Researchers close in on technology for making renewable petroleum

University of Minnesota researchers are a key step closer to making renewable petroleum fuels using bacteria, sunlight and carbon dioxide.

Graduate student Janice Frias, who earned her doctorate in January, made the critical step by figuring out how to use a protein to transform fatty acids produced by the bacteria into ketones, which can be cracked to make hydrocarbon fuels. The university is filing patents on the process.

The research is published in the April 1 issue of the Journal of Biological Chemistry. Frias, whose advisor was Larry Wackett, Distinguished McKnight Professor of Biochemistry, is lead author. Other team members include organic chemist Jack Richman, a researcher in the College of Biological Sciences' Department of Biochemistry, Molecular Biology and Biophysics, and undergraduate Jasmine Erickson, a junior in the College of Biological Sciences. Wackett, who is senior author, is a faculty member in the College of Biological Sciences and the university's BioTechnology Institute.

Aditya Bhan and Lanny Schmidt, chemical engineering professors in the College of Science and Engineering, are turning the ketones into diesel fuel using catalytic technology they have developed. The ability to produce ketones opens the door to making petroleum-like hydrocarbon fuels using only bacteria, sunlight and carbon dioxide.

"There is enormous interest in using carbon dioxide to make hydrocarbon fuels," Wackett says. "CO2 is the major greenhouse gas mediating global climate change, so removing it from the atmosphere is good for the environment. It's also free. And we can use the same infrastructure to process and transport this new hydrocarbon fuel that we use for fossil fuels."

The research is funded by a $2.2 million grant from the U.S. Department of Energy's Advanced Research Projects Agency-energy (ARPA-e) program, created to stimulate American leadership in renewable energy technology.

Wackett is principal investigator for the ARPA-e grant. His team of co-investigators includes Jeffrey Gralnick, assistant professor of microbiology and Marc von Keitz, chief technical officer of BioCee, as well as Bhan and Schmidt. They are the only group using a photosynthetic bacterium and a hydrocarbon-producing bacterium together to make hydrocarbons from carbon dioxide.

The U of M team is using Synechococcus, a bacterium that fixes carbon dioxide in sunlight and converts CO2 to sugars. Next, they feed the sugars to Shewanella, a bacterium that produces hydrocarbons. This turns CO2, a greenhouse gas produced by combustion of fossil fuel petroleum, into hydrocarbons.

Hydrocarbons (made from carbon and hydrogen) are the main component of fossil fuels. It took hundreds of millions of years of heat and compression to produce fossil fuels, which experts expect to be largely depleted within 50 years.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Minnesota.

Research produces novel sensor with improved detection selectivity

A highly sensitive sensor that combines a variety of testing means (electrochemistry, spectroscopy and selective partitioning) into one device has been developed at the University of Cincinnati. It's already been tested in a variety of settings -- including testing for components in nuclear waste.

The sensor is unusual in that most sensors only have one or two modes of selectivity, while this sensor has three. In practical terms, that means the UC sensor has three different ways to find and identify a compound of interest. That's important because settings like a nuclear waste storage tank are a jumbled mix of chemical and radioactive wastes. The sensor, however, would have a variety of applications, including testing in other environments and even medical applications.

Research related to this novel sensor will be presented at the American Chemical Society biannual meeting March 27-31 in Anaheim, Calif., in a presentation titled "Using Spectroelectrochemistry to Improve Sensor Selectivity."

That presentation will be made March 28 by William Heineman, distinguished research professor of chemistry at the University of Cincinnati. He is one of six international scientists invited to speak by electrochemistry students involved in planning a conference symposium. Heineman has published more than 400 research articles on the topics of spectroelectrochemistry, electroanalytical chemistry, bioanalytical chemistry and chemical sensors, and has won numerous national and international awards for his work.

Research on this sensor concept began more than a decade ago and has received support from the United States Department of Energy for most of that time. "They wanted a sensor that can be lowered in a tank to make lots of measurements quickly or have the option of leaving it in there to monitor what's going on over months or a year," said Heineman, who added that the ideal sensor is both rugged and very selective and sensitive.

The sensor has, in fact, been tested at the Hanford site, a mostly decommissioned nuclear production complex in Washington state, where it was used to detect one important component of the radioactive and hazardous wastes stored inside the giant tanks there.

The basic design and concept for this monitor could be used in many other environmental or medical settings. These include detection of toxic heavy metals and polycyclic aromatic hydrocarbons at superfund sites.

The three-way selectivity comes from the use of coatings, electrochemistry, and spectroscopy. The selective coating only allows certain compounds to enter the sensing region. For example, all negatively charged ions might be able to enter the sensor while all positively charged ions are excluded. Next comes the electrochemistry. A potential is applied, and an even smaller group of compounds are electrolyzed. Finally, a very specific wavelength of light is used to detect the actual compound of interest.

The end result is that compounds, even those present in very low concentrations, can be detected and analyzed. This is especially important in medical monitoring and other applications requiring high selectivity and sensitivity.

"Our goal in this research was to demonstrate that the concept works, and that goal has been met as it's now been tested in several ways. Maybe that's why the students at the ACS meeting wanted to hear about it," said UC's Heineman.

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The above story is reprinted (with editorial adaptations ) from materials provided by University of Cincinnati, via EurekAlert!, a service of AAAS.

Purdue startup hopes to change the way we test cancer drugs

A Purdue University scientist's nanopolymer would make it easier and cheaper for drug developers to test the effectiveness of a widely used class of cancer inhibitors.

W. Andy Tao, an associate professor of biochemistry analytical chemistry and a member of the Purdue Center for Cancer Research team, created the Purdue-patented pIMAGO nanopolymer that can be used to determine whether cancer drugs have been effective against biochemical processes that can lead to cancer cell formation. The nanopolymers would attach themselves to target proteins that would later be detected by a relatively simple laboratory procedure called chemiluminescence.

Tymora Analytical, a company Tao started in the Purdue Research Park, will manufacture the pIMAGO nanopolymers. The 'p' stands for phosphor, and the IMAGO comes from the Greek word for image.

Tao's pIMAGO nanopolymers are coated in titanium ions and would attract and bond with phosphorylated proteins, ones in which a phosphate group has been added to a protein activating an enzyme called kinase. Kinase, when overactive, is known to cause cancer cell formation, and many cancer drugs are aimed at inhibiting kinase activity.

"It is universal. You can detect any kind of phosphorylation in a protein," said Tao, whose findings were reported in the early online version of the journal Analytical Chemistry. "It is also cheaper and would be more widely available."

The nanopolymers would be added to a solution of proteins, a chemical agent to start phosphorylation and a drug to inhibit kinase activity. Phosphorylated proteins would only be present if the drug is ineffective.

Avidin-HRP - the protein Avidin bound with the enzyme horseradish peroxidase - would be added. Avidin would bind with a vitamin B acid called biotin that is also on the nanopolymers' surfaces. A chemical called a substrate, added later, would cause a reaction with HRP, causing the solution to change color.

A lightly colored solution would mean there had been little kinase activity and few phosphorylated proteins and that the drug was effective. A darker solution would signal more kinase activity and a less effective drug.

"This could have a lot of applications in pharmaceuticals for drug discovery," Tao said.

Screening kinase inhibitors using antibodies can be cost-prohibitive for many laboratories because antibodies are in short supply and aren't available for many types of cells. Radioisotope tests are highly regulated and possibly dangerous because of radiation involved.

"We want to develop this as a commercial application to replace radioisotopes and antibodies as a universal method for screening kinase inhibitors," Tao said.

Provided by Purdue University (news : web)

Scientists find a key to maintaining our DNA

DNA contains all of the genetic instructions that make us who we are, and maintaining the integrity of our DNA over the course of a lifetime is a critical, yet complex part of the aging process. In an important, albeit early step forward, scientists have discovered how DNA maintenance is regulated, opening the door to interventions that may enhance the body's natural preservation of genetic information.

The new findings may help researchers delay the onset of aging and aging-related diseases by curbing the loss or damage of our genetic makeup, which makes us more susceptible to cancers and neurodegenerative diseases, such as Alzheimer's. Keeping our DNA intact longer into our later years could help eliminate the sickness and suffering that often goes hand-in-hand with old age.

"Our research is in the very early stages, but there is great potential here, with the capacity to change the human experience," said Robert Bambara, Ph.D., chair of the Department of Biochemistry and Biophysics at the University of Rochester Medical Center and leader of the research. "Just the very notion is inspiring."

In the Journal of Biological Chemistry, Bambara and colleagues report that a process called acetylation regulates the maintenance of our DNA. The team has discovered that acetylation determines the degree of fidelity of both DNA replication and repair.

The finding builds on past research, which established that as humans evolved, we created two routes for DNA replication and repair – a standard route that eliminates some damage and a moderate amount of errors, and an elite route that eliminates the large majority of damage and errors from our DNA.

Only the small portion of our DNA that directs the creation of all the proteins we are made of – proteins in blood cells, heart cells, liver cells and so on – takes the elite route, which uses much more energy and so "costs" the body more. The remaining majority of our DNA, which is not responsible for creating proteins, takes the standard route, which requires fewer resources and moves more quickly.

But, scientists have never understood what controls which pathway a given piece of DNA would go down. Study authors found, that like a policeman directing traffic at a busy intersection, acetylation directs which proteins take which route, favoring the protection of DNA that creates proteins by shuttling them down the elite, more accurate course.

"If we found a way to improve the protection of DNA that guides protein production, basically boosting what our body already does to eliminate errors, it could help us live longer," said Lata Balakrishnan, Ph.D., postdoctoral research associate at the Medical Center, who helped lead the work. "A medication that would cause a small alteration in this acetylation-based regulatory mechanism might change the average onset of cancers or neurological diseases to well beyond the current human lifespan."

"Clearly, a simple preventative approach would be a key, not to immortality, but to longer, disease-free lives," added Bambara.

DNA replication is an intricate, error-prone process, which takes place when our cells divide and our DNA is duplicated. Duplicate copies of DNA are first made in separate pieces, that later must be joined to create a new, full strand of DNA. The first half of each separate DNA segment usually contains the most errors, while mistakes are less likely to appear in the latter half.

For DNA that travels down the standard route, the first 20 percent of each separate DNA segment is tagged, cut off and removed. This empty space is then backfilled with the latter part – which is the more accurate section – of the adjoining piece of DNA as the two segments come together to form a full strand.

In contrast, DNA that travels down the elite route gets special treatment: the first 30 to 40 percent of each separate DNA segment is tagged, removed and backfilled, meaning more mistakes and errors are eliminated before the segments are joined. The end result is a more accurate copy of DNA.

The same situation occurs with the DNA repair process, as the body works to remove damaged pieces of DNA.

Unlike the current work, the majority of aging-related research zeroes in on specific agents that damage our DNA, called reactive oxygen species, and how to reduce them. The new research represents a small piece of the pie, but has the potential to be a very important one.

Bambara's team is investigating the newly identified acetylation regulatory process further to figure out how they might be able to intervene to augment the body's natural safeguarding of important genetic information. They are studying human and yeast cell systems to determine how proteins in cells work together to trigger acetylation, which adds a specific chemical to the proteins involved in DNA replication and repair. Researchers are manipulating cells in various ways, through damage or genetic alterations, to see if these changes activate or influence acetylation in any way.

Though they are far from identifying compounds or existing drugs to test, they do see this research having an impact in the future.

"The translational rate is becoming better and better. Today, the course between initial discovery and drug development is intrinsically faster. I could see having some sort of therapeutic that helps us live longer and healthier lives in 25 years," said Bambara.

Provided by University of Rochester Medical Center (news : web)

Rapid, high-definition chemistry with new imaging technique

With intensity a million times brighter than sunlight, a new synchrotron-based imaging technique offers high-resolution pictures of the molecular composition of tissues with unprecedented speed and quality. Carol Hirschmugl, a physicist at the University of Wisconsin-Milwaukee (UWM), led a team of researchers from UWM, the University of Illinois at Urbana-Champaign and University of Illinois at Chicago (UIC) to demonstrate these new capabilities.

Hirschmugl and UWM scientist Michael Nasse have built a facility called "Infrared Environmental Imaging (IRENI)," to perform the technique at the Synchrotron Radiation Center (SRC) at UW-Madison. The new technique employs multiple beams of synchrotron light to illuminate a state-of-the-art camera, instead of just one beam.

IRENI cuts the amount of time needed to image a sample from hours to minutes, while quadrupling the range of the sample size and producing high-resolution images of samples that do not have to be tagged or stained as they would for imaging with an optical microscope.

"Since IRENI reveals the molecular composition of a tissue sample, you can choose to look at the distribution of functional groups, such as proteins, carbohydrates and lipids," says Hirschmugl, "so you concurrently get detailed structure and chemistry."

The technique could have broad applications not only in medicine, but also in pharmaceutical drug analysis, art conservation, forensics, biofuel production, and advanced materials, such as graphene, she says.

Funded by $1 million grant from the National Science Foundation's Major Research Instrumentation Program, the development of the facility has quickly attracted other projects supported by the NSF and the National Institutes of Health. It is published online today in Nature Methods.

The work is a collaboration with the labs of Rohit Bhargava, assistant professor of bioengineering at the University of Illinois at Urbana-Champaign and pathologists Dr. Virgilia Macias and Dr. André Kajdacsy-Balla at UIC. "It has taken three years to establish IRENI as a national user facility located at the SRC," says Nasse. "It is the only facility of its kind worldwide."

Chemical fingerprints

The unique features of the synchrotron make it a highly versatile light source in spectroscopy. Streams of speeding electrons emit continuous light across the entire electromagnetic spectrum so that researchers can access whatever wavelength is best absorbed for a particular purpose.

Although not visible to the human eye, the mid-infrared range of light used by the team documents the light absorbed at thousands of locations on the sample, forming graphic "fingerprints" of biochemically important molecules.

Using 12 beams of synchrotron light in this range allows researchers to collect thousands of these chemical fingerprints simultaneously, producing an image that is 100 times less-pixelated than in conventional infrared imaging.

"We did not realize until now the improvement in detail and quality that sampling at this pixel size would bring," says Bhargava. "The quality of the chemical images is now quite similar to that of optical microscopy and the approach presents exciting new possibilities."

Testing for future applications

The team tested the technique on breast and prostate tissue samples to determine its capabilities for potential use in diagnostics for cancer and other diseases. The researchers were able to detect features that distinguished the epithelial cells, in which cancers begin, from the stromal cells, which are the type found in deeper tissues, with unprecedented detail.

Separating the two layers of cells is a "basement membrane" which prevents malignant cells from spreading from the epithelial cells into the stromal cells. Early-stage cancers are concentrated in the epithelial cells, but metastasis occurs when the basement membrane is breached. Using a prostate cancer sample, the team had encouraging results in locating spectra of the basement membrane, but more work needs to be done.

"IRENI provides us a new opportunity to study tissues and provides lessons for the development of the next generation of IR imaging instruments," says Michael Walsh, a Carle Foundation Hospital-Beckman Institute post-doctoral fellow at the University of Illinois at Urbana-Champaign and co-author on the paper.

It opens the door for development of synchrotron-based imaging that can monitor cellular processes, from simple metabolism to stem cell specialization.

Provided by University of Wisconsin - Milwaukee

PepsiCo unveils 100 percent plant-based bottle

Remember the Cola Wars? Get ready for the Bottle Wars. PepsiCo Inc. on Tuesday unveiled a bottle made entirely of plant material, which it says bests the technology of competitor Coca-Cola and reduces its potential carbon footprint.

The bottle is made from switch grass, pine bark, corn husks and other materials. Ultimately, Pepsi plans to also use orange peels, oat hulls, potato scraps and other leftovers from its food business.

The new bottle looks, feels and protects the drink inside exactly the same as its current bottles, Papalia said. “It’s indistinguishable.”

PepsiCo says it is the world’s first bottle of a common type of plastic called PET made entirely of plant-based materials. Coca-Cola Co. currently produces a bottle using 30 per cent plant-based materials and recently estimated it would be several years before it has a 100 per cent plant bottle that’s commercially viable.

“We’ve cracked the code,” said Rocco Papalia, senior vice-president of advanced research of PepsiCo.

The discovery potentially changes the industry standard for plastic packaging. Traditional plastic, called PET, is used in beverage bottles, food pouches, coatings and other common products.

The plastic is the go-to because it’s lightweight and shatter-resistant, its safety is well-researched and it doesn’t affect flavours. It is not biodegradable or compostable. But it is fully recyclable, a characteristic both companies maintain in their new creations.

Traditional PET plastic is made using fossil fuels, like petroleum, a limited resource that’s rising in price. By using plant material instead, companies reduce their environmental impact. Pepsi says the new plastic will cost about the same as traditional plastic.

The company, based in Purchase, N.Y., said it has had dozens of people working on the process for years. While PepsiCo wouldn’t specify the cost to research and design the new bottle, Papalia said it is in the millions of dollars.

It’s one of several steps PepsiCo has taken recently to reduce its environmental impact. The company created a fully compostable bag for its SunChips line. It cut the amount of plastic in its Aqua-Fina bottle in 2009. And its Naked Juice line is in the midst of switching to a bottle made entirely of recycled plastic bottles.

PepsiCo says of its 19 biggest brands, those that generate more than $1 billion (dollar figures U.S.) in revenue, 11 are beverage brands that use PET. The company says the packaging will cost roughly the same as it does today.

PepsiCo plans to test the product in 2012 in a few hundred thousand bottles. Once the company is sure it can successfully produce the bottle at that scale, it will begin converting all its products.

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