said that NIH expects to continue to provide access to this data, if through a more secure process.
She added that NIH is still considering how it will handle these types of databases in the future, and she admitted “this issue is broader than dbGaP now,” and that NIH is “aware of the bigger picture. She also admits that they were taken by surprise.
“People really didn’t think this could be true,” she said.
TGen Scientists Uncover New Field of Research that could Help Police in Crime Scene Forensics
[Source: TGen] - A team of investigators led by scientists at the Translational Genomics Research Institute (TGen) have found a way to identify possible suspects at crime scenes using only a small amount of DNA, even if it is mixed with hundreds of other genetic fingerprints.
Using genotyping microarrays, the scientists were able to identify an individuals DNA from within a mix of DNA samples, even if that individual represented less than 0.1 percent of the total mix, or less than one part per thousand. They were able to do this even when the mix of DNA included more than 200 individual DNA samples.
The results appear today in PLoS Genetics, a peer-reviewed open-access journal published by the Public Library of Science.
The discovery could help police investigators better identify possible suspects, even when dozens of people over time have been at a crime scene. It also could help reassess previous crime scene evidence, and it could have other uses in various genetic studies and in statistical analysis.
"This is a potentially revolutionary advance in the field of forensics," said the paper's senior author, Dr. David W. Craig, associate director of TGen's Neurogenomics Division, which otherwise is charged with finding ways to treat diseases and conditions of the brain and nervous system. "By employing the powers of genomic technology, it is now possible to know with near certainty that a particular individual was at a particular location, even with only trace amounts of DNA and even if dozens or even hundreds of others were there, too."
The researchers analyzed complex mixes of genomic DNA using high-density Single Nucleotide Polymorphism (SNP) genotyping microarrays. This approach enabled them to accurately identify individuals from DNA mixes of at least 200 people using less than one in one-thousandth of the total mix. Theoretically, they showed that individuals could be identified in mixes of more than 1,000 people.
Currently, it is difficult for police forensic investigators to detect an individual if their genomic DNA is less than 10 percent of a mix, or if it is from a large mix of DNA material. A long-held assumption within the field of forensic science was that it was not possible to identify individuals using pooled data — until now.
According to Commander Brent Vermeer, director of the Phoenix Police Department crime lab, much DNA evidence is rendered useless because of contamination, and that to eventually put the TGen theoretical research into a cost-effective police practice “would be an amazing asset.’’
A new Arizona law, Senate Bill 1412, passed in June by the Legislature, requires police agencies to keep DNA evidence in cases of homicide or felony sexual assault for as long as convicts are in prison or on supervised release, or at least 55 years in unsolved cases. Some like Phoenix keep it indefinitely.
"As technology advances, we need to be prepared to keep evidence that, down the road, could prove again to be useful," said Vermeer, who heads a bureau of nearly 130 analysts and crime scene investigators.
Craig said the findings presented in the paper should foster more scientific investigation that could lead to cost-effective ways of using the TGen technology to fight crime.
"It opens up ideas never considered before," Craig said.
Dr. Stanley F. Nelson, director of the UCLA site of the National Institute of Health’s Neuroscience Microarray Consortium, said forensics investigators are "often stymied" because they now search for fewer than 20 DNA markers. The TGen researchers looked at hundreds of thousands of markers to make their identifications, he said."
It opens up a whole new can of worms of what’s possible to do forensically," said Nelson, professor of Human Genetics and Psychiatry at UCLA’s David Geffen School of Medicine. Nelson contributed to the TGen paper.
Nelson said that, using current police methods, DNA processing costs less than $50, while a similar process for genomic research costs several hundred dollars. However, with advances in technology, those costs should come down, he said.
The TGen study resulted from what Nelson described as "an intellectual curiosity" by Craig while investigating diseases. Nils Homer, a former TGen intern who now is working on his doctorate degree in computer science at UCLA, brought Nelson and Craig together. Homer is the paper’s first author.
"We demonstrate an approach for rapidly and sensitively determining whether a trace amount... of genomic DNA from an individual is present within a complex DNA mixture," the paper said.
Using genotyping microarrays, the scientists were able to identify an individuals DNA from within a mix of DNA samples, even if that individual represented less than 0.1 percent of the total mix, or less than one part per thousand. They were able to do this even when the mix of DNA included more than 200 individual DNA samples.
The results appear today in PLoS Genetics, a peer-reviewed open-access journal published by the Public Library of Science.
The discovery could help police investigators better identify possible suspects, even when dozens of people over time have been at a crime scene. It also could help reassess previous crime scene evidence, and it could have other uses in various genetic studies and in statistical analysis.
"This is a potentially revolutionary advance in the field of forensics," said the paper's senior author, Dr. David W. Craig, associate director of TGen's Neurogenomics Division, which otherwise is charged with finding ways to treat diseases and conditions of the brain and nervous system. "By employing the powers of genomic technology, it is now possible to know with near certainty that a particular individual was at a particular location, even with only trace amounts of DNA and even if dozens or even hundreds of others were there, too."
The researchers analyzed complex mixes of genomic DNA using high-density Single Nucleotide Polymorphism (SNP) genotyping microarrays. This approach enabled them to accurately identify individuals from DNA mixes of at least 200 people using less than one in one-thousandth of the total mix. Theoretically, they showed that individuals could be identified in mixes of more than 1,000 people.
Currently, it is difficult for police forensic investigators to detect an individual if their genomic DNA is less than 10 percent of a mix, or if it is from a large mix of DNA material. A long-held assumption within the field of forensic science was that it was not possible to identify individuals using pooled data — until now.
According to Commander Brent Vermeer, director of the Phoenix Police Department crime lab, much DNA evidence is rendered useless because of contamination, and that to eventually put the TGen theoretical research into a cost-effective police practice “would be an amazing asset.’’
A new Arizona law, Senate Bill 1412, passed in June by the Legislature, requires police agencies to keep DNA evidence in cases of homicide or felony sexual assault for as long as convicts are in prison or on supervised release, or at least 55 years in unsolved cases. Some like Phoenix keep it indefinitely.
"As technology advances, we need to be prepared to keep evidence that, down the road, could prove again to be useful," said Vermeer, who heads a bureau of nearly 130 analysts and crime scene investigators.
Craig said the findings presented in the paper should foster more scientific investigation that could lead to cost-effective ways of using the TGen technology to fight crime.
"It opens up ideas never considered before," Craig said.
Dr. Stanley F. Nelson, director of the UCLA site of the National Institute of Health’s Neuroscience Microarray Consortium, said forensics investigators are "often stymied" because they now search for fewer than 20 DNA markers. The TGen researchers looked at hundreds of thousands of markers to make their identifications, he said."
It opens up a whole new can of worms of what’s possible to do forensically," said Nelson, professor of Human Genetics and Psychiatry at UCLA’s David Geffen School of Medicine. Nelson contributed to the TGen paper.
Nelson said that, using current police methods, DNA processing costs less than $50, while a similar process for genomic research costs several hundred dollars. However, with advances in technology, those costs should come down, he said.
The TGen study resulted from what Nelson described as "an intellectual curiosity" by Craig while investigating diseases. Nils Homer, a former TGen intern who now is working on his doctorate degree in computer science at UCLA, brought Nelson and Craig together. Homer is the paper’s first author.
"We demonstrate an approach for rapidly and sensitively determining whether a trace amount... of genomic DNA from an individual is present within a complex DNA mixture," the paper said.
Wednesday, August 27, 2008
Despite rocky start, medical school presses on
[Source: Ken Alltucker, The Arizona Republic ] - Arizona leaders see the new University of Arizona medical-school campus in downtown Phoenix as an anchor of a biomedical hub that will train more doctors, foster cutting-edge research and spur the state's economy.
But as 48 students usher in the Phoenix college's second year of instruction, much has changed from the original vision.
The medical school's leadership is being overhauled. Plans for a new downtown teaching hospital have stalled. And the school's Tucson faculty members have raised questions about whether the Phoenix campus will take away limited resources.
University officials acknowledge a rocky start in some respects for the nearly 2-year-old Phoenix campus.
"Any new concept will have some growing pains," said Robert Bulla, a member of the Arizona Board of Regents and a regents committee overseeing development of the biomedical campus.
"I am not disappointed that it has been slow, but it has taken a little longer than I hoped to get things in place," Bulla added.
Still, no one doubts the University of Arizona College of Medicine-Phoenix in partnership with Arizona State University has made significant strides since its official October 2006 dedication.
The school has assembled its curriculum, hired faculty and welcomed the first two classes of medical students. It also has secured funds to pursue an ambitious expansion that will add a new educational and a state-of-the-art research lab that will be shared by the state's three public universities.
The school is a key part of the state's strategy, pushed by Gov. Janet Napolitano and others, to build a research-based economy and improve medical care.
Phoenix and the state have invested millions to develop and expand the medical school and to launch bioscience research facilities such as the Translational Genomics Research Institute to attract top-tier scientists. At the downtown campus, medical students rub elbows with top-notch genetic researchers who are developing advanced medical treatments.
Among the goals are to graduate more doctors in a state with one of the lowest per capita figures of physicians and to expand the state's access to clinical trials and other treatments.
Changing visions
The Phoenix medical school's challenges are not unique.
Expanding medical schools often must grapple with changes in funding, staffing and training locations for students, said Sarah Bunton, a senior research analyst with the Association of American Medical Colleges.
"There are no formulaic answers to increasing class size," said Bunton, who added that administrators must be flexible when planning medical-school expansions.
Some factors that slowed the pace of the Phoenix medical school's progress over the past two years:
• The dean of the medical school in Phoenix resigned in April after his title was changed to vice dean by Tucson's medical dean. The Tucson dean later resigned as part of a restructuring orchestrated by UA President Robert Shelton. UA hired a new vice president for health affairs, William Crist, who will be in charge of both medical campuses as well as the university's other health schools.
• Plans for a new downtown teaching hospital are on hold. The university no longer is soliciting new bids for hospital partners, and the newly appointed Crist sees no immediate need for a new hospital.
• A committee report issued this spring revealed fresh evidence that some UA faculty are concerned that the Phoenix campus is "draining human and financial resources" from the Tucson campus.
• The campus is building-rich but budget-challenged. A $470 million stimulus package will fund the buildings needed to expand the campus at the same time the state's budget cuts have forced administrators to scale back hiring new faculty and staff. And private fundraising has been slow to materialize.
Leadership shakeup
Perhaps the downtown medical school's most pressing need comes at the top.
The Phoenix campus has not had a permanent dean since Edward "Ted" Shortliffe stepped down this spring. Shortliffe resigned his position after the Tucson-based dean, Keith Joiner, changed Shortliffe's title from dean to vice dean.
At the time, Joiner cited confusion of having two deans on separate campuses, but Joiner was not long for his position at the time, either. He relinquished his deanship as part of a restructuring orchestrated by Shelton.
Shelton created a single position responsible for UA's vast health-sciences area, including both medical campuses. Crist was hired for the $650,000-a-year position of vice president for health affairs. He expects to start Oct. 31.
Many factors brought about the leadership change. The Committee of Eleven, which investigates faculty complaints, issued a report in April that revealed low morale and concerns about the direction of the medical school. Faculty expressed worry about decision making, academic freedom and other factors. Some faculty members said they were worried about the emergence of the Phoenix medical school.
Michael Cusanovich, who chairs the Committee of Eleven, said Tucson faculty members are worried that the Phoenix campus will divert financial resources and brainpower.
"The biggest concern is how much money gets diverted out of here (Tucson) to Phoenix," Cusanovich said, adding that the Tucson campus will have to share state funding and research grants. "Those are dollars, from a parochial point of view, that will not be available here."
Budget woes hit Phoenix
Valley residents believe a full-time dean at the Phoenix campus is important for many reasons, from sustaining relationships with area hospitals and doctors groups to fundraising.
Stuart Flynn has served as interim dean in Phoenix since Shortliffe stepped down, and he has piloted the campus through cuts that stripped 4 percent from this year's budget.
Flynn said the budget cuts have hurt the ability to add more faculty, but he said it has not affected services to the school's 48 first-year and 24 second-year students.
"It will slow down our ability to grow our faculty on this campus," Flynn said of the budget cuts.
Mining the Valley and out-of-state donors for charitable giving is an important role for Crist and the new dean. Such contributions support important things such as recruiting faculty and providing scholarships for students.
UA Foundation President Jim Moore said the university has secured some contributions but needs to attract more donors for the new Phoenix school.
Hospital plan on hold
While the students are busy learning the basics, the prospects for a downtown teaching hospital are less clear.
Plans for such a hospital have been on hold since talks between Banner Health and UA broke down over disagreements about the size of the proposed hospital and faculty salary. UA put out a request for information among potential new suitors last January. Only Maricopa Integrated Health System responded with a hospital plan.
Now, UA representatives say it will be Crist's job to sort out the hospital proposal, and he said there is no pressing need for a teaching hospital in downtown Phoenix.
Crist said he visited several Phoenix-area hospitals that already train UA students and chatted with executives. With several area hospitals such as St. Joseph's Hospital and Medical Center, Banner Good Samaritan, Carl T. Hayden Veterans Affairs Medical Center and others already training UA medical students, he doesn't see an immediate need to build a new hospital in downtown Phoenix to train students.
"I saw no obvious need, at my first pass level, for more teaching facilities," Crist said.
Maricopa Integrated's chief executive, Betsey Bayless, wants to continue talks with the university when Crist takes over.
"The (MIHS) board several years ago adopted a resolution that they want to build a hospital in conjunction with UA," Bayless said. "I think they are still interested."
Maricopa Integrated needs to replace its Maricopa Medical Center whether it is in tandem with UA or not.
Bayless said the district spends up to $20 million a year on repairs to the aging facility. She estimates it would cost the district $40 million a year in debt and interest payments for a new hospital.
Maricopa Integrated, however, must find the money to pay for such a hospital.
Bayless said the one potential source of money could be federal funds that help hospitals pay for uncompensated-care costs.
Arizona funneled $55 million, called disproportionate-share funds, to the state's general fund to support the state's program for low-income patients. Maricopa Integrated has appealed the state's decision to keep the money, arguing that it needs the money to support its role as a "safety net" hospital that provides care for the poor and uninsured.
Another potential funding source, Bayless said, could be a voter-approved bond to pay construction costs. The health district's board would need to approve a measure to pursue such a funding plan and has not done so yet.
"The (Maricopa Integrated) board has the capability of going to the ballot and going for a bond issue," Bayless said. "I know their preference has been to get the disproportionate-share money and get those funds that were intended for indigent patients so we could go ahead and build using that money."
Although no other Phoenix-area hospital has expressed interest in building a new hospital with UA, at least one government hospital shares a similar challenge with Maricopa. The VA hospital, built in 1951, faces high maintenance needs.
Executive Director Donald Moore said his facility will continue to be an important training ground for UA medical students, but he has not talked about the possibility of building a hospital jointly with UA or Maricopa Integrated.
But as 48 students usher in the Phoenix college's second year of instruction, much has changed from the original vision.
The medical school's leadership is being overhauled. Plans for a new downtown teaching hospital have stalled. And the school's Tucson faculty members have raised questions about whether the Phoenix campus will take away limited resources.
University officials acknowledge a rocky start in some respects for the nearly 2-year-old Phoenix campus.
"Any new concept will have some growing pains," said Robert Bulla, a member of the Arizona Board of Regents and a regents committee overseeing development of the biomedical campus.
"I am not disappointed that it has been slow, but it has taken a little longer than I hoped to get things in place," Bulla added.
Still, no one doubts the University of Arizona College of Medicine-Phoenix in partnership with Arizona State University has made significant strides since its official October 2006 dedication.
The school has assembled its curriculum, hired faculty and welcomed the first two classes of medical students. It also has secured funds to pursue an ambitious expansion that will add a new educational and a state-of-the-art research lab that will be shared by the state's three public universities.
The school is a key part of the state's strategy, pushed by Gov. Janet Napolitano and others, to build a research-based economy and improve medical care.
Phoenix and the state have invested millions to develop and expand the medical school and to launch bioscience research facilities such as the Translational Genomics Research Institute to attract top-tier scientists. At the downtown campus, medical students rub elbows with top-notch genetic researchers who are developing advanced medical treatments.
Among the goals are to graduate more doctors in a state with one of the lowest per capita figures of physicians and to expand the state's access to clinical trials and other treatments.
Changing visions
The Phoenix medical school's challenges are not unique.
Expanding medical schools often must grapple with changes in funding, staffing and training locations for students, said Sarah Bunton, a senior research analyst with the Association of American Medical Colleges.
"There are no formulaic answers to increasing class size," said Bunton, who added that administrators must be flexible when planning medical-school expansions.
Some factors that slowed the pace of the Phoenix medical school's progress over the past two years:
• The dean of the medical school in Phoenix resigned in April after his title was changed to vice dean by Tucson's medical dean. The Tucson dean later resigned as part of a restructuring orchestrated by UA President Robert Shelton. UA hired a new vice president for health affairs, William Crist, who will be in charge of both medical campuses as well as the university's other health schools.
• Plans for a new downtown teaching hospital are on hold. The university no longer is soliciting new bids for hospital partners, and the newly appointed Crist sees no immediate need for a new hospital.
• A committee report issued this spring revealed fresh evidence that some UA faculty are concerned that the Phoenix campus is "draining human and financial resources" from the Tucson campus.
• The campus is building-rich but budget-challenged. A $470 million stimulus package will fund the buildings needed to expand the campus at the same time the state's budget cuts have forced administrators to scale back hiring new faculty and staff. And private fundraising has been slow to materialize.
Leadership shakeup
Perhaps the downtown medical school's most pressing need comes at the top.
The Phoenix campus has not had a permanent dean since Edward "Ted" Shortliffe stepped down this spring. Shortliffe resigned his position after the Tucson-based dean, Keith Joiner, changed Shortliffe's title from dean to vice dean.
At the time, Joiner cited confusion of having two deans on separate campuses, but Joiner was not long for his position at the time, either. He relinquished his deanship as part of a restructuring orchestrated by Shelton.
Shelton created a single position responsible for UA's vast health-sciences area, including both medical campuses. Crist was hired for the $650,000-a-year position of vice president for health affairs. He expects to start Oct. 31.
Many factors brought about the leadership change. The Committee of Eleven, which investigates faculty complaints, issued a report in April that revealed low morale and concerns about the direction of the medical school. Faculty expressed worry about decision making, academic freedom and other factors. Some faculty members said they were worried about the emergence of the Phoenix medical school.
Michael Cusanovich, who chairs the Committee of Eleven, said Tucson faculty members are worried that the Phoenix campus will divert financial resources and brainpower.
"The biggest concern is how much money gets diverted out of here (Tucson) to Phoenix," Cusanovich said, adding that the Tucson campus will have to share state funding and research grants. "Those are dollars, from a parochial point of view, that will not be available here."
Budget woes hit Phoenix
Valley residents believe a full-time dean at the Phoenix campus is important for many reasons, from sustaining relationships with area hospitals and doctors groups to fundraising.
Stuart Flynn has served as interim dean in Phoenix since Shortliffe stepped down, and he has piloted the campus through cuts that stripped 4 percent from this year's budget.
Flynn said the budget cuts have hurt the ability to add more faculty, but he said it has not affected services to the school's 48 first-year and 24 second-year students.
"It will slow down our ability to grow our faculty on this campus," Flynn said of the budget cuts.
Mining the Valley and out-of-state donors for charitable giving is an important role for Crist and the new dean. Such contributions support important things such as recruiting faculty and providing scholarships for students.
UA Foundation President Jim Moore said the university has secured some contributions but needs to attract more donors for the new Phoenix school.
Hospital plan on hold
While the students are busy learning the basics, the prospects for a downtown teaching hospital are less clear.
Plans for such a hospital have been on hold since talks between Banner Health and UA broke down over disagreements about the size of the proposed hospital and faculty salary. UA put out a request for information among potential new suitors last January. Only Maricopa Integrated Health System responded with a hospital plan.
Now, UA representatives say it will be Crist's job to sort out the hospital proposal, and he said there is no pressing need for a teaching hospital in downtown Phoenix.
Crist said he visited several Phoenix-area hospitals that already train UA students and chatted with executives. With several area hospitals such as St. Joseph's Hospital and Medical Center, Banner Good Samaritan, Carl T. Hayden Veterans Affairs Medical Center and others already training UA medical students, he doesn't see an immediate need to build a new hospital in downtown Phoenix to train students.
"I saw no obvious need, at my first pass level, for more teaching facilities," Crist said.
Maricopa Integrated's chief executive, Betsey Bayless, wants to continue talks with the university when Crist takes over.
"The (MIHS) board several years ago adopted a resolution that they want to build a hospital in conjunction with UA," Bayless said. "I think they are still interested."
Maricopa Integrated needs to replace its Maricopa Medical Center whether it is in tandem with UA or not.
Bayless said the district spends up to $20 million a year on repairs to the aging facility. She estimates it would cost the district $40 million a year in debt and interest payments for a new hospital.
Maricopa Integrated, however, must find the money to pay for such a hospital.
Bayless said the one potential source of money could be federal funds that help hospitals pay for uncompensated-care costs.
Arizona funneled $55 million, called disproportionate-share funds, to the state's general fund to support the state's program for low-income patients. Maricopa Integrated has appealed the state's decision to keep the money, arguing that it needs the money to support its role as a "safety net" hospital that provides care for the poor and uninsured.
Another potential funding source, Bayless said, could be a voter-approved bond to pay construction costs. The health district's board would need to approve a measure to pursue such a funding plan and has not done so yet.
"The (Maricopa Integrated) board has the capability of going to the ballot and going for a bond issue," Bayless said. "I know their preference has been to get the disproportionate-share money and get those funds that were intended for indigent patients so we could go ahead and build using that money."
Although no other Phoenix-area hospital has expressed interest in building a new hospital with UA, at least one government hospital shares a similar challenge with Maricopa. The VA hospital, built in 1951, faces high maintenance needs.
Executive Director Donald Moore said his facility will continue to be an important training ground for UA medical students, but he has not talked about the possibility of building a hospital jointly with UA or Maricopa Integrated.
Tuesday, August 26, 2008
Finding answers in MRIs
[Source: BY WILLIAM ROLLER, SUN STAFF WRITER] - The medical research lab may lack the drama of the Emmy Award-winning "ER" TV show but a Yuma pre-med student applied her passion for science to search for possible discoveries that can impact health and the community at large.
Norianne Pimentel, 19, a 2006 Cibola graduate and now a pre-physiological sciences junior at the University of Arizona, is enjoying her summer investigating ways magnetic resonance imaging (MRI) could someday lead to answers about life-threatening disease.
Supported by grants from the National Institutes of Health and the Howard Hughes Medical Institute, Pimentel is an intern assistant of primary investigator Dr. Natarajan Raghunand in the Undergraduate Biology Research Program at the UA.
The program is strictly lab work but may provide vital links in cancer research, Pimentel said. Cancer can be difficult to detect but the sooner it is found, the better the chances are of treating it.
Imaging techniques, procedures used to photograph inside the body, can play a critical role. Imaging alone is not a treatment but does aid in making proper decisions about treatment.
"I don't do X-rays but only MRIs that use pictures to see what's there," Pimentel said. "A lot of imaging scans use a contrast, iodine, injected in the blood. But an MRI is much less invasive than a CT (computed tomography) scan."
Using MRIs, Pimentel is examining mouse kidneys while assessing two imaging techniques: Flow-sensitive Alternating Inversion Recovery Arterial Spin Labeling (FAIR-ASL) MRI and Dynamic Contrast Enhanced (DCE) MRI.
FAIR-ASL uses water already in the blood as a contrast medium, while DCE uses tracers like the rare metal gadolinium. Both are safer than present methods and could be used to examine blood flow in people, she said.
"So, if you see a bright patch, a different contrast, it will modulate the signals the tissue sends to the machine," Pimentel said.
By examining kidneys of laboratory mice, the goal is to optimize imaging techniques so that when there is a malfunction, doctors can assess it more quickly and with greater accuracy. One of the ailments it can spot are tumors.
"I can look at the blood flow and tell whether a tumor is vascular (receiving blood flow) and what area of the tumor is getting nourishment."
She went on that if a tumor is getting blood supply, it can metastasize (spread), which is of critical concern while nonvascular tumors tend to be less dangerous. The MRI also aids to pinpoint the area to perform a biopsy, the extraction of tissue for examination.
"My job is to see how it's working in terms of imaging, which provides another piece of information to treat the ailment," Pimentel said. "It provides bigger pieces of the puzzle of what may be malfunctioning."
Different researchers have different goals, she said. But the ultimate goal is to provide more insight into the health and well-being of the human body, she explained.
"Whatever your goal in medical research is, you're looking for an advancement that can change somebody's life down the line."
Of the many fields that fall under the medical umbrella, Pimentel said she wants to remain open to several. Medical school is definitely on her agenda and she is leaning toward a career in radiology, neurology or diagnostic medicine.
Pimentel recommended, that high school seniors pondering a career path seriously consider research because it affords so many opportunities.
"I always thought about returning to Yuma. I love the city and loved growing up there. I would be glad to return and work at YRMC (Yuma Regional Medical Center)."
Norianne Pimentel, 19, a 2006 Cibola graduate and now a pre-physiological sciences junior at the University of Arizona, is enjoying her summer investigating ways magnetic resonance imaging (MRI) could someday lead to answers about life-threatening disease.
Supported by grants from the National Institutes of Health and the Howard Hughes Medical Institute, Pimentel is an intern assistant of primary investigator Dr. Natarajan Raghunand in the Undergraduate Biology Research Program at the UA.
The program is strictly lab work but may provide vital links in cancer research, Pimentel said. Cancer can be difficult to detect but the sooner it is found, the better the chances are of treating it.
Imaging techniques, procedures used to photograph inside the body, can play a critical role. Imaging alone is not a treatment but does aid in making proper decisions about treatment.
"I don't do X-rays but only MRIs that use pictures to see what's there," Pimentel said. "A lot of imaging scans use a contrast, iodine, injected in the blood. But an MRI is much less invasive than a CT (computed tomography) scan."
Using MRIs, Pimentel is examining mouse kidneys while assessing two imaging techniques: Flow-sensitive Alternating Inversion Recovery Arterial Spin Labeling (FAIR-ASL) MRI and Dynamic Contrast Enhanced (DCE) MRI.
FAIR-ASL uses water already in the blood as a contrast medium, while DCE uses tracers like the rare metal gadolinium. Both are safer than present methods and could be used to examine blood flow in people, she said.
"So, if you see a bright patch, a different contrast, it will modulate the signals the tissue sends to the machine," Pimentel said.
By examining kidneys of laboratory mice, the goal is to optimize imaging techniques so that when there is a malfunction, doctors can assess it more quickly and with greater accuracy. One of the ailments it can spot are tumors.
"I can look at the blood flow and tell whether a tumor is vascular (receiving blood flow) and what area of the tumor is getting nourishment."
She went on that if a tumor is getting blood supply, it can metastasize (spread), which is of critical concern while nonvascular tumors tend to be less dangerous. The MRI also aids to pinpoint the area to perform a biopsy, the extraction of tissue for examination.
"My job is to see how it's working in terms of imaging, which provides another piece of information to treat the ailment," Pimentel said. "It provides bigger pieces of the puzzle of what may be malfunctioning."
Different researchers have different goals, she said. But the ultimate goal is to provide more insight into the health and well-being of the human body, she explained.
"Whatever your goal in medical research is, you're looking for an advancement that can change somebody's life down the line."
Of the many fields that fall under the medical umbrella, Pimentel said she wants to remain open to several. Medical school is definitely on her agenda and she is leaning toward a career in radiology, neurology or diagnostic medicine.
Pimentel recommended, that high school seniors pondering a career path seriously consider research because it affords so many opportunities.
"I always thought about returning to Yuma. I love the city and loved growing up there. I would be glad to return and work at YRMC (Yuma Regional Medical Center)."
Take chances
[Source: Norma Coile, AZStarsNet.com] - Vicki L. Chandler, 57, helps cure cancer and other diseases, feeds the hungry in the world and could bring a Nobel Prize to the University of Arizona some day.
She is the director of The BIO5 Institute, which draws scientists from five University of Arizona colleges to work on creating lifesaving therapies and cures for diseases. Chandler is also a renowned researcher, Regents' Professor and Endowed Chair in her own right: She helped decipher the genetic code for corn, important to feeding global populations, and she wins prestigious grants to explore the genetics of various human diseases.
As a researcher in a major university, my students and I work in uncharted territory. We are discovering things for the first time. Each of our experiments is designed to test a hypothesis, and many times our hypotheses turn out to be right and that is certainly gratifying.
However, the most stimulating times in my career were when our experiments revealed a whole new way of thinking about our science. That is unbelievably exciting and it happens every few years. For example, in 2006, we uncovered a new pathway for genetic information to be passed from parents to their children. Discover Magazine cited that work as one of the top six discoveries that year.
A key aspect of experimental science is taking chances. … It is a given that not everything will work perfectly, mistakes will happen, experiments will fail, and rejection will occur. When any of the above happens, I don't blame others for the situation or spend too much time focusing on aspects that I can't control. Instead I try to look deeply at myself and learn from my mistakes, grow stronger from rejections; what could be done differently next time, how can I improve?
One person who had a strong influence on me was Barbara McClintock, who won the Nobel Prize for Medicine in 1983. One of the most important things I learned from her was to keep an open mind and be prepared for the unusual and unexpected.
She is the director of The BIO5 Institute, which draws scientists from five University of Arizona colleges to work on creating lifesaving therapies and cures for diseases. Chandler is also a renowned researcher, Regents' Professor and Endowed Chair in her own right: She helped decipher the genetic code for corn, important to feeding global populations, and she wins prestigious grants to explore the genetics of various human diseases.
As a researcher in a major university, my students and I work in uncharted territory. We are discovering things for the first time. Each of our experiments is designed to test a hypothesis, and many times our hypotheses turn out to be right and that is certainly gratifying.
However, the most stimulating times in my career were when our experiments revealed a whole new way of thinking about our science. That is unbelievably exciting and it happens every few years. For example, in 2006, we uncovered a new pathway for genetic information to be passed from parents to their children. Discover Magazine cited that work as one of the top six discoveries that year.
A key aspect of experimental science is taking chances. … It is a given that not everything will work perfectly, mistakes will happen, experiments will fail, and rejection will occur. When any of the above happens, I don't blame others for the situation or spend too much time focusing on aspects that I can't control. Instead I try to look deeply at myself and learn from my mistakes, grow stronger from rejections; what could be done differently next time, how can I improve?
One person who had a strong influence on me was Barbara McClintock, who won the Nobel Prize for Medicine in 1983. One of the most important things I learned from her was to keep an open mind and be prepared for the unusual and unexpected.
Alzheimer's research earns Joseph Rogers Lifetime Achievement Award at Health Care Heroes breakfast
[Phoenix Business Journal] - Joseph Rogers, president and senior scientist at Sun Health Research Institute, received the Lifetime Achievement Award at the 2008 Health Care Heroes Awards breakfast presented by the Phoenix Business Journal Thursday.
Rogers has been a research pioneer on the damage inflammation does to brain tissue in Alzheimer's patients. The work by Rogers and collaborating scientists allows researchers to test different treatments that may have a positive impact on Alzheimer's and other disorders.
Eleven others also were honored at the event sponsored by Blue Cross Shield of Arizona, Abrazo Health Care, Phoenix Children's Hospital, A.T. Still University, Delta Dental and The Plaza Cos. Thirty-one finalists were nominated in 11 categories. The other winners are:
First Responder: Chris Crockett, commander, Public Affairs Bureau, Phoenix Police Department.
Education: Barbara Kavanagh, president and founder, Arizona Myeloma Network; Dr. Craig Phelps, provost, A.T. Still University.
Service Philanthropy: Judy Mohraz, president, The Virginia G. Piper Charitable Trust.
Community Outreach: James Washington, director of school based clinics, Abrazo Health Care.
Dental: Dr. Doug Beischel, chief of staff, John C. Lincoln Children's Dental Care.
Nurse: Elizabeth Campbell, clinical program manager, Translational Genomics Institute.
Nurse Leader: Sue Hanauer, vice president, patient care services, John C. Lincoln North Mountain Hospital.
Physician: Dr. Oliver Harper, senior physician and co-founder, Banner Arizona Medical Clinic.
Research/Innovator: William Duckworth, VA researcher, Phoenix VA Health Care System.
Volunteer: Gary Held, president, My Guy Remodeling.
Rogers has been a research pioneer on the damage inflammation does to brain tissue in Alzheimer's patients. The work by Rogers and collaborating scientists allows researchers to test different treatments that may have a positive impact on Alzheimer's and other disorders.
Eleven others also were honored at the event sponsored by Blue Cross Shield of Arizona, Abrazo Health Care, Phoenix Children's Hospital, A.T. Still University, Delta Dental and The Plaza Cos. Thirty-one finalists were nominated in 11 categories. The other winners are:
First Responder: Chris Crockett, commander, Public Affairs Bureau, Phoenix Police Department.
Education: Barbara Kavanagh, president and founder, Arizona Myeloma Network; Dr. Craig Phelps, provost, A.T. Still University.
Service Philanthropy: Judy Mohraz, president, The Virginia G. Piper Charitable Trust.
Community Outreach: James Washington, director of school based clinics, Abrazo Health Care.
Dental: Dr. Doug Beischel, chief of staff, John C. Lincoln Children's Dental Care.
Nurse: Elizabeth Campbell, clinical program manager, Translational Genomics Institute.
Nurse Leader: Sue Hanauer, vice president, patient care services, John C. Lincoln North Mountain Hospital.
Physician: Dr. Oliver Harper, senior physician and co-founder, Banner Arizona Medical Clinic.
Research/Innovator: William Duckworth, VA researcher, Phoenix VA Health Care System.
Volunteer: Gary Held, president, My Guy Remodeling.
SPIE Announces Newly-Elected 2009 Officers and Directors
Source: MARKET WIRE via COMTEX] - SPIE 2008 President Kevin Harding announced the recent election results at the Annual General Meeting of the Society, 12 August, 2008, in San Diego, California. Terms begin January 1, 2009.
The 2009 Society Officers:
Maria J. Yzuel was elected by SPIE members to serve as the 2009 President. Yzuel is a professor with the Department of Physics, Group of Optics, Universidad Autonoma de Barcelona (UAB), Spain. She received her Ph. D. in Physics from the Universidad of Zaragoza, Spain. An SPIE Fellow, she lists some of her technical interests as diffraction image theory, image quality evaluation, apodization, applications to photolithography optical pattern recognition, color information in correlators, design of filters and liquid crystal devices. Yzuel has published more than 200 scientific papers and presented about 20 invited papers and more than 200 regular contributions in scientific conferences. She has supervised more than 20 Ph.D. theses.
Ralph B. James was elected by SPIE members to serve as the 2009 President Elect. James is Program Manager and Senior Scientist for the Brookhaven National Laboratory. He received his M.S. and Ph.D. degree in Applied Physics at the California Institute of Technology. An SPIE Fellow, he lists his technical interests as photonic and electro-optical instrumentation, sensors, imaging, lasers, laser processing of materials, nanotechnology, nonlinear optics, semiconductor detectors, and biomedical imaging. James has published over 400 journal articles, conference proceedings, book chapters and invited review papers, has 10 patents granted, and is the editor of 13 books on sensors, spectroscopy and imaging.
Katarina Svanberg was elected by SPIE members to serve as the 2009 Vice President. Svanberg is Professor of Oncology and Chief Physician in Oncology at Lund University, Lund, Sweden. She received her M.D. and Ph.D. in Medical Science from Lund University. Svanberg is an SPIE Fellow, a recipient of the SKAPA Innovation Prize, and has given invited talks at 85 international conferences and 30 foreign universities. She lists some of her technical interests as clinical oncology for the abatement of human malignant diseases and optical spectroscopy for detection and treatment of malignant tumors. She has supervised activities for a large number of Ph.D. students in biomedical optics.
Brian A. Lula was elected by SPIE members to serve as the 2009 Secretary/Treasurer. Lula is the president and CEO of PI Physik Instrumente LP. He graduated in mechanical engineering from Centennial College, Ontario, Canada, and completed advanced engineering courses at the University of Michigan. His technical interests include micro and nanopositioning technologies, telescope mechanical/optical system design and fabrication, astronomical imaging, optical manufacturing and testing. Lula is a world class CCD astronomical imager/educator with published photos in popular astronomy magazines such as Sky & Telescope, Astronomy, CBS National and local TV news, NASA's Astrophoto of the Day (APOD) and was featured in a personal exhibit at the Smithsonian Air & Space Museum in Washington DC.
The newly elected Society Directors; three-year terms, 2009-2011:
Jennifer K. Barton; associate professor/tissue optics lab director, University of Arizona.
Bahram Javidi; distinguished professor, University of Connecticut.
Upendra N. Singh; chief technologist, NASA Langley Research Center.
Hugo Thienpont; director of research, Vrije University Brussel.
Appointed Director; one-year term, 2009-2011:
Donis G. Flagello; ASML Fellow, ASML US, Inc.
About SPIE
SPIE is an international optics and photonics society founded in 1955 advancing light-based technologies. Serving the interests of its more than 188,000 active constituents representing 138 different countries, SPIE acts as a catalyst for collaboration among technical disciplines for information exchange, continuing education, publishing opportunities, patent precedent, and career and professional growth. As the organizer and sponsor of approximately 25 major conferences and education programs annually in North America, Europe, Asia, and the South Pacific, SPIE provides publishing, speaking, and learning opportunities on emerging technologies. For more information, visit http://SPIE.org.
The 2009 Society Officers:
Maria J. Yzuel was elected by SPIE members to serve as the 2009 President. Yzuel is a professor with the Department of Physics, Group of Optics, Universidad Autonoma de Barcelona (UAB), Spain. She received her Ph. D. in Physics from the Universidad of Zaragoza, Spain. An SPIE Fellow, she lists some of her technical interests as diffraction image theory, image quality evaluation, apodization, applications to photolithography optical pattern recognition, color information in correlators, design of filters and liquid crystal devices. Yzuel has published more than 200 scientific papers and presented about 20 invited papers and more than 200 regular contributions in scientific conferences. She has supervised more than 20 Ph.D. theses.
Ralph B. James was elected by SPIE members to serve as the 2009 President Elect. James is Program Manager and Senior Scientist for the Brookhaven National Laboratory. He received his M.S. and Ph.D. degree in Applied Physics at the California Institute of Technology. An SPIE Fellow, he lists his technical interests as photonic and electro-optical instrumentation, sensors, imaging, lasers, laser processing of materials, nanotechnology, nonlinear optics, semiconductor detectors, and biomedical imaging. James has published over 400 journal articles, conference proceedings, book chapters and invited review papers, has 10 patents granted, and is the editor of 13 books on sensors, spectroscopy and imaging.
Katarina Svanberg was elected by SPIE members to serve as the 2009 Vice President. Svanberg is Professor of Oncology and Chief Physician in Oncology at Lund University, Lund, Sweden. She received her M.D. and Ph.D. in Medical Science from Lund University. Svanberg is an SPIE Fellow, a recipient of the SKAPA Innovation Prize, and has given invited talks at 85 international conferences and 30 foreign universities. She lists some of her technical interests as clinical oncology for the abatement of human malignant diseases and optical spectroscopy for detection and treatment of malignant tumors. She has supervised activities for a large number of Ph.D. students in biomedical optics.
Brian A. Lula was elected by SPIE members to serve as the 2009 Secretary/Treasurer. Lula is the president and CEO of PI Physik Instrumente LP. He graduated in mechanical engineering from Centennial College, Ontario, Canada, and completed advanced engineering courses at the University of Michigan. His technical interests include micro and nanopositioning technologies, telescope mechanical/optical system design and fabrication, astronomical imaging, optical manufacturing and testing. Lula is a world class CCD astronomical imager/educator with published photos in popular astronomy magazines such as Sky & Telescope, Astronomy, CBS National and local TV news, NASA's Astrophoto of the Day (APOD) and was featured in a personal exhibit at the Smithsonian Air & Space Museum in Washington DC.
The newly elected Society Directors; three-year terms, 2009-2011:
Jennifer K. Barton; associate professor/tissue optics lab director, University of Arizona.
Bahram Javidi; distinguished professor, University of Connecticut.
Upendra N. Singh; chief technologist, NASA Langley Research Center.
Hugo Thienpont; director of research, Vrije University Brussel.
Appointed Director; one-year term, 2009-2011:
Donis G. Flagello; ASML Fellow, ASML US, Inc.
About SPIE
SPIE is an international optics and photonics society founded in 1955 advancing light-based technologies. Serving the interests of its more than 188,000 active constituents representing 138 different countries, SPIE acts as a catalyst for collaboration among technical disciplines for information exchange, continuing education, publishing opportunities, patent precedent, and career and professional growth. As the organizer and sponsor of approximately 25 major conferences and education programs annually in North America, Europe, Asia, and the South Pacific, SPIE provides publishing, speaking, and learning opportunities on emerging technologies. For more information, visit http://SPIE.org.
Brain Mechanisms Underlying Attention, Awareness Being Probed
[Source: MedIndia.com] - U.S. scientists have joined forces with world-famous magicians to discover the brain mechanisms that underlie attention and awareness.
Dr. Stephen Macknik and Dr. Susana Martinez-Conde, two neuroscientists at Barrow Neurological Institute at St. Joseph's Hospital and Medical Center, believe that this collaboration may benefit the fields of education and medical rehabilitation by using magical techniques to help treat ADHD, Alzheimer's disease and brain trauma.
"Magicians have developed powerful cognitive principles and intuitions about attention and awareness that are not understood scientifically. We've been able to learn more about cognition from magicians who have developed illusions that trick audiences," says Dr. Martinez-Conde.
The scientists have studied how magicians mix humor into their performances because a laughing audience is unable to pay attention to the magician's hand.
They have also determined that there are various levels of misdirection that magicians use to trick an audience.
The insights, which were previously unknown, suggest that humour and misdirection may help manipulate levels of attention.
"The collaboration on this project has led to many exciting insights to help us understand the brain's underlying cognition," says Dr. Martinez-Conde.
The magicians associated with the project include James Randi (The Amazing Randi), Teller (of Penn and Teller), Apollo Robbins, Mac King, and John Thomson (The Great Tomsoni).
Dr. Stephen Macknik and Dr. Susana Martinez-Conde, two neuroscientists at Barrow Neurological Institute at St. Joseph's Hospital and Medical Center, believe that this collaboration may benefit the fields of education and medical rehabilitation by using magical techniques to help treat ADHD, Alzheimer's disease and brain trauma.
"Magicians have developed powerful cognitive principles and intuitions about attention and awareness that are not understood scientifically. We've been able to learn more about cognition from magicians who have developed illusions that trick audiences," says Dr. Martinez-Conde.
The scientists have studied how magicians mix humor into their performances because a laughing audience is unable to pay attention to the magician's hand.
They have also determined that there are various levels of misdirection that magicians use to trick an audience.
The insights, which were previously unknown, suggest that humour and misdirection may help manipulate levels of attention.
"The collaboration on this project has led to many exciting insights to help us understand the brain's underlying cognition," says Dr. Martinez-Conde.
The magicians associated with the project include James Randi (The Amazing Randi), Teller (of Penn and Teller), Apollo Robbins, Mac King, and John Thomson (The Great Tomsoni).
Southern Arizona bioscience industry is doing amazing things
[Source: Joe Pangburn, Inside Tucson Business] - Southern Arizona is quickly becoming one of the nation’s more recognized bioscience centers and a global leader in innovation.
This is thanks to the more than 100 companies in Southern Arizona’s bioscience industry that are doing some amazing things.
"We are the world leaders in providing systems to detect cancer in tissue," said Chris Gleeson, chief executive officer of Ventana Medical Systems, 1910 E. Innovation Park Drive, which last year was acquired by Swiss-based Roche Group. "[Roche] has effectively doubled our R & D spending. We are probably going to spend more than all of our competitors combined in the next year on tissue diagnostic research and it is all being done here in Tucson and Oro Valley."
Ventana Medical develops and manufactures diagnostic instruments and reagent systems that provide leading-edge automation technology. In addition, the company has premier workflow solutions designed to improve laboratory workflow efficiency.
Across the street, Integrated Biomolecule Corporation, 2005 E. Innovation Park Drive, contracts with smaller pharmaceutical companies testing raw material and finished product.
"We have the technical ability to take a pill and spilt it apart into its different parts and then measure each to tell you exactly whether or not you have 20 mg of copper or if you have 18 or zero," said Robert Green, president of Integrated Biomolecule. "We can also tell you how much lead, if any, is present in a substance. Which is especially important with raw materials that are coming from China and the recent lead scares."
Moving in as a new neighbor on Innovation Park Drive will be Sanofi-Aventis, currently at 1580 E. Hanley Blvd. along Oracle Road.
The Paris-based, global pharmaceutical company has more than 100,000 employees in more than 100 countries. The research arm in Oro Valley houses 57 scientists who are testing incalculable drug molecule combinations to see what may go together and has potential to require further testing.
"There are 10 to the 40th possible drug-like molecules and we would want to test them all to be comprehensive," said Ken Wertman, scientific director of the Oro Valley research site. "But if you wanted to make a milligram of each of those molecules, there is enough matter in the universe to do so."
Wertman said it takes around $1.2 billion and around 12 to 15 years to bring a drug to the market.
"That is the most challenging thing emotionally about this business; you plug away year after year working on a compound and find out after years of work, it isn’t viable and you have to go back to the drawing board," he said.
Years ago it would take a scientist a year to get through and research 1,000 to 2,000 molecules; today’s technology allows two scientists to look at 5,000 in two weeks.
We’re not just looking for a needle in a haystack," he said. "but we’re looking for a particular piece of hay in an entire field of hay."
Sanofi-Aventis made the move into Oro Valley because of the work of a few University of Arizona professors who began work in that field and were eventually bought out.
The university is a huge player in the bioscience industry in Southern Arizona.
The UA has become one of the nation’s top 20 public research institutions featuring a world-class faculty. The National Science Foundation ranks the UA No. 13 among public research institutions.
"Biotech companies have the most difficult path to emerging success than any new startup company," said Bruce Wright, the associate vice president for economic development at the University of Arizona. "That’s why having an incubator in place to nurture and support them through that stage is really critical."
The business incubator at the Science and Technology Park on the southeast side allows companies to come in and begin working on their business, products and devices and have access to laboratories for far less than it would cost in a stand-alone building.
"That is often the most expensive part of getting started for these companies and by letting them come in and grow, we increase their success rate," Wright said.
Wright said there is still a long way to go in the biotech commercialization infrastructure to make sure Southern Arizona plays a big role in the field. But he is pleased with the direction it is heading.
"With the kind of development happening out there, I think we are beginning to put the pieces in place that will allow us to compete for the attraction of bioscience companies and to grow and retain the homegrown companies," he said. "We’ve got a ways to go but I am encouraged that all of the major players in the bioscience field are now working together through the Southern Arizona Bioscience Steering Committee."
The Committee is made up of members from area governments, TREO, the university and members of the industry. They are working to advance bioscience in the area by bringing to light need and issues companies are facing and working to address them.
The university’s Office of Economic Development has mapped out as many companies in the area involved in the bioscience industry and is about to begin contacting them and finding out what issues they are facing in Southern Arizona. The map is available at http://econdev.web.arizona.edu/Biomap.html.
"We can’t be competitors in this," Wright said. "We all need to be working in a complementary fashion to advance bioscience in this area. I think if we can demonstrate that this is a community with an aptitude and an interest in growing biotechnology that will be helpful in attracting other companies into the region from around the world."
Also located at the UA is the BIO5 Institute. BIO5 works on bringing together faculty and other researchers from five disciplines to tackle complex biology-base problems affecting humans today, such as trying to address world hunger while preserving the environment, and diagnose, treat and prevent disease.
Another asset the industry has in Southern Arizona is the C-Path Institute.
C-Path works as a neutral third party with scientists from government, industry and academia to create and foster transparent efficient partnerships that support the U.S. Food and Drug Administration’s efforts to identify methods that will better serve the industry in the rapid development of safe medical products.
The need for this was outlined in 2004 by the FDA itself. It is referred to as the Critical Path Initiative. The FDA called attention to the alarming decline in the number of new medical products submitted to them for approval, and cited the need for new methods in drug development. Only 16 new medicines were approved in 2007, one of the lowest numbers in more than two decades.
"We’ve identified seven new tests to replace two tests for the FDA that were 100 years old," said Ray Woosley, president of the C-Path Institute. "We want to serve as a trusted third party to enable innovative collaborations between government, academia and business. Companies like Ventana will tell us their secrets and we don’t tell it to anyone else. But when they are preparing to bring something to the FDA we can go first and say, we have not taken any money from this company, but we want to tell about this product and let you know the science is good on it."
With that kind of advocation and support, and the world-class companies located here, Tucson could become the Silicon Valley of the biotech world, at least developer Roger Ford thinks so.
"Silicon Valley was born out of two companies locating there," Ford said. "But the lure of being around like-minded people attracted all kinds of companies. That is what is going to happen here."
In preparation, Ford is developing Innovation Campus, just north of Innovation Park.
"Companies want to be able to move to a space that already exists, not one they have to build before they can move here," he said. "If you build it they will come."
There is certainly enough support for biotech, and Southern Arizona is well poised to become a leader.
Contact reporter Joe Pangburn at jpangburn@azbiz.com or (520) 295-4259.
This is thanks to the more than 100 companies in Southern Arizona’s bioscience industry that are doing some amazing things.
"We are the world leaders in providing systems to detect cancer in tissue," said Chris Gleeson, chief executive officer of Ventana Medical Systems, 1910 E. Innovation Park Drive, which last year was acquired by Swiss-based Roche Group. "[Roche] has effectively doubled our R & D spending. We are probably going to spend more than all of our competitors combined in the next year on tissue diagnostic research and it is all being done here in Tucson and Oro Valley."
Ventana Medical develops and manufactures diagnostic instruments and reagent systems that provide leading-edge automation technology. In addition, the company has premier workflow solutions designed to improve laboratory workflow efficiency.
Across the street, Integrated Biomolecule Corporation, 2005 E. Innovation Park Drive, contracts with smaller pharmaceutical companies testing raw material and finished product.
"We have the technical ability to take a pill and spilt it apart into its different parts and then measure each to tell you exactly whether or not you have 20 mg of copper or if you have 18 or zero," said Robert Green, president of Integrated Biomolecule. "We can also tell you how much lead, if any, is present in a substance. Which is especially important with raw materials that are coming from China and the recent lead scares."
Moving in as a new neighbor on Innovation Park Drive will be Sanofi-Aventis, currently at 1580 E. Hanley Blvd. along Oracle Road.
The Paris-based, global pharmaceutical company has more than 100,000 employees in more than 100 countries. The research arm in Oro Valley houses 57 scientists who are testing incalculable drug molecule combinations to see what may go together and has potential to require further testing.
"There are 10 to the 40th possible drug-like molecules and we would want to test them all to be comprehensive," said Ken Wertman, scientific director of the Oro Valley research site. "But if you wanted to make a milligram of each of those molecules, there is enough matter in the universe to do so."
Wertman said it takes around $1.2 billion and around 12 to 15 years to bring a drug to the market.
"That is the most challenging thing emotionally about this business; you plug away year after year working on a compound and find out after years of work, it isn’t viable and you have to go back to the drawing board," he said.
Years ago it would take a scientist a year to get through and research 1,000 to 2,000 molecules; today’s technology allows two scientists to look at 5,000 in two weeks.
We’re not just looking for a needle in a haystack," he said. "but we’re looking for a particular piece of hay in an entire field of hay."
Sanofi-Aventis made the move into Oro Valley because of the work of a few University of Arizona professors who began work in that field and were eventually bought out.
The university is a huge player in the bioscience industry in Southern Arizona.
The UA has become one of the nation’s top 20 public research institutions featuring a world-class faculty. The National Science Foundation ranks the UA No. 13 among public research institutions.
"Biotech companies have the most difficult path to emerging success than any new startup company," said Bruce Wright, the associate vice president for economic development at the University of Arizona. "That’s why having an incubator in place to nurture and support them through that stage is really critical."
The business incubator at the Science and Technology Park on the southeast side allows companies to come in and begin working on their business, products and devices and have access to laboratories for far less than it would cost in a stand-alone building.
"That is often the most expensive part of getting started for these companies and by letting them come in and grow, we increase their success rate," Wright said.
Wright said there is still a long way to go in the biotech commercialization infrastructure to make sure Southern Arizona plays a big role in the field. But he is pleased with the direction it is heading.
"With the kind of development happening out there, I think we are beginning to put the pieces in place that will allow us to compete for the attraction of bioscience companies and to grow and retain the homegrown companies," he said. "We’ve got a ways to go but I am encouraged that all of the major players in the bioscience field are now working together through the Southern Arizona Bioscience Steering Committee."
The Committee is made up of members from area governments, TREO, the university and members of the industry. They are working to advance bioscience in the area by bringing to light need and issues companies are facing and working to address them.
The university’s Office of Economic Development has mapped out as many companies in the area involved in the bioscience industry and is about to begin contacting them and finding out what issues they are facing in Southern Arizona. The map is available at http://econdev.web.arizona.edu/Biomap.html.
"We can’t be competitors in this," Wright said. "We all need to be working in a complementary fashion to advance bioscience in this area. I think if we can demonstrate that this is a community with an aptitude and an interest in growing biotechnology that will be helpful in attracting other companies into the region from around the world."
Also located at the UA is the BIO5 Institute. BIO5 works on bringing together faculty and other researchers from five disciplines to tackle complex biology-base problems affecting humans today, such as trying to address world hunger while preserving the environment, and diagnose, treat and prevent disease.
Another asset the industry has in Southern Arizona is the C-Path Institute.
C-Path works as a neutral third party with scientists from government, industry and academia to create and foster transparent efficient partnerships that support the U.S. Food and Drug Administration’s efforts to identify methods that will better serve the industry in the rapid development of safe medical products.
The need for this was outlined in 2004 by the FDA itself. It is referred to as the Critical Path Initiative. The FDA called attention to the alarming decline in the number of new medical products submitted to them for approval, and cited the need for new methods in drug development. Only 16 new medicines were approved in 2007, one of the lowest numbers in more than two decades.
"We’ve identified seven new tests to replace two tests for the FDA that were 100 years old," said Ray Woosley, president of the C-Path Institute. "We want to serve as a trusted third party to enable innovative collaborations between government, academia and business. Companies like Ventana will tell us their secrets and we don’t tell it to anyone else. But when they are preparing to bring something to the FDA we can go first and say, we have not taken any money from this company, but we want to tell about this product and let you know the science is good on it."
With that kind of advocation and support, and the world-class companies located here, Tucson could become the Silicon Valley of the biotech world, at least developer Roger Ford thinks so.
"Silicon Valley was born out of two companies locating there," Ford said. "But the lure of being around like-minded people attracted all kinds of companies. That is what is going to happen here."
In preparation, Ford is developing Innovation Campus, just north of Innovation Park.
"Companies want to be able to move to a space that already exists, not one they have to build before they can move here," he said. "If you build it they will come."
There is certainly enough support for biotech, and Southern Arizona is well poised to become a leader.
Contact reporter Joe Pangburn at jpangburn@azbiz.com or (520) 295-4259.
Monday, August 25, 2008
Global Warming Forecasts Not Taking Into Account Nanoscale Atmospheric Aerosols
[Source: ScienceDaily ] - Arizona State University researchers have made a breakthrough in understanding the effect on climate change of a key component of urban pollution. The discovery could lead to more accurate forecasting of possible global-warming activity, say Peter Crozier and James Anderson.
Crozier is an associate professor in ASU's School of Materials, which is jointly administered by the College of Liberal Arts and Sciences and the Ira A. Fulton School of Engineering. Anderson is a senior research scientist in the engineering school's Department of Mechanical and Aerospace Engineering.
As a result of their studies of aerosols in the atmosphere, they assert that some measures used in atmospheric science are oversimplified and overlook important factors that relate to climatic warming and cooling.
The research findings are detailed in the Aug. 8 issue of Science magazine, in the article "Brown Carbon Spheres in East Asian Outflow and Their Optical Properties," co-authored by Crozier, Anderson and Duncan Alexander, a former postdoctoral fellow at ASU in the area of electron microscopy, and the paper's lead author.
So-called brown carbons – a nanoscale atmospheric aerosol species – are largely being ignored in broad-ranging climate computer models, Crozier and Anderson say.
Studies of the greenhouse effect that contribute directly to climate change have focused on carbon dioxide and other greenhouse gases. But there are other components in the atmosphere that can contribute to warming – or cooling – including carbonaceous and sulfate particles from combustion of fossil fuels and biomass, salts from oceans and dust from deserts. Brown carbons from combustion processes are the least understood of these aerosol components.
The parameter typically used to measure degrees of warming is radiative forcing, which is the difference in the incoming energy from sunlight and outgoing energy from heat and reflected sunlight. The variety of gasses and aerosols that compose the atmosphere will, under different conditions, lead to warming (positive radiative forcing) or cooling (negative radiative forcing).
The ASU researchers say the effect of brown carbon is complex because it both cools the Earth's surface and warms the atmosphere.
"Because of the large uncertainty we have in the radiative forcing of aerosols, there is a corresponding large uncertainty in the degree of radiative forcing overall," Crozier says. "This introduces a large uncertainty in the degree of warming predicted by climate change models."
A key to understanding the situation is the light-scattering and light-absorbing properties – called optical properties – of aerosols.
Crozier and Anderson are trying to directly measure the light-absorbing properties of carbonaceous aerosols, which are abundant in the atmosphere.
"If we know the optical properties and distribution of all the aerosols over the entire atmosphere, then we can produce climate change models that provide more accurate prediction," Anderson says.
Most of the techniques used to measure optical properties of aerosols involve shining a laser through columns of air.
"The problem with this approach is that it gives the average properties of all aerosol components, and at only a few wavelengths of light," Anderson says.
He and Crozier have instead used a novel technique based on a specialized type of electron microscope. This technique – monochromated electron energy-loss spectroscopy – can be used to directly determine the optical properties of individual brown carbon nanoparticles over the entire visible light spectrum as well as over the ultraviolet and infrared areas of the spectrum.
"We have used this approach to determine the complete optical properties of individual brown carbon nanoparticles sampled from above the Yellow Sea during a large international climate change experiment," Crozier says.
"This is the first time anyone has determined the complete optical properties of single nanoparticles from the atmosphere," Anderson says.
It's typical for climate modelers to approximate atmospheric carbon aerosols as either non-absorbing or strongly absorbing. "Our measurements show this approximation is too simple," Crozier says. "We show that many of the carbons in our sample have optical properties that are different from those usually assumed in climate models."
Adds Anderson: "When you hear about predictions of future warming or changes in precipitation globally, or in specific regions like the Southwestern United States, the predictions are based on computer model output that is ignoring brown carbon, so they are going to tend to be less accurate."
The research was funded for a six-year period with grants to ASU from the National Science Foundation (NSF) Chemistry Program ($319,000) and the National Aeronautics and Space Administration (NASA) Radiation Science Program ($327,000).
The work is part of the Aerosol Characterization Experiment (ACE) program, which encompasses three projects to date carried out by hundreds of researchers from multiple countries.
Crozier and Anderson have been involved in the U.S. component of the ACE-Asia experiment, a large-scale, multi-agency effort to characterize aerosols from East Asia, involving the NSF, NASA, the National Oceanic and Atmospheric Administration, the Department of Energy and others.
Crozier is an associate professor in ASU's School of Materials, which is jointly administered by the College of Liberal Arts and Sciences and the Ira A. Fulton School of Engineering. Anderson is a senior research scientist in the engineering school's Department of Mechanical and Aerospace Engineering.
As a result of their studies of aerosols in the atmosphere, they assert that some measures used in atmospheric science are oversimplified and overlook important factors that relate to climatic warming and cooling.
The research findings are detailed in the Aug. 8 issue of Science magazine, in the article "Brown Carbon Spheres in East Asian Outflow and Their Optical Properties," co-authored by Crozier, Anderson and Duncan Alexander, a former postdoctoral fellow at ASU in the area of electron microscopy, and the paper's lead author.
So-called brown carbons – a nanoscale atmospheric aerosol species – are largely being ignored in broad-ranging climate computer models, Crozier and Anderson say.
Studies of the greenhouse effect that contribute directly to climate change have focused on carbon dioxide and other greenhouse gases. But there are other components in the atmosphere that can contribute to warming – or cooling – including carbonaceous and sulfate particles from combustion of fossil fuels and biomass, salts from oceans and dust from deserts. Brown carbons from combustion processes are the least understood of these aerosol components.
The parameter typically used to measure degrees of warming is radiative forcing, which is the difference in the incoming energy from sunlight and outgoing energy from heat and reflected sunlight. The variety of gasses and aerosols that compose the atmosphere will, under different conditions, lead to warming (positive radiative forcing) or cooling (negative radiative forcing).
The ASU researchers say the effect of brown carbon is complex because it both cools the Earth's surface and warms the atmosphere.
"Because of the large uncertainty we have in the radiative forcing of aerosols, there is a corresponding large uncertainty in the degree of radiative forcing overall," Crozier says. "This introduces a large uncertainty in the degree of warming predicted by climate change models."
A key to understanding the situation is the light-scattering and light-absorbing properties – called optical properties – of aerosols.
Crozier and Anderson are trying to directly measure the light-absorbing properties of carbonaceous aerosols, which are abundant in the atmosphere.
"If we know the optical properties and distribution of all the aerosols over the entire atmosphere, then we can produce climate change models that provide more accurate prediction," Anderson says.
Most of the techniques used to measure optical properties of aerosols involve shining a laser through columns of air.
"The problem with this approach is that it gives the average properties of all aerosol components, and at only a few wavelengths of light," Anderson says.
He and Crozier have instead used a novel technique based on a specialized type of electron microscope. This technique – monochromated electron energy-loss spectroscopy – can be used to directly determine the optical properties of individual brown carbon nanoparticles over the entire visible light spectrum as well as over the ultraviolet and infrared areas of the spectrum.
"We have used this approach to determine the complete optical properties of individual brown carbon nanoparticles sampled from above the Yellow Sea during a large international climate change experiment," Crozier says.
"This is the first time anyone has determined the complete optical properties of single nanoparticles from the atmosphere," Anderson says.
It's typical for climate modelers to approximate atmospheric carbon aerosols as either non-absorbing or strongly absorbing. "Our measurements show this approximation is too simple," Crozier says. "We show that many of the carbons in our sample have optical properties that are different from those usually assumed in climate models."
Adds Anderson: "When you hear about predictions of future warming or changes in precipitation globally, or in specific regions like the Southwestern United States, the predictions are based on computer model output that is ignoring brown carbon, so they are going to tend to be less accurate."
The research was funded for a six-year period with grants to ASU from the National Science Foundation (NSF) Chemistry Program ($319,000) and the National Aeronautics and Space Administration (NASA) Radiation Science Program ($327,000).
The work is part of the Aerosol Characterization Experiment (ACE) program, which encompasses three projects to date carried out by hundreds of researchers from multiple countries.
Crozier and Anderson have been involved in the U.S. component of the ACE-Asia experiment, a large-scale, multi-agency effort to characterize aerosols from East Asia, involving the NSF, NASA, the National Oceanic and Atmospheric Administration, the Department of Energy and others.
M&Ms As Diet Food? 100-calorie Pack Misconceptions
[Source: ScienceDaily] - Beware of mini-packs and mini-foods, especially if you're a dieter.
Chronic dieters tend to consume more calories when foods and packages are smaller, according to a new study in the Journal of Consumer Research. Authors Maura L. Scott, Stephen M. Nowlis, Naomi Mandel, and Andrea C. Morales (all Arizona State University) examined consumer behavior regarding "mini-packs," 100-calorie food packages that are marketed to help people control calorie intake.
"Interestingly, one group that over-consumes the mini-packs is chronic dieters—individuals constantly trying to manage their weight and food intake," write the authors.
The researchers believe their research shows that the ubiquitous small packages may actually undermine dieters' attempts to limit calories. "On the one hand, consumers perceive the mini-packs to be a generous portion of food (numerous small food morsels in each pack and multiple mini-packs in each box); on the other hand, consumers perceive the mini-packs to be diet food. For chronic dieters, this perceptual dilemma causes a tendency to overeat, due to their emotion-laden relationship with food."
In a series of studies, the researchers assessed peoples' perceptions of M&Ms in mini-packs versus regular-sized packages. They found that participants tended to have conflicting thoughts about the mini-packs: They thought of them as "diet food," yet they overestimated how many calories the packages contained. In subsequent studies, the researchers assessed participants' relationship with food, dividing them into "restrained" and "unrestrained" eaters. The "restrained" eaters tended to consume more calories from mini-packs than "unrestrained" participants.
The authors conclude that dieters should keep an eye on small packages: "While restrained eaters may be attracted to smaller foods in smaller packages initially, presumably because these products are thought to help consumers with their diets, our research shows that restrained eaters actually tend to consume more of these foods than they would of regular foods."
Chronic dieters tend to consume more calories when foods and packages are smaller, according to a new study in the Journal of Consumer Research. Authors Maura L. Scott, Stephen M. Nowlis, Naomi Mandel, and Andrea C. Morales (all Arizona State University) examined consumer behavior regarding "mini-packs," 100-calorie food packages that are marketed to help people control calorie intake.
"Interestingly, one group that over-consumes the mini-packs is chronic dieters—individuals constantly trying to manage their weight and food intake," write the authors.
The researchers believe their research shows that the ubiquitous small packages may actually undermine dieters' attempts to limit calories. "On the one hand, consumers perceive the mini-packs to be a generous portion of food (numerous small food morsels in each pack and multiple mini-packs in each box); on the other hand, consumers perceive the mini-packs to be diet food. For chronic dieters, this perceptual dilemma causes a tendency to overeat, due to their emotion-laden relationship with food."
In a series of studies, the researchers assessed peoples' perceptions of M&Ms in mini-packs versus regular-sized packages. They found that participants tended to have conflicting thoughts about the mini-packs: They thought of them as "diet food," yet they overestimated how many calories the packages contained. In subsequent studies, the researchers assessed participants' relationship with food, dividing them into "restrained" and "unrestrained" eaters. The "restrained" eaters tended to consume more calories from mini-packs than "unrestrained" participants.
The authors conclude that dieters should keep an eye on small packages: "While restrained eaters may be attracted to smaller foods in smaller packages initially, presumably because these products are thought to help consumers with their diets, our research shows that restrained eaters actually tend to consume more of these foods than they would of regular foods."
Friday, August 22, 2008
A new weapon to fight cancer - tobacco plants
[Source: Ken Alltucker, The Arizona Republic] - Tobacco is better known as a cause of cancer rather than a potential cure.
But scientists in Arizona and elsewhere believe tobacco plants may hold the key to developing a personalized cancer vaccine as well as treatments for other diseases.
The experiments are part of a growing field of plant-based biotechnology, and the cancer treatment has gained enough traction to interest the likes of German drug giant Bayer.
"Most important is that the vaccine has been successfully used in human clinical trials," said Charles Arntzen, director of the ASU Biodesign Institute's Center for Infectious Diseases and Vaccinology.
The made-to-order vaccine has been tested in an early-stage clinical trial, and it showed an immune response in 70 percent of non-Hodgkin's lymphoma patients without harmful side effects.
Even though it is called a vaccine, it will not prevent a person from getting non-Hodgkin's lymphoma, which is the seventh-leading cause of cancer-related deaths in the United States. Rather, the vaccine is made from a person's diseased cells and programmed to attack that individual's cancer.
Bayer has spent nearly $15 million on a facility in Germany that initially will grow the tobacco plants to make personalized vaccines for lymphoma patients. The German drug manufacturer plans to explore treatments for other diseases, too.
"It is a huge investment by a company to gamble that they will make it through clinical trials," said Arntzen, who wrote about the personalized plant-based vaccines in an article published Thursday in the journal Science.
Arntzen said he has collaborated with scientists at Stanford University who are developing plant-based vaccines. Earlier this year, the Biodesign Institute secured a $1.5 million grant from the federal government to study whether tobacco plants can yield a vaccine that blocks the West Nile virus from attacking a person's central nervous system. It is a similar technology that is being studied and used by Bayer and Stanford researchers, Arntzen said.
Although scientists are excited about the prospect of using plants to develop individual cancer treatments, no one has yet estimated how much such personalized treatments would cost to make.
Plant-based biotechnology already has been used to produce drugs for diseases such as cystic fibrosis and Gaucher's disease, but some of these personalized drugs can be pricey for consumers.
Avastin, a cancer drug made by South San Francisco-based Genentech, can cost up to $8,800 per month, and Genzyme's Cerezyme, which is used for Gaucher disease, costs about $200,000 a year.
Experts say drug development increasingly is shifting from a one-size-fits-all approach. Drug manufacturers realize that personalized drugs hold great promise as being more effective with fewer side effects. Yet producing such individualized drugs can be expensive and fraught with regulatory challenges.
It would be tough to replicate such a personalized drug in a manner consistent enough to pass muster with the Food and Drug Administration.
"It is going to take some innovative methods to generate that kind of product," said Ray Woosley, president and chief executive officer of the Tucson-based Critical Path Institute, which works to make the drug-development process quicker, safer and more effective.
"It is going to be a challenge to have that kind of individuality and to make sure you produce it the same way (to pass the FDA's review)," Woosley said.
How it works
Bayer envisions a personalized vaccine that is made based on a patient's unique genetic makeup. The vaccine is produced by taking DNA from a person's cancer cells, genetically modifying the DNA strands and transferring the virus to a tobacco plant. The plant responds by producing a protein that can help a cancer patient battle the disease.
The plant-based vaccine works by prodding a person's immune system to attack cancer tumors.
Other scientists have explored the possibility of using animals to make the vaccine, but the tobacco-plant vaccine can be produced much more quickly.
Indeed, speed is a key to growing these personalized treatments.
Scientists estimate that such vaccines can take just six to 10 weeks to produce from the time of a patient's biopsy. That would give doctors a quick time frame to administer the vaccine rather than revert to traditional cancer treatment such as chemotherapy, which has harmful side effects.
Arntzen said that non-Hodgkin's lymphoma is a relatively low-moving cancer, so it gives researchers time to grow, cultivate and give the vaccine to patients.
But scientists in Arizona and elsewhere believe tobacco plants may hold the key to developing a personalized cancer vaccine as well as treatments for other diseases.
The experiments are part of a growing field of plant-based biotechnology, and the cancer treatment has gained enough traction to interest the likes of German drug giant Bayer.
"Most important is that the vaccine has been successfully used in human clinical trials," said Charles Arntzen, director of the ASU Biodesign Institute's Center for Infectious Diseases and Vaccinology.
The made-to-order vaccine has been tested in an early-stage clinical trial, and it showed an immune response in 70 percent of non-Hodgkin's lymphoma patients without harmful side effects.
Even though it is called a vaccine, it will not prevent a person from getting non-Hodgkin's lymphoma, which is the seventh-leading cause of cancer-related deaths in the United States. Rather, the vaccine is made from a person's diseased cells and programmed to attack that individual's cancer.
Bayer has spent nearly $15 million on a facility in Germany that initially will grow the tobacco plants to make personalized vaccines for lymphoma patients. The German drug manufacturer plans to explore treatments for other diseases, too.
"It is a huge investment by a company to gamble that they will make it through clinical trials," said Arntzen, who wrote about the personalized plant-based vaccines in an article published Thursday in the journal Science.
Arntzen said he has collaborated with scientists at Stanford University who are developing plant-based vaccines. Earlier this year, the Biodesign Institute secured a $1.5 million grant from the federal government to study whether tobacco plants can yield a vaccine that blocks the West Nile virus from attacking a person's central nervous system. It is a similar technology that is being studied and used by Bayer and Stanford researchers, Arntzen said.
Although scientists are excited about the prospect of using plants to develop individual cancer treatments, no one has yet estimated how much such personalized treatments would cost to make.
Plant-based biotechnology already has been used to produce drugs for diseases such as cystic fibrosis and Gaucher's disease, but some of these personalized drugs can be pricey for consumers.
Avastin, a cancer drug made by South San Francisco-based Genentech, can cost up to $8,800 per month, and Genzyme's Cerezyme, which is used for Gaucher disease, costs about $200,000 a year.
Experts say drug development increasingly is shifting from a one-size-fits-all approach. Drug manufacturers realize that personalized drugs hold great promise as being more effective with fewer side effects. Yet producing such individualized drugs can be expensive and fraught with regulatory challenges.
It would be tough to replicate such a personalized drug in a manner consistent enough to pass muster with the Food and Drug Administration.
"It is going to take some innovative methods to generate that kind of product," said Ray Woosley, president and chief executive officer of the Tucson-based Critical Path Institute, which works to make the drug-development process quicker, safer and more effective.
"It is going to be a challenge to have that kind of individuality and to make sure you produce it the same way (to pass the FDA's review)," Woosley said.
How it works
Bayer envisions a personalized vaccine that is made based on a patient's unique genetic makeup. The vaccine is produced by taking DNA from a person's cancer cells, genetically modifying the DNA strands and transferring the virus to a tobacco plant. The plant responds by producing a protein that can help a cancer patient battle the disease.
The plant-based vaccine works by prodding a person's immune system to attack cancer tumors.
Other scientists have explored the possibility of using animals to make the vaccine, but the tobacco-plant vaccine can be produced much more quickly.
Indeed, speed is a key to growing these personalized treatments.
Scientists estimate that such vaccines can take just six to 10 weeks to produce from the time of a patient's biopsy. That would give doctors a quick time frame to administer the vaccine rather than revert to traditional cancer treatment such as chemotherapy, which has harmful side effects.
Arntzen said that non-Hodgkin's lymphoma is a relatively low-moving cancer, so it gives researchers time to grow, cultivate and give the vaccine to patients.
Thursday, August 21, 2008
A Trained Eye Finally Solved the Anthrax Puzzle
[Source New York Times, By NICHOLAS WADE] - When the Federal Bureau of Investigation announced it had cracked the long-unsolved anthrax case, the turning point cited by the bureau was its identification of a laboratory flask as the source of the anthrax.
The dots, or in this case more than a thousand separate anthrax samples, were connected with the help of a group of scientists working secretly for some seven years. They succeeded by using a combination of new techniques not even invented in late 2001 when the anthrax-laced letters were sent, and that most old-fashioned attribute of expert scientists and detectives: a trained eye.
Now, in their first interviews, after being released this week from their vows of silence, several scientists explained how they charted a new frontier in microbial forensics, one that could have the same evidentiary power as DNA fingerprinting in criminal cases.
The scientists say they are confident the F.B.I. has identified the source of the anthrax, a flask in the custody of Bruce E. Ivins, whom the F.B.I. considers to have been the perpetrator of the attacks. But almost a hundred other people were known to have had access to cultures from the flask, and the scientists say they have no opinion as to whether Dr. Ivins, who committed suicide last month, was the culprit. Some former colleagues and other experts have questioned whether the government was right in suspecting Dr. Ivins, a researcher at the Army Medical Institute of Infectious Diseases in Fort Detrick, Md. But the technical feat of matching the attack anthrax to its source is itself a gripping tale of scientific detection.
The scientific chase began in late 2001 as the first person to contract anthrax from powder in a letter lay dying in a Florida hospital. The victim, Robert Stevens, 63, a photo editor at The Sun, a tabloid, was suffering from pulmonary anthrax, and the F.B.I. needed to know whether the anthrax in the attacks, which began a week after Sept. 11, was natural, or a biological weapon.
A sample of anthrax from Mr. Stevens’s body was flown to Paul Keim, a biologist at Northern Arizona University who two years earlier had developed a test for distinguishing the various strains of anthrax found in nature and in biological weapons laboratories. Of the anthrax strains used as weapons, the most virulent was one known as the Ames strain.
Dr. Keim confirmed the fears of intelligence agencies: it was the Ames strain that infected and eventually killed Mr. Stevens.
Dr. Keim’s test could tell two strains of anthrax apart but it could not tell the bureau what it needed to know next, which of the many cultures of Ames anthrax around the world the attack anthrax might have come from.
The F.B.I. decided to go back to basics and to try decoding the entire DNA sequence — some five million units — of the anthrax genome to see if some clues to its source might be developed. For this job it turned to the Institute for Genomic Research or TIGR, a leader in decoding the genomes of microbes. Its director was then Claire Fraser-Liggett, who is now at the University of Maryland. The F.B.I. asked her to form a group, with as few people as possible, to decode an anthrax genome, without telling her it was the one that had killed Mr. Stevens.
In contrast to the way science is usually done, the research overseen by the F.B.I., which took seven years to finish, was highly compartmentalized. The scientists, who work at academic institutions, say they did not understand important details of the case until a news conference on Monday — which they and their scientific directors in the F.B.I. attended.
For the bureau, the compartmentalization was an essential safeguard against the nightmare that one of their many advisers might turn out to have prepared the attack anthrax. “It may have been in people’s minds that someone in the room could have been one of the perpetrators, which ended up being the case,” said Dr. Chris Hassell, the F.B.I. laboratory director.
By early 2002, the TIGR team had completed the genome and were able to compare it with a culture of Ames anthrax maintained at Porton Down, the British biological weapons establishment. Anthrax is a highly stable organism that changes very little from one generation to another. But the scientists found several differences between the Stevens and Porton Down genomes, raising the possibility that the source of the attack strain might be distinguishable from other cultures of Ames anthrax.
“The finding was very good news for the investigation by giving hope that molecular forensics might bear fruit but, if so, large numbers of samples would need to be analyzed,” Dr. Fraser-Liggett said.
All Ames anthrax is derived from a cow that died in Texas in April 1981. The F.B.I. acquired a sample from Fort Detrick of the original strain, known as the Ames ancestor. Decoding began on that, with the idea of constructing a genealogy that would show the Ames ancestor begat the source culture which begat the attack strain.
The TIGR team decoded the Ames ancestor and then turned to decoding the anthrax from one of the attack mailings. Each decoding took three to four months and cost about $250,000, said Jacques Ravel, a leading member of the TIGR team who is also now at the University of Maryland.
But when the decoding of the attack genome was finished in 2002, the TIGR scientists had a major surprise and disappointment. In virtually all of its five billion units, the attack anthrax was identical to the Ames ancestor. There were no differences that could tie the attack strain to any of the many known cultures of Ames held in laboratories around the world.
At the regular meetings the TIGR scientists held with the F.B.I., they received very little information or feedback. But they could tell that their counterpart scientists in the bureau were as discouraged as they were, Dr. Fraser-Liggett said. Anthrax genomes looked like a dead end.
Then an Army microbiologist from Fort Detrick made an unexpected discovery. Using an old-fashioned microbiological technique, he spread out some attack spores on a bed of nutrient and let each form its own colony. All the colonies looked identical except one, which, to his trained eye, seemed very slightly different. Different-looking colonies are called morphotypes or just “morphs.”
“Had that task been assigned to someone less experienced, these morphotypes might never have been seen or their significance never realized,” Dr. Fraser-Liggett said.
Because of the obvious possibility that the morph might look different because its genome was different, the F.B.I. asked the TIGR team to decode its genome. Four months later, the TIGR scientists were elated when they discovered the morph had a major genetic change in its genome, known as an indel, short for insertion or deletion of DNA. “We were extremely excited,” Dr. Fraser-Liggett said.
With the morph, the attack strain was at last developing a genetic signature of its own. Though 99 percent of its spores were identical with the Ames ancestor, some 1 percent or less were morphs.
Dr. Ravel was asked to decode seven more morph genomes, a task that took two years. He could do only one at a time for fear of cross-contamination in his laboratory. Dr. Fraser-Liggett said she did not know why the F.B.I. did not ask other laboratories to share the task and speed up the critical process.
One of the many mysteries the TIGR team had to live with under the bureau’s management was the puzzle of why the attack spores contained as many morphs as they did. At the news conference they learned why, when an F.B.I. scientist explained that the flask in Dr. Ivins’s custody, known as RMR-1029, held the product of 13 production runs of anthrax made at the Army’s Dugway Proving Ground and 22 spore preparations made at Fort Detrick. Some 160 liters of material, the scientist said, had been concentrated into the liter held in the RMR-1029 flask.
The vast number of spores, and the many different culturing procedures, Dr. Keim said, “guarantees you will see these mutants, and when you mix them together you will have a characteristic signature.”
Other scientists chosen by the F.B.I. selected four of the morphs as having the most reliable indels. All the attack letters contained these four morphs as well as the predominant form of Ames ancestor-type spores. The bureau at last had a signature of the attack strain.
Hoping for just this breakthrough, the bureau had been building a repository of Ames anthrax samples, taken under subpoena from laboratories around the world. As the morphs became available, the F.B.I. started testing samples. At first, some had one or two of the morphs. None had three of the morphs.
By late 2005 to 2006 it became clear that just eight of the 1,070 samples collected included all four morphs. And one of the samples was the ancestor of the other seven. The seven samples came from Fort Detrick and one other laboratory in the United States, F.B.I. scientists said at the Monday news conference, held at F.B.I. headquarters.
The source of the seven was a master flask of Ames anthrax known as RMR-1029 which was kept by Dr. Bruce Ivins. “That’s when the genetics caught up with the investigators,” a Department of Justice prosecutor said.
There, the scientific conclusions end. The bureau then began a second phase of the inquiry, that of ascertaining who had access to the flask and its seven descendants. The F.B.I. investigated almost 100 scientists who had had access to cultures from the flask or were in some way associated with them.
At the news conference, it emerged that Dr. Ivins had in fact submitted two samples of RMR-1029, one in February 2002 and a second in April 2002. The second tested negative. The F.B.I. rejected and destroyed the first sample because it had not been prepared according to a strict protocol that the F.B.I. says Dr. Ivins helped in devising.
A duplicate of the first sample was later located in Dr. Keim’s laboratory, where all duplicates were sent, and tested positive. Asked why Dr. Ivins would submit a true sample of his flask in February but a false one in April, the F.BI. scientists said they could not speculate about his motives.
Dr. Keim said he believed the bureau had correctly identified the source of the attack anthrax. “The science on that is pretty solid,” he said. As to whether Dr. Ivins was the perpetrator, Dr. Keim said that only a jury could make that decision. He said Dr. Ivins had been a friend and he faulted the F.B.I. for not having prevented his suicide. “Whether Bruce did it or not I prefer not to think about,” he said.
Dr. Fraser-Liggett said, “I am absolutely convinced the F.B.I. has the right source flask,” but added that she had no opinion as to who the perpetrator might be.
Scott Shane contributed reporting from Washington.
The dots, or in this case more than a thousand separate anthrax samples, were connected with the help of a group of scientists working secretly for some seven years. They succeeded by using a combination of new techniques not even invented in late 2001 when the anthrax-laced letters were sent, and that most old-fashioned attribute of expert scientists and detectives: a trained eye.
Now, in their first interviews, after being released this week from their vows of silence, several scientists explained how they charted a new frontier in microbial forensics, one that could have the same evidentiary power as DNA fingerprinting in criminal cases.
The scientists say they are confident the F.B.I. has identified the source of the anthrax, a flask in the custody of Bruce E. Ivins, whom the F.B.I. considers to have been the perpetrator of the attacks. But almost a hundred other people were known to have had access to cultures from the flask, and the scientists say they have no opinion as to whether Dr. Ivins, who committed suicide last month, was the culprit. Some former colleagues and other experts have questioned whether the government was right in suspecting Dr. Ivins, a researcher at the Army Medical Institute of Infectious Diseases in Fort Detrick, Md. But the technical feat of matching the attack anthrax to its source is itself a gripping tale of scientific detection.
The scientific chase began in late 2001 as the first person to contract anthrax from powder in a letter lay dying in a Florida hospital. The victim, Robert Stevens, 63, a photo editor at The Sun, a tabloid, was suffering from pulmonary anthrax, and the F.B.I. needed to know whether the anthrax in the attacks, which began a week after Sept. 11, was natural, or a biological weapon.
A sample of anthrax from Mr. Stevens’s body was flown to Paul Keim, a biologist at Northern Arizona University who two years earlier had developed a test for distinguishing the various strains of anthrax found in nature and in biological weapons laboratories. Of the anthrax strains used as weapons, the most virulent was one known as the Ames strain.
Dr. Keim confirmed the fears of intelligence agencies: it was the Ames strain that infected and eventually killed Mr. Stevens.
Dr. Keim’s test could tell two strains of anthrax apart but it could not tell the bureau what it needed to know next, which of the many cultures of Ames anthrax around the world the attack anthrax might have come from.
The F.B.I. decided to go back to basics and to try decoding the entire DNA sequence — some five million units — of the anthrax genome to see if some clues to its source might be developed. For this job it turned to the Institute for Genomic Research or TIGR, a leader in decoding the genomes of microbes. Its director was then Claire Fraser-Liggett, who is now at the University of Maryland. The F.B.I. asked her to form a group, with as few people as possible, to decode an anthrax genome, without telling her it was the one that had killed Mr. Stevens.
In contrast to the way science is usually done, the research overseen by the F.B.I., which took seven years to finish, was highly compartmentalized. The scientists, who work at academic institutions, say they did not understand important details of the case until a news conference on Monday — which they and their scientific directors in the F.B.I. attended.
For the bureau, the compartmentalization was an essential safeguard against the nightmare that one of their many advisers might turn out to have prepared the attack anthrax. “It may have been in people’s minds that someone in the room could have been one of the perpetrators, which ended up being the case,” said Dr. Chris Hassell, the F.B.I. laboratory director.
By early 2002, the TIGR team had completed the genome and were able to compare it with a culture of Ames anthrax maintained at Porton Down, the British biological weapons establishment. Anthrax is a highly stable organism that changes very little from one generation to another. But the scientists found several differences between the Stevens and Porton Down genomes, raising the possibility that the source of the attack strain might be distinguishable from other cultures of Ames anthrax.
“The finding was very good news for the investigation by giving hope that molecular forensics might bear fruit but, if so, large numbers of samples would need to be analyzed,” Dr. Fraser-Liggett said.
All Ames anthrax is derived from a cow that died in Texas in April 1981. The F.B.I. acquired a sample from Fort Detrick of the original strain, known as the Ames ancestor. Decoding began on that, with the idea of constructing a genealogy that would show the Ames ancestor begat the source culture which begat the attack strain.
The TIGR team decoded the Ames ancestor and then turned to decoding the anthrax from one of the attack mailings. Each decoding took three to four months and cost about $250,000, said Jacques Ravel, a leading member of the TIGR team who is also now at the University of Maryland.
But when the decoding of the attack genome was finished in 2002, the TIGR scientists had a major surprise and disappointment. In virtually all of its five billion units, the attack anthrax was identical to the Ames ancestor. There were no differences that could tie the attack strain to any of the many known cultures of Ames held in laboratories around the world.
At the regular meetings the TIGR scientists held with the F.B.I., they received very little information or feedback. But they could tell that their counterpart scientists in the bureau were as discouraged as they were, Dr. Fraser-Liggett said. Anthrax genomes looked like a dead end.
Then an Army microbiologist from Fort Detrick made an unexpected discovery. Using an old-fashioned microbiological technique, he spread out some attack spores on a bed of nutrient and let each form its own colony. All the colonies looked identical except one, which, to his trained eye, seemed very slightly different. Different-looking colonies are called morphotypes or just “morphs.”
“Had that task been assigned to someone less experienced, these morphotypes might never have been seen or their significance never realized,” Dr. Fraser-Liggett said.
Because of the obvious possibility that the morph might look different because its genome was different, the F.B.I. asked the TIGR team to decode its genome. Four months later, the TIGR scientists were elated when they discovered the morph had a major genetic change in its genome, known as an indel, short for insertion or deletion of DNA. “We were extremely excited,” Dr. Fraser-Liggett said.
With the morph, the attack strain was at last developing a genetic signature of its own. Though 99 percent of its spores were identical with the Ames ancestor, some 1 percent or less were morphs.
Dr. Ravel was asked to decode seven more morph genomes, a task that took two years. He could do only one at a time for fear of cross-contamination in his laboratory. Dr. Fraser-Liggett said she did not know why the F.B.I. did not ask other laboratories to share the task and speed up the critical process.
One of the many mysteries the TIGR team had to live with under the bureau’s management was the puzzle of why the attack spores contained as many morphs as they did. At the news conference they learned why, when an F.B.I. scientist explained that the flask in Dr. Ivins’s custody, known as RMR-1029, held the product of 13 production runs of anthrax made at the Army’s Dugway Proving Ground and 22 spore preparations made at Fort Detrick. Some 160 liters of material, the scientist said, had been concentrated into the liter held in the RMR-1029 flask.
The vast number of spores, and the many different culturing procedures, Dr. Keim said, “guarantees you will see these mutants, and when you mix them together you will have a characteristic signature.”
Other scientists chosen by the F.B.I. selected four of the morphs as having the most reliable indels. All the attack letters contained these four morphs as well as the predominant form of Ames ancestor-type spores. The bureau at last had a signature of the attack strain.
Hoping for just this breakthrough, the bureau had been building a repository of Ames anthrax samples, taken under subpoena from laboratories around the world. As the morphs became available, the F.B.I. started testing samples. At first, some had one or two of the morphs. None had three of the morphs.
By late 2005 to 2006 it became clear that just eight of the 1,070 samples collected included all four morphs. And one of the samples was the ancestor of the other seven. The seven samples came from Fort Detrick and one other laboratory in the United States, F.B.I. scientists said at the Monday news conference, held at F.B.I. headquarters.
The source of the seven was a master flask of Ames anthrax known as RMR-1029 which was kept by Dr. Bruce Ivins. “That’s when the genetics caught up with the investigators,” a Department of Justice prosecutor said.
There, the scientific conclusions end. The bureau then began a second phase of the inquiry, that of ascertaining who had access to the flask and its seven descendants. The F.B.I. investigated almost 100 scientists who had had access to cultures from the flask or were in some way associated with them.
At the news conference, it emerged that Dr. Ivins had in fact submitted two samples of RMR-1029, one in February 2002 and a second in April 2002. The second tested negative. The F.B.I. rejected and destroyed the first sample because it had not been prepared according to a strict protocol that the F.B.I. says Dr. Ivins helped in devising.
A duplicate of the first sample was later located in Dr. Keim’s laboratory, where all duplicates were sent, and tested positive. Asked why Dr. Ivins would submit a true sample of his flask in February but a false one in April, the F.BI. scientists said they could not speculate about his motives.
Dr. Keim said he believed the bureau had correctly identified the source of the attack anthrax. “The science on that is pretty solid,” he said. As to whether Dr. Ivins was the perpetrator, Dr. Keim said that only a jury could make that decision. He said Dr. Ivins had been a friend and he faulted the F.B.I. for not having prevented his suicide. “Whether Bruce did it or not I prefer not to think about,” he said.
Dr. Fraser-Liggett said, “I am absolutely convinced the F.B.I. has the right source flask,” but added that she had no opinion as to who the perpetrator might be.
Scott Shane contributed reporting from Washington.
Wednesday, August 20, 2008
NHGRI SEEKS DNA SEQUENCING TECHNOLOGIES FIT FOR ROUTINE LABORATORY AND MEDICAL USE
[Source NIH Press] - The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today awarded more than $20 million in grants to develop innovative sequencing technologies inexpensive and efficient enough to sequence a person's DNA as a routine part of biomedical research and health care.
"The ability to comprehensively sequence any person's genome is the type of quantum leap needed to usher in an age of personalized medicine where healthcare providers can use an individual's genetic code to prevent, diagnose, and treat diseases," said Alan E. Guttmacher, M.D., acting director of the National Human Genome Research Institute.
DNA sequencing costs have fallen dramatically over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the successful effort to sequence the human genome. NHGRI subsequently launched programs in 2004 to accelerate the development of sequencing technologies and the rate of reduction of genome sequencing cost. Significant progress has been made towards the goal of producing high quality genome sequence of 3 billion base pairs -- the amount of DNA found in humans and other mammals -- for $100,000. Ultimately, NHGRI's vision is to cut the cost of whole-genome sequencing of an individual's genome to $1,000 or less, which will enable sequencing as part of routine medical care.
"A new generation of sequencing technologies is stepping in front of the already impressive technologies that enabled initial sequencing of the human genome," said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "We continue to seek further innovation to enable routine sequencing of genomes to advance scientific knowledge and healthcare."
The new grants will fund eight investigator teams to develop revolutionary technologies that would make it possible to sequence a genome for $1,000, as well as three investigators developing nearer-term technologies to sequence a genome for $100,000. The collective approaches incorporate many complementary elements that integrate biochemistry, chemistry and physics with engineering to enhance the whole effort to develop the next generation of DNA sequencing and analysis technologies.
"$1,000 GENOME" GRANTS
NHGRI's Revolutionary Genome Sequencing Technologies grants have as their goal the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less. Stuart Lindsey of ASU's Biodesign Institute is an Arizona recipient and details of his project are below.
STUART LINDSAY, PH.D., ARIZONA STATE UNIVERSITY, TEMPE $370,000 (1 YEAR) SEQUENCING BY RECOGNITION
This team will test a method in which molecules that are tethered to electrodes will bind transiently to DNA. Binding would complete an electron tunneling circuit, signaling the presence of a particular base -- A, C, G or T -- within the DNA. If successful, this method would be deployed in a nanopore with different binding molecules for each of the four nucleotide bases.
"The ability to comprehensively sequence any person's genome is the type of quantum leap needed to usher in an age of personalized medicine where healthcare providers can use an individual's genetic code to prevent, diagnose, and treat diseases," said Alan E. Guttmacher, M.D., acting director of the National Human Genome Research Institute.
DNA sequencing costs have fallen dramatically over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the successful effort to sequence the human genome. NHGRI subsequently launched programs in 2004 to accelerate the development of sequencing technologies and the rate of reduction of genome sequencing cost. Significant progress has been made towards the goal of producing high quality genome sequence of 3 billion base pairs -- the amount of DNA found in humans and other mammals -- for $100,000. Ultimately, NHGRI's vision is to cut the cost of whole-genome sequencing of an individual's genome to $1,000 or less, which will enable sequencing as part of routine medical care.
"A new generation of sequencing technologies is stepping in front of the already impressive technologies that enabled initial sequencing of the human genome," said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "We continue to seek further innovation to enable routine sequencing of genomes to advance scientific knowledge and healthcare."
The new grants will fund eight investigator teams to develop revolutionary technologies that would make it possible to sequence a genome for $1,000, as well as three investigators developing nearer-term technologies to sequence a genome for $100,000. The collective approaches incorporate many complementary elements that integrate biochemistry, chemistry and physics with engineering to enhance the whole effort to develop the next generation of DNA sequencing and analysis technologies.
"$1,000 GENOME" GRANTS
NHGRI's Revolutionary Genome Sequencing Technologies grants have as their goal the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less. Stuart Lindsey of ASU's Biodesign Institute is an Arizona recipient and details of his project are below.
STUART LINDSAY, PH.D., ARIZONA STATE UNIVERSITY, TEMPE $370,000 (1 YEAR) SEQUENCING BY RECOGNITION
This team will test a method in which molecules that are tethered to electrodes will bind transiently to DNA. Binding would complete an electron tunneling circuit, signaling the presence of a particular base -- A, C, G or T -- within the DNA. If successful, this method would be deployed in a nanopore with different binding molecules for each of the four nucleotide bases.
Tuesday, August 19, 2008
Drier, Warmer Springs In US Southwest Stem From Human-caused Changes In Winds
[Source: ScienceDaily] - Human-driven changes in the westerly winds are bringing hotter and drier springs to the American Southwest, according to new research from The University of Arizona in Tucson.
Since the 1970s the winter storm track in the western U.S. has been shifting north, particularly in the late winter. As a result, fewer winter storms bring rain and snow to Southern California, Arizona, Nevada, Utah, western Colorado and western New Mexico.
"We used to have this season from October to April where we had a chance for a storm," said Stephanie A. McAfee. "Now it's from October to March."
The finding is the first to link the poleward movement of the westerly winds to the changes observed in the West's winter storm pattern. The change in the westerlies is driven by the atmospheric effects of global warming and the ozone hole combined.
"When you pull the storm track north, it takes the storms with it," said McAfee, a doctoral candidate in the UA's department of geosciences.
"During the period it's raining less, it also tends to be warmer than it used to be," McAfee said. "We're starting to see the impacts of climate change in the late winter and early spring, particularly in the Southwest. It's a season-specific kind of drought."
Having drier, warmer conditions occur earlier in the year will affect snowpack, hydrological processes and water resources, McAfee said.
Other researchers, including the UA's Laboratory of Tree-Ring Research Director Tom Swetnam, have linked warmer, drier springs to more and larger forest fires.
McAfee's co-author Joellen L. Russell said, "We're used to thinking about climate change as happening sometime in the future to someone else, but this is right here and affects us now. The future is here."
McAfee and Russell, a UA assistant professor of geosciences, will publish their paper, Northern Annular Mode Impact on Spring Climate in the Western United States, in Geophysical Research Letters, a journal of the American Geophysical Union. The National Oceanic and Atmospheric Administration funded the research via the Climate Assessment for the Southwest program at the UA.
Atmospheric scientists have documented that the westerly winds, or storm track, have been shifting poleward for several decades. The southwestern U.S. has experienced less winter precipitation during the same period.
Computer models of future climate and atmospheric conditions suggest the storm track will continue to move north and that precipitation will continue to decrease in the southwestern U.S.
The timing of the change from wet, cool winter weather to the warmer dry season is important for many ecological processes in the arid Southwest. Therefore, McAfee wanted to know how the shift in the storm track affected precipitation during the transition from winter to spring.
For the period 1978 to 1998, the researchers compared the month-to-month position of the winter storm track, temperature and precipitation records from the western U.S., and pressure at different levels in the atmosphere.
The team used a statistical method called Monte Carlo simulations to test whether the coincidence of storm track and weather patterns had occurred by chance.
Russell said the results of the simulation showed, "It's very rare that you get this distribution by chance." Therefore, she said, the changes in late winter precipitation in the West from 1978 to 1998 are related to the changes in the storm track path for that same time period.
McAfee said her next step is investigating whether western vegetation has changed as the storm track has changed.
Since the 1970s the winter storm track in the western U.S. has been shifting north, particularly in the late winter. As a result, fewer winter storms bring rain and snow to Southern California, Arizona, Nevada, Utah, western Colorado and western New Mexico.
"We used to have this season from October to April where we had a chance for a storm," said Stephanie A. McAfee. "Now it's from October to March."
The finding is the first to link the poleward movement of the westerly winds to the changes observed in the West's winter storm pattern. The change in the westerlies is driven by the atmospheric effects of global warming and the ozone hole combined.
"When you pull the storm track north, it takes the storms with it," said McAfee, a doctoral candidate in the UA's department of geosciences.
"During the period it's raining less, it also tends to be warmer than it used to be," McAfee said. "We're starting to see the impacts of climate change in the late winter and early spring, particularly in the Southwest. It's a season-specific kind of drought."
Having drier, warmer conditions occur earlier in the year will affect snowpack, hydrological processes and water resources, McAfee said.
Other researchers, including the UA's Laboratory of Tree-Ring Research Director Tom Swetnam, have linked warmer, drier springs to more and larger forest fires.
McAfee's co-author Joellen L. Russell said, "We're used to thinking about climate change as happening sometime in the future to someone else, but this is right here and affects us now. The future is here."
McAfee and Russell, a UA assistant professor of geosciences, will publish their paper, Northern Annular Mode Impact on Spring Climate in the Western United States, in Geophysical Research Letters, a journal of the American Geophysical Union. The National Oceanic and Atmospheric Administration funded the research via the Climate Assessment for the Southwest program at the UA.
Atmospheric scientists have documented that the westerly winds, or storm track, have been shifting poleward for several decades. The southwestern U.S. has experienced less winter precipitation during the same period.
Computer models of future climate and atmospheric conditions suggest the storm track will continue to move north and that precipitation will continue to decrease in the southwestern U.S.
The timing of the change from wet, cool winter weather to the warmer dry season is important for many ecological processes in the arid Southwest. Therefore, McAfee wanted to know how the shift in the storm track affected precipitation during the transition from winter to spring.
For the period 1978 to 1998, the researchers compared the month-to-month position of the winter storm track, temperature and precipitation records from the western U.S., and pressure at different levels in the atmosphere.
The team used a statistical method called Monte Carlo simulations to test whether the coincidence of storm track and weather patterns had occurred by chance.
Russell said the results of the simulation showed, "It's very rare that you get this distribution by chance." Therefore, she said, the changes in late winter precipitation in the West from 1978 to 1998 are related to the changes in the storm track path for that same time period.
McAfee said her next step is investigating whether western vegetation has changed as the storm track has changed.
Genes And Nutrition Influence Caste In Unusual Species Of Harvester Ant
[Source: ScienceDaily] - Researchers trying to determine whether nature or nurture determines an ant’s status in the colony have found a surprising answer.
Both.
Nature (that is, the ant’s genetic makeup) and nurture (what it eats, for example) play a role in determining the fate of the Florida harvester ant, Pogonomyrmex badius, a resilient creature found in many parts of the southeastern United States.
The research team included scientists from the University of Illinois, the University of Arizona, Linfield College and Arizona State University. The findings appear this month in American Naturalist.
In the hierarchy of an ant colony, status is everything. If you are a “gyne” and thus destined to become a queen, you can expect the very best accommodations and generous portions at mealtimes. If you are a worker, you must be ready to sacrifice your health, welfare and reproductive capacity for the betterment of the colony.
The researchers were drawn to P. badius because its social structure is more complex than most. Its caste system includes two categories of workers: majors and minors. Major workers are nearly four times heavier than minors, but the minors outnumber them by 20 to 1. Gynes (pronounced jines) are about eight times heavier than minors.
The researchers wanted to know whether the ant’s genetic endowment dictated its caste and size or whether nutrition also played a role.
“Basically what we found is that things are more complicated than previously thought,” said Christopher R. Smith, a former graduate student in the School of Integrative Biology at Illinois and corresponding author on the study.
“Our study shows that there is a large genetic component to caste determination, but that there is also a very strong environmental component.”
The researchers found that the genetic makeup of the colonies they studied was quite diverse. The average P. badius queen had mated with at least 20 males (the norm for ants is one to five). The genetic analysis also suggested that the offspring of most males could develop into any caste, but that some male lineages (patrilines) were more likely to become gynes while others were more likely to become major or minor workers.
A recent study of honey bees found that colonies with a lot of genetic diversity were better at nest building and finding and storing food than their less diverse counterparts.
It was long assumed that castes are environmentally determined, but recent studies on Pogonomyrmex harvester ants have found colonies in which becoming a worker or gyne is determined exclusively by genetic differences. Such rigidity constrains the colony’s ability to adaptively adjust to environmental realities. For example, colonies that have few workers and yet produce a lot of larvae that are destined to become gynes fail to grow to maturity because they lack the resources to feed the voracious gynes. On the other hand, colonies that can respond to environmental factors and alter the ratio of the castes they produce are often more successful in a changing environment. They can produce more workers when resources are scarce and more gynes when food is plentiful.
“Flexibility in caste determination is essential as it allows the colony to respond to changes in need or environmental fluctuations,” said principal investigator Andrew Suarez, an Illinois professor of animal biology and of entomology and an affiliate of the Institute for Genomic Biology.
In the new study, the researchers analyzed what the P. badius ants were eating. Using stable isotope analysis, which looks for different versions of elements such as nitrogen and carbon in the diet, the researchers could tell whether individual ants were eating higher or lower on the food chain. Those at the top would have a more carnivorous diet, with a higher nitrogen content in their foods. They would also ingest more of a specific isotope of nitrogen in their foods than those eating seeds or plants.
The analysis showed that gynes were at the top of the dietary food chain and had the highest proportion of nitrogen in their diets. The minor workers had the lowest nitrogen content and were eating primarily from plant rather than animal sources. The majors were getting a better diet than the minors, but were not eating as well as the gynes.
“Differences in the nutrition that an individual assimilated during larval growth are strong predictors of caste,” the authors wrote.
The researchers also found that genetic differences predict size in major workers and gynes, but not minor workers. Minor workers increase in size only as the colony grows, probably because larger colonies have more resources available to them.
The exact mechanisms by which genetics or diet influence caste are not yet known, Smith said, but in P. badius both play an important role. There may be a hormonal response, for example, that is driven in part by genetics and in part by nutrition that determines the trajectory of an individual ant’s development, he said. Smith, currently a postdoctoral researcher at Arizona State University, continues to explore how genetic differences interact with variation in diet to generate diversity in the form and function of all ants.
The fact that nutrition can alter the genetic destiny of some ants in the colony probably allows it to adjust the ratio of workers to gynes to survive in tough times, he said.
“But there are still ‘haves’ and ‘have nots’ in the colony: those genetic variants who have a reproductive advantage and those that don’t,” Smith said. “The ant colony and human society have striking parallels.” He quotes Marx and Engels: “The history of all past society has consisted in the development of class antagonisms … the exploitation of one part of society by the other.”
Both.
Nature (that is, the ant’s genetic makeup) and nurture (what it eats, for example) play a role in determining the fate of the Florida harvester ant, Pogonomyrmex badius, a resilient creature found in many parts of the southeastern United States.
The research team included scientists from the University of Illinois, the University of Arizona, Linfield College and Arizona State University. The findings appear this month in American Naturalist.
In the hierarchy of an ant colony, status is everything. If you are a “gyne” and thus destined to become a queen, you can expect the very best accommodations and generous portions at mealtimes. If you are a worker, you must be ready to sacrifice your health, welfare and reproductive capacity for the betterment of the colony.
The researchers were drawn to P. badius because its social structure is more complex than most. Its caste system includes two categories of workers: majors and minors. Major workers are nearly four times heavier than minors, but the minors outnumber them by 20 to 1. Gynes (pronounced jines) are about eight times heavier than minors.
The researchers wanted to know whether the ant’s genetic endowment dictated its caste and size or whether nutrition also played a role.
“Basically what we found is that things are more complicated than previously thought,” said Christopher R. Smith, a former graduate student in the School of Integrative Biology at Illinois and corresponding author on the study.
“Our study shows that there is a large genetic component to caste determination, but that there is also a very strong environmental component.”
The researchers found that the genetic makeup of the colonies they studied was quite diverse. The average P. badius queen had mated with at least 20 males (the norm for ants is one to five). The genetic analysis also suggested that the offspring of most males could develop into any caste, but that some male lineages (patrilines) were more likely to become gynes while others were more likely to become major or minor workers.
A recent study of honey bees found that colonies with a lot of genetic diversity were better at nest building and finding and storing food than their less diverse counterparts.
It was long assumed that castes are environmentally determined, but recent studies on Pogonomyrmex harvester ants have found colonies in which becoming a worker or gyne is determined exclusively by genetic differences. Such rigidity constrains the colony’s ability to adaptively adjust to environmental realities. For example, colonies that have few workers and yet produce a lot of larvae that are destined to become gynes fail to grow to maturity because they lack the resources to feed the voracious gynes. On the other hand, colonies that can respond to environmental factors and alter the ratio of the castes they produce are often more successful in a changing environment. They can produce more workers when resources are scarce and more gynes when food is plentiful.
“Flexibility in caste determination is essential as it allows the colony to respond to changes in need or environmental fluctuations,” said principal investigator Andrew Suarez, an Illinois professor of animal biology and of entomology and an affiliate of the Institute for Genomic Biology.
In the new study, the researchers analyzed what the P. badius ants were eating. Using stable isotope analysis, which looks for different versions of elements such as nitrogen and carbon in the diet, the researchers could tell whether individual ants were eating higher or lower on the food chain. Those at the top would have a more carnivorous diet, with a higher nitrogen content in their foods. They would also ingest more of a specific isotope of nitrogen in their foods than those eating seeds or plants.
The analysis showed that gynes were at the top of the dietary food chain and had the highest proportion of nitrogen in their diets. The minor workers had the lowest nitrogen content and were eating primarily from plant rather than animal sources. The majors were getting a better diet than the minors, but were not eating as well as the gynes.
“Differences in the nutrition that an individual assimilated during larval growth are strong predictors of caste,” the authors wrote.
The researchers also found that genetic differences predict size in major workers and gynes, but not minor workers. Minor workers increase in size only as the colony grows, probably because larger colonies have more resources available to them.
The exact mechanisms by which genetics or diet influence caste are not yet known, Smith said, but in P. badius both play an important role. There may be a hormonal response, for example, that is driven in part by genetics and in part by nutrition that determines the trajectory of an individual ant’s development, he said. Smith, currently a postdoctoral researcher at Arizona State University, continues to explore how genetic differences interact with variation in diet to generate diversity in the form and function of all ants.
The fact that nutrition can alter the genetic destiny of some ants in the colony probably allows it to adjust the ratio of workers to gynes to survive in tough times, he said.
“But there are still ‘haves’ and ‘have nots’ in the colony: those genetic variants who have a reproductive advantage and those that don’t,” Smith said. “The ant colony and human society have striking parallels.” He quotes Marx and Engels: “The history of all past society has consisted in the development of class antagonisms … the exploitation of one part of society by the other.”
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