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Oct 2, 2008

Deep biosphere research points to new methods for recovering petroleum

Release Date: October 2, 2008

Miles below us, deep within Earth's crust, life is astir. Organisms there are not the large creatures typically envisioned when thinking of life. Instead, thriving there are microbes, the smallest and oldest form of life on Earth. Although the biological diversity of these deep biosphere microorganisms may surpass that of the more familiar surface biosphere, much about them is still unknown, including the origin of the organic compounds they consume. Arizona State University researchers are using a novel approach that integrates physical organic chemistry with organic geochemistry and biogeochemistry to uncover the source of these organic compounds.

Carbon, the building block of organic matter, is one of the most dynamic elements on the planet; it responds to biological, physical and chemical processes in many ways and on many timescales. Understanding how carbon is formed, where it comes from, and how much of it exists, is important for a more detailed and coherent picture of the global carbon cycle. Yet a complete understanding of how carbon is produced and consumed in the environment still evades researchers because much of what is known is based on processes that act on short time-scales and at Earth's surface.

Deep biosphere microbes, like any living organism, require energy to survive; for many, their sustenance comes in the form of organic compounds. Over time, organic compounds are buried and pushed deeper into the Earth's crust. Harsh conditions on the journey to the deep Earth cause the organic compounds to become "recalcitrant," meaning they are no longer in a form that microbes can use. Some of the consumable organic compounds are produced by other subsurface microbes, but a large portion is most likely the end product of a mysterious geochemical process.

Theoretical biogeochemist Everett Shock, a professor in ASU's School of Earth and Space Exploration and the Department of Chemistry and Biochemistry in the College of Liberal Arts and Sciences, leads an interdisciplinary group of researchers who are investigating how this geochemical transformation from recalcitrant matter to usable organic compounds occurs deep in Earth's crust.

"The secret appears to lie in how temperature and pressure affect the reactivity of organic compounds, and, maybe more importantly, how the properties of water change deep in sediments and sedimentary rocks," says Shock. "The transformation in how water behaves is so enormous that we would hardly recognize it as the same stuff that comes out of our kitchen taps."

Most organic reactions at the Earth's surface do not work very well in water; either they need an organism that has evolved the mechanisms to promote organic reactions in water or they need an organic solvent, hexane or benzene, for example. The very deep Earth, below where microbial life has been shown to exist, has lots of rocks but no organic solvents. It does, however, have very hot water.

Hilairy Hartnett, an assistant professor in the School of Earth and Space Exploration and ASU's Department of Chemistry and Biochemistry, is part of Shock's interdisciplinary group examining the mechanisms of the sub-surface carbon cycle. The team hypothesizes that conditions deep in the Earth might be good for complex organic reactions.

"Evidence suggests that hot water at high pressures - conditions we'd find in the subsurface - is actually a very good solvent for organic reactions," Hartnett says. "It might be possible for these reactions to occur without biology if the conditions are right." She explains, "Biological processes can promote reactions to generate complex organic molecules even at unfavorable low temperatures and pressures - the difference for the deep Earth is the high-temperature and pressure."

Spurred by a $1.5M grant from the National Science Foundation, the team will apply new theoretical models of how water at high temperatures and pressures can transform organic compounds in unexpected ways. Through a series of high-temperature/pressure experiments involving organic compounds, water, and common minerals found in sedimentary rocks such as iron oxides and clays, the team plans to reveal how organic transformation reactions occur in natural geologic conditions.

Team member John Holloway, emeritus faculty in the School of Earth and Space Exploration and ASU's Department of Chemistry and Biochemistry, designed and built the hydrothermal reaction vessels necessary for testing. At ASU's new Omni-pressure Lab, simple compounds such as water and carbon dioxide are placed in the inert gold capsules and then tested.

"The samples are held at temperatures up to 300 degrees Celsius and pressures of 250 atmospheres, equivalent to the bottom of the ocean (2,500 meters) or slightly higher, for periods of hours to weeks," explains Holloway. "They are then quenched to ambient conditions and we analyze the products using gas chromatography and mass-spectrometry."

The results of past similar experiments have shown that the concentration, variety, and complexity of compounds all increase with time, and are strongly influenced by contact with minerals during the experiments.

"It will be important to find out if the mixture of compounds we make in the lab looks anything like the organic compounds that are found in the deep subsurface," says Hartnett. "If they do, then maybe this is how they formed - just rocks, hot water and simple carbon compounds. If they don't, well, we need to figure out what else is required." "Lots of researchers have looked at individual aspects of the questions we're asking, but this is one of the first - or maybe the first - attempt to look at these high-temperature water-rock-organic processes from an integrated experimental and theoretical standpoint," Hartnett says.

A project of this caliber requires a team with a wide-range of expertise from thermodynamic modeling, reaction mechanisms, and organic characterization, to clay minerals and high-temperature/pressure experiments. Many different techniques and backgrounds are necessary to understand the complexities of the process.

"Some of the known organic reactions under hydrothermal conditions are fascinating to me as an organic chemist. But this

is a not a research field that I can enter in my own, I don't know how to do the experiments and I don't know which are the important observations," says chemistry professor Ian Gould, "but I can bring expertise in the area of choosing useful and informative reactions to study." "No one person is an expert in all aspects of the project. As a team, we all think about the same questions, but we each bring a different set of skills and ideas to the forum. That often means we can find answers more quickly, or find answers that come from a direction any one of us by ourselves might have overlooked," says Hartnett.

"What we're learning may be applied to hydrocarbon exploration, carbon dioxide sequestration, environmental reclamation, and microbial sustainability," says team member Lynda Williams, an associate research professor in the School of Earth and Space Exploration who focuses on the chemical composition of clay and sedimentary minerals. "It could also lead toward understanding primordial conditions on Earth and similar planets where carbon-based life has evolved," she adds.

This interdisciplinary approach to exploring organic reactions in hot water may also have important implications for "green" chemistry. By learning more about how to promote organic reactions in hot water, other researchers may be able to take that knowledge and develop new chemical processes that don't have to use environmentally unfriendly, toxic solvents.

Funded through NSF's Emerging Topics in Biogeochemical Cycles program, Shock and his team will be the first to link organic geochemical reactions deep in the Earth's crust to the support of microbes in the deep biosphere. In the process, the researchers plan to test new ideas about how petroleum forms from deeply buried organic matter, including the direct involvement of deep biosphere microbes. That deeply buried organic material is the precursor to petroleum, but it may also be the food that many microbes need to survive.

"By understanding organic synthesis reactions in the deep biosphere, we may find better organic and inorganic tracers to aid in finding petroleum resources and recovering them in more environmentally friendly ways," says Williams.

Nikki Staab, nstaab@asu.edu


September 3, 2008

New NIH 'EUREKA' program to fund two 'exceptionally innovative' ASU research projects

ASU can now shout the classic exclamation of discovery-Eureka!-twice. Fueled by a new initiative at the National Institutes of Health called the EUREKA program, two 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 have each 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," said NIH Director Elias A. Zerhouni, M.D. "The program reflects NIH's commitment to supporting potentially transformative research, even if it carries a greater than usual degree of scientific risk."

"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," said ASU President Michael Crow.

Chaput and Diaz's projects were two of 38 proposals deemed exceptional. This is an impressive showing for ASU and 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," said John Chaput, a Biodesign Institute researcher and ASU assistant professor in the Department of Chemistry and Biochemistry.

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, or arrangement 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, have 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," said Chaput "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. "We expect that many of these sites will coincide with regions of the genome that contain known genes, but we also expect to find many areas previously thought to contain no protein-coding information whatsoever. It is these areas that interest us most, as they are a possible treasure-trove of new protein-coding information."

Neural nanomachines

Research to be led by Rudy 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 at ASU.

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 explained.

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

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 nano-sensors 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 micro-surgery, and advancing the understanding of cellular biology.

"Once you have such capabilities, it has the potential for application in deep brain stimulation, the treatment of brain damage, or such things as multiple sclerosis and Parkinson's disease," Diaz said.

Joe Caspermeyer, Media Relations Manager & Science Editor
(480) 727-0369 | joseph.caspermeyer@asu.edu
September 3, 2008


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