The Gold Standard: Nanoparticles Used To Make 3-D DNA Nanotubes

[Source: ScienceDaily ] - Arizona State University researchers Hao Yan and Yan Liu imagine and assemble intricate structures on a scale almost unfathomably small. Their medium is the double-helical DNA molecule, a versatile building material offering near limitless construction potential.

In the January 2, 2009 issue of Science, Yan and Liu, researchers at ASU's Biodesign Institute and faculty in the Department of Chemistry and Biochemistry, reveal for the first time the three-dimensional character of DNA nanotubules, rings and spirals, each a few hundred thousandths the diameter of a human hair. These DNA nanotubes and other synthetic nanostructures may soon find their way into a new generation of ultra-tiny electronic and biomedical innovations.

Yan and Liu are working in the rapidly proliferating field of structural DNA nanotechnology. By copying a page from nature's guidebook, they capitalize on the DNA molecule's remarkable properties of self-assembly. When ribbonlike strands of the molecule are brought together, they fasten to each other like strips of Velcro, according to simple rules governing the pairing of their four chemical bases, (labeled A, C, T and G). From this meager alphabet, nature has wrung a mind-bending multiplicity of forms. DNA accomplishes this through the cellular synthesis of structural proteins, coded for by specific sequences of the bases. Such proteins are fundamental constituents of living matter, forming cell walls, vessels, tissues and organs. But DNA itself can also form stable architectural structures, and may be artificially cajoled into doing so.

In his research, Yan has been much inspired by nanoscale ingenuity in the natural world: "Unicellular creatures like oceanic diatoms," he points out, "contain self-assembled protein architectures." These diverse forms of enormous delicacy and organismic practicality are frequently the result of the orchestrated self-assembly of both organic and inorganic material.
Scientists in the field of structural DNA nanotechnology, including Dr. Yan's team, have previously demonstrated that pre-fab DNA elements could be induced to self-assemble, forming useful nanostructural platforms or "tiles." Such tiles are able to snap together—with jigsaw puzzle-piece specificity—through base pairing, forming larger arrays.

Yan and Liu's work in Science responds to one of the fundamental challenges in nanotechnology and materials science, the construction of molecular-level forms in three dimensions. To do so, the team uses gold nanoparticles, which can be placed on single-stranded DNA, compelling these flexible molecular tile arrays to bend away from the nanoparticles, curling into closed loops or forming spring-like spirals or nested rings, roughly 30 to 180 nanometers in diameter.

The gold nanoparticles, which coerce DNA strands to arc back on themselves, produce a force known as "steric hindrance," whose magnitude depends on the size of particle used. Using this steric hindrance, Yan and Liu have shown for the first time that DNA nanotubules can be specifically directed to curl into closed rings with high yield.

When 5 nanometer gold particles were used, a milder steric hindrance directed the DNA tiles to curl up and join complementary neighboring segments, often forming spirals of varying diameter in addition to closed rings. A 10 nanometer gold particle however, exerted greater steric hindrance, directing a more tightly constrained curling which, produced mostly closed tubules. Yan stresses that the particle not only participates in the self-assembly process as the directed material, but also as an active agent, inducing and guiding formation of the nanotube.

With the assistance of Anchi Cheng and Jonanthan Brownell at the Scripps Research Institute, they have used an imaging technique known as electron cryotomography to provide the first glimpses of the elusive 3-D architecture of DNA nanotubules. "You quickly freeze the sample in vitreous ice," he explains, describing the process. "This will preserve the native conformation of the structure." Subsequent imaging at various tilted angles allows the reconstruction of the three-dimensional nanostructure, with the gold particles providing enough electron density for crisp visualization.

DNA nanotubules will soon be ready to join their carbon nanotube cousins, providing flexible, resilient and manipulatable structures at the molecular level. Extending control over 3-D architectures will lay the foundation for future applications in photometry, photovoltaics, touch screen and flexible displays, as well as for far-reaching biomedical advancements.

"The ability to build three-dimensional structures through self-assembly is really exciting, " Yan says. "It's massively parallel. You can simultaneously produce millions or trillions of copies."
Yan and Liu believe that controlled tubular nanostructures bearing nanoparticles may be applied to the design of electrical channels for cell-cell communication or used in the construction of various nanoelectrical devices.

Gut Instinct: Salmonella Bacteria's Molecular Tactics To Cause Illness

[Source: ScienceDaily] - Hundreds of trillions of bacteria make their home in the vertebrate gut. Though many of these microbes perform helpful duties for their host, others—the pathogens—are unwelcome visitors, causing disease.

Salmonella typhimurium is one such pathogenic bacterium. It has evolved sophisticated means of growth, replication, transport and survival within the forbidding environment of the body, where it is responsible for most cases of food-borne illness. Yixin Shi, a researcher at Arizona State University's Biodesign Institute, has taken a keen interest in the regulatory mechanisms that allow Salmonella bacteria to overcome their surroundings and continuously modify both their own and their host's responses in order to stay alive.

By cooperating with the Dr. Roy Curtiss' lab in the Biodesign Institute, Shi's research, which appears in the Proceedings of the National Academy of Sciences, (PNAS) unveils a key survival circuit, which activates a signaling cascade, switching on or off a suite of genes necessary to circumvent the body's multiple defense mechanisms.

A corrosive course

The bacteria are tenacious, surviving acidic pH conditions, digestive enzymes, bile salts, antimicrobial peptides, and other hazards as they pass through the stomach and intestine, and invade the mucosa of the small intestine. Once they make contact with the intestinal lumen, their goal is to secure a safe haven—within the cells of the intestinal epithelium.

To reach this sanctuary, Salmonella first invite themselves in by secreting specific protein factors derived from a region of DNA known as the Salmonella Pathogenicity Island 1 or SPI-1. These factors trick the body, inducing the reorganization of the host cell's cytoskeleton. Epithelial cells respond to the Salmonella secretions by surrounding the bacterial cell in a membrane-bound balloon—the Salmonella Containing Vacuole or SCV. Once the bacterium is taken up in the SCV by the epithelial cell, this secretion system is no longer needed and is switched off. At the same time, another system, SPI-2 is activated and will respond to the altered environment of the internalized Salmonella.

Starving the beast

As the Salmonella penetrates through the epithelial layer, it encounters a dense population of macrophages that normally act to engulf and digest pathogens and debris. Unlike other gut commensal microbes—E. coli for example—Salmonella is able to survive and replicate within SCV of these macrophages, which eventually transport it to organs including the liver and spleen. "The host cells isolate nutrients from bacteria," Shi explains. "They may deplete metal ions, nucleotides, and amino acids which are essential for bacterial life and growth. In this way, Salmonella are essentially starved to death."

But the Salmonella are prepared, and respond— first by sensing the new conditions, then synthesizing proteins allowing them to acquire nutrients from this new environment while switching on genes girding the bacteria against destructive host peptides.
A switch in time

As Shi explains, a regulatory system allowing Salmonella to monitor and respond to rapidly changing conditions is made up of two proteins: PhoP and PhoQ. The PhoP/PhoQ regulators act as a master control, switching off invasion proteins when they are no longer required while switching on a new set of protein factors necessary for intracellular survival. In a domino effect, part of this transition activates magnesium transporters, which act to reestablish metal ion levels in the depleted conditions of the vacuole.

But now a problem arises. Salmonella must maintain proper Mg2+ concentration in their cytoplasm, though PhoP, once turned on, acts to continually increase these levels. The single master switch PhoP/PhoQ is not sufficient to provide this level of control. Salmonella uses an RNA Mg2+ riboswitch to ensure downregulation of Mg2+ transporters without shutting down bacterial resistance to antimicrobial peptides. Likewise, instead of one regulatory switch, two are needed to properly mitigate conditions of resistance to the bacteriocidal peptides, and amino acid starvation. Enter SlyA.

Two to tango

SlyA is a regulatory protein which cleverly integrates itself into the PhoP/PhoQ regulatory system, allowing for multivariable control. Only when both the PhoP/PhoQ and SlyA regulatory systems are activated can the proper activation of genes for intracellular survival be switched on and delicately maintained.

The sequence of events appears as follows: after cellular invasion and formation of the vacuole, PhoP responds to antimicrobial peptides and/or low levels of Mg2+ within the vacuole by switching on, activating Mg2+ transporters and stimulating the production of SlyA. The PhoP/PhoQ system is sufficient to maintain proper Mg2+ levels, but it is SlyA's job to respond to nutrient starvation. Shi believes SlyA does this by sensing the presence of a particular chemical signal—ppGpp, (guanosine tetraphosphate), indicative of amino acid depletion. If SlyA detects this chemical, it will act in consort with the PhoP/PhoQ system. With both PhoP/PhoQ and SlyA switches thrown, all the necessary regulatory genes are brought into play, as conditions warrant.

Shi emphasizes that the cluster of genes responsible for this sequence of environmental adaptations to adversity in virulent bacteria like Salmonella are arranged in particular chromosomal regions, the so-called horizontally acquired loci, which are absent in helpful gut bacteria like E. coli.

Disabling either PhoP or SlyA renders Salmonella virtually impotent, its virulence severely attenuated. The bacteria lose their survivability within the macrophage environment, succumbing either to nutrient starvation or direct obliteration by host antimicrobial peptides.
Shi suggests that the specificity of SlyA's activity within Salmonella's regulatory universe may be good news for those hoping to target this system through vaccine development or other therapeutic intervention. Discovering competitive analogs of ppGpp, for instance, could provide an alternate approach, curtailing SlyA's function.

Shi is optimistic that a firmer grasp of such regulatory mechanisms of virulence as PhoP/PhoQ and SlyA will ultimately lead to life-saving applications. "I never think I'm doing basic science," Shi stresses. "I always think I'm working on the first steps of an application. "

Yixin Shi is an assistant professor of ASU's School of Life Sciences and researcher in the Biodesign Institute's Center for Infectious Diseases and Vaccinology.

The Medium Is The Message: Manipulating Salmonella In Spaceflight Curtails Infectiousness

[Source: ScienceDaily] - Infectious pathogens like Salmonella typhimurium employ a startling array of techniques to skillfully outwit the body's defense mechanisms and produce illness. Through their expression of genes—the fundamental building blocks of cellular physiology—such microbes ingeniously adapt to varied environments, modifying their disease-causing potential or virulence.

Although the study of a broad range of microbial virulence factors is now well advanced, many pieces of the puzzle are still missing. Cheryl Nickerson, a researcher at Arizona State University's Biodesign Institute, has explored the novel environment of space to investigate the cellular and molecular machinery of virulence. There, the space shuttle crew grow the bacteria in triple-enclosed containers under conditions of minimized gravity (or microgravity). Nickerson's spaceflight experiments have shown that Salmonella gene expression and virulence are profoundly altered by microgravity, with the pathogenic cells undergoing a significant increase in their infectious disease potential.

Nickerson's latest findings, published in the journal PLoS ONE, are derived from experiments aboard NASA space shuttle mission STS-123, launched in March, 2008. This research validated results and broadened the scope of spaceflight experiments from STS-115, conducted two years earlier.

In addition to confirming the effects of microgravity observed in the STS-115 experiments (known as MICROBE), the new study homed in on the importance of the microbial growth medium to gene expression and virulence during spaceflight. "Pathogenic cells are smart," Nickerson stresses, pointing to their remarkable ability to fine-tune virulence factors in response to subtle environmental cues.

S. typhimurium, Nickerson's pathogen of choice, is a rod-shaped, motile bacterium and occasional unwelcome visitor to the human gastrointestinal tract, where it is a leading cause of food poisoning and related illnesses.

In both spaceflights, bacteria cultured in a nutrient-rich medium known as Lennox Broth (LB) consistently displayed a heightened virulence and exhibited differential expression of 167 distinct genes. These results were largely consistent with previous earthbound experiments in the laboratory, in which microgravitational conditions were simulated using a rotating wall vessel bioreactor—a device designed by NASA engineers to replicate elements of spaceflight.

Nickerson was able to examine the activity of genes in fine-grained detail through a technique known as microarray analysis, which allowed for a complete profile of gene expression across the entire 4.8 million DNA base pairs that make up the circular Salmonella chromosome. The 167 changes in gene levels produce a tremendous diversity of protein products, pointing to a global transformation in response to microgravity.

Interestingly, many of the 167 differentially expressed genes observed in the space-traveling microbes coded for an assortment of ionic response pathways. To Nickerson, these compelling results now suggested a possible means of limiting or eliminating the enhanced virulence imparted by spaceflight, through manipulation of the ionic content of the bacterium's surrounding environment.

In both the STS-115 and STS-123 missions, Nickerson compared the spaceflight response of Salmonella grown in Lennox Broth to the same bacteria grown in a minimal medium—one requiring the cells to synthesize most of their metabolic needs from scratch. This alternate growth medium, dubbed M9, contained high concentrations of five critical ions. The effects of this medium were dramatic, with the M9 cultures exhibiting a decrease in virulence in response to microgravity, despite exhibiting altered expression of many of the same genes and gene families that were observed in the LB cultures, where virulence under microgravity was intensified.

To test the hypothesis that ionic concentrations present in the M9 medium played a role in virulence reduction, a hybridized culture media known as LB-M9 was prepared for the March 2008 mission, consisting of the LB formula supplemented with five ions occurring in the M9 medium, but which were found to be at lower concentrations in LB. Bacteria cultured with LB-M9 again displayed a decreased virulence in response to microgravity. Subsequent bioreactor studies conducted by Nickerson's team on earth have hinted that phosphate ions may be a principle component of the observed virulence reduction.

One of Nickerson's most intriguing findings involves a specific RNA-binding protein known as Hfq, which appears to regulate central aspects of S. typhimurium's response to the spaceflight environment, acting as a "global molecular master switch." Hfq is known to regulate one third of the 167 differentially expressed genes in the spaceflight LB cultures. Interestingly, a large number of Hfq-regulated genes were also found to be differentially expressed in the M9 flight samples. In addition to Hfq's known properties as a virulence factor, the protein also acts to regulate ion response pathways,and has been associated with phosphate regulation. Moreover, Hfq appears to be an evolutionarily conserved regulatory factor, and may serve to globally modify bacterial responses to microgravity, regardless of the phenotypic outcome—a decrease in virulence for M9 cultures grown in microgravity environments and an increase for bacteria steeped in the LB medium.

But what was causing Salmonella to undergo such a dramatic transformation under conditions of microgravity? At least part of the answer, Nickerson believes, is related to the mechanical forces exerted upon the bacterial cell's membrane by the growth conditions—a property known as fluid shear. Specifically, the microgravity conditions aboard the space shuttle produce a condition of reduced fluid shear, an effect that appears to trigger an intensification of virulence in Salmonella grown in LB medium. As Nickerson points out, "No one had thought to look at a mechanical force like fluid shear on the disease-causing properties of a microorganism."

If a rolling stone gathers no moss, a bacterium like S. typhimurium appears to gather virulence when its movement is slowed down and fluid shear across its surface is minimized. Nickerson speculates that Salmonella encounters just such conditions not only during spaceflight but also in vivo in an infected individual when the bacterium makes contact with an intestinal host cell and becomes ensnared in the fingerlike projections known as microvilli.

Thus, space travel may trick the microbes into behaving as though they were in an environment hospitable to cell infection, thereby switching on an increased virulence response, given appropriate environmental preconditions. "They're responding to an environmental signal that they're used to seeing right here on earth, during the natural course of the infectious disease process," Nickerson states, emphasizing that this response is masked in traditional microbial studies performed using lab cell cultures, which fail to replicate the low fluid shear conditions found in vivo, particularly in the gastrointestinal tract—Salmonella's favored site of infection.

One result of spaceflight not replicated in the earthly bioreactor simulations was the formation of what appear to be biofilms—conglomerations of bacterial cells associated with infectious virulence. Nickerson emphasizes the potential importance, should such findings be confirmed. Up to 70 percent of bacterial infections in humans may be associated with the formation of such biofilms, which seem to arm bacterial pathogens with formidable resistance to the host's immune system as well as to antibiotics.

How do the disparate variables—extracellular phosphate concentration, mechanical forces like fluid shear and genetic regulation of pathogenic virulence—combine and interact during the infection process? While the current research provides tantalizing hints, a full understanding of the complex interplay of forces and the in vivo mechanisms of Salmonella pathogenesis await further research.

Fortunately, new opportunities for study are opening up, which may illuminate these issues. NASA is one of the primary partners in the construction and operation of the International Space Station (ISS), a semi-permanent research platform allowing for further investigations into microbial responses to low fluid shear environments. Because cells cultured in microgravity exhibit biomedically relevant phenotypes that can not be observed using traditional experimental approaches, Nickerson believes the therapeutic benefits of such research will extend beyond infectious pathogens like S. typhimurium, eventually inspiring new clinical approaches to cancer, aging, bone and muscle wasting diseases, among other earthly afflictions.
"We can use the innovative research platform of the ISS to contribute to these new translational advances for the development of new strategies to globally advance human health."

Cutting The Cord To Determine Babies' Health Risk From Toxic Exposure

[Source: ScienceDaily] - Despite the well-known dangers of first- and secondhand smoke, an estimated ten percent of pregnant women in the U.S. are smokers. Exposure of a developing baby to harmful cigarette byproducts from mothers who smoke affects an estimated 420,000 newborns each year and poses a significant health care burden.

Now, in the first study of its kind, a team of researchers has completed a global assessment of newborns' umbilical cord blood to better understand the fetal health risks from smoking mothers. The research was led by Johns Hopkins University and included Rolf Halden, a researcher from the Biodesign Institute at Arizona State University.

"Cigarette smoking is a massive onslaught on human physiology," said Halden, who works in the institute's Center for Environmental Biotechnology. Cigarette smoke is known to contain more than 4,000 chemicals, potentially affecting the health of a newborn baby on multiple levels, including low birth weight, premature delivery and small size for gestational age. The exact cause of these health effects continues to be the subject of investigation.

"Unfortunately, maternal cigarette smoking puts babies at risk of adverse birth outcomes and increases susceptibility to other diseases later in life," said Halden.

The research team's goal was to provide the first assessment of proteins detectable in infant blood and to identify possible molecular predictors, or biomarkers, of fetal health risks.
The emergence of improved analytical tools allowed the researchers to address newborn health risks and explore the environmental effects of a well-known toxin in a level of detail not previously available. These tools include high-speed DNA sequencing, a powerful instrumental analysis called proteomic mass spectrometry to enhance the detection of proteins in complex samples, and bioinformatics, or the raw computing power to perform massive data crunching to tease out and identify biomarkers.

In doing so, the team described over 200 serum proteins contained in umbilical cord blood, the vital link between mother and developing baby that shares between the pair both essential nutrients as well as unwanted toxins absorbed by the mother.

"Modern tools in mass spectrometry and bioinformatics have enabled us to obtain a first view of proteins contained in fetal cord blood serum and to single out among these more than a dozen interesting ones whose concentrations change as a function of chemical exposure. These biomarkers of exposure and early effect are the gold of protein mining," said Halden, who is also an associate professor in the Ira A. Fulton School of Engineering.

Halden, who joined ASU's Biodesign Institute in 2008, initiated the study while at Hopkins along with lead author David R. Colquhoun, and colleagues Lynn R. Goldman, Frank R. Witter, Robert N. Cole, Marjan Gucek, Malini Mansharamani, and Benjamin J. Apelberg. The results were published in the early online edition of the journal Environmental Health Perspectives (http://www.ehponline.org).

To best obtain a snapshot of fetal proteins at birth, the study needed to obtain cord blood samples as soon as possible after newborn delivery. This required the coordinated efforts of multiple investigators and the resources of the large teaching hospital at Hopkins to recruit study subjects. Among the participants were many doctors and nurses to help with deliveries and obtain cord blood samples along with graduate students who were on call and had to rush out in the middle of the night to collect samples, transfer and process them, and analyze the data from the study population.

The group started with a large pool of more than 300 cord blood samples, and after adjusting for parameters such as the age of the mothers, narrowed down their focus to a dozen babies, half from non-smoking mothers and the other half from pregnant smokers.

"The study was a little bit challenging in that we went out on a fishing expedition," said Halden. "We wanted to look at everything at the same time, and the ability to tease out from the soup of proteins only those of interest was the chief technical challenge of this project."

The team looked for new proteins or proteins levels that may have changed between the smoking and non-smoking groups. After analyzing more than 200 proteins through mass spectrometry in smoke-exposed and control groups, they found small changes in the levels of some proteins, which represented biomarkers of cigarette smoke exposure.

"Of 17 proteins that were significantly up- or down-regulated in the cord blood of babies born to smoking mothers, 14 have previously been described to be related to smoking in either adults or in the fetus," said Lyne Goldman, a professor in the Department of Environmental Health Sciences at Johns Hopkins' School of Public Health.

The protein biomarkers have been linked to key metabolic pathways involved in regulating nutrients, oxygen and inflammation processes. After their analysis, the team also discovered some surprising results that illustrate the subtlety of using biomarkers as an approach to peer into the molecular makeup of human health. "There was not a single protein unique to either the smoking or non-smoking group," said Halden. "The remarkable finding is that there were no unique biomarkers."

Halden explains that only through the combined use of the new technologies was the research team able to tease out the small differences in the proteins levels between the two study groups.
Asked about the reliability of the biomarkers that the research team identified? Halden said, "The truth is that we don't know yet. We only took a first snapshot of the protein profile in baby blood right after birth. But does it change over time and will the differences we detected persist? We don't know."

The group hopes to use the same techniques to examine a wide range of environmental exposures and their effect on human health. "These findings confirm and underscore the serious metabolic alterations that are occurring in utero to children of smoking mothers, alterations that may increase risk for chronic disease over a lifetime," said Hopkins colleague Frank Witter. "We hope that this method will be sensitive enough to detect proteomic changes associated with environmental exposures as well."

The ultimate hope is that through the use of biomarkers identified by the team, it may become possible to detect effects of toxic exposures early on, before the onset of disease. "This may open opportunities to improve health outcomes by reducing the occurrence and severity of disease from environmental exposures, said Halden."

Turbocharged Nanomotors

[Source: PhysOrg.com] -- Nanorobots that are introduced into the body to eradicate tumor cells or clean out clogged arteries are not just science fiction; they are a realistic vision of the technological possibilities of the not-so-distant future. Efficient nanomotors will be needed to drive these nanomachines.

A team of scientists from University of California, San Diego (USA) and Arizona State University (Tempe, USA) has now developed nanorods that swim extremely fast. “These nanorods travel about 75 times their own length in one second,” report Joseph Wang and his co-workers in the journal Angewandte Chemie. “We are approaching the speed of the most efficient biological nanomotors, including flagellated bacteria.”

The first simple applications for nanomotors could include rapid transportation of pharmaceutical agents to specific target areas, or the passage of specimen molecules through the tiny channels of diagnostic systems on a microchip. However, forward motion through a liquid is not as trivial as one would like to think. One method for the construction of nanomotors that can achieve this is the fuel-driven catalytic nanowire. These are tiny nanoscopic rods whose ends are made of two different metals. Unlike macroscopic motors, they do not have a fuel tank; instead they move through a medium that contains the fuel they need.

The “classic” example of such a system is a gold–platinum nanotube that can travel at speeds of 10 to 20 µm per second with hydrogen peroxide as its fuel. Wang and his team have now dramatically accelerated these nanorod motors: they have achieved speeds of over 150 µm per second by replacing the gold portion with an alloy of silver and gold.

How does the nanomotor work? The platinum segment catalyzes the splitting of hydrogen peroxide (H2O2) into oxygen (O2) and protons (H+). It absorbs the excess electrons. These are transferred to the silver/gold segment, where they speed up the reduction reaction of H2O2 and protons to make water. The release of oxygen and water produces a small current, which drives the nanorod through the fluid, platinum side first. “The silver/gold alloy causes the electrons to be transferred more quickly,” explains Wang. “This increases the fuel decomposition rate and the nanorod is accelerated faster.” The speed of the nanorods can be tailored by changing the proportion of silver in the alloy. “Fuel additives or variations of the platinum segment will make these rods even faster,” predicts Wang.

UA researchers are finding a new way to reduce food-borne illness in humans

[Source: Susan McGinley, UA College of Agriculture and Life Sciences] - Most people are familiar with Salmonella and its potential to make people ill. But fewer know about Campylobacter jejuni – even though it makes more people sick. Raw chicken is one of the most common carriers of the bacteria, often encountered when cooked meat is placed on unwashed cutting boards previously used for trimming raw chicken, or when chicken is not cooked to 165 degrees Fahrenheit.

"Campylobacter is now the No. 1 food-borne pathogen in the United States and the world, surpassing Salmonella," said Lynn Joens, a professor in The University of Arizona department of veterinary science and microbiology and a BIO5 member. "In the United States alone, 2.4 million cases are reported annually, with costs exceeding $1 billion."

A new poultry vaccine in development at the UA offers a unique approach in controlling Campylobacter jejuni infection in chickens before it reaches the dinner table. In research trials the vaccine has significantly reduced the pathogen's ability to colonize young chickens' intestines, where the infection begins. The goal is to halt the contamination before it spreads and survives on raw chicken sold in stores.

"Yet chickens don't actually cause the disease (nor does it make them ill). It's the organism they carry that makes people sick," Joens said. "Right now you can go to any grocery store, get a raw chicken, test it in a laboratory and find Campylobacter jejuni. Twenty to 80 percent of all broiler houses become contaminated with Campylobacter."

The most common symptoms of human Campylobacter poisoning, which mimic those of Salmonella and other gastrointestinal pathogens, include fever, cramps, watery diarrhea and sometimes dysentery. More severe infections can lead to peritonitis, autoimmune disease or death.

Funded by the U.S. Department of Agriculture, Joens and UA graduate students started analyzing Campylobacter's infection process about four years ago, looking for a way to interrupt it. The laboratory team, which included graduate research associate James Theoret and assistant research professor Bibiana Law, eventually discovered that the pathogen first attached itself to the surface of the chick's intestines and then began to multiply. Attacking the "sticking" mechanism seemed to be the key.

When the UA researchers sequenced the intestinal surface protein they identified the gene responsible for producing Campylobacter’s adherence protein. Then they built a trial vaccine around it using Salmonella bacteria as a vector, with the assistance of Roy Curtiss, professor and director of the Center for Infectious Diseases and Vaccinology at Arizona State University. Curtiss’ group inserted the adherence gene into Salmonella bacteria, which is nonpathogenic for poultry. The resulting live vaccine – containing Salmonella programmed to make the Campylobacter adhering protein – was fed to young chickens to protect them.

“Once the Salmonella in the vaccine produced the Campylobacter protein, the chicks made antibodies against it in their intestines,” Joens says. "In our first study of 15 birds we got a very significant reduction – 98 percent – in Campylobacter infection, compared with a control group. We're now repeating the trial on a larger scale."

The vaccination process is simple, easy to produce and protective to the chick, according to Joens. The Salmonella lives four to five days, enough time to stimulate antibody production, and dies. Chickens need to be vaccinated early because they become infected at just two to three weeks of age.

Joens' preliminary figures show that 270 million Campylobacter organisms were present in non-vaccinated birds, compared with 67,000 organisms in the vaccinated birds.

"You need at least 500 organisms to produce disease in humans," he explained. "The chlorine in the packinghouse chillers usually reduces numbers of bacteria by 1,000 to 100,000 organisms, so the chickens should be free of Campylobacter after processing."

The UA group was the first to discover the adherence protein, which is only produced when Campylobacter jejuni colonizes certain surfaces, like chicken intestine and skin. They have a patent pending in both the United States and the European Union for the gene that produces it.

"If everything goes right we could have a commercial vaccine in three to five years," Joens said. The vaccine's effect could be significant: About 8.9 billion broilers go to market annually in the U.S., with a value of $21.5 billion. Europe has similar broiler production figures. Americans consumed 86 pounds of chicken per person in 2006, the most recent numbers available.

"The vaccine would be a great intervention method for Campylobacter when the USDA and FDA (Food and Drug Administration) mandate reduced numbers of food-borne pathogens in chicken – probably in two to three years," Joens said. "Once it becomes available, the vaccine should cost about a penny per chick. More importantly, it should greatly reduce the number of cases of human Campylobacter gastroenteritis."

Making Flies Sick Reveals New Role For Growth Factors In Immunity

[Source: ScienceDaily] - Salmonella infection is not a positive experience. However, by infecting the common laboratory fruit fly Drosophila melanogaster with a Salmonella strain known for causing humans intestinal grief, researchers in the School of Life Sciences at Arizona State University have shed light on some key cell regulatory processes – with broad implications for understanding embryonic development, immune function and congenital diseases in humans.
Associate Professor Stuart Newfeld and laboratory coordinator Joel Frandsen, along with colleagues in the College of Liberal Arts and Sciences and Biodesign Institute at ASU, released their findings online on September 24 in the journal Proceedings of the National Academy of Sciences.

Strong parallels exist in the regulation of immune system function in animals as diverse as flies, mice, and humans. Newfeld's own investigative connection between fly and human immune systems came about through his research with a well-studied family of proteins called Bone Morphogenetic Proteins (BMP).

"Bones and flies?" one might scoff. These proteins are named because of their involvement in the formation of bone and cartilage in humans; however, they have also been linked to many other aspects of early development and to essential cellular processes in virtually all animals.
One type of morphogenetic protein, intensively studied in fruit flies and the focus of the published study by the Newfeld group, is the growth factor Decapentaplegic (Dpp). Dpp acts as a hormonal signaling device, binding to cells and communicating, for instance, whether to divide or to stop growing or even to become a different type of cell.

Studies have shown that Dpp in the fruit fly and its counterparts in other animals have diverged little from one another in evolutionary time. Although there are tiny changes in the genes that code for this protein from animal to animal, the morphogenetic proteins are still structurally and functionally very similar – a testament to their crucial role as signaling devices in all animals, including humans.

"Dpp from flies has been shown to be completely functional in mammalian cells, and the human version of Dpp – BMP 2/4 – also works just fine when injected into flies," explains Newfeld.

Newfeld's research builds on earlier observations made by Aaron Johnson, then a graduate student in the Newfeld lab, now a postdoctoral fellow with University of Texas Southwestern Medical Center in Dallas, Tex. Johnson first observed that fruit fly mutants that lacked the ability to generate Dpp protein in one tissue (at a particular time in embryonic development) suffered from excess cell growth in the neighboring tissue. The lack of communication between the tissues resulted in uncontrolled cell growth, in this case in the heart. "Dpp mutant flies have large hearts which are stiffer and beat inefficiently," says Newfeld.

Johnson went on to uncover Dpp's role in heart development. He discovered that when the embryo is nearly ready to hatch, Dpp signals tell heart cells to stop growing. These instructions also insure a proper boundary between the heart and surrounding muscle tissue.

While these were fundamentally exciting discoveries, Newfeld made them even more so when he extended Johnson's project. Since both the heart and the lymph glands in the fly originate from the same tissue (cardiogenic mesoderm), he postulated that when heart development goes awry in fruit fly Dpp mutants that the lymph glands might also be affected.

"One of the functions of the lymph gland in fruit flies is to produce blood cells," notes Newfeld. "This is in contrast to humans where the processes take place in our bone marrow."

With support from Science Foundation Arizona, Frandsen built on Johnson and Newfeld's early discoveries by looking into the mutant fruit fly's immune system and blood cells. He noticed that, in addition to excess cell growth during heart development, Dpp mutants also had an excess of plasmatocytes (blood cells involved in digesting small infectious particles) – an important clue that Dpp was affecting the regulation of the immune system of the flies.
Plasmatocytes are one of three types of immune cells that arise from hematopoietic stem cells – embryonic cells that only take on their adult roles based on signals they receive from signaling molecules, including Dpp. However, how Dpp might specifically function in blood cell formation remained a mystery, and required fresh thinking.

With help from School of Life Sciences Professor Roy Curtiss, director of the Center for Infectious Diseases and Vaccinology at the Biodesign Institute at ASU, and his technician Bronwyn Gunn, Frandsen and Newfeld developed a novel experimental approach. Rather than curing their fly patients, they sought instead to make the Dpp mutants sick, hoping the infection with Salmonella would provide a new avenue to study their immune system defects in greater detail.

"The problem with the traditional approaches to studying immunity is that we keep our flies in a pretty clean lab – they see few, if any, pesticides or parasites or anything they would need to defend themselves from," says Newfeld.

Getting flies sick wasn't trouble free, Frandsen says. At first, the fruit flies wouldn't eat the type of Salmonella that infects humans. But, with some clever cookery, a feeding technique was identified that led to Salmonella-infected flies. Once inside the flies, the Salmonella activated their immune systems. Newfeld points out that it was then that Frandsen made a key observation: Dpp mutant flies are unable to produce one type of immune cell that normal flies do in response to an attack by pathogens. This was the first piece of evidence that Dpp might regulate the options available to hematopoietic stem cells.

The lack of Dpp in fly mutants meant that their stem cells would only become plasmatocytes. The inability of Dpp mutant fruit flies to produce a particular immune cell type was not obvious under regular lab conditions. This type of defect is considered "cryptic"; a defect that is not immediately obvious because until the fly requires an immune response there is no way to know that something is wrong.

"Up to this point Dpp had not been implicated in hematopoiesis in flies," states Newfeld.
The discovery that Dpp plays a direct role in immune system regulation in flies may have some direct implications for humans, offering new insight into human diseases caused by mutations in bone morphogenetic proteins. Newfeld says too, that scientists who study these morphogenetic proteins in mammals (proteins very similar to Dpp) have known for some time that these proteins are involved in the hematopoietic stem cell growth in the bone marrow. The similarities between the two organisms are intriguing.

"These are exciting parallels; ones which can stimulate collaboration, provide inspiration and reveal new research directions relevant to the understanding of development and immune diseases," Newfeld notes.

Using Living Cells As Nanotechnology Factories

[Source: ScienceDaily] - In the tiny realm of nanotechnology, scientists have used a wide variety of materials to build atomic scale structures. But just as in the construction business, nanotechnology researchers can often be limited by the amount of raw materials. Now, Biodesign Institute at Arizona State University researcher Hao Yan has avoided these pitfalls by using cells as factories to make DNA based nanostructures inside a living cell.

The results were published in the early online edition of the Proceedings of the National Academy of Sciences.

Yan specializes in a fast-growing field within nanotechnology -- commonly known as structural DNA nanotechnology -- that uses the basic chemical units of DNA, abbreviated as C, T, A, or G, to self-fold into a number of different building blocks that can further self-assemble into patterned structures.

"This is a good example of artificial nanostructures that can be replicated using the machineries in live cells" said Yan. "Cells are really good at making copies of double stranded DNA and we have used the cell like a copier machine to produce many, many copies of complex DNA nanostructures."

DNA nanotechnologists have made some very exciting achievements during the past five to 10 years. But DNA nanotechnology has been limited by the need to chemically synthesize all of the material from scratch. To date, it has strictly been a test tube science, where researchers have developed many toolboxes for making different DNA nanostructures to attach and organize other molecules including nanoparticles and other biomolecules.

"If you need to make a single gram of a DNA nanostructure, you need to order one gram of the starting DNA materials. Scientists have previously used chemical methods to copy branched DNA structures, and there has also been significant work in using long-stranded DNA sequences replicated from cells or phage viruses to scaffold short helper DNA sequences to form 2-D or 3-D objects," said Yan, who is also a professor in the Department of Chemistry and Biochemistry at ASU.

"We have always dreamed of scaling up DNA nanotechnology. One way to scale that it up is to use the cellular system because simple DNA can be replicated inside the cell. We wanted to know if the cell's copy machine could tolerate single stranded DNA nanostructures that contain complicated secondary structures."

To test the nanoscale manufacturing capabilities of cells, Yan and his fellow researchers, Chenxiang Lin, Sherri Rinker and Yan Liu at ASU and their collaborators Ned Seeman and Xing Wang at New York University went back to reproducing the very first branched nanostructure made up of DNA- a cross-shaped, four-arm DNA junction and another DNA junction structure containing a different crossover topology.

To copy these branched DNA nanostructures inside a living cell, the ASU and NYU research team first shipped the cargo inside a bacteria cell. They cut and pasted the DNA necessary to make these structures into a phagemid, a virus-like particle that infects a bacteria cell. Once inside the cell, the phagemid used the cell just like a photocopier machine to reproduce millions of copies of the DNA. By theoretically starting with just a single phagemid infection, and a single milliliter of cultured cells, Yan found that the cells could churn out trillions of the DNA junction nanostructures.

The DNA nanostructures produced in the cells were also found to fold correctly, just like the previously built test tube structures. According to Yan, the results also proved the key existence of the DNA nanostructures during the cell's routine DNA replication and division cycles. "When a DNA nanostructure gets replicated, it does exist and can survive the complicated cellular machinery. And it looks like the cell can tolerate this kind of structure and still do its job. It's amazing," said Yan.

Yan acknowledges that this is just the first step, but foresees there are many interesting DNA variations to consider next. "The fact that the natural cellular machinery can tolerate artificial DNA objects is quite intriguing, and we don't know what the limit is yet."

Yan's group may be able to change and evolve DNA nanostructures and devices using the cellular system and the technology may also open up some possibilities for synthetic biology applications.

"I'm very excited about the future of DNA nanotechnology, but there is a lot of work to be done. An interesting research topic to pursue is the interface of DNA nanostructures with live cells; it is full of opportunities," said Yan.

Neural nanomachines project funded by NIH's EUREKA program

[Source: Nanowerk News] - Fueled by a new initiative at the National Institutes of Health called the EUREKA program, two Arizona State University (ASU) teams have received million-dollar grants to pursue the next frontiers in biomedical research.

EUREKA, an acronym for Exceptional, Unconventional Research Enabling Knowledge Acceleration, is intended to boost exceptionally innovative research.

Biodesign Institute researcher John Chaput and Ira A. Fulton School of Engineering associate professor Rudy Diaz each have received $1.2 million research grants from the new, high-impact NIH program. The EUREKA program represents the NIH’s increased emphasis on supporting unconventional, paradigm-shifting research.

“EUREKA projects promise remarkable outcomes that could revolutionize science,” says Elias Zerhouni, NIH’s director. “The program reflects NIH’s commitment to supporting potentially transformative research, even if it carries a greater-than-usual degree of scientific risk.”

Adds ASU President Michael Crow: “The National Institute of Health’s decision to fund these key biomedical research projects not only speaks to the intellectual merits of ASU’s outstanding proposals, but also confirms ASU’s success in attracting federal investment in bold, high-risk, high-impact research central to our mission.”

Chaput and Diaz’s projects were two of 38 proposals deemed exceptional. This is an impressive showing for ASU, and it demonstrates the university’s ability to compete with the best and brightest scientists from across the nation.

“The EUREKA competition provided a unique forum for our Biodesign team to develop a transformative platform that represents a convergence of chemistry, biology and informatics,” says John Chaput, a Biodesign Institute researcher and ASU assistant professor in the Department of Chemistry and Biochemistry.

Neural nanomachines

Research to be led by Diaz will focus on assembling nanomachines designed to deliver electrical signals to neurons on command. Applications of the technology would include bio-sensing and delivery devices that could be used to detect and treat a variety of human neurological disorders.

Diaz, an associate professor in the Department of Electrical Engineering and the Center for Nanophotonics in ASU’s Ira A. Fulton School of Engineering, will work professors Thomas Moore and Hao Yan in the Department of Chemistry and Biochemistry. Yan also works in the Center for Single Molecule Biophysics in the Biodesign Institute.

The team’s goal is to gain new insights into the pathological obstruction of neural signals and the development of new and more precise neural-stimulation technology.

With existing technology, viewing the “microscopic dynamics” of what is occurring in the human body at a cellular level “is like observing human activity on Earth from an orbiting satellite,” Diaz says.

Even with the development of laser tweezers and nanoelectrodes, “most of our cellular bio-chemistry knowledge is still extracted from circumstantial evidence,” Diaz says.

The method Diaz’s team proposes would permit “direct interaction with cells at the local level.” That would be achieved with a nanoscale structure that could be injected into the body, targeted to attach itself to certain clusters of cells and then controlled by chemical reactions triggered by light delivered either through the skin or via microscopic optical fibers.

The team will molecularly assemble a nanodevice that is best described as a remotely powered and remotely controlled pacemaker.

It will be built on a DNA chassis that includes antennas for receiving power and commands from the outside world, and batteries to store and deliver that power.

The antennas are built of Noble metal nanospheres that take advantage of the plasmon resonance to amplify and focus light with nanometer precision.

Artificial electrocytes – electric organ cells that work like batteries, such as those that naturally occur in fish such as electric eels – will be constructed from liposomes (fat cells) that will have ion pumps and ion gate molecules incorporated into their lipid membranes.

The whole structure will have to be encapsulated in a DNA “cage” to prevent the components from being short-circuited by the body’s fluids.

Under the correct wavelength of light, the power-receiving antennae would amplify the incident light to drive the electric charging of the artificial electrocyte.

The structure would include a set of plasmonic antennae. These are microscopic metal nanostructures that behave as antennae in the presence of photons (light) the way metal antennas behave in the presence of radio waves.

The antennas would be tuned to a different wavelength and coupled to the ion gates in the membranes to serve as light-activated switches to perform a “gate-opening” process that triggers the discharge of the artificial electrocyte chain, thus delivering an electrical impulse that can stimulate neurons.

The group hopes to prove the functionality of each component independently and to demonstrate that the entire assembly works as designed.

These nanostructures could lead to advanced neuro-imaging sensors operating at the cellular scale. Such nanosensors delivered to their targets by chemical tags, or during surgical intervention, could reveal new details about the transmission of neural signals and of their pathological interruption.

The light-powered artificial electrocyte could become a critical tool for improving microsurgery, and advancing the understanding of cellular biology.
Discovering ‘hidden’ proteins

During his four-year research project, Chaput will lead a Biodesign Institute team on a project that plans to search the human genome for regions of DNA that contain important, but as of yet unidentified genetic information.

If successful, Chaput’s project may confirm the possible existence of novel protein-coding regions that remain hidden in the shadows of the classic proteome. Determining how and when such proteins are made could have a major impact in diseases, such as cancer, by helping us to understand how cellular function is deposited in our genomes.

Within the code of life, three polymers – DNA, RNA and proteins – provide nearly all of the information content. Each is made from a slightly different set of chemical building blocks, and the exact sequence of these blocks within each chain carries out the instructions of the genetic code. Fifty years ago, Francis Crick, co-discoverer of the DNA double helix, first postulated the “central dogma” of molecular biology, where DNA information is transcribed to make RNA, and RNA is translated to make proteins.

The bounty of the Human Genome Project has identified nearly 25,000 genes. It’s estimated that the human body could make more than a million different proteins, the majority of which remain to be discovered. This entourage of proteins, the proteome, is ultimately responsible for everything good or bad that is related to human health and disease.

Chaput’s team, which includes fellow Biodesign colleagues Sudhir Kumar and Bertram Jacobs, has produced tantalizing clues that suggest there may be many proteins hidden within the DNA sequences of our genome. Together, they will combine their expertise in molecular and cellular biology, bioinformatics and virology to uncover how and when such proteins are made.

“We have developed a combined experimental-bioinformatics approach that allows us to quickly search entire genomes for sequences that enhance the translation of a downstream gene,” Chaput says. “By determining the identity and location of these motifs, it should be possible to determine when specific genes are being made and possibly discover new genes that contribute to our proteome. Since many of these genes will likely be made by non-traditional methods, this technology will also allow us to investigate new mechanisms of protein translation.”

The motifs they hope to identify help recruit ribosomes, the protein translation machinery of the cell, to the correct translation start site on the RNA message. By identifying these landing sites, the team can use bioinformatics to learn where these motifs are located in the genome.

This information will enable Chaput’s team to create an annotated map of the human genome showing all possible locations where protein translation could occur.

Poultry Vaccines May also Improve Human Health

[Source: Stacy Kish, CSREES Staff] - The United States is the world leader in the poultry industry, with annual profits of $50 billion; however, food pathogens threaten the industry. Scientists are especially concerned about Avian Pathogenic Escherichia coli (APEC), which caused an estimated $80 million in losses in 2002.

APEC has the potential to be as harmful as E. coli O157:H7, the strain responsible for human illness and death after consumption of contaminated meat. The genetic similarity between APEC and human E. coli has led scientists to suspect poultry as a source of Extra-intestinal Pathogenic E. coli (ExPEC), which is associated with urethral infections, sepsis, and meningitis.

With funding from USDA's Cooperative State Research, Education, and Extension Service (CSREES) National Research Initiative (NRI), scientists in Arizona are developing a new vaccine for this poultry disease, which, in turn, may improve animal and human health.

Dr. Roy Curtiss and colleagues at Arizona State University began by identifying how E. coli evaded the host's immune system. The researchers used the E. coli bacterial genome to identify the specific genes responsible for triggering its harmful effects. The vaccine produced during this project may lead to additional protection for humans against another pathogen, Salmonella.
"We have to understand how bacteria cause disease so that we can know the best way to fight them," associate research scientist Melha Mellata said. "We came up with a project where we would protect chickens, not only from E. coli infection, but also Salmonella, and in doing so, improve human health."

Antibiotics, the long-time first line of defense to prevent APEC, have lost their potency as the bacteria have grown more resistant to treatment.

"It's becoming increasingly important to develop a vaccine to prevent bacterial infection in poultry," Mellata said. "Poultry is not only a daily food staple, but also a key to human health. For example, the entire supply of annual human flu vaccine production is made from eggs."

Vaccine production for E. coli and Salmonella groups is complicated by the genetic diversity of each bacterium. The new vaccine under development in Curtiss' laboratory is designed to be effective against both E. coli and Salmonella. Curtiss has already developed three vaccines that are effective against multiple strains of Salmonella in livestock. By freeing animals from Salmonella, the vaccine may prevent it from traveling down the food chain to people. The vaccines, which were approved by the FDA for use in swine and poultry, are currently on the market.

CSREES funded this research project through the NRI Food Safety program. Through federal funding and leadership for research, education and extension programs, CSREES focuses on investing in science and solving critical issues impacting people's daily lives and the nation's future. For more information, visit www.csrees.usda.gov.

A new weapon to fight cancer - tobacco plants

[Source: Ken Alltucker, The Arizona Republic] - Tobacco is better known as a cause of cancer rather than a potential cure.

But scientists in Arizona and elsewhere believe tobacco plants may hold the key to developing a personalized cancer vaccine as well as treatments for other diseases.

The experiments are part of a growing field of plant-based biotechnology, and the cancer treatment has gained enough traction to interest the likes of German drug giant Bayer.

"Most important is that the vaccine has been successfully used in human clinical trials," said Charles Arntzen, director of the ASU Biodesign Institute's Center for Infectious Diseases and Vaccinology.

The made-to-order vaccine has been tested in an early-stage clinical trial, and it showed an immune response in 70 percent of non-Hodgkin's lymphoma patients without harmful side effects.

Even though it is called a vaccine, it will not prevent a person from getting non-Hodgkin's lymphoma, which is the seventh-leading cause of cancer-related deaths in the United States. Rather, the vaccine is made from a person's diseased cells and programmed to attack that individual's cancer.

Bayer has spent nearly $15 million on a facility in Germany that initially will grow the tobacco plants to make personalized vaccines for lymphoma patients. The German drug manufacturer plans to explore treatments for other diseases, too.

"It is a huge investment by a company to gamble that they will make it through clinical trials," said Arntzen, who wrote about the personalized plant-based vaccines in an article published Thursday in the journal Science.

Arntzen said he has collaborated with scientists at Stanford University who are developing plant-based vaccines. Earlier this year, the Biodesign Institute secured a $1.5 million grant from the federal government to study whether tobacco plants can yield a vaccine that blocks the West Nile virus from attacking a person's central nervous system. It is a similar technology that is being studied and used by Bayer and Stanford researchers, Arntzen said.

Although scientists are excited about the prospect of using plants to develop individual cancer treatments, no one has yet estimated how much such personalized treatments would cost to make.

Plant-based biotechnology already has been used to produce drugs for diseases such as cystic fibrosis and Gaucher's disease, but some of these personalized drugs can be pricey for consumers.

Avastin, a cancer drug made by South San Francisco-based Genentech, can cost up to $8,800 per month, and Genzyme's Cerezyme, which is used for Gaucher disease, costs about $200,000 a year.

Experts say drug development increasingly is shifting from a one-size-fits-all approach. Drug manufacturers realize that personalized drugs hold great promise as being more effective with fewer side effects. Yet producing such individualized drugs can be expensive and fraught with regulatory challenges.

It would be tough to replicate such a personalized drug in a manner consistent enough to pass muster with the Food and Drug Administration.

"It is going to take some innovative methods to generate that kind of product," said Ray Woosley, president and chief executive officer of the Tucson-based Critical Path Institute, which works to make the drug-development process quicker, safer and more effective.

"It is going to be a challenge to have that kind of individuality and to make sure you produce it the same way (to pass the FDA's review)," Woosley said.

How it works

Bayer envisions a personalized vaccine that is made based on a patient's unique genetic makeup. The vaccine is produced by taking DNA from a person's cancer cells, genetically modifying the DNA strands and transferring the virus to a tobacco plant. The plant responds by producing a protein that can help a cancer patient battle the disease.

The plant-based vaccine works by prodding a person's immune system to attack cancer tumors.
Other scientists have explored the possibility of using animals to make the vaccine, but the tobacco-plant vaccine can be produced much more quickly.

Indeed, speed is a key to growing these personalized treatments.

Scientists estimate that such vaccines can take just six to 10 weeks to produce from the time of a patient's biopsy. That would give doctors a quick time frame to administer the vaccine rather than revert to traditional cancer treatment such as chemotherapy, which has harmful side effects.

Arntzen said that non-Hodgkin's lymphoma is a relatively low-moving cancer, so it gives researchers time to grow, cultivate and give the vaccine to patients.

ImmuneRegen’s Adjuvant to Be Tested with the Biodesign Institute’s Vaccine against Norwalk Viruses

[Source: GEN News Highlights] - The Biodesign Institute at Arizona State University (ASU) will help ImmuneRegen® BioSciences assess Viprovex® as an adjuvant to plant-derived vaccines against noroviruses, or Norwalk-like viruses.

Biodesign Institute's center for infectious diseases and vaccinology (CIDV) will use engineered tobacco plants to produce high levels of Norwalk-virus capsid protein (NVCP), which is the antigen used to elicit an immune response during vaccination. Viprovex will be administered in conjunction with NVCP to assess if the molecule enhances the immune response in mice.

“The ability of Viprovex' active ingredient, Sar9, Met (O2)11-Substance P, to generate not only antibody-mediated responses but also support cellular responses via activation of specific immune cells gives us strong reason to expect adjuvant activity when coupled with vaccines such as those being developed by the Biodesign Institute,” says Hal Siegel, Ph.D., of ImmuneRegen.

Plant-derived vaccines serve as an efficient and cost-effective alternative to producing large amounts of protein for recombinant vaccines, according to the companies.

ASU scientist part of team developing giant biomass plant

[Source: Phoenix Business Journal, Angela Gonzales] - Bruce Rittmann, director of the Center for Environmental Biotechnology at Arizona State University's Biodesign Institute, is on a mission to use bacteria to produce energy.

"What we're going to do is use our ultimate energy source directly from the sun and capture some of that energy by growing photosynthetic microorganisms," he said. "These organisms are new sources of renewable biomass energy."

His goal is to use bacteria to produce biomass that can be turned into liquid fuels, such as biodiesel, in a large-scale commercial operation. Rittmann is collaborating with other ASU professors to replace fossil fuels with these photosynthetic systems.

"We must succeed at this," he said. "We have to have something that's massive. This is the only thing that's massive."

The 2-year-old project has about $5 million in funding from the Science Foundation of Arizona and British Petroleum.

Neal Woodbury, director of the Center for BioOptical Nanotechnology at the Biodesign Institute, said the idea of the project is to grow cyanobacteria in large quantities, then isolate a diesel-like product from the organisms. Cyanobacteria commonly are found in ponds and unattended swimming pools that have turned green with algae.

Another ASU professor, Willem Vermaas, has been able to increase the amount of lipids, or fats, in the organisms for use in the production of biodiesel fuel.

"There's a lot of interest in taking that organism and growing it and understanding how to remove the lipid from it, taking that lipid down and using that as a fuel source," Woodbury said.

Cyanobacteria grow rapidly. "Unlike plants, these organisms will double about once a day under normal circumstances. So you can harvest half of the mass of material each day, and the next day that half will reappear again," he said. "If you don't put chlorine in your pool, it doesn't take very long."

The professors are hammering out a deal with a local utility to conduct the project on a major commercial scale. Because the agreement hasn't been signed, they are reluctant to name the utility, but they hope to have the deal done this fall.

The scientists plan to set up shop next to the utility's fossil-fuel plant to pipe carbon dioxide emitted by the plant into tubes containing the bacteria. The bacteria need to consume carbon dioxide to make oil, which creates a carbon-neutral energy source; and, as a bonus, they keep the fossil-fuel plant from emitting carbon dioxide into the atmosphere.

"The question really becomes how you scale this up, and how you make it economical," Woodbury said, adding that the size of the biomass plant would be one hectare, or 10,000 square meters.

The first phase of the project will end next spring, and the ASU researchers are working on a grant request to the Science Foundation and British Petroleum, explaining how they plan to take the project to the next level.

Rittmann said he's been working on environmental sustainability issues since he was an undergraduate student in the 1970s.

"The needs of society have transformed themselves over the years, and I've tried to orient myself," he said. "What I do is address the pressing environmentally related needs of society. It's always a motivation for me. As new needs arise, I try to jump in when I have something to offer."

Bruce Rittmann
Title: Director, Center for Environmental Biotechnology
Company: Biodesign Institute at Arizona State University
Industry: Research and development
Years on the job: 3.5
Web: www.biodesign.asu.edu
Why it's green: Developing new technologies for energy sustainability

ASU institute working on improving health worldwide

[Source: Nick Smith , The Arizona Republic]- The key to unlocking some of the most complex health issues facing society today may be found in some of the research being conducted in Tempe.

At the Biodesign Institute at Arizona State University, doctors, scientists and students are using state-of-the-art technology to improve the quality of life for people all over the world.

Some of the projects at the institute include pursuing nanotechnology improvements in solar energy, creating in-home diagnostic and treatment devices and developing a bio-diesel fuel from photosynthetic bacteria. Research at the institute has been going on for nearly four years and has resulted in patented inventions.

"The work being done there is pretty incredible," said Mike Hicks, a recent ASU graduate who works on a research team at the institute. "It really could make a big difference."

The institute receives funding from contributors that include state and federal government, industry grants and different philanthropies.

For the past year, researchers have been working on a system that simultaneously purifies dirty water on a mass level and turns the extracted bacteria into bio-diesel, according to institute staff. The research is being conducted on a small level inside labs, but the ultimate goal would be to receive funding to produce it on a marketable level. Other researchers are working on a personalized diagnostic and treatment system known as "Doc-in-a-Box." The goal is to have the system in every home to serve as a personalized doctor, according to Stephen Albert Johnson, the director for the Center for Innovations in Medicine at the Biodesign Institute.

"Doc-in-a-Box" would allow for detection of diseases before any symptoms arise by analyzing blood samples on a regular basis.

ASU Biodesign director moves into research post

[Source: Ken Alltucker, The Arizona Republic] - Arizona State University has appointed its Biodesign Institute Director George Poste to a new research position.

Poste will take on the role of chief scientist for an ASU endeavor called the "complex adaptive systems initiative" that seeks to pool the university's intellectual firepower and bolster its research reputation.

Poste, who was appointed May 2003 to his director post, will remain as executive director of Biodesign until his replacement is hired.

ASU's Neal Woodbury is now Biodesign's deputy director and will shoulder some of the institute's workload as Poste establishes the new initiative.

"The deal I had with George was to take five years and get Biodesign established as an internationally prominent institute, and we achieved that," ASU President Michael Crow said. "Now, I want him to develop the broader scientific trajectory for ASU."

Poste will be charged with boosting ASU's research competitiveness in emerging areas such as synthetic biology, sensor technologies and health-care informatics.

Crow said Poste will have a small staff and budget in excess of $1 million.

Under Poste, the Biodesign Institute has generated $199 million in funding and filed many patents.

TGen Awarded $1.99 Million Grant to Advance Highly Parallel Supercomputing

[Source: TGen] - The National Institutes of Health (NIH) today awarded a $1.99 million grant to the Translational Genomics Research Institute (TGen) to enhance its supercomputing capabilities. The grant was one of only 20 funded by the Center for Research Resources (NCRR), part of the National Institutes of Health (NIH). The project aligns TGen with Arizona State University’s Ira A. Fulton School of Engineering and Biodesign Institute, as computational and bioinformatics teams will build a scalable supercomputing system and work to develop various computational and statistical tools that address complex biomedical questions. When up and running, the new system doubles the supercomputing capabilities currently in place.

“In today’s genomic research environment, high-throughput instruments allow scientists to collect increasingly large amounts of data,” said Dr. Ed Suh, Senior Investigator & Director Chief Information Officer of TGen’s Computational Biology division and the grant’s Principle Investigator. “This scalable computing system will allow TGen and ASU scientists to explore those large volumes of complex data more thoroughly and at an accelerated pace.”

TGen and ASU scientists are collaborating on a variety of research projects that develop and examine molecular profiles of human diseases and fundamental pathways involved in disease states. The focus is to discern complex or simple sets of biomarkers useful for disease diagnosis and prognosis, as well as to develop molecular classification for directing optimal therapeutic choice and identifying new targets. The molecular profile datasets being analyzed cover diseases including: Alzheimer's, autism, diabetes, coronary heart disease, malignant gliomas, melanoma, pancreatic cancer, prostate cancer, colon cancer, multiple myeloma, and breast cancer.

“The parallel supercomputing system supported by this NIH grant provides a powerful resource for ASU and TGen engineers, researchers, biomedical informaticians, computer scientists and biologists to interact in solving complex computational problems that will lead to better disease diagnosis and prognosis. This is a great opportunity to enhance our supercomputing capability with a dedicated system for biomedical research,” said Dr. Deirdre Meldrum, dean of ASU’s School of Engineering and director of the Center for Ecogenomics at the Biodesign Institute at ASU.

For the complexities of many of today’s biomedical computational research, handling vast amounts of raw data creates a bottleneck in research due to the slow computer processing time. Technology has evolved quite rapidly in the last five years, making it possible to greatly increase the amount of processing power available to researchers. The system to be developed by TGen and ASU will possess higher-bandwidth and storage to allow efficient development and use of computational models and algorithms at a rate of nearly 24 trillion operations per second.
According to Dr. Dan Stanzione, director of ASU’s High Performance Computing Initiative (HPCI), this means answers will come faster.

“The success of TGen and ASU scientists to date has come at the sacrifice of time. However, individuals affected with disease do not have the luxury of time. The parallel cluster-computing system will optimize TGen and ASU researchers’ ability to meet their data analyses and systems modeling needs, and hopefully accelerate timely and effective discovery toward improved human health,” said Dr. Stanzione.

The TGen and ASU high performance computing groups have also developed various parallel computing techniques such as domain decomposition and dynamic load balancing methods to achieve optimal efficiency in solving computing and memory intensive problems on parallel computing machines. All of the techniques take full advantage of the parallel cluster computer system.

“In an era of highly-competitive grant funding, this award speaks to the quality of research happening at TGen and ASU, and illustrates yet again, the collaborative nature of Arizona’s biomedical research environment,” said Dr. Jeffrey Trent, TGen’s President and Scientific Director.

The parallel cluster computer system will be installed in the HPCI facility located on the ASU campus. HPCI staff will provide management and operational support for the system in conjunction with TGen’s HPBC team.

Microorganisms may help produce renewable energy in large quantities

[Source: ThaiIndian.com] - Scientists at the Biodesign Institute at Arizona State University say that two complementary approaches may help use microorganisms to produce renewable energy in large quantities, without damaging the environment or competing with the food supply.

The researchers say that the first approach is to use microbes to convert biomass to useful energy.

According to them, different microorganisms can grow without oxygen to take this abundant organic matter, and convert it to useful forms of energy such as methane, hydrogen or even electricity.

The second approach, they say, is to use bacteria or algae that can capture sunlight to produce new biomass that can be turned into liquid fuels like biodiesel, or converted by other microorganisms to useful energy.

Biodesign Institute’’s Bruce Rittmann, Rosa Krajmalnik-Brown, and Rolf Halden say that both approaches currently are intensive areas of biofuel research at the institute, which has a joint project with petroleum giant BP to harvest photosynthetic bacteria to produce renewable liquid fuels, such as biodiesel.

The researchers believe that the future of microbial bioenergy is brightened by recent advancements in genome technologies, and other molecular-biology techniques.

They, however, add that even if one picks the idea bug for generating bioenergy, growing, maintaining, and optimising conditions for its use remains a daunting challenge in terms of scalability and reliability.

“Microbial communities that are used to harvest energy must be resilient to fluctuations in environmental conditions, variations in nutrient and energy inputs and intrusion by microbial invaders that might consume the desired energy product,” Nature magazine quoted the authors as saying.

They say that the key to large-scale success in microbial bioenergy is managing the microbial community so that that it delivers the desired bioenergy product reliably and at high rate.
The authors say that in the absence of such molecular techniques, scientists understanding of methanogenic communities progressed through slow, incremental advances over several decades. They believe that society cannot wait decades for new bioenergy sources.

The researchers feel that scientists should now take full advantage of the existing pre-genomic, genomic, and post-genomic tools to understand microorganisms involved in bioenergy production so as to speed up scientific and technological advances.

The authors conclude: “Information from these tools, when properly integrated with advanced engineering tools and material, should accelerate the rate at which microbial bioenergy processes can be converted from the realm of intriguing science to real world practice.” (ANI)

From Foe To Friend: Researchers Use Salmonella As A Way To Administer Vaccines In The Body

[Source: ScienceDaily] - Researchers at the Biodesign Institute at Arizona State University have made a major step forward in their work to develop a biologically engineered organism that can effectively deliver an antigen in the body. The researchers report that they have been able to use live salmonella bacterium as the containment/delivery method for an antigen.

The work is a major step forward in development of a new means of biological containment that would be a key component to a new way to deliver vaccines in animals and humans. If fully developed, the new method could be used to administer vaccines to many of those who do not benefit from traditional vaccines because of their cost, because of drug resistance or because of limited effects on children.

Outlined in the paper, "Regulated programmed lysis of recombinant Salmonella in host tissues to release protective antigens and confer biological containment," published on the online version (July 7) of the Proceedings of the National Academy of Sciences, the researchers describe a new, novel and effective means of biological containment for antigen delivery. The method not only effectively delivers the antigen in the body, but does so in a way that does not infect the body with salmonella and does not leave any vaccine cells in the environment.

The research team includes scientists formally at Washington University, St. Louis, and Megan Health Inc., St. Louis, who are now at ASU's Biodesign Institute and the School of Life Sciences.

"Our goal is to design, engineer and evaluate a live bacterial (using salmonella) antigen delivery system that would display regulated delayed lysis in vivo after invasion into and colonizing internal lymphoid tissues in an immunized individual," said Roy Curtiss, director of the Center for Infectious Diseases and Vaccinology at the Biodesign Institute and a professor in ASU's School of Life Sciences. Curtiss was part of the research team that made the discovery.

"We wanted to do this in a way so that no disease symptoms due to salmonella would arise, a protective immune response would be induced to the pathogen whose protective antigen was delivered by the vaccine construction (in this case against S. pneumoniae due to an immune response to PspA), and there would be no ability for live bacterial vaccine cells to either persist in vivo or to survive if shed into the environment," Curtiss added.

"The biological containment system we developed is sufficient by itself on conferring attenuation, the inability to cause disease symptoms, and ability to deliver an antigen to induce protective immunity," Curtiss said. "We have high expectations that this delivery system will be safe and effective when administered to animals and humans."

A key to the project, according to Curtiss, is "turning a foe into a friend." That foe is the salmonella bacterium--the leading cause of human food-borne illness and which is currently in the news due to contaminated tomatoes and other food crops. Curtiss' team, through genetic know-how, has developed a variety of ways to tame salmonella in the lab and use it as a delivery vector for vaccines.

"We try to genetically modify the salmonella bacterium to eliminate its harmful effects -- the diarrhea, gut inflammation and fluid secretion -- while keeping the wherewithal to induce immunity against the bacteria causing pneumonia or other infectious diseases," Curtiss said. Several in his research team attack the problem from different angles, with some focusing on weakening salmonella, others boosting the immune response and others optimizing the self-destruct mechanism.

Speaking about the application of a pneumonia antigen, team leader Wei Kong, of the Biodesign Institute, said: "If we tried to use live Streptococcus pneumoniae causing pneumonia for a vaccine, we would obviously kill the patient. The benefit of a live vaccine that uses a weakened form of salmonella, is that the salmonella can be taken up through the intestinal lining and stimulate an immune response by using just a portion of the bacteria causing pneumonia that itself is not deadly."

In experiments, the genetically modified Salmonella enterica bacterium colonizes the lymph tissues of the host and manufactures a protein from the S. pneumoniae bacterium, which then triggers a strong antibody response. Unlike most vaccines that are entirely manufactured by a vaccine company, the attenuated recombinant salmonella vaccine after entry into the immunized individual serves as its own factory to produce (manufacture) the protective antigens (proteins) from the S. pneumoniae pathogen. This ability to cause manufacture in the immunized individual dramatically decreases the cost of such vaccines to make them affordable for use in the developing world, Curtiss said.

An important factor for the research team was to genetically program the S. enterica bacterium to destroy itself so that it is not released into the environment, Curtiss said.

"Biological containment systems are important to address the potential risk posed by any unintentional release of the modified salmonella into the environment," he explained. The salmonella life cycle is balanced to allow enough time to enter the body and build an immune response, while leading to cell death by bursting the cells and preventing the vaccine strain from spreading into the environment.

"The data show that the system we have devised results in cell lysis in the absence of arabinose and clearance of the strain from host tissues," the researchers state in the PNAS article.

"More importantly, our strain was fully capable of delivering a test antigen and inducing a robust immune response comparable to that of a vaccine strain without this containment system, thereby demonstrating that this system has all of the features required for biological containment of a recombinant attenuated salmonella vaccine," they added.

The research was funded by the U.S. Department of Agriculture and the National Institutes of Health.

Internship programs expand as experts worry over future work force

[Source: Phoenix Business Journal, Angela Gonzales] - Bioscience internships slowly are taking a foothold in Arizona's fledgling life sciences industry, as schools and hospitals work together to give a practical experience to tomorrow's work force.

Arizona State University is beginning its third summer, inviting 26 high school students to its Biodesign Institute. It has grown from 18 students last year.

There aren't enough spots for these scientific minds, since more than 140 students applied for the 26 spots.

"These students who applied for these programs tend to be very top students -- valedictorians; fantastic kids," said Rick Fisher, who last year was named director of education and outreach programs at ASU's Biodesign Institute.

In its seventh year of providing internships for 18 students a summer, Sun Health is looking for funding to expand its internship program to add more students. Existing funding comes from donations.

Applications come from all over the nation, including students at Yale and Harvard universities, said Brian Browne, director of education and community relations for Sun Health. Browne said he is seeing fewer students opting for math, science and health careers.

Home-grown scientists needed

"We're seeing a large increase in foreign-born scientists and health care professionals," he said. "This increase is alarming because we are not preparing the next generation of home-grown scientists and other professionals. We're having a harder time attracting students to go into the fields like science and technology."

Sun Health partners with two West Valley high school districts -- Dysart and Agua Fria -- to give students a glimpse of health care careers.

"For example, students are going to be exposed to careers of what a scientist does," Browne said. "It's my job to expose students to all of these careers and give them information on what they can be in the fields of science, technology and health care."

The Apple A Day Program not only provides tours of Sun Health's two hospitals and research institute, but it also takes health care professionals into the classrooms, where they talk about how real life -- such as steroids or drug addiction -- is rooted in science.

"We're hoping to pique their curiosity so they want to learn more and potentially go into a field like that," he said.

Browne said he hopes to get more funding to expand the Apple A Day program to other local school districts.

University of Arizona in Tucson also wants students to get excited about careers in biosciences, tripling its internship program to 28 students this summer with a $28,000 budget.

First-generation students

Kevin Hall, director of research, training and career development at UA's BIO5 Institute in Tucson, is making a big effort to reach out to economically disadvantaged students, to give them a chance at these competitive internship spots.

Sixty percent of students this summer are coming from the underserved population, and many are first-generation college students, Hall said. Students receive an $800 stipend for their work during the summer; enticing those who may need to earn money during the summer but who don't want to miss out on training.

"I would like to double it again next year," Hall said.

While universities and hospitals work to beef up their internship programs, the Translational Genomics Research Institute in January received a whopping $6.5 million from the Helios Education Foundation to start its own internship program.

Last year, Helios gave TGen $383,000 to pilot the internship program, followed by the $6.5 million over the next 25 years.

Candice Nulsen, program manager for education and outreach at TGen, said this summer will be its first official year, kicking off with 45 scholars for an eight-week session.

"From TGen's perspective, part of our strategic partnership with Helios is not only to give fantastic opportunities to students but to help grow and maintain the brain trust here in Arizona," Nulsen said.

The students accepted into the program are a mix of high school, undergraduate and a few graduate-level students.

Paul Luna, president and CEO of Helios Education Foundation, said he hopes the Helios Scholars Program at TGen will attract more students to the biosciences.

"We hope to be incubating the future scientists in Arizona by investing in this program," he said.

At trade show, Arizona competes for a piece of the biotech cake

[Source: Ken Alltucker, The Arizona Republic] - The state of Georgia hosted biotech executives from across the globe aboard a decommissioned aircraft carrier. Pennsylvania raffled away a Harley-Davidson motorcycle. And Minnesota handed out a $500 shopping spree at the Mall of America.

Economic-development representatives from 31 states, including Arizona, and more than two dozen foreign nations courted biotechnology executives and investors this week in San Diego at the Biotechnology Industry Organization's annual convention.

They are desperate to woo biotech companies and research, which they see as an environmentally friendly industry that offers high-wage jobs, innovation and improved health care.

The states offered trips, trinkets and lots of cash to capture the industry's attention.

One day after Massachusetts Gov. Deval Partick signed a $1 billion biotech bill, Maryland proposed its own $1.1 billion funding plan to sprinkle investments across that state's biotech sector.

Not to be outdone, California Gov. Arnold Schwarzenegger, one of a dozen or so governors at the convention, chatted up his state's $3 billion stem-cell research initiative and pitched California as a business destination.

"Let's face it, California is the biotech capital of the world," Schwarzenegger said during a luncheon speech. "If you are a biotech scientist, or an entrepreneur or an investor, California is one of the best places to set up shop."

Arizona's contingent of public and private bioscience interests wasn't far behind when it came to chatting up the state's burgeoning biotech efforts.

Representatives from the University of Arizona's Bio5 Institute, Arizona State University's Biodesign Institute, Northern Arizona University, the Flinn Foundation and others were on hand to promote the Grand Canyon State.

Arizona made no splashy announcement of any new funding deal at the conference.

But the state Department of Commerce issued a news release Wednesday listing some of Arizona's bio-related accomplishments.

Walt Plosila, a consultant who helped draft the state's bioscience road map, said Arizona's planned approach to grow its research base is the smartest way to expand its biotech efforts.

"The goal is not to be good at everything," said Plosila, senior adviser to Cleveland-based Technology Partnership Practice. "It's not to try to be like Massachusetts or Silicon Valley. They are so far ahead, and they have such a deep base - you can't do that."

Arizona has notched some positive momentum in recent years, Plosila said, noting the state ranked No. 27 among all states in federal National Institutes of Health grants and No. 20 in bioscience venture-capital investment during the 2007 fiscal year.

A state-funded measure helped build new state-of-the-art research labs in Tucson and Tempe. And the Translational Genomics Research Institute has expanded the state's molecular know-how.

Even though Arizona has made strides in the area of research funding, the state still has not spawned a strong cluster of privately owned biotech companies, he added. "Arizona is not yet at a critical mass of companies," Plosila said.

That is true of many states across the United States.

But those states work hard to woo companies at the annual biotechnology industry show.

"This has evolved over the years from being an industry show to an economic-development show," said Curt Bilby, chief executive officer of the Austin-based biotech company Terapio. "Everybody is trying to become the next biotech cluster."

Contest among states

Louisiana's pavilion featured an amateur ventriloquist handling a stuffed ostrich. A pavilion for Nebraska offered biotech executives a drawing for Omaha steaks.

Kansas took on a sporting theme, with the state's biotech organization, called the Kansas Bio Authority, circulated a pamphlet featuring a picture of the state's college-basketball championship aftermath. The message: "Kansas: Home of Champions."

Economic development representatives from Georgia acknowledged that competition among the states remains tough.

"You look at Boston, San Diego and the Silicon Valley - they are the leaders," said Michael Starling, a senior project manager with the DeKalb County Office of Economic Development in suburban Atlanta. "Everybody else is reaching for that second rung."

Reach the reporter at ken.alltucker@arizonarepubic.com or 602-444-8285.