Wednesday, May 30, 2007

Detecting and identifying contamination from bacteria, viruses, and other microbes at UA

Self-decontaminating surfaces and inexpensive devices that can be used anywhere to rapidly diagnose disease are two areas of research for new BIO5 member Linda S. Powers, PhD. The projects are part of her interest in developing technology to detect and identify contamination from bacteria, viruses and other microbes. Microbe detection is accomplished with light (the intrinsic florescence of the microbes) and the detection instrument is very sensitive and measures small numbers of microbes in real time. Once the microbe is detected, a second test (small molecules that binds to specific microbes) reveals what it is within a few seconds.

Dr. Powers joined The University of Arizona (UA) faculty this year, coming from Utah State University. Also moving to Tucson this year is the company Dr. Powers founded, MicroBioSystems, which manufactures and licenses the detection and identification of microbes. The company builds and tests prototypes for other companies, and licenses the technology. Dr. Powers is a professor of electrical and computer engineering and the Thomas R. Brown Chair of Bioengineering, and director of the National Center for the Design of Molecular Function at the UA.

Dr. Powers is joined by BIO5 member Walther R. Ellis, Jr., PhD, who also relocated to the UA from Utah State University. He is a research professor of Chemical and Environmental Engineering and associate director of the National Center for the Design of Molecular Function.

Sunday, May 27, 2007

BNI's Dr. Pipe to serve on International Society for Magnetic Resonance in Medicine Board of Trustees

Jim Pipe, Ph.D., of the Barrow Neurological Institute and St. Joseph’s Hospital, was recently elected to serve on the Board of Trustees of the International Society for Magnetic Resonance in Medicine (ISMRM). The ISMRM is the premier international society for research, development, and applications in the field of magnetic resonance in medicine and biology and other related topics. Its multidisciplinary membership of over 5,000 members and consists of clinicians, physicists, engineers, biochemists, and technologists. Each year the ISMRM elects four new members to the board, a scientist and a clinician from both inside and outside of North America. Dr. Pipe was elected by his peers as the North American scientist from a slate of four candidates, and will serve a 3-year term starting in May 2007.

According to ASU, there's a new wrinkle in evolution -- man-made proteins

Nature, through the trial and error of evolution, has discovered a vast diversity of life from what can only presumed to have been a primordial pool of building blocks. Inspired by this success, a new Biodesign Institute research team, led by John Chaput, is now trying to mimic the process of Darwinian evolution in the laboratory by evolving new proteins from scratch. Using new tricks of molecular biology, Chaput and co-workers have evolved several new proteins in a fraction of the 3 billion years it took nature. Their most recent results, published in the May 23rd edition of the journal PLoS ONE, have led to some surprisingly new lessons on how to optimize proteins which have never existed in nature before, in a process they call ‘synthetic evolution.’

"The goal of our research is to understand certain fundamental questions regarding the origin and evolution of proteins," said Chaput, a researcher in the institute’s Center for BioOptical Nanotechnology and assistant professor in Arizona State University’s department of chemistry and biochemistry. "Would proteins that we evolve in the lab look like proteins we see today in nature or do they look totally different from the set of proteins nature ultimately chose" By gaining a better understanding of these questions, we hope to one day create new tailor-made catalysts that can be used as therapeutics in molecular medicine or biocatalysts in biotechnology."

The building blocks of proteins are 20 different amino acids that are strung together and folded to make the unique globular shape, stability and function of every protein. The mixing and matching of the amino acid chain like numbers in the lottery are what favor the odds in nature of finding just the right combinations to help generate biological diversity. Yet no one can predict how the string of amino acids sequence folds to make the 3-D functional structure of a protein.

John Chaput, a researcher at the Biodesign Institute at Arizona State University, has used molecular biology tricks to rapidly evolve proteins that have improved stability when compared to naturally occuring... To select the raw ingredients to create the proteins, Chaput’s group (which includes Harvard collaborator Jack Szostak, and ASU colleagues Jim Allen, Meitian Wang, Matthew Rosenow and Matthew Smith) began their quest by further evolving a protein that had been previously selected from a pool of random sequences.

Jack Szostak and Anthony Keefe first made the parental protein in 2001. To achieve their feat, they stacked the odds of finding just one or two new proteins and generated a library of random amino acid sequences so vast — 400 trillion — that it dwarfs the number of items in the entire Library of Congress (134 million). They started with a small protein stretch 80 amino acids long. This basic protein segment acts as a protein scaffold that can be selected for the ability to strongly clutch its target molecule, ATP. There was only one problem, the parental protein could bind ATP, but it wasn’t very stable without it. "It turns out that protein stability is a major problem in biology," said Chaput. "As many as half of the 30,000 genes discovered from the human genome project contain proteins that we really don’t know what their structure is or whether or not they would be stable. So for our goal, we wanted to learn more about the evolution of protein folding and stability."

Chaput’s group decided to speed up protein evolution once again by randomly mutating the parental sequence with a selection specically designed to improve protein stability. The team upped the ante and added increasing amounts of a salt, guanidine hydrochloride, making it harder for the protein fragment to bind its target (only the top 10 percent of strongest ATP binders remained). After subjecting the protein fragments to several rounds of this selective environmental pressure, only the ‘survival of the fittest’ ATP binding protein fragments remained. The remaining fragments were identified and amino acid sequences compared with one another. Surprisingly, Chaput had bested nature’s designs, as the test tube derived protein was not only stable, but could bind ATP twice as tight as anything nature had come up with before. To understand how this information is encoded in a protein sequence, Chaput and colleagues solved the 3-D crystal structures for their evolutionary optimized protein, termed DX, and the parent sequence.

In a surprising result, just two amino acids changes in the protein sequence were found to enhance the binding, solubility and heat stability. "We were shocked, because when we compared the crystal structures of the parent sequence to the DX sequence, we didn’t see any significant changes," said Chaput. "Yet no one could have predicted that these two amino acids changes would improve the function of the DX protein compared to the parent. The results have helped provide a new understanding of how subtle amino acid changes contribute to the protein folding and stability. Chaput’s team has developed the technology potential to take any of nature’s proteins and further improve its stability and function. "We have the distinct advantage over nature of being able to freeze the evolution of our lab-evolved proteins at different time points to begin to tease apart this random process and relate it to the final protein function," said Chaput. Next, Chaput plans on further expanding his efforts to evolve proteins with new therapeutic features or catalytic functions.

For more information, contact Joe Caspermeyer,, 480-727-0369

Saturday, May 26, 2007

Biodesign Institute scientists offer new view of photosynthesis

A research team led by Neal Woodbury, at ASU's Biodesign Institute, has come up with a new insight into the mechanism of photosynthesis, which involves the orchestrated movement of proteins on the timescale of a millionth of a millionth of a second. Their findings are described in in the May 4 issue of Science, "Protein Dynamics Control the Kinetics of Initial Electron Transfer in Photosynthesis."

During photosynthesis, plants are capable of scavenging nearly every photon of available light energy to produce food. In order to examine the processes involved in photosynthesis, Dr Woodbury’s team used the earliest photosynthetic bacteria to evolve called Rhodobacter sphaeroides and created mutants that allowed them to uncover more of the physical mechanism driving photosynthesis and theoretically tweak the electron transfer relationships between molecules in the reaction center. The reaction center is where light energy is funneled into specialized chlorophyll binding proteins that form a scaffold, holding chlorophyll molecules at a highly optimized distances and orientations so that electrons can hop from one chlorophyll to another.

The research team includes lead author Haiyu Wang, Biodesign Institute; Su Lin, Biodesign Institute; James Allen, ASU Department of Chemistry and Biochemistry; JoAnn Williams, ASU Department of Chemistry and Biochemistry; Sean Blankert and Christa Laser, Biodesign Institute.

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Monday, May 21, 2007

Biodesign Institute scientists study new ways to generate hydrogen

As researchers look for new sources of energy, hydrogen is considered a potential answer. As one of the key components of water, it is abundant and produces no pollution. But several technical challenges have hampered hydrogen development, including those pertaining to the splitting of water to produce hydrogen molecules. A group of ASU researchers at the Biodesign Institute has received a $1.5 million grant from the U.S. Department of Energy to explore innovative methods for generating hydrogen.

The four-year grant is part of a new round of DOE funded projects in support of President George W. Bush’s Hydrogen Fuel Initiative, to address the technical and economic challenges in developing renewable and distributed hydrogen production technologies. Neal Woodbury, director of the Center for BioOptical Nanotechnology at the Biodesign Institute, is the principal investigator on the ASU grant, which he says will explore new ways to efficiently convert water into hydrogen. The research will focus on the development of new catalysts – materials that facilitate chemical conversion processes – for converting water to hydrogen.

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Sunday, May 20, 2007

Arizona high school graduate makes the USA Today’s 2007 All-USA academic team

Veronica Shi, a new graduate of Corona del Sol High School, has been working in the laboratory of Dr. Susana Martinez-Conde at the Barrow Neurological Institute for the last three years, where she has made a new discovery of great importance. She has discovered that the brightness of an object’s surface depends on the size of the surface’s image on the retina of the eye. This outstanding discovery, which propelled her into the USA Today’s 2007 All-USA High School Academic Team, and into the 2007 freshman class at Harvard University, has major implications for how we see, and could be used, in part, as a method to increase visibility in the partially blind.

The project has been a three year study on human volunteers to measure how perceived brightness varies as a function of the size of an object’s surface on the retina. The neural cells of the retina are sensitive to light and each cell is sensitive to a specific area of the visual field, called a receptive field. The hypothesis of the project is that the apparent brightness of an object’s surface should increase when the size of the surface matches the size of the retinal cells’ receptive fields. The subjects viewed grayscale visual stimuli presented on a computer monitor. The subjects, who did not know the purpose of the study, indicated whether a surface was brighter or darker than a standard stimulus of known luminance. The experimenters varied the size of the surfaces and found that, when the surface size matched the size of retinal receptive fields, the apparent brightness increased, thus verifying the hypothesis. This result has far reaching implications for improving the visibility of visual objects for the partially blind, and also has important implications for how the brain processes information about object luminance.

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Tuesday, May 1, 2007

Sun Health Institute opens research building, adds staff

Source: Erin Zlomek, The Arizona Republic

Along with opening a second 36,000-square-foot medical research building, the Sun Health Research Institute announced the hirings of four new employees expected to investigate the puzzles presented by Alzheimer's and Parkinson's diseases.

At the new research center's unveiling April 9, the company announced these new staff additions:

Paul Coleman, Ph.D., senior scientist and co-director of the L.J. Roberts Center for Alzheimer's research. Dr, Coleman plans to research how early Alzheimer's begins.

Dr. Philip Khairallah, M.D., fellow of the American College of Cardiology, and former head of cardiovascular research at the Cleveland Clinic, will develop cardiovascular research at the center and study a drug thought to play a role in hypertension.

Dr. Jeffrey Stern, M.D., MPH, will lead the new Center for Prostate Cancer and Urologic Research. His first project will be a Food and Drug Administration study of a drug treatment for bladder cancer.

Dr. Sandra Ann Jacobson, M.D., Ph.D. will be a geriatric neuropsychiatrist with the Center for Healthy Aging at the Institute. She will focus her research on the causes of dementia.

The new building, at 10515 Santa Fe Drive, Sun City, will provide more room for clinical research trials and can accommodate more patients willing to participate in those trials, according to the company.

The Sun Health Research Institute employs 80 medical professionals. The staff has conducted more than 70 clinical trials. The new center consists of three floors. While the first two floors will be used for trials and research, the third floor will house the newly expanded tissue repository for the institute's Brain and Body Donation program. Expansion of the repository will enhance the institute's ability to research Alzheimer's disease, Parkinson's disease, orthopedics and cancer, according to the company.