[Source: ScienceDaily (Feb. 6, 2008)] — University of Arizona optical scientists have broken a technological barrier by making three-dimensional holographic displays that can be erased and rewritten in a matter of minutes.
The holographic displays -- which are viewed without special eyewear -- are the first updatable three-dimensional displays with memory ever to be developed, making them ideal tools for medical, industrial and military applications that require "situational awareness."
"This is a new type of device, nothing like the tiny hologram of a dove on your credit card," UA optical sciences professor Nasser Peyghambarian said. "The hologram on your credit card is printed permanently. You cannot erase the image and replace it with an entirely new three-dimensional picture."
"Holography has been around for decades, but holographic displays are really one of the first practical applications of the technique," UA optical scientist Savas Tay said.
Dynamic hologram displays could be made into devices that help surgeons track progress during lengthy and complex brain surgeries, show airline or fighter pilots any hazards within their entire surrounding airspace, or give emergency response teams nearly real-time views of fast-changing flood or traffic problems, for example.
And no one yet knows where the advertising and entertainment industries will go with possible applications, Peyghambarian said. "Imagine that when you walk into the supermarket or department store, you could see a large, dynamic, three-dimensional product display," he said. It would be an attention-grabber.
Tay, Peyghambarian, their colleagues from the UA College of Optical Sciences and collaborators from Nitto Denko Technical Corp., which is an Oceanside, Calif., subsidiary of Nitto Denko, Japan, report on the research in the Feb. 7 issue of the journal Nature.
Their device basically consists of a special plastic film sandwiched between two pieces of glass, each coated with a transparent electrode. The images are "written" into the light-sensitive plastic, called a photorefractive polymer, using laser beams and an externally applied electric field. The scientists take pictures of an object or scene from many two-dimensional perspectives as they scan their object, and the holographic display assembles the two-dimensional perspectives into a three-dimensional picture.
The Air Force Office of Scientific Research, which has funded Peyghambarian's team to develop updatable holographic displays, has used holographic displays in the past. But those displays have been static. They did not allow erasing and updating of the images. The new holographic display can show a new image every few minutes.
The four-inch by four-inch prototype display that Peyghambarian, Tay and their colleagues created now comes only in red, but the researchers see no problem with developing much larger displays in full color. They next will make one-foot by one-foot displays, then three-foot by three-foot displays.
"We use highly efficient, low-cost recording materials capable of very large sizes, which is very important for life-size, realistic 3D displays," Peyghambarian said. "We can record complete scenes or objects within three minutes and can store them for three hours."
The researchers also are working to write images even faster using pulsed lasers.
"If you can write faster with a pulsed laser, then you can write larger holograms in the same amount of time it now takes to write smaller ones," Tay said. "We envision this to be a life-size hologram. We could, for example, display an image of a whole human that would be the same size as the actual person."
Tay emphasized how important updatable holographic displays could be for medicine.
"Three-dimensional imaging techniques are already commonly used in medicine, for example, in MRI (Magnetic Resonance Imaging) or CAT scan (Computerized Axial Tomography) techniques," Tay said. "However, the huge amount of data that is created in three dimensions is still being displayed on two-dimensional devices, either on a computer screen or on a piece of paper. A great amount of data is lost by displaying it this way. So I think when we develop larger, full-color 3D holograms, every hospital in the world will want one."
Friday, February 29, 2008
Key To Life Before Its Origin On Earth May Have Been Discovered
[Source: ScienceDaily (Feb. 29, 2008)] — An important discovery has been made with respect to the mystery of "handedness" in biomolecules. Researchers led by Sandra Pizzarello, a research professor at Arizona State University, found that some of the possible abiotic precursors to the origin of life on Earth have been shown to carry "handedness" in a larger number than previously thought.
Pizzarello, in ASU's Department of Chemistry and Biochemistry, worked with Yongsong Huang and Marcelo Alexandre, of Brown University, in studying the organic materials of a special group of meteorites that contain among a variety of compounds, amino acids that have identical counterparts in terrestrial biomolecules. These meteorites are fragments of asteroids that are about the same age as the solar system (roughly 4.5 billion years.)
Scientists have long known that most compounds in living things exist in mirror-image forms. The two forms are like hands; one is a mirror reflection of the other. They are different, cannot be superimposed, yet identical in their parts.
When scientists synthesize these molecules in the laboratory, half of a sample turns out to be "left-handed" and the other half "right-handed." But amino acids, which are the building blocks of terrestrial proteins, are all "left-handed," while the sugars of DNA and RNA are "right-handed." The mystery as to why this is the case, "parallels in many of its queries those that surround the origin of life," said Pizzarello.
Years ago Pizzarello and ASU professor emeritus John Cronin analyzed amino acids from the Murchison meteorite (which landed in Australia in 1969) that were unknown on Earth, hence solving the problem of any contamination. They discovered a preponderance of "left-handed" amino acids over their "right-handed" form.
"The findings of Cronin and Pizzarello are probably the first demonstration that there may be natural processes in the cosmos that generate a preferred amino acid handedness," Jeffrey Bada of the Scripps Institution of Oceanography, La Jolla, Calif., said at the time.
The new PNAS work* was made possible by the finding in Antarctica of an exceptionally pristine meteorite. Antarctic ices are good "curators" of meteorites. After a meteorite falls -- and meteorites have been falling throughout the history of Earth -- it is quickly covered by snow and buried in the ice. Because these ices are in constant motion, when they come to a mountain, they will flow over the hill and bring meteorites to the surface.
"Thanks to the pristine nature of this meteorite, we were able to demonstrate that other extraterrestrial amino acids carry the left-handed excesses in meteorites and, above all, that these excesses appear to signify that their precursor molecules, the aldehydes, also carried such excesses," Pizzarello said. "In other words, a molecular trait that defines life seems to have broader distribution as well as a long cosmic lineage.""
This study may provide an important clue to the origin of molecular asymmetry," added Brown associate professor and co-author Huang.
*The work is being published in the Early Edition of the Proceedings of the National Academy of Sciences. The paper is titled, "Molecular asymmetry in extraterrestrial chemistry: Insights from a pristine meteorite," and is co-authored by Pizzarello, Huang and Alexandre.
Pizzarello, in ASU's Department of Chemistry and Biochemistry, worked with Yongsong Huang and Marcelo Alexandre, of Brown University, in studying the organic materials of a special group of meteorites that contain among a variety of compounds, amino acids that have identical counterparts in terrestrial biomolecules. These meteorites are fragments of asteroids that are about the same age as the solar system (roughly 4.5 billion years.)
Scientists have long known that most compounds in living things exist in mirror-image forms. The two forms are like hands; one is a mirror reflection of the other. They are different, cannot be superimposed, yet identical in their parts.
When scientists synthesize these molecules in the laboratory, half of a sample turns out to be "left-handed" and the other half "right-handed." But amino acids, which are the building blocks of terrestrial proteins, are all "left-handed," while the sugars of DNA and RNA are "right-handed." The mystery as to why this is the case, "parallels in many of its queries those that surround the origin of life," said Pizzarello.
Years ago Pizzarello and ASU professor emeritus John Cronin analyzed amino acids from the Murchison meteorite (which landed in Australia in 1969) that were unknown on Earth, hence solving the problem of any contamination. They discovered a preponderance of "left-handed" amino acids over their "right-handed" form.
"The findings of Cronin and Pizzarello are probably the first demonstration that there may be natural processes in the cosmos that generate a preferred amino acid handedness," Jeffrey Bada of the Scripps Institution of Oceanography, La Jolla, Calif., said at the time.
The new PNAS work* was made possible by the finding in Antarctica of an exceptionally pristine meteorite. Antarctic ices are good "curators" of meteorites. After a meteorite falls -- and meteorites have been falling throughout the history of Earth -- it is quickly covered by snow and buried in the ice. Because these ices are in constant motion, when they come to a mountain, they will flow over the hill and bring meteorites to the surface.
"Thanks to the pristine nature of this meteorite, we were able to demonstrate that other extraterrestrial amino acids carry the left-handed excesses in meteorites and, above all, that these excesses appear to signify that their precursor molecules, the aldehydes, also carried such excesses," Pizzarello said. "In other words, a molecular trait that defines life seems to have broader distribution as well as a long cosmic lineage.""
This study may provide an important clue to the origin of molecular asymmetry," added Brown associate professor and co-author Huang.
*The work is being published in the Early Edition of the Proceedings of the National Academy of Sciences. The paper is titled, "Molecular asymmetry in extraterrestrial chemistry: Insights from a pristine meteorite," and is co-authored by Pizzarello, Huang and Alexandre.
UA researchers help unlock the genetic secrets of corn
[Source: Deborah Daun, BIO5] - Relying on a genetic "physical map" developed by University of Arizona plant scientists, researchers from Washington University, Cold Spring Harbor Laboratory, Iowa State University, and the UA have completed a working draft of the corn genome. By unlocking the genetic secrets of this crop vital to U.S. agriculture, the researchers have gained information that could ultimately help society deal with drought, global warming, population pressures, and increasing energy needs.
"The impact is going to be tremendous," says Rod Wing, PhD, co-principal investigator on the project and leader of the group that developed the physical map. Wing, a BIO5 member and director of the Arizona Genomics Institute in the UA College of Agriculture and Life Sciences, says that the data contained in the draft genome could be used, for instance, to develop new strains of maize that need less water or can better respond to climate change, as well as to develop strains with higher yields to help feed the planet's growing population. "It will also have an impact on the biofuel industry," Wing says.
The genetic blueprint was announced Feb. 28, 2008 by the project's leader, Richard K. Wilson, Ph.D., director of Washington University's Genome Sequencing Center, at the 50th Annual Maize Genetics Conference in Washington, D.C.
The $29.5 million project was initiated in 2005 and is funded by the National Science Foundation (NSF), the U.S. Department of Agriculture and the U.S. Department of Energy. "Corn is one of the most economically important crops for our nation," says NSF director Arden L. Bement, Jr. "Completing this draft sequence of the corn genome constitutes a significant scientific advance and will foster growth of the agricultural community and the economy as a whole."
The process of unlocking the corn genome began at the UA, where Wing's team, together with UA computer scientist Cari Soderlund, led the development of the genome's physical map by, essentially, taking some 18,000 pieces of genetic material and assembling them in the proper order. Wing’s team also included scientists from the University of Missouri and Rutgers University.
"Imagine that the genome was divided up into pieces and that these pieces are all scrambled in a box, like a puzzle," Wing says. "Using various physical and genetic mapping techniques we put the pieces into the correct order and orientation." Researchers at Washington University in St. Louis sequenced the ordered pieces to create the draft genome, which is available to scientists worldwide through GenBank, an online public DNA database. The genetic data is also available at maizesequence.org.
The draft covers about 95 percent of the corn genome. Scientists from Washington University, the University of Arizona, and Cold Spring Harbor Laboratory will spend the remaining year of the grant refining and finalizing the sequence. "Although it's still missing a few bits, the draft genome sequence is empowering," Wilson explains. "Virtually all the information is there, and while we may make some small modifications to the genetic sequence, we don't expect major changes."
The group sequenced a variety of corn known as B73, developed at Iowa State University decades ago. It is noted for its high grain yields and has been used extensively in both commercial corn breeding and in research laboratories. The genome will be a key tool for researchers working to improve varieties of corn and other cereal crops, including rice, wheat and barley.
The genetic code of corn consists of 2 billion bases of DNA, the chemical units that are represented by the letters T, C, G and A, making it similar in size to the human genome, which is 2.9 billion letters long. By comparison, the rice genome is far smaller, containing about 430 million bases.
The United States is the world's top corn producer. In 2007, U.S. farmers produced a record 13.1 billion bushels of corn, an increase of nearly 25 percent over the previous year, according to the U.S. Department of Agriculture. The 2007 production value of corn was estimated at more than $3 billion dollars. Favorable prices, a growing demand for ethanol and strong export sales have fueled an increase in farmland acreage devoted to corn production.
"The impact is going to be tremendous," says Rod Wing, PhD, co-principal investigator on the project and leader of the group that developed the physical map. Wing, a BIO5 member and director of the Arizona Genomics Institute in the UA College of Agriculture and Life Sciences, says that the data contained in the draft genome could be used, for instance, to develop new strains of maize that need less water or can better respond to climate change, as well as to develop strains with higher yields to help feed the planet's growing population. "It will also have an impact on the biofuel industry," Wing says.
The genetic blueprint was announced Feb. 28, 2008 by the project's leader, Richard K. Wilson, Ph.D., director of Washington University's Genome Sequencing Center, at the 50th Annual Maize Genetics Conference in Washington, D.C.
The $29.5 million project was initiated in 2005 and is funded by the National Science Foundation (NSF), the U.S. Department of Agriculture and the U.S. Department of Energy. "Corn is one of the most economically important crops for our nation," says NSF director Arden L. Bement, Jr. "Completing this draft sequence of the corn genome constitutes a significant scientific advance and will foster growth of the agricultural community and the economy as a whole."
The process of unlocking the corn genome began at the UA, where Wing's team, together with UA computer scientist Cari Soderlund, led the development of the genome's physical map by, essentially, taking some 18,000 pieces of genetic material and assembling them in the proper order. Wing’s team also included scientists from the University of Missouri and Rutgers University.
"Imagine that the genome was divided up into pieces and that these pieces are all scrambled in a box, like a puzzle," Wing says. "Using various physical and genetic mapping techniques we put the pieces into the correct order and orientation." Researchers at Washington University in St. Louis sequenced the ordered pieces to create the draft genome, which is available to scientists worldwide through GenBank, an online public DNA database. The genetic data is also available at maizesequence.org.
The draft covers about 95 percent of the corn genome. Scientists from Washington University, the University of Arizona, and Cold Spring Harbor Laboratory will spend the remaining year of the grant refining and finalizing the sequence. "Although it's still missing a few bits, the draft genome sequence is empowering," Wilson explains. "Virtually all the information is there, and while we may make some small modifications to the genetic sequence, we don't expect major changes."
The group sequenced a variety of corn known as B73, developed at Iowa State University decades ago. It is noted for its high grain yields and has been used extensively in both commercial corn breeding and in research laboratories. The genome will be a key tool for researchers working to improve varieties of corn and other cereal crops, including rice, wheat and barley.
The genetic code of corn consists of 2 billion bases of DNA, the chemical units that are represented by the letters T, C, G and A, making it similar in size to the human genome, which is 2.9 billion letters long. By comparison, the rice genome is far smaller, containing about 430 million bases.
The United States is the world's top corn producer. In 2007, U.S. farmers produced a record 13.1 billion bushels of corn, an increase of nearly 25 percent over the previous year, according to the U.S. Department of Agriculture. The 2007 production value of corn was estimated at more than $3 billion dollars. Favorable prices, a growing demand for ethanol and strong export sales have fueled an increase in farmland acreage devoted to corn production.
Wednesday, February 27, 2008
BIO5 researcher identifies cities at risk to bioterrorism
[Source: Deborah Daun, BIO5] - A University of Arizona researcher has created a new system to dramatically show American cities their relative level of vulnerability to bioterrorism.Walter W. Piegorsch, PhD, an expert on environmental risk, has placed 132 major cities – on a list from Albany, N.Y., to Youngstown, Ohio -- on a color-coded map that identifies their level of risk based on factors like critical industries, ports, railroads, population, natural environment and other factors.
Piegorsch is the director of a new UA graduate program in interdisciplinary statistics and a professor of mathematics in the College of Science, as well as a member of the UA’s BIO5 Institute.
The map marks high risk areas as red (for example, Houston or, surprisingly, Boise, Idaho), midrange risk as yellow (San Francisco) and lower risk as green (Tucson). The map shows a wide swath of highest-risk urban areas running from New York down through the Southeast and into Texas. That swath includes all of the high risk urban areas in the United States except for Boise.
The model employs what risk experts call a benchmark vulnerability metric, which shows risk managers each city’s level of risk for urban terrorism.
Piegorsch says terrorism vulnerability involves three dimensions of risk -- social aspects, natural hazards and how the city and its infrastructure have been constructed.
He concludes that the allocation of funds for preparedness and response to terrorism should take into account these factors of risk and underlying vulnerability.
“Our capacity to adequately prepare for and respond to these vulnerabilities varies widely across the country, especially in urban areas,” he writes. He argues that “any one-size-fits–all strategy” of resource allocation and training ignores the reality of the geographic differences identified in his study. Such failures, he says, would “limit urban areas’ abilities to prepare for and respond to terrorist events.”
The research was published in the December 2007 issue of Risk Analysis, a journal published by the Society for Risk Analysis. It was funded by the U.S. Department of Homeland Security. Piegorsch was the lead author in collaboration with Susan L. Cutter, PhD, director, Hazards & Vulnerability Research Institute, and Carolina Distinguished Professor of Geography, University of South Carolina; and Frank Hardisty, PhD, Research Faculty, GeoVISTA Center, Pennsylvania State University.
To access the journal article, go to:http://www.blackwell-synergy.com/doi/abs/10.1111/j.1539-6924.2007.00977.x
Thursday, February 21, 2008
Project focuses on production of hydrogen from bacteria and sunlight
[Source: Skip Derra, ASU] - If we wanted to create the ideal environmentally friendly energy source, it would be a fuel that is easy and economical to produce, and one that does not pollute our air when burned. That is exactly what researchers at Arizona State University intend to develop in a new program that uses bacteria and sunlight to generate hydrogen, a clean fuel that produces no greenhouse gases.
The project is one of the first to be funded by the ASU President’s Intellectual Fusion fund. This endowed fund is supported by two recent gifts totaling $22 million, and is used to make seed investments in research areas that push the boundaries of traditional academic disciplines.
Funding for the biohydrogen project ($2.5 million over five years) is being administered through the Global Institute of Sustainability, which, with ASU’s School of Sustainability has the goals of researching new, environmentally friendly technologies and educating students on sustainability.
ASU’s biohydrogen project aims to harness the energy in sunlight using microbial photosynthesis to produce hydrogen. A second part of this project is to convert waste materials from the initial process to produce even more hydrogen.
“Hydrogen is the purest fuel you can think of,” said microbiologist Willem “Wim” Vermaas, a professor in ASU’s School of Life Sciences and the lead investigator on the project. “It generates energy without releasing CO2 into the atmosphere. It is the ultimate clean energy technology because you are splitting water to make the hydrogen. If you burn the hydrogen, you get water back. In essence, with our process you are converting solar energy into a clean fuel.”
“Of course,” he adds, “there are many challenges to making this process work efficiently.” Splitting water into its chemical constituents of hydrogen and oxygen can be done through other methods, like electrolysis. ASU’s process is more elegant and does not require any energy other than sunlight. What makes the process work is finely tuned cyanobacteria to carry out the reaction.
Vermaas, a member of ASU’s Center for Bioenergy and Photosynthesis, said that in the laboratory researchers have used a cyanobacterial system to generate a small amount of hydrogen using only solar energy. To optimize the system, the microorganism must be retooled to put most of the energy it gathers from sunlight into compounds useful for biohydrogen production.
The ASU researchers, who have years of experience working in this field, are using a cyanobacterium with a known genome and have developed it into a model organism for genetic and metabolic engineering studies. Using its natural photosynthesis machinery, “we are now starting to direct more of the photosynthetic activity into biofuel production, yielding organisms that convert substantially more of the harvested energy into biofuels,” Vermaas said.
One of the main challenges for the researchers is finding an enzyme for hydrogen production, called hydrogenase, which can operate in the presence of oxygen. Hydrogenase enzymes are a key component to hydrogen production through the photosynthesis process. However, they currently are very sensitive to oxygen, a natural by-product of the splitting of water (H2O).
“If you make photosynthetic hydrogen, you also make oxygen and you have a problem because oxygen inactivates the very enzyme that you want to have working,” Vermaas explained. One part of the project, headed up by Ferran Garcia-Pichel in the School of Life Sciences, is to find heartier forms of hydrogenase. Garcia-Pichel will be looking at systems that occur in nature. "Preliminary data suggest that in a variety of natural habitats cyanobacteria can produce hydrogen, which means that unless there is some way the cells exclude oxygen from the process, their hydrogenase enzyme must be oxygen tolerant,” Vermaas said.
“Boosting the oxygen tolerance of the hydrogenase is really a key to the overall system,” he added. With a robust hydrogenase enzyme, the next step is to incorporate their genes into the model cyanobacterial system. But the way they are incorporated and how the oxygen-tolerant hydrogenase is aligned with other enzymes in the cyanobacteria are critical to getting the system to work efficiently.
“We need to be able to effectively connect the hydrogenase to the photosynthetic reaction center complexes of the cyanobacteria,” Vermaas says. “We can do that through metabolic engineering.”
Each cyanobacterial cell is about 1.5 µm in size, much smaller than what can be seen individually by the human eye. Bacteria’s evolutionary drive is to multiply and in that process electrons and protons are used for the generation of energy and as building blocks for growth of the organism. In the modified cyanobacterial system, Vermaas wants to divert electrons from their normal pathways and push them into new pathways that result in hydrogen production.
“That can be done by more directly linking hydrogenase to where electrons come out of the photosynthetic pathway,” he said. “So we are essentially hijacking the electrons to go to the hydrogenase where they, together with protons, form hydrogen.”
The third part of the project is to create a microbial fuel cell technology that uses the left over cyanobacterial biomass generated in the hydrogen production process as the energy source for additional hydrogen production. Bruce Rittmann, director of the Environmental Biotechnology Center at the Biodesign Institute at ASU is leading the effort in this area.
The researchers will develop the scientific and technological basis for microbial fuel cells that oxidize organic materials in biomass at their anodes, while generating hydrogen gas at their cathode. This work is expected to not only capture energy from cyanobacterial biomass, but it will lay the scientific groundwork for microbial conversion of energy from all kinds of biomass, including human and animal wastes, agricultural crops and residues, and ethanol. The process already has demonstrated that it can produce some energy, but Vermaas said there still is a long way to go to make it economical and efficient.
All of this work is based on many years of research that has been done at ASU, especially groundbreaking biochemical and molecular studies carried out by Tom and Ana Moore, Devens Gust, Jim Allen, Andrew Webber, Neal Woodbury and Anne Jones in the Center for Bioenergy and Photosynthesis. Jens Appel, a leading researcher on cyanobacterial hydrogenases, joined the team in January.
The key now is that with the steady funding that will be provided by the President’s Intellectual Fusion fund, the team can perform the necessary research that will yield results.
“We know the space we need to look in, and where to look in nature for solutions,” Vermaas said. “We have the tools to do the work. We have good ideas on how to do metabolic engineering of the cyanobacteria. We just need to do more research to make it work effectively.”
For more information: Contact Willem Vermaas, (480) 965-6250, wim@asu.edu
The project is one of the first to be funded by the ASU President’s Intellectual Fusion fund. This endowed fund is supported by two recent gifts totaling $22 million, and is used to make seed investments in research areas that push the boundaries of traditional academic disciplines.
Funding for the biohydrogen project ($2.5 million over five years) is being administered through the Global Institute of Sustainability, which, with ASU’s School of Sustainability has the goals of researching new, environmentally friendly technologies and educating students on sustainability.
ASU’s biohydrogen project aims to harness the energy in sunlight using microbial photosynthesis to produce hydrogen. A second part of this project is to convert waste materials from the initial process to produce even more hydrogen.
“Hydrogen is the purest fuel you can think of,” said microbiologist Willem “Wim” Vermaas, a professor in ASU’s School of Life Sciences and the lead investigator on the project. “It generates energy without releasing CO2 into the atmosphere. It is the ultimate clean energy technology because you are splitting water to make the hydrogen. If you burn the hydrogen, you get water back. In essence, with our process you are converting solar energy into a clean fuel.”
“Of course,” he adds, “there are many challenges to making this process work efficiently.” Splitting water into its chemical constituents of hydrogen and oxygen can be done through other methods, like electrolysis. ASU’s process is more elegant and does not require any energy other than sunlight. What makes the process work is finely tuned cyanobacteria to carry out the reaction.
Vermaas, a member of ASU’s Center for Bioenergy and Photosynthesis, said that in the laboratory researchers have used a cyanobacterial system to generate a small amount of hydrogen using only solar energy. To optimize the system, the microorganism must be retooled to put most of the energy it gathers from sunlight into compounds useful for biohydrogen production.
The ASU researchers, who have years of experience working in this field, are using a cyanobacterium with a known genome and have developed it into a model organism for genetic and metabolic engineering studies. Using its natural photosynthesis machinery, “we are now starting to direct more of the photosynthetic activity into biofuel production, yielding organisms that convert substantially more of the harvested energy into biofuels,” Vermaas said.
One of the main challenges for the researchers is finding an enzyme for hydrogen production, called hydrogenase, which can operate in the presence of oxygen. Hydrogenase enzymes are a key component to hydrogen production through the photosynthesis process. However, they currently are very sensitive to oxygen, a natural by-product of the splitting of water (H2O).
“If you make photosynthetic hydrogen, you also make oxygen and you have a problem because oxygen inactivates the very enzyme that you want to have working,” Vermaas explained. One part of the project, headed up by Ferran Garcia-Pichel in the School of Life Sciences, is to find heartier forms of hydrogenase. Garcia-Pichel will be looking at systems that occur in nature. "Preliminary data suggest that in a variety of natural habitats cyanobacteria can produce hydrogen, which means that unless there is some way the cells exclude oxygen from the process, their hydrogenase enzyme must be oxygen tolerant,” Vermaas said.
“Boosting the oxygen tolerance of the hydrogenase is really a key to the overall system,” he added. With a robust hydrogenase enzyme, the next step is to incorporate their genes into the model cyanobacterial system. But the way they are incorporated and how the oxygen-tolerant hydrogenase is aligned with other enzymes in the cyanobacteria are critical to getting the system to work efficiently.
“We need to be able to effectively connect the hydrogenase to the photosynthetic reaction center complexes of the cyanobacteria,” Vermaas says. “We can do that through metabolic engineering.”
Each cyanobacterial cell is about 1.5 µm in size, much smaller than what can be seen individually by the human eye. Bacteria’s evolutionary drive is to multiply and in that process electrons and protons are used for the generation of energy and as building blocks for growth of the organism. In the modified cyanobacterial system, Vermaas wants to divert electrons from their normal pathways and push them into new pathways that result in hydrogen production.
“That can be done by more directly linking hydrogenase to where electrons come out of the photosynthetic pathway,” he said. “So we are essentially hijacking the electrons to go to the hydrogenase where they, together with protons, form hydrogen.”
The third part of the project is to create a microbial fuel cell technology that uses the left over cyanobacterial biomass generated in the hydrogen production process as the energy source for additional hydrogen production. Bruce Rittmann, director of the Environmental Biotechnology Center at the Biodesign Institute at ASU is leading the effort in this area.
The researchers will develop the scientific and technological basis for microbial fuel cells that oxidize organic materials in biomass at their anodes, while generating hydrogen gas at their cathode. This work is expected to not only capture energy from cyanobacterial biomass, but it will lay the scientific groundwork for microbial conversion of energy from all kinds of biomass, including human and animal wastes, agricultural crops and residues, and ethanol. The process already has demonstrated that it can produce some energy, but Vermaas said there still is a long way to go to make it economical and efficient.
All of this work is based on many years of research that has been done at ASU, especially groundbreaking biochemical and molecular studies carried out by Tom and Ana Moore, Devens Gust, Jim Allen, Andrew Webber, Neal Woodbury and Anne Jones in the Center for Bioenergy and Photosynthesis. Jens Appel, a leading researcher on cyanobacterial hydrogenases, joined the team in January.
The key now is that with the steady funding that will be provided by the President’s Intellectual Fusion fund, the team can perform the necessary research that will yield results.
“We know the space we need to look in, and where to look in nature for solutions,” Vermaas said. “We have the tools to do the work. We have good ideas on how to do metabolic engineering of the cyanobacteria. We just need to do more research to make it work effectively.”
For more information: Contact Willem Vermaas, (480) 965-6250, wim@asu.edu
Monday, February 11, 2008
Researchers decode genetics of rare photosynthetic bacterium
[Source: Skip Derra, ASU] – A bacterium that harvests far-red light by making a rare form of chlorophyll (chlorophyll d) has revealed its genetic secrets, according to a team of researchers who recently sequenced the bacteria’s genome. The researchers, from Arizona State University and Washington University, St. Louis, report in the current online edition (Feb. 4) of the Proceedings of the National Academy of Sciences, that they have sequenced the genome of the cyanobacterium, Acaryochloris marina, which through its production of chlorophyll d can absorb “red edge,” near infrared long wavelength light -- light that is invisible to the naked eye. Acaryochloris marina has a massive genome (8.3 million base pairs) and is among the largest of 55 cyanobacterial strains in the world. It is the first chlorophyll-d containing organism to be sequenced.
The advance has applications in plant research, said Jeffrey Touchman, an assistant professor ASU’s School of Life Sciences and lead author of the paper, “Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.”
“Chlorophyll d harvests light from a spectrum of light that few other organisms can, and that enables this organism to carve out its own special niche in the environment to pick up far-red light,” Touchman explained. “The agricultural implications could be significant. One could imagine the transfer of this biochemical mechanism to other plants where they could then use a wider range of the light spectrum and become sort of ‘plant powerhouses,’ deriving increased energy by employing this new photosynthetic pigment.”
There is a bioenergy link to this work, said Touchman, who is a member of ASU’s Center for Bioenergy and Photosynthesis. It could be used for crops that are turned into fuels or to generate biomass. Touchman worked with Robert Blankenship of Washington University on the sequencing project, which involved collaborators from Australia and Japan. Touchman also has an appointment with Translational Genomics Research Institute (TGen), Scottsdale, Ariz., where he operates a high-throughput DNA sequencing facility. The work is supported by the National Science Foundation.
Blankenship said with every gene of Acaryochloris marina now sequenced and annotated, the immediate goal is to find the enzyme that causes a chemical structure change in chlorophyll d, making it different from the more common chlorophyll a, and b, but also from about nine other forms of chlorophyll. “The synthesis of chlorophyll by an organism is complex, involving 17 different steps in all,” Blankenship said. “Someplace near the end of this process, an enzyme transforms a vinyl group to a formyl group to make chlorophyll d. This transformation of chemical forms is not known in any other chlorophyll molecules.”
Touchman and Blankenship said they have some candidate genes they will test. They plan to insert these genes into an organism that only makes chlorophyll a. If the organism learns to synthesize chlorophyll d with one of the genes, the mystery of chlorophyll d synthesis will be solved, and then the excitement will begin.
The researchers said harvesting solar power through plants or other organisms that would be genetically altered with the chlorophyll d gene could make them “solar power factories” that generate and store solar energy. Consider a seven-foot tall corn plant genetically tailored with the chlorophyll d gene to be expressed at the very base of the stalk. While the rest of the plant synthesized chlorophyll a, absorbing short wave light, the base is absorbing “red edge” light in the 710 nanometer range.
Energy could be stored in the base without competing with any other part of the plant for photosynthesis, as the rest only makes chlorophyll a. Also, the altered corn using the chlorophyll d gene could become a super plant because of its enhanced ability to harness energy from the Sun.
That model is similar to how Acaryochloris marina actually operates in the South Pacific, specifically Australia’s Great Barrier Reef. Discovered just 11 years ago, the cyanobacterium lives in a symbiotic relationship with a sponge-like marine animal popularly called a sea squirt. The Acaryochloris marina lives beneath the sea squirt, which is a marine animal that lives attached to rocks just below the surface of the water. The cyanobacterium absorbs “red edge” light through the tissues of the sea squirt.
The genome, said Blankenship, is “fat and happy. Acaryochloris marina lies down there using far red light that no one else can use. The organism has never been under very strong selection pressure to maintain a modest genome size. It’s in kind of a sweet spot. Living in this environment is what allowed it to have such dramatic genome expansion.”
Touchman said that once the gene that causes the late-step chemical transformation is found and inserted successfully into other plants or organisms, that it could potentially represent a five percent increase in available light for organisms to use. “We now have the complete genetic information of a novel organism that makes this type of pigment that no other organism does,” he said. “We don’t yet know what every gene does, but this presents a fertile area for future studies. When we find the chlorophyll-d enzyme and then look into transferring it into other organisms, we’ll be working to extend the range of potentially useful radiation from our Sun.”
The advance has applications in plant research, said Jeffrey Touchman, an assistant professor ASU’s School of Life Sciences and lead author of the paper, “Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.”
“Chlorophyll d harvests light from a spectrum of light that few other organisms can, and that enables this organism to carve out its own special niche in the environment to pick up far-red light,” Touchman explained. “The agricultural implications could be significant. One could imagine the transfer of this biochemical mechanism to other plants where they could then use a wider range of the light spectrum and become sort of ‘plant powerhouses,’ deriving increased energy by employing this new photosynthetic pigment.”
There is a bioenergy link to this work, said Touchman, who is a member of ASU’s Center for Bioenergy and Photosynthesis. It could be used for crops that are turned into fuels or to generate biomass. Touchman worked with Robert Blankenship of Washington University on the sequencing project, which involved collaborators from Australia and Japan. Touchman also has an appointment with Translational Genomics Research Institute (TGen), Scottsdale, Ariz., where he operates a high-throughput DNA sequencing facility. The work is supported by the National Science Foundation.
Blankenship said with every gene of Acaryochloris marina now sequenced and annotated, the immediate goal is to find the enzyme that causes a chemical structure change in chlorophyll d, making it different from the more common chlorophyll a, and b, but also from about nine other forms of chlorophyll. “The synthesis of chlorophyll by an organism is complex, involving 17 different steps in all,” Blankenship said. “Someplace near the end of this process, an enzyme transforms a vinyl group to a formyl group to make chlorophyll d. This transformation of chemical forms is not known in any other chlorophyll molecules.”
Touchman and Blankenship said they have some candidate genes they will test. They plan to insert these genes into an organism that only makes chlorophyll a. If the organism learns to synthesize chlorophyll d with one of the genes, the mystery of chlorophyll d synthesis will be solved, and then the excitement will begin.
The researchers said harvesting solar power through plants or other organisms that would be genetically altered with the chlorophyll d gene could make them “solar power factories” that generate and store solar energy. Consider a seven-foot tall corn plant genetically tailored with the chlorophyll d gene to be expressed at the very base of the stalk. While the rest of the plant synthesized chlorophyll a, absorbing short wave light, the base is absorbing “red edge” light in the 710 nanometer range.
Energy could be stored in the base without competing with any other part of the plant for photosynthesis, as the rest only makes chlorophyll a. Also, the altered corn using the chlorophyll d gene could become a super plant because of its enhanced ability to harness energy from the Sun.
That model is similar to how Acaryochloris marina actually operates in the South Pacific, specifically Australia’s Great Barrier Reef. Discovered just 11 years ago, the cyanobacterium lives in a symbiotic relationship with a sponge-like marine animal popularly called a sea squirt. The Acaryochloris marina lives beneath the sea squirt, which is a marine animal that lives attached to rocks just below the surface of the water. The cyanobacterium absorbs “red edge” light through the tissues of the sea squirt.
The genome, said Blankenship, is “fat and happy. Acaryochloris marina lies down there using far red light that no one else can use. The organism has never been under very strong selection pressure to maintain a modest genome size. It’s in kind of a sweet spot. Living in this environment is what allowed it to have such dramatic genome expansion.”
Touchman said that once the gene that causes the late-step chemical transformation is found and inserted successfully into other plants or organisms, that it could potentially represent a five percent increase in available light for organisms to use. “We now have the complete genetic information of a novel organism that makes this type of pigment that no other organism does,” he said. “We don’t yet know what every gene does, but this presents a fertile area for future studies. When we find the chlorophyll-d enzyme and then look into transferring it into other organisms, we’ll be working to extend the range of potentially useful radiation from our Sun.”
Friday, February 8, 2008
First documented case of pest resistance to biotech cotton
[Source: Mari N. Jensen, UA College of Science] - A pest insect known as bollworm is the first to evolve resistance in the field to plants modified to produce an insecticide called Bt, according to a new research report. Bt-resistant populations of bollworm, Helicoverpa zea, were found in more than a dozen crop fields in Mississippi and Arkansas between 2003 and 2006. "What we're seeing is evolution in action," said lead researcher Bruce Tabashnik. "This is the first documented case of field-evolved resistance to a Bt crop.”
Bt crops are so named because they have been genetically altered to produce Bt toxins, which kill some insects. The toxins are produced in nature by the widespread bacterium Bacillus thuringiensis, hence the abbreviation Bt.
The bollworm resistance to Bt cotton was discovered when a team of University of Arizona entomologists analyzed published data from monitoring studies of six major caterpillar pests of Bt crops in Australia, China, Spain and the U.S. The data documenting bollworm resistance were first collected seven years after Bt cotton was introduced in 1996. "Resistance is a decrease in pest susceptibility that can be measured over human experience," said Tabashnik, professor and head of UA's entomology department and an expert in insect resistance to insecticides. "When you use an insecticide to control a pest, some populations eventually evolve resistance."
The researchers write in their report that Bt cotton and Bt corn have been grown on more than 162 million hectares (400 million acres) worldwide since 1996, “generating one of the largest selections for insect resistance ever known." Even so, the researchers found that most caterpillar pests of cotton and corn remained susceptible to Bt crops. "The resistance occurred in one particular pest in one part of the U.S.,"Tabashnik said. "The other major pests attacking Bt crops have not evolved resistance. And even most bollworm populations have not evolved resistance."
The field outcomes refute some experts' worst-case scenarios that predicted pests would become resistant to Bt crops in as few as three years, he said. “The only other case of field-evolved resistance to Bt toxins involves resistance to Bt sprays," Tabashnik said. He added that such sprays have been used for decades, but now represent a small proportion of the Bt used against crop pests.
The bollworm is a major cotton pest in the southeastern U.S. and Texas, but not in Arizona. The major caterpillar pest of cotton in Arizona is a different species known as pink bollworm, Pectinophora gossypiella, which has remained susceptible to the Bt toxin in biotech cotton.
Tabashnik and his colleagues' article, "Insect resistance to Bt crops: evidence versus theory," will be published in the February issue of Nature Biotechnology. His co-authors are Aaron J. Gassmann, a former UA postdoctoral fellow now an assistant professor at Iowa State University; David W. Crowder, a UA doctoral student; and Yves Carrière, a UA professor of entomology. Tabashnik and Carrière are members of UA's BIO5 Institute.
The U.S. Department of Agriculture funded the research."Our research shows that in Arizona, Bt cotton reduces use of broad-spectrum insecticides and increases yield," said Carrière. Such insecticides kill both pest insects and beneficial insects. To delay resistance, non-Bt crops are planted near Bt crops to provide "refuges" for susceptible pests. Because resistant insects are rare, the only mates they are likely to encounter would be susceptible insects from the refuges. The hybrid offspring of such a mating generally would be susceptible to the toxin. In most pests, offspring are resistant to Bt toxins only if both parents are resistant.In bollworm, however, hybrid offspring produced by matings between susceptible and resistant moths are resistant. Such a dominant inheritance of resistance was predicted to make resistance evolve faster.
The UA researchers found that bollworm resistance evolved fastest in the states with the lowest abundance of refuges. The field outcomes documented by the global monitoring data fit the predictions of the theory underlying the refuge strategy, Tabashnik said. Although first-generation biotech cotton contained only one Bt toxin called Cry1Ac, a new variety contains both Cry1Ac and a second Bt toxin, Cry2Ab. The combination overcomes pests that are resistant to just one toxin. The next steps, Tabashnik said, include conducting research to understand inheritance of resistance to Cry2Ab and developing designer toxins to kill pests resistant to Cry1Ac.
Bt crops are so named because they have been genetically altered to produce Bt toxins, which kill some insects. The toxins are produced in nature by the widespread bacterium Bacillus thuringiensis, hence the abbreviation Bt.
The bollworm resistance to Bt cotton was discovered when a team of University of Arizona entomologists analyzed published data from monitoring studies of six major caterpillar pests of Bt crops in Australia, China, Spain and the U.S. The data documenting bollworm resistance were first collected seven years after Bt cotton was introduced in 1996. "Resistance is a decrease in pest susceptibility that can be measured over human experience," said Tabashnik, professor and head of UA's entomology department and an expert in insect resistance to insecticides. "When you use an insecticide to control a pest, some populations eventually evolve resistance."
The researchers write in their report that Bt cotton and Bt corn have been grown on more than 162 million hectares (400 million acres) worldwide since 1996, “generating one of the largest selections for insect resistance ever known." Even so, the researchers found that most caterpillar pests of cotton and corn remained susceptible to Bt crops. "The resistance occurred in one particular pest in one part of the U.S.,"Tabashnik said. "The other major pests attacking Bt crops have not evolved resistance. And even most bollworm populations have not evolved resistance."
The field outcomes refute some experts' worst-case scenarios that predicted pests would become resistant to Bt crops in as few as three years, he said. “The only other case of field-evolved resistance to Bt toxins involves resistance to Bt sprays," Tabashnik said. He added that such sprays have been used for decades, but now represent a small proportion of the Bt used against crop pests.
The bollworm is a major cotton pest in the southeastern U.S. and Texas, but not in Arizona. The major caterpillar pest of cotton in Arizona is a different species known as pink bollworm, Pectinophora gossypiella, which has remained susceptible to the Bt toxin in biotech cotton.
Tabashnik and his colleagues' article, "Insect resistance to Bt crops: evidence versus theory," will be published in the February issue of Nature Biotechnology. His co-authors are Aaron J. Gassmann, a former UA postdoctoral fellow now an assistant professor at Iowa State University; David W. Crowder, a UA doctoral student; and Yves Carrière, a UA professor of entomology. Tabashnik and Carrière are members of UA's BIO5 Institute.
The U.S. Department of Agriculture funded the research."Our research shows that in Arizona, Bt cotton reduces use of broad-spectrum insecticides and increases yield," said Carrière. Such insecticides kill both pest insects and beneficial insects. To delay resistance, non-Bt crops are planted near Bt crops to provide "refuges" for susceptible pests. Because resistant insects are rare, the only mates they are likely to encounter would be susceptible insects from the refuges. The hybrid offspring of such a mating generally would be susceptible to the toxin. In most pests, offspring are resistant to Bt toxins only if both parents are resistant.In bollworm, however, hybrid offspring produced by matings between susceptible and resistant moths are resistant. Such a dominant inheritance of resistance was predicted to make resistance evolve faster.
The UA researchers found that bollworm resistance evolved fastest in the states with the lowest abundance of refuges. The field outcomes documented by the global monitoring data fit the predictions of the theory underlying the refuge strategy, Tabashnik said. Although first-generation biotech cotton contained only one Bt toxin called Cry1Ac, a new variety contains both Cry1Ac and a second Bt toxin, Cry2Ab. The combination overcomes pests that are resistant to just one toxin. The next steps, Tabashnik said, include conducting research to understand inheritance of resistance to Cry2Ab and developing designer toxins to kill pests resistant to Cry1Ac.
Tuesday, February 5, 2008
Arizona’s first dedicated bioscience venture fund launches
[Source: Eric Tooker] - Leading Phoenix-area bioscience and investment professionals today announced the formation of the Translational Accelerator, LLC (TRAC), a private, Arizona-based $20 million bioscience venture capital group. TRAC becomes Arizona’s first venture fund established to target early-stage bioscience companies. TRAC investments will only support firms located in Arizona or those planning to move to the state.
The establishment of TRAC begins to address one of Arizona’s most pressing needs in its quest to build a thriving bioscience sector: the need to attract venture capital.
“Funds such as TRAC are essential to a successful bioscience region,” said Walt Plosila, Ph.D., vice president of the Battelle Technology Partnership Practice and principle author of Battelle’s 2002 report, Arizona’s Bioscience Roadmap. “Having early-stage venture capital available in Arizona can speed the commercialization of research discoveries into local firms and jobs rather than being developed elsewhere.”
In addition to authoring the report, Plosila has been instrumental in providing research and expertise to help state leaders implement the plan.
Fledgling bioscience companies typically face what Battelle references as the “Valley of Death”—the dry spell between research discovery, often financed by government or corporate grants, and late-stage clinical trials, when pharmaceutical firms and other investors typically begin to take interest. Established venture capital firms are increasingly hesitant to provide capital during the preclinical or early clinical stage of development, though without it, young firms cannot validate their discoveries or develop prototypes.
TRAC will generally invest between $500,000 and $2 million in any one company. Investments will focus on companies devoted to developing diagnostics, services, prevention agents and treatments directed to cancer and diseases of the central nervous system, such as Alzheimer’s and multiple sclerosis. Funding will support those efforts to move a scientific discovery from the lab into the clinic, the so-called translational stage.
TRAC is managed by four Phoenix-area bioscience and investment professionals: Richard Love, a former senior executive of the Translational Genomics Research Institute (TGen) and former CEO of ILEX Oncology Inc.; Dan Von Hoff, M.D., Physician-in-Chief of TGen, Director of TGen’s Translational Drug Development Division and Chief Scientific Officer of Scottsdale Healthcare; Eric Tooker, J.D., president and chief executive officer of Medical Consultant Services; and John Bentley, a partner with Grayhawk Venture Partners. The concept for TRAC formed and gained support while Love was at TGen, as he recognized the need to attract investor funding to seed early discoveries that have commercial potential—whether developed at TGen or any of Arizona’s research institutions.
“A venture fund’s success depends in large part on the expertise of its managers and advisors,” Love said. “We have a top-notch team of individuals recognized nationally and beyond for their extensive experience in biomedical research and initiating successful commercial ventures.”
“Successful bioscience venture funds tend to attract the attention of investors nationwide,” Tooker said. “If done right, this could be the catalyst to leveraging significant out-of-state capital into Arizona.”
“Early-stage venture funding in biotech is very complex and sophisticated, and the TRAC fund is an example of the investors’ commitment in taking the needed risk to help drive Arizona’s economy,” said Barry Broome, Greater Phoenix Economic Council president and CEO.
The Fund is supported by a number of individual investors plus the Flinn Foundation, a Phoenix-based private foundation which commissioned Arizona’s Bioscience Roadmap.
”Much as information technologies drove economic progress in the past 25 years, many economists predict that the new discoveries in biology will be a driving force for the next 25 years”, said John Murphy, Flinn Foundation president and CEO. “The Foundation’s investment in TRAC is another way that we can support the growth of Arizona’s bioscience enterprise.”
Interested parties should contact Eric Tooker to request additional information at 480.268.2006 or at etooker@tracvc.com.
The establishment of TRAC begins to address one of Arizona’s most pressing needs in its quest to build a thriving bioscience sector: the need to attract venture capital.
“Funds such as TRAC are essential to a successful bioscience region,” said Walt Plosila, Ph.D., vice president of the Battelle Technology Partnership Practice and principle author of Battelle’s 2002 report, Arizona’s Bioscience Roadmap. “Having early-stage venture capital available in Arizona can speed the commercialization of research discoveries into local firms and jobs rather than being developed elsewhere.”
In addition to authoring the report, Plosila has been instrumental in providing research and expertise to help state leaders implement the plan.
Fledgling bioscience companies typically face what Battelle references as the “Valley of Death”—the dry spell between research discovery, often financed by government or corporate grants, and late-stage clinical trials, when pharmaceutical firms and other investors typically begin to take interest. Established venture capital firms are increasingly hesitant to provide capital during the preclinical or early clinical stage of development, though without it, young firms cannot validate their discoveries or develop prototypes.
TRAC will generally invest between $500,000 and $2 million in any one company. Investments will focus on companies devoted to developing diagnostics, services, prevention agents and treatments directed to cancer and diseases of the central nervous system, such as Alzheimer’s and multiple sclerosis. Funding will support those efforts to move a scientific discovery from the lab into the clinic, the so-called translational stage.
TRAC is managed by four Phoenix-area bioscience and investment professionals: Richard Love, a former senior executive of the Translational Genomics Research Institute (TGen) and former CEO of ILEX Oncology Inc.; Dan Von Hoff, M.D., Physician-in-Chief of TGen, Director of TGen’s Translational Drug Development Division and Chief Scientific Officer of Scottsdale Healthcare; Eric Tooker, J.D., president and chief executive officer of Medical Consultant Services; and John Bentley, a partner with Grayhawk Venture Partners. The concept for TRAC formed and gained support while Love was at TGen, as he recognized the need to attract investor funding to seed early discoveries that have commercial potential—whether developed at TGen or any of Arizona’s research institutions.
“A venture fund’s success depends in large part on the expertise of its managers and advisors,” Love said. “We have a top-notch team of individuals recognized nationally and beyond for their extensive experience in biomedical research and initiating successful commercial ventures.”
“Successful bioscience venture funds tend to attract the attention of investors nationwide,” Tooker said. “If done right, this could be the catalyst to leveraging significant out-of-state capital into Arizona.”
“Early-stage venture funding in biotech is very complex and sophisticated, and the TRAC fund is an example of the investors’ commitment in taking the needed risk to help drive Arizona’s economy,” said Barry Broome, Greater Phoenix Economic Council president and CEO.
The Fund is supported by a number of individual investors plus the Flinn Foundation, a Phoenix-based private foundation which commissioned Arizona’s Bioscience Roadmap.
”Much as information technologies drove economic progress in the past 25 years, many economists predict that the new discoveries in biology will be a driving force for the next 25 years”, said John Murphy, Flinn Foundation president and CEO. “The Foundation’s investment in TRAC is another way that we can support the growth of Arizona’s bioscience enterprise.”
Interested parties should contact Eric Tooker to request additional information at 480.268.2006 or at etooker@tracvc.com.
Monday, February 4, 2008
Sifting the genome for clues to cancer
[Source: Jennifer Couzin, ScienceNOW Daily] - Biologists have hunted for weak spots in cancer cells for years, hoping to find clues to the disease that can be exploited. That should get easier thanks to a mass-screening technique reported in the 1 February issue of Science that may provide a cost-effective and powerful way to pick out new drug targets against cancer.
As genetic technology has grown more sophisticated and cheaper, scientists have begun dissecting a cancer cell's arsenal on a massive scale. In 2005, the National Institutes of Health in Bethesda, Maryland, launched The Cancer Genome Atlas (TCGA), a $1.5 billion search for genes that are mutated in a host of cancers (Science, 16 December 2005, p. 1751). Some scientists have criticized TCGA for focusing on gene sequencing while diverting funds from functional studies that can determine which of the hundreds of mutations are most important. One person with such concerns is geneticist Stephen Elledge of Harvard Medical School in Boston.
With molecular biologist Gregory Hannon of Cold Spring Harbor Laboratory in New York state, Elledge developed genetic tools that examine how genes function in human cancer cells. As they report in two new studies, the pair and their colleagues constructed viral vectors, each one containing an RNA molecule designed to shut down a gene with a complementary sequence. The vectors also contained DNA bar codes, sequences that the researchers could look for later to determine which small RNAs were having a big effect on a cell's behavior. The researchers inserted between 10,000 and 40,000 of these small RNAs at once into breast cancer, colon cancer, and normal human cells in the lab. The main analysis, of 10,000 short hairpin RNAs, targeted about 3000 different genes, says Elledge. Then they waited to see which small RNAs would blunt survival or growth of cancer cells without affecting normal ones. The theory is that those genes hit by RNAi are acting in concert with abnormalities in the cancer cell to cause out-of-control proliferation.
On this first pass, roughly two dozen genes fit the bill, says Elledge. "It looks like you can get a lethality signature," a pattern of genes that affect how tumor cells proliferate. Elledge cautions that this is just a start in determining which proteins might make good drug targets and that the technique won't pick up every one. The work cost about $30,000 to conduct once the tools were in place. Other experts are hopeful that this approach will pay dividends. "I'm a very big fan," says cancer geneticist Ronald DePinho of the Dana-Farber Cancer Institute in Boston, who also chairs TCGA’s advisory board. He believes that given cancer's complexity, it is necessary to both survey the genomes of tumor cell and examine how the cells respond when genes are silenced. If the two methods independently come up with genes that are interconnected, "it would be a much more powerful way of prioritizing" what to study next, says computational biologist Michael Bittner of the Translational Genomics Research Institute in Phoenix, Arizona.
Related sites
· The Cancer Genome Atlas
· Findings from TCGA
As genetic technology has grown more sophisticated and cheaper, scientists have begun dissecting a cancer cell's arsenal on a massive scale. In 2005, the National Institutes of Health in Bethesda, Maryland, launched The Cancer Genome Atlas (TCGA), a $1.5 billion search for genes that are mutated in a host of cancers (Science, 16 December 2005, p. 1751). Some scientists have criticized TCGA for focusing on gene sequencing while diverting funds from functional studies that can determine which of the hundreds of mutations are most important. One person with such concerns is geneticist Stephen Elledge of Harvard Medical School in Boston.
With molecular biologist Gregory Hannon of Cold Spring Harbor Laboratory in New York state, Elledge developed genetic tools that examine how genes function in human cancer cells. As they report in two new studies, the pair and their colleagues constructed viral vectors, each one containing an RNA molecule designed to shut down a gene with a complementary sequence. The vectors also contained DNA bar codes, sequences that the researchers could look for later to determine which small RNAs were having a big effect on a cell's behavior. The researchers inserted between 10,000 and 40,000 of these small RNAs at once into breast cancer, colon cancer, and normal human cells in the lab. The main analysis, of 10,000 short hairpin RNAs, targeted about 3000 different genes, says Elledge. Then they waited to see which small RNAs would blunt survival or growth of cancer cells without affecting normal ones. The theory is that those genes hit by RNAi are acting in concert with abnormalities in the cancer cell to cause out-of-control proliferation.
On this first pass, roughly two dozen genes fit the bill, says Elledge. "It looks like you can get a lethality signature," a pattern of genes that affect how tumor cells proliferate. Elledge cautions that this is just a start in determining which proteins might make good drug targets and that the technique won't pick up every one. The work cost about $30,000 to conduct once the tools were in place. Other experts are hopeful that this approach will pay dividends. "I'm a very big fan," says cancer geneticist Ronald DePinho of the Dana-Farber Cancer Institute in Boston, who also chairs TCGA’s advisory board. He believes that given cancer's complexity, it is necessary to both survey the genomes of tumor cell and examine how the cells respond when genes are silenced. If the two methods independently come up with genes that are interconnected, "it would be a much more powerful way of prioritizing" what to study next, says computational biologist Michael Bittner of the Translational Genomics Research Institute in Phoenix, Arizona.
Related sites
· The Cancer Genome Atlas
· Findings from TCGA
ASU scientists study Arizona water
[Source: Claudia Koerner , ASU] - Though water coming from the tap or flowing in the Salt River may look clean, researchers said it could be hiding something.
The Water Quality Center at ASU has been researching microbes and chemicals that contaminate Arizona rivers and tap water since 2001 through funding from the National Science Foundation. "Anytime we look for these bugs, they are there," said Morteza Abbaszadegan, director of the center. But that doesn't necessarily mean Arizonans are in danger, Abbaszadegan added."So far, so good," he said. "We do not find them in finished water."The center's research affirms the importance of water treatment plants in Arizona, Abbaszadegan added. Because drinking water flows 280 miles from Lake Havasu in open canals, it is even more susceptible to contamination.
The research is compiled into reports, which are available to city governments."Now the utilities companies know there are such contaminants," Abbaszadegan said. Determining what particles are in Arizona water also helps utility companies update their facilities and keeps the community aware of potential health concerns, he said. "The level of microbes dictates the level of treatment the cities should provide," Abbaszadegan said. He added that knowing which microbes are in Arizona rivers can help treatment plants target other factors as well. "One thing that is especially important for central Arizona is taste and odor," Abbaszadegan said. Through various projects, the center is not only identifying what is in the water, but also finding new methods to treat it, he said.
In 2006, center researchers developed a new tool to detect bacteria in water samples. Unlike standard tests, which take 24 hours, the new machine can determine if water is contaminated within 20 minutes to an hour and a half. "A lot of time, 24 hours is too late," Abbaszadegan said. BioSense, a bioscience company, has already picked up the new technology, and Abbaszadegan said it has "huge commercial potential." Graduate students are critical to the research the center performs, and the center's research has helped at least 15 of them meet graduation requirements, he added.
Tamer Helmy, a life sciences doctoral candidate, is working on a new way of concentrating viruses in a sample to make them easier to detect. "It is important because we need a quick method to alert the public if there is any outbreak of a virus," Helmy said. "It's important to everybody."Other student researchers agreed that the importance of their work to society was one of the reasons they enjoy it.
Dan Gerrity, a civil and environmental engineering doctoral candidate, is working on disinfecting water using a combination of ultraviolet light and semiconductor powder. Gerrity said he thinks this method will be very common in future water treatment plants, which are already changing their technology dramatically. "As we find more chemical and microbial contaminants, we'll need new ways to treat them," Gerrity said.
Fellow civil and environmental engineering doctoral candidate Brooke Mayer said she attributes the changing treatment methods to the advances researchers, like those at the Water Quality Center, are making with contaminants. "We're starting to understand [microbes] better," Mayer said.
The Water Quality Center at ASU has been researching microbes and chemicals that contaminate Arizona rivers and tap water since 2001 through funding from the National Science Foundation. "Anytime we look for these bugs, they are there," said Morteza Abbaszadegan, director of the center. But that doesn't necessarily mean Arizonans are in danger, Abbaszadegan added."So far, so good," he said. "We do not find them in finished water."The center's research affirms the importance of water treatment plants in Arizona, Abbaszadegan added. Because drinking water flows 280 miles from Lake Havasu in open canals, it is even more susceptible to contamination.
The research is compiled into reports, which are available to city governments."Now the utilities companies know there are such contaminants," Abbaszadegan said. Determining what particles are in Arizona water also helps utility companies update their facilities and keeps the community aware of potential health concerns, he said. "The level of microbes dictates the level of treatment the cities should provide," Abbaszadegan said. He added that knowing which microbes are in Arizona rivers can help treatment plants target other factors as well. "One thing that is especially important for central Arizona is taste and odor," Abbaszadegan said. Through various projects, the center is not only identifying what is in the water, but also finding new methods to treat it, he said.
In 2006, center researchers developed a new tool to detect bacteria in water samples. Unlike standard tests, which take 24 hours, the new machine can determine if water is contaminated within 20 minutes to an hour and a half. "A lot of time, 24 hours is too late," Abbaszadegan said. BioSense, a bioscience company, has already picked up the new technology, and Abbaszadegan said it has "huge commercial potential." Graduate students are critical to the research the center performs, and the center's research has helped at least 15 of them meet graduation requirements, he added.
Tamer Helmy, a life sciences doctoral candidate, is working on a new way of concentrating viruses in a sample to make them easier to detect. "It is important because we need a quick method to alert the public if there is any outbreak of a virus," Helmy said. "It's important to everybody."Other student researchers agreed that the importance of their work to society was one of the reasons they enjoy it.
Dan Gerrity, a civil and environmental engineering doctoral candidate, is working on disinfecting water using a combination of ultraviolet light and semiconductor powder. Gerrity said he thinks this method will be very common in future water treatment plants, which are already changing their technology dramatically. "As we find more chemical and microbial contaminants, we'll need new ways to treat them," Gerrity said.
Fellow civil and environmental engineering doctoral candidate Brooke Mayer said she attributes the changing treatment methods to the advances researchers, like those at the Water Quality Center, are making with contaminants. "We're starting to understand [microbes] better," Mayer said.
Pharmacy Dean J. Lyle Bootman wins top honor
[Source: UA News] - J. Lyle Bootman, dean of The University of Arizona College of Pharmacy, has been awarded the 2008 Remington Honor Medal, widely considered to be the profession's highest honor. Administered by the American Pharmacists Association, the award will be presented to Bootman during its annual meeting and exposition on March 16. Bootman was selected to receive the award because of his lifetime of achievement in pharmacy. His studies on drug-related morbidity and mortality in the mid-1990s were a wake-up call to health care providers to better understand the high cost of medication-related errors and to appreciate the role of pharmacists in reducing harm by managing patients' pharmaceutical care.
He is one of only eight pharmacists to be admitted to the Institute of Medicine of the National Academies of Science and was the first pharmacist to serve on its Board of Health Care Services. In 2006, he served as co-chairman of the Institute of Medicine Committee that produced the influential report "Preventing Medication Errors."
Bootman is the founder and executive director of the UA Center for Health Outcomes and PharmacoEconomic Research, one of the first such centers in the world. He has been dean of the UA College of Pharmacy since 1990, following three years as acting dean. Bootman holds a bachelor of science degree in pharmacy from the UA and a master of science and doctorate in pharmacy administration from the University of Minnesota. He also was awarded an honorary doctor of science degree from the University of the Sciences in Philadelphia.
Named for eminent community pharmacist, manufacturer and educator Joseph P. Remington, the award was established in 1918 to recognize distinguished service and/or outstanding achievement on behalf of American pharmacy during the preceding year, culminating in the past year, or for a sustained period of time. The American Pharmacists Association's awards program is pharmacy's most comprehensive recognition program. The American Pharmacists Association, founded in 1852 as the American Pharmaceutical Association, represents more than 63,000 practicing pharmacists, pharmaceutical scientists, student pharmacists, pharmacy technicians and others interested in advancing the profession. The association, dedicated to helping all pharmacists improve medication use and advance patient care, is the first-established and largest association of pharmacists in the United States.
He is one of only eight pharmacists to be admitted to the Institute of Medicine of the National Academies of Science and was the first pharmacist to serve on its Board of Health Care Services. In 2006, he served as co-chairman of the Institute of Medicine Committee that produced the influential report "Preventing Medication Errors."
Bootman is the founder and executive director of the UA Center for Health Outcomes and PharmacoEconomic Research, one of the first such centers in the world. He has been dean of the UA College of Pharmacy since 1990, following three years as acting dean. Bootman holds a bachelor of science degree in pharmacy from the UA and a master of science and doctorate in pharmacy administration from the University of Minnesota. He also was awarded an honorary doctor of science degree from the University of the Sciences in Philadelphia.
Named for eminent community pharmacist, manufacturer and educator Joseph P. Remington, the award was established in 1918 to recognize distinguished service and/or outstanding achievement on behalf of American pharmacy during the preceding year, culminating in the past year, or for a sustained period of time. The American Pharmacists Association's awards program is pharmacy's most comprehensive recognition program. The American Pharmacists Association, founded in 1852 as the American Pharmaceutical Association, represents more than 63,000 practicing pharmacists, pharmaceutical scientists, student pharmacists, pharmacy technicians and others interested in advancing the profession. The association, dedicated to helping all pharmacists improve medication use and advance patient care, is the first-established and largest association of pharmacists in the United States.
Friday, February 1, 2008
Agreement between the Translational Genomics Research Institute Accelerators and Abraxis Bioscience to bring Innovative Discoveries to Market
Source: Arizona Department of Commerce] - Further solidifying Arizona as a leader in the bioscience industry, Governor Janet Napolitano today announced a cooperative agreement between two major bioscience entities, the Translational Genomics Research Institute Accelerators (TGenAccel) and Abraxis Bioscience to bring innovative, promising discoveries and therapies to market.
TGen and Abraxis Chairman and Founder Patrick Soon-Shiong, M.D., have entered into a letter of intent (LOI) to establish two initiatives to further biomedical development across Arizona, and extend TGen’s Clinical Research Services nationally. The LOI, facilitated by the Greater Phoenix Economic Council (GPEC), calls for a total of $21.5 million to fund the initial phases of both programs."This is significant for Arizona; we have the infrastructure and bioscience capital in place to conduct clinical trials and bring to market important bioscientific work," said Governor Napolitano. "There are a multitude of discoveries occurring each day that these initiatives – the critical links necessary – will enable to become globally viable and accessible. I am pleased to commend TGen, Abraxis and our statewide partners in this effort.”
Of the total $21.5 million, $14 million will be used to establish Catapult Bio – a new, nonprofit organization that will focus on bringing promising life sciences research with a focus on diagnostics, prognostics, therapeutics, devices and services to market. The remaining $7.5 million is earmarked toward launching a National Personalized Health Network (NPHN), a new platform to increase evidence-based personalized medicine clinical trials. The NPHN will operate from Greater Phoenix and initially establish eight Individualized Therapy Centers throughout the country to determine the effectiveness of this type of treatment.“Our agreement represents an important partnership that will transform and advance worldwide health care,” Dr. Patrick Soon-Shiong, chairman and CEO of Abraxis Bioscience, said. “It is my hope that Catapult Bio and the National Personalized Health Network will play a critical role in helping to accelerate and extend my vision for personalized medicine throughout the world.”
The creation of Catapult Bio addresses a gap highlighted in the recently released 2007 Battelle report, Arizona's Bioscience Roadmap: Toward 2012, which indicated Arizona’s need to establish an entity with the expertise to further develop and commercialize the increasing number of research discoveries emerging from Arizona-based life sciences research efforts. Additionally, Catapult Bio helps fulfill significant funding shortfalls in shepherding late stage research discoveries into development and commercialization.“Catapult Bio will focus on creating exciting new programs that bridge the expertise and funding gaps, and provide the necessary support to efficiently enhance, accelerate and develop technology into commercially available products and services,” MaryAnn Guerra, president of TGen Accelerators, said. “Our National Personalized Health Network will leverage TGen’s clinical expertise and allow increased patient access to important information relating to their treatment, additional clinical care services and an expanded clinical trial network focused on personalized medicine.”
“This pioneering effort to create Catapult Bio and the National Personalized Health Network in Greater Phoenix is the result of an emerging technology practice driving next-generation economic development,” Barry Broome, president and CEO of GPEC, said. “Dr. Soon-Shiong is a philanthropist and a visionary leader whose incredible investment will literally change the health of individuals around the world for the better.”
For more information about the Office of the Governor, please visit www.azgovernor.gov.
TGen and Abraxis Chairman and Founder Patrick Soon-Shiong, M.D., have entered into a letter of intent (LOI) to establish two initiatives to further biomedical development across Arizona, and extend TGen’s Clinical Research Services nationally. The LOI, facilitated by the Greater Phoenix Economic Council (GPEC), calls for a total of $21.5 million to fund the initial phases of both programs."This is significant for Arizona; we have the infrastructure and bioscience capital in place to conduct clinical trials and bring to market important bioscientific work," said Governor Napolitano. "There are a multitude of discoveries occurring each day that these initiatives – the critical links necessary – will enable to become globally viable and accessible. I am pleased to commend TGen, Abraxis and our statewide partners in this effort.”
Of the total $21.5 million, $14 million will be used to establish Catapult Bio – a new, nonprofit organization that will focus on bringing promising life sciences research with a focus on diagnostics, prognostics, therapeutics, devices and services to market. The remaining $7.5 million is earmarked toward launching a National Personalized Health Network (NPHN), a new platform to increase evidence-based personalized medicine clinical trials. The NPHN will operate from Greater Phoenix and initially establish eight Individualized Therapy Centers throughout the country to determine the effectiveness of this type of treatment.“Our agreement represents an important partnership that will transform and advance worldwide health care,” Dr. Patrick Soon-Shiong, chairman and CEO of Abraxis Bioscience, said. “It is my hope that Catapult Bio and the National Personalized Health Network will play a critical role in helping to accelerate and extend my vision for personalized medicine throughout the world.”
The creation of Catapult Bio addresses a gap highlighted in the recently released 2007 Battelle report, Arizona's Bioscience Roadmap: Toward 2012, which indicated Arizona’s need to establish an entity with the expertise to further develop and commercialize the increasing number of research discoveries emerging from Arizona-based life sciences research efforts. Additionally, Catapult Bio helps fulfill significant funding shortfalls in shepherding late stage research discoveries into development and commercialization.“Catapult Bio will focus on creating exciting new programs that bridge the expertise and funding gaps, and provide the necessary support to efficiently enhance, accelerate and develop technology into commercially available products and services,” MaryAnn Guerra, president of TGen Accelerators, said. “Our National Personalized Health Network will leverage TGen’s clinical expertise and allow increased patient access to important information relating to their treatment, additional clinical care services and an expanded clinical trial network focused on personalized medicine.”
“This pioneering effort to create Catapult Bio and the National Personalized Health Network in Greater Phoenix is the result of an emerging technology practice driving next-generation economic development,” Barry Broome, president and CEO of GPEC, said. “Dr. Soon-Shiong is a philanthropist and a visionary leader whose incredible investment will literally change the health of individuals around the world for the better.”
For more information about the Office of the Governor, please visit www.azgovernor.gov.
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