From EMSL: “A Series of New Videos for Users”

EMSL

at PNNL

EMSL recently posted a collection of eight new videos on its YouTube channel and website to help users improve their research.

The short videos – around two minutes each – feature EMSL scientists describing how certain capabilities can advance users’ projects, particularly those relevant to DOE Office of Biological and Environmental Research.

Featured scientists and capabilities include:

Amir Ahkami and Kim Hixson – Plant Sciences Laboratory
Mark Engelhard – X-ray Photoelectron Spectrometer
Libor Kovarik – Environmental Transmission Electron Microscope
Scott Lea – Helium Ion Microscope
Malak Tfaily – 21 Tesla FTICR Mass Spectrometer
Tamas Varga – X-ray Computed Tomography
Zheming Wang – Sum-frequency Generation Vibrational Spectroscopy
Zihua Zhu – Time of Flight Secondary Ion Mass Spectrometry

Or check out all the videos under EMSL’s “Accelerate Your Research” YouTube playlist.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Welcome to EMSL. EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

Team’s in Our DNA. We approach science differently than many institutions. We believe in – and have proven – the value of drawing together members of the scientific community and assembling the people, resources and facilities to solve problems. It’s in our DNA, since our founder Dr. Wiley’s initial call to create a user facility that would facilitate “synergism between the physical, mathematical, and life sciences.” We integrate experts across disciplines; experiment with theory; and our user program proposal calls with other user facilities.

We proudly provide an enriched, customized experience that allows users to connect with our people and capabilities in an environment where we focus on solving problems. We collaborate with researchers from academia, government labs and industry, and from nearly all 50 states and from other countries.

From PNNL: “New catalyst meets challenge of cleaning exhaust from modern engines”

PNNL Lab

EMSL

December 14, 2017
Susan Bauer
susan.bauer@pnnl.gov
(509) 372-6083

Innovation also uses less platinum, expensive component of catalytic converters.

Researchers discovered a new type of active site (dashed green circles) which meets the dual challenge of achieving high activity and thermal stability in single-atom catalysts to improve vehicle emissions. No image credit.

As cars become more fuel-efficient, less heat is wasted in the exhaust, which makes it harder to clean up the pollutants are being emitted. But researchers have recently created a catalyst capable of reducing pollutants at the lower temperatures expected in advanced engines. Their work, published this week in Science magazine, a leading peer-reviewed research journal, presents a new way to create a more powerful catalyst while using smaller amounts of platinum, the most expensive component of emission-control catalysts.

The recent findings grew out of a collaboration between research groups led by Yong Wang, who holds a joint appointment at the Department of Energy’s Pacific Northwest National Laboratory and is a Voiland Distinguished Professor at Washington State University’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering and Abhaya Datye, a distinguished professor at the University of New Mexico.

Catalysts have been an integral part of the exhaust systems of diesel- and gasoline-powered engines since the mid-1970s when federal regulations called for reductions of carbon monoxide, hydrocarbons and nitrogen oxides. Catalytic converters transform the pollutants to nitrogen, carbon dioxide and water.

The researchers addressed the daunting challenge of designing a catalyst that could endure engine exhaust temperatures of up to nearly 1,500 degrees Fahrenheit encountered under high engine loads. Yet the catalyst would still have to work when an engine is started cold and must clean up the exhaust before reaching 300 degrees Fahrenheit, significantly lower than current systems. The lower operating temperatures during cold start are due to increasing fuel efficiency in advanced combustion engines, which leaves less energy in the tailpipe exhaust, said Datye, a study co-author.

The recent findings build on research, published in Science last year, in which the Wang and Datye groups found a novel way to trap and stabilize individual platinum atoms on the surface of cerium oxide, a commonly used component in emissions control catalysts. The so-called single-atom catalyst uses platinum more efficiently while remaining stable at high temperatures. Platinum typically trades at prices close to or even greater than gold.

For their latest paper [Science], the researchers steam-treated the catalyst at nearly 1,400 degrees Fahrenheit. This made the already stable catalyst become very active at the low cold-start temperatures.

“We were able to meet the challenges of both the high-temperature stability and the low-temperature activity,” Wang said. “This demonstration of hydrothermal stability, along with high reactivity, makes it possible to bring single-atom catalysis closer to industrial application.”

Multiple types of spectroscopy and electron microscopy capabilities available at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility on the PNNL campus, allowed the scientists to understand the catalyst surface at the atomic level and provide mechanistic insight into how oxygen vacancies migrate to the surface of the cerium oxide, creating pathways for highly active carbon monoxide conversion.

The work was funded by DOE’s Office of Science and Office of Energy Efficiency and Renewable Energy’s Vehicle Technologies Office.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

From Science Magazine: “Emails shed light on controversial DOE request to remove ‘climate change’ from abstracts”

Science Magazine

Dec. 12, 2017
Christa Marshall

The U.S. Department of Energy’s Pacific Northwest National Laboratory in Richland, Washington. Borgendorf/Wikipedia.

A U.S. Department of Energy (DOE) official’s controversial request this summer for scientists to remove “climate change” from research abstracts was ordered by senior national lab managers and was intended to satisfy President Trump’s budget request, according to emails obtained by E&E News and confirmed by a lab aide.

The communications, obtained through a Freedom of Information Act request, suggest officials at Pacific Northwest National Laboratory (PNNL) in Richland, Washington, a national lab funded by DOE, were trying to protect scientists. But the emails also leave unanswered questions about why decisions were made on a Trump plan that was not law.

The senior officials “don’t have the authority to say … ‘We don’t care whether Congress appropriated the funds,'” said Andrew Rosenberg, director of the Center for Science and Democracy at the Union of Concerned Scientists in Cambridge, Massachusetts.

In August, Northeastern University associate professor Jennifer Bowen started a social media frenzy by posting a letter on Facebook from a DOE employee asking for the removal of climate language from her research summary on salt marsh carbon sequestration. Later, additional scientists who received similar DOE requests identified the sender as Ashley Gilbert, a project coordinator at PNNL (Greenwire, Aug. 29).

According to emails sent between 23 August and 25 August, Gilbert acted at the request of Terry Law, a manager of user services at the Environmental Molecular Sciences Laboratory (EMSL), a user facility at PNNL.

PNNL spokesman Greg Koller said Law was further directed by “EMSL management” but did not name which officials. It was a “team decision,” he said.

While the identities of affected scientists were previously known, Lane’s directive, the role of senior management and the lab’s full reasoning were not.

Law said removing climate language was necessary because President Trump’s budget proposal called for the elimination of user access for EMSL research related to “climate feedbacks and carbon.”

“Can you look at the 14 abstracts … and find those that talk about global warming or climate change? Then contact the PIs to get different wording? Just explain to them we still have to meet the president budget language restrictions,” Law said to Gilbert on 23 August.

The proposals were from 14 grant winners supported by EMSL and the Joint Genome Institute.

Gilbert then contacted Bowen, University of Arizona assistant professor Scott Saleska and Concordia University biologist David Walsh, who told E&E News he was asked to scrub language in his abstract on terrestrial organic matter transformations in the Arctic Ocean.

“Holy cow, really?” Walsh wrote to Gilbert when first asked to change wording.

“I understand that you are just doing your job, so I will refrain from comment. I redacted the offensive clause,” Bowen wrote to Gilbert.

In an email to Saleska on Aug. 25, Law said the accepted research proposals likely follow the president’s budget request but require revision to “eliminate confusion by others who may not understand the nuances” and “falsely assume we’re funding research that was specifically eliminated for EMSL.” Law did not define who the “others” were.

Once Bowen posted her letter publicly, inquiries from journalists started flowing in to Bowen and Law. Eventually, inquiries were kicked over to DOE headquarters.

In one exchange, Koller floated text to lab officials stating that “we routinely ask folks to modify their abstracts for length, clarity, etc. In this case, it could have been as simple as someone wanting to just highlight the parts of the research that are priorities for this administration.”

In an email interview, Koller said there was a misunderstanding about the intent of the revisions, emphasizing that they occurred after proposals were accepted, and were never a condition of funding.

“There have been no other incidents where PNNL has asked scientists to remove climate change from research proposals,” he said.

“Asking authors to clarify abstracts isn’t unusual in the science community,” he said when asked why DOE was basing decisions on a budget request. The revisions were made so scientists could “clarify the focus of their research plans,” he added.

Rosenberg at the Union of Concerned Scientists said he had never heard of federal officials making such requests based on a president’s budget proposal, which is just a suggestion to Congress.

“I think that’s crazy,” he said.

It didn’t help the situation that Congress so rarely meets budget deadlines, but the revisions still should not have happened, he said.

DOE spokeswoman Shaylyn Hynes said “the short answer is no” when asked whether DOE headquarters directed PNNL managers.

After Bowen’s post this summer, Hynes said “there is no departmental-wide policy banning the term ‘climate change’ from being used in DOE materials. That is completely false.” Koller said that includes PNNL.

It’s uncertain whether the PNNL incident was an isolated one. When told of the abstracts, one employee at a national lab said he is free to attend conferences on climate change.

Privately, other DOE workers outside PNNL say they’ve been asked to alter climate change language on documents, but internally.

“There are some program offices discouraging the use of the term, but none of these instances are from political guidance,” said one DOE staffer.

Jeff Navin, a former acting chief of staff at DOE in the Obama administration, said the Trump administration created “this mess” by putting the lab in a tough spot.

“They want to fund good science, but they also want to be seen as a team player with the department that funds them. But the question shouldn’t be why PNNL asked for these changes; the question should be who in the administration suggested this prohibition and why.”

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

From EMSL: “Microbial Communities Thrive by Transferring Electrons”

EMSL

February 03, 2017 [Blew right by tis when it first came out. Glad to see they re-issued it.]
Haluk Beyenal
Washington State University
beyenal@wsu.edu

Alice Dohnalkova
EMSL
Alice.Dohnalkova@pnnl.gov

New cooperative photosynthesis studied for applications to waste treatment and bioenergy production. No image credit.

The Science

Photosynthetic bacteria are major primary producers on Earth, using sunlight to convert inorganic compounds in the environment into more complex organic compounds that fuel all living systems on the planet. A team of researchers recently discovered a new microbial metabolic process, which they termed syntrophic anaerobic photosynthesis, and which could represent an important, widespread form of carbon metabolism in oxygen-depleted zones of poorly mixed freshwater lakes.

The Impact

The discovery of syntrophic anaerobic photosynthesis reveals new possibilities for bioengineering microbial communities that could be used for waste treatment and bioenergy production.

Summary

Almost all life on Earth relies directly or indirectly on primary production—the conversion of inorganic compounds in the environment into organic compounds that store chemical energy and fuel the activity of organisms. Nearly half the global primary productivity occurs through photosynthetic carbon dioxide (CO2) fixation by sulfur bacteria and cyanobacteria. In oxygen-depleted environments, photosynthetic bacteria use inorganic compounds such as water, hydrogen gas and hydrogen sulfide to provide electrons needed to convert CO2 into organic compounds. These organic compounds also make their way into the food web, where they support the growth of heterotrophs—organisms that cannot manufacture their own food. A recent study revealed a new metabolic process, called syntrophic anaerobic photosynthesis, in which photosynthetic and heterotrophic bacteria cooperate to support one another’s growth in oxygen-depleted environments. Researchers from Washington State University, Pacific Northwest National Laboratory (PNNL), China University of Geoscience, and Southern Illinois University made this discovery using the Quanta scanning electron microscope and the FEI Tecnai T-12 cryo-transmission electron microscope at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility.

Quanta scanning electron microscope

FEI Tecnai T-12 cryo-transmission electron microscope

Their analysis revealed that a heterotrophic bacterial species, Geobacter sulfurreducens, directly transfers electrons to a photosynthetic bacterial species, Prosthecochloris aestuarii, which uses electrons to fix CO2 into cell material. At the same time, donating electrons allows G. sulfurreducens to support its own metabolic needs by converting acetate into CO2 and water. This potentially widespread, symbiotic form of metabolism, which links anaerobic photosynthesis directly to anaerobic respiration, could be harnessed to develop new strategies for waste treatment and bioenergy production.

P.T. Ha, S.R. Lindemann, L. Shi, A.C. Dohnalkova, J.K. Fredrickson, M.T. Madigan and H. Beyenal, “Syntrophic anaerobic photosynthesis via direct interspecies electron transfer.” 2017 Nature Communications doi:10.1038/ncomms13924

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Welcome to EMSL. EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

Team’s in Our DNA. We approach science differently than many institutions. We believe in – and have proven – the value of drawing together members of the scientific community and assembling the people, resources and facilities to solve problems. It’s in our DNA, since our founder Dr. Wiley’s initial call to create a user facility that would facilitate “synergism between the physical, mathematical, and life sciences.” We integrate experts across disciplines; experiment with theory; and our user program proposal calls with other user facilities.

We proudly provide an enriched, customized experience that allows users to connect with our people and capabilities in an environment where we focus on solving problems. We collaborate with researchers from academia, government labs and industry, and from nearly all 50 states and from other countries.

From PNNL: “Microbes take their vitamins – for the good of science”

PNNL Lab

January 21, 2016
Tom Rickey

Illustration of the PNNL team’s technology where a vitamin mimic (small blue structure) binds to a protein (larger coiled structure) to gain entry into the bacterium Chloroflexus aurantiacus. Illustration by Nathan Johnson, PNNL

The bacterium Chloroflexus aurantiacus helps give the greenish color to this pool of water in Yellowstone National Park.
Image courtesy of Wikimedia Commons

Chloroflexus aurantiacus under the microscope. Image courtesy of Sylvia Herter and the Joint Genome Institute

Microbes need their vitamins just like people do. Vitamins help keep both organisms healthy and energetic by enabling proteins to do their work. For bacteria, a dearth of vitamins can spell death.

Now scientists at the Department of Energy’s Pacific Northwest National Laboratory have made a “vitamin mimic” — a molecule that looks and acts just like the natural vitamin to bacteria, but can be tracked and measured by scientists in live cells. The research offers a new window into the inner workings of living microbes that are crucial to the world’s energy future, wielding great influence in the planet’s carbon and nutrient cycle and serving as actors in the creation of new fuels.

Vitamins are a powerful currency for researchers seeking to compel microbes to give up their secrets.

“We have a lot to learn about how microbes accumulate and use nutrients that are necessary for their survival and growth. This provides a window for doing so,” said chemist Aaron Wright, the corresponding author of the study published in ACS Chemical Biology.

“Perhaps we will be able to make a microbial community do what we want, by controlling its access to a specific nutrient,” Wright added.

To control the bacteria via vitamins, Wright and his team have to know what other proteins in the cell the vitamins are consorting with, and where and when.

Think of a planner analyzing emergency services for a large city. Knowing that an ambulance enters the city occasionally and transports some people somewhere, for instance, is not nearly as useful as knowing the precise address of the caller, the identity of the injured, and the location of the nearest hospital.

It’s the same for scientists trying to understand microbial cells. While a cell is infinitesimally small, the activity within resembles the hustle and bustle of a large city, with many functions within carried out by thousands of entities. Knowing precisely which vitamins aid which proteins, under what circumstances, to keep things running is a must if scientists are to maximize microorganisms for energy production and other processes.

“Microbial communities are organized based on their ability to get the resources they need to survive and grow,” said Wright. “We need to understand how the availability of nutrients, like vitamins, helps determine the structure of a microbial community as a step toward controlling that community in ways we would like to be able to do.”

An anchor for pond scum

Wright’s team studied the bacterium Chloroflexus aurantiacus J-10-fl, which is a common member of microbial mats — gloopy natural structures (think pond scum) where layers containing different groups of microbes band together. In these collections, C. aurantiacus often plays the role of anchor, helping to hold together an assortment of microbes. The bacteria, which resemble strands of string under the microscope, are usually found in hot springs, since they enjoy temperatures above 100 degrees Fahrenheit.

Wright’s team performed a series of synthetic chemical steps to alter three vitamins that C. aurantiacus needs to survive: vitamin B1 (thiamine), vitamin B2 (riboflavin), and vitamin B7 (biotin). While the bacteria recognized the substances as normal vitamins, the researchers can monitor the mimics much more easily than their natural counterparts.

Wright’s team used the mimics to relay a treasure trove of information about how vitamins enter the cell and interact within the cell, by analyzing the precise location of the molecules’ activity in living cells. Through a system called affinity-based protein profiling, Wright’s group effectively tagged these molecules where they’re active, then used techniques such as mass spectrometry to sort and measure proteins of interest.

One of the team’s findings suggests multiple vitamins may share the same molecular machinery to gain entry into the cell. The team is still investigating these data. These findings can provide a road map for scientists like Wright who are trying to direct microbes as part of broad efforts to create clean, renewable fuels and reduce the effects of climate change.

The work was funded by the U.S. Department of Energy Office of Science. The mass spectrometry-based measurements and microscopy were performed at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility at PNNL.

Reference: Lindsey N. Anderson, Phillip K. Koech, Andrew E. Plymale, Elizabeth V. Landorf, Allan Konopka, Frank R. Collart, Mary S. Lipton, Margaret F. Romine and Aaron T. Wright, Live cell discovery of microbial vitamin transport and enzyme-cofactor interactions, ACS Chemical Biology, Dec. 15, 2015, DOI: 10.1021/acschembio.5b00918.

EMSL, the Environmental Molecular Sciences Laboratory, is a national scientific user facility sponsored by the Department of Energy’s Office of Science. Located at Pacific Northwest National Laboratory in Richland, Wash., EMSL offers an open, collaborative environment for scientific discovery to researchers around the world. Its integrated computational and experimental resources enable researchers to realize important scientific insights and create new technologies. Follow EMSL on Facebook, LinkedIn and Twitter.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

From EMSL: “Scarcity Drives Efficiency”

EMSL

September 28, 2015 [This just became available.]
Tim Scheibe tim.scheibe@pnnl.gov at EMSL
Younan Xia younan.xia@bme.gatech.edu

Platinum can be an efficient fuel cell catalyst

Researchers developed a new class of catalysts by putting essentially all of the platinum atoms on the surface material and minimized the use of atoms in the core, thereby increasing the utilization efficiency of precious metals for fuel cells.

The Science

Platinum is an excellent catalyst for reactions in fuel cells, but its scarcity and cost have driven scientists to look for more efficient ways to use the precious metal. In a recent study, researchers developed a new class of catalysts by putting essentially all of the platinum atoms on the surface and minimizing the use of atoms in the core, thereby increasing efficient utilization of platinum for fuel cells.

The Impact

The novel nanocage catalyst will help promote the sustainable use of platinum and other precious metals for energy and other industrial applications. The reduced costs associated with the novel nanostructures will encourage commercialization of this technology for the development of zero-emission energy sources.

Summary

Researchers from Georgia Institute of Technology and Emory University, Xiamen University, University of Wisconsin–Madison, Oak Ridge National Laboratory and Arizona State University fabricated cubic and octahedral nanocages by depositing a few atomic layers of platinum on palladium nanocrystals, and then completely etching away the palladium core. Density functional theory (DFT) calculations suggested the etching process was initiated by the formation of vacancies through the removal of palladium atoms incorporated into the outermost layer during the deposition of platinum. Some of the computational work was performed using computer resources at EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Biological and Environmental Research user facility. DFT calculations were performed at supercomputing centers at EMSL, Argonne National Laboratory and the National Energy Research Scientific Computing Center.

Based on the findings, researchers propose that during platinum deposition, some palladium atoms are incorporated into the outermost platinum layers. Upon contact with the etchant—an acid or corrosive chemical—the palladium atoms in the outermost layer of the platinum shell are oxidized to generate vacancies in the surface of the nanostructure. The underlying palladium atoms then diffuse to these vacancies and are continuously etched away, leaving behind atom-wide channels. Over time, the channels grow in size to allow direct corrosion of palladium from the core. This process leads to a nanocage with a few layers of platinum atoms in the shell and a hollow interior.

Compared to a commercial platinum/carbon catalyst, the nanocages showed enhanced catalytic activity and durability. The findings demonstrate it is possible to design fuel cell catalysts with efficient use of precious metals without sacrificing performance. Moreover, it is possible to tailor the arrangement of atoms or the surface structure of catalytic particles to optimize their catalytic performance for a specific type of chemical reaction. The researchers are testing these catalysts in fuel cell devices to determine how to further improve their design for clean energy applications.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

Welcome to EMSL. EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

Team’s in Our DNA. We approach science differently than many institutions. We believe in – and have proven – the value of drawing together members of the scientific community and assembling the people, resources and facilities to solve problems. It’s in our DNA, since our founder Dr. Wiley’s initial call to create a user facility that would facilitate “synergism between the physical, mathematical, and life sciences.” We integrate experts across disciplines; experiment with theory; and our user program proposal calls with other user facilities.

We proudly provide an enriched, customized experience that allows users to connect with our people and capabilities in an environment where we focus on solving problems. We collaborate with researchers from academia, government labs and industry, and from nearly all 50 states and from other countries.

From PNNL: “Tiny grains of rice hold big promise for greenhouse gas reductions, bioenergy”

PNNL Lab

July 28, 2015
Dawn Zimmerman

Rice serves as the staple food for more than half of the world’s population, but it’s also the one of the largest manmade sources of atmospheric methane, a potent greenhouse gas. Now, with the addition of a single gene, rice can be cultivated to emit virtually no methane from its paddies during growth. It also packs much more of the plant’s desired properties, such as starch for a richer food source and biomass for energy production, according to a study in Nature.

In addition to a near elimination of greenhouse gases associated with its growth, SUSIBA2 rice produces substantially more grains for a richer food source. The new strain is shown here (right) compared to the study’s control.
Image courtesy of Swedish University of Agricultural Sciences

With their warm, waterlogged soils, rice paddies contribute up to 17 percent of global methane emissions, the equivalent of about 100 million tons each year. While this represents a much smaller percentage of overall greenhouse gases than carbon dioxide, methane is about 20 times more effective at trapping heat. SUSIBA2 rice, as the new strain is dubbed, is the first high-starch, low-methane rice that could offer a significant and sustainable solution.

Researchers created SUSIBA2 rice by introducing a single gene from barley into common rice, resulting in a plant that can better feed its grains, stems and leaves while starving off methane-producing microbes in the soil.

The results, which appear in the July 30 print edition of Nature and online, represent a culmination of more than a decade of work by researchers in three countries, including Christer Jansson, director of plant sciences at the Department of Energy’s Pacific Northwest National Laboratory and EMSL, DOE’s Environmental Molecular Sciences Laboratory. Jansson and colleagues hypothesized the concept while at the Swedish University of Agricultural Sciences and carried out ongoing studies at the university and with colleagues at China’s Fujian Academy of Agricultural Sciences and Hunan Agricultural University.

“The need to increase starch content and lower methane emissions from rice production is widely recognized, but the ability to do both simultaneously has eluded researchers,” Jansson said. “As the world’s population grows, so will rice production. And as the Earth warms, so will rice paddies, resulting in even more methane emissions. It’s an issue that must be addressed.”
Channeling carbon

During photosynthesis, carbon dioxide is absorbed and converts to sugars to feed or be stored in various parts of the plant. Researchers have long sought to better understand and control this process to coax out desired characteristics of the plant. Funneling more carbon to the seeds in rice results in a plumper, starchier grain. Similarly, carbon and resulting sugars channeled to stems and leaves increases their mass and creates more plant biomass, a bioenergy feedstock.

In early work in Sweden, Jansson and his team investigated how distribution of sugars in plants could be controlled by a special protein called a transcription factor, which binds to certain genes and turns them on or off.

“By controlling where the transcription factor is produced, we can then dictate where in a plant the carbon — and resulting sugars — accumulate,” Jansson said.

To narrow down the mass of gene contenders, the team started with grains of barley that were high in starch, then identified genes within that were highly active. The activity of each gene then was analyzed in an attempt to find the specific transcription factor responsible for regulating the conversion of sugar to starch in the above-ground portions of the plant, primarily the grains.

The master plan

Upon discovery of the transcription factor SUSIBA2, for SUgar SIgnaling in BArley 2, further investigation revealed it was a type known as a master regulator. Master regulators control several genes and processes in metabolic or regulatory pathways. As such, SUSIBA2 had the ability to direct the majority of carbon to the grains and leaves, and essentially cut off the supply to the roots and soil where certain microbes consume and convert it to methane.

Researchers introduced SUSIBA2 into a common variety of rice and tested its performance against a non-modified version of the same strain. Over three years of field studies in China, researchers consistently demonstrated that SUSIBA2 delivered increased crop yields and a near elimination of methane emissions.

Next steps

Jansson will continue his work with SUSIBA2 this fall to further investigate the mechanisms involved with the allocation of carbon using mass spectrometry and imaging capabilities at EMSL. Jansson and collaborators also want to analyze how roots and microbial communities interact to gain a more holistic understanding of any impacts a decrease in methane-producing bacteria may have.

Funding for this research was provided by The Swedish University of Agricultural Sciences, the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, the National Natural Science Foundation of China and the Carl Tryggers Foundation.

See the full article here.

Please help promote STEM in your local schools.

Stem Education Coalition

Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

From EMSL: “How atmospheric ice forms”

Environmental Molecular Sciences Laboratory (EMSL)

No Date
No Writer Credit

New insights into atmospheric ice formation could improve climate models

The formation of ice crystals in the atmosphere strongly affects cloud dynamics, cloud radiative properties and the water vapor budget, and thus plays an important role in climate. To gain new insights into this poorly understood process, researchers used state-of-the-art micro-spectroscopy and chemical imaging methods to characterize the physical and chemical properties of ice-nucleating particles sampled from ambient air.

The Impact

The study reveals the abundance of a given type of particle in the atmosphere can play a stronger role in ice formation than the particle-specific ice-nucleation propensity determined by the specific chemical and physical particle properties. These findings significantly advance our understanding of the underlying mechanisms that lead to ice formation in the atmosphere and could improve the accuracy of predictive cloud and climate models.

Summary

Researchers from Stony Brook University, EMSL, Lawrence Berkeley National Laboratory and University of the Pacific developed a novel methodology that enables comprehensive analyses of individual particles that act as ice nuclei, which trigger the formation of ice crystals in the atmosphere, as well as the entire population of particles found in ambient air. To characterize the particles’ physical and chemical properties, the researchers used micro-spectroscopy and chemical imaging methods, including computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS). These methods provide information on the size, shape and elemental composition of a large number of individual particles.

By classifying the particles into categories based on physical and chemical properties, the researchers discovered ice-nucleating particles are not distinct from other particles. In other words, unique particle composition and shape were not sufficient to assess the potential to act as ice nuclei. Instead, the ice-nucleating particles are common in the atmosphere and do not always pose a “needle-in-the-haystack” challenge. This is in contrast to the traditional view that there are very few, but exceptional particles in the atmosphere with the right properties to become ice nuclei. Even particles that are not especially efficient at forming ice crystals can play an important role in this process when sufficiently abundant in the entire particle population, due to the large collective surface area for ice-nucleating reactions. The findings suggest cloud models should take into account the properties of the entire particle population in addition to those of individual ice-nucleating particles to accurately reflect the important role of particle abundance and total available surface area in ice formation.

Funding: Funding for sample collection was provided by the Atmospheric Radiation Measurement (ARM) Program sponsored by the DOE’s Office of Science’s Office of Biological and Environmental Research (OBER), Climate and Environmental Sciences Division (CESD). Funding for data analysis was provided by the U.S. DOE’s Atmospheric System Research (ASR) Program, OBER, CESD. Laboratory Directed Research and Development funds were provided by PNNL.

See the full article here.

EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

ScienceSprings relies on technology from

MAINGEAR computers

Lenovo

Dell

From EMSL: “Developing Better Biomass Feedstock”

Environmental Molecular Sciences Laboratory (EMSL)

No Date
No Writer Credit

Multi-omics unlocking the workings of plants

Biomass holds great promise as a fuel source to generate renewable energy to help the United States achieve energy independence. Kim Hixson is applying what she’s learned from a lowly weed to bioengineer better biomass feedstock.

Hixson, an EMSL senior research scientist, is collaborating with Norman Lewis, a regents professor and director of the Institute of Biological Chemistry at Washington State University in Pullman. Together they are using EMSL’s multi-omics capabilities to better understand how manipulating the genes in one plant can be applied to other plants to improve their potential as biofuel and biochemical feedstock.

“Our research is hypothesis driven, but there’s also a lot of discovery,” says Hixson. “The more we study biology, the more we see how interconnected things are in nature.”

More Than a Weed

Central to this research is Arabidopsis, a model plant system. A small flowering plant related to cabbage, Arabidopsis makes for an ideal plant model. Its genome has been sequenced and is easy to genetically modify. Hixson calls it the “lab rat of the plant world.”

Thale cress (Arabidopsis thaliana)

Arabidopsis is a small flowering plant related to cabbage and a model organism used to research plant biology. The plant on the left is wild-type Arabidopsis at five weeks. The plant on the right is Arabidopsis at five weeks with ADT-related genes knocked out, reducing the levels of lignin.

Arabidopsis has a six-member isoenzyme family of arogenate dehydratases, or ADTs. These enzymes are involved in the catalytic reactions that turn arogenic acid, a metabolite, into phenylalanine, an essential metabolite which is incorporated directly into proteins or is further modified into other chemicals such as flavonoids, coumarins, anthocyanins and lignin.

Hixson’s research found hundreds of different changes occurring in the plant due to the modifications in the ADT composition. The collaborators at WSU discovered that out of the six ADTs in Arabidopsis, five ADTs are seemingly linked to the production of phenylalanine utilized in the phenylpropanoid pathway, which is involved in lignin production. Lignin gives plants their recalcitrance; it’s hydrophobic and difficult to degrade. Lignin is the structural material that makes the sugars in plants difficult to extract when making biofuels.

“It is well known that a significant amount of the carbon dioxide that Arabidopsis fixes goes into the phenylpropanoid pathway and ultimately ends up as lignin,” says Hixson. “This is very important from the perspective of turning plant material into biofuel.”

Hixson’s Arabidopsis studies earned her an American Chemical Society Withycombe-Charalambous Graduate Student Symposium Award. At the symposium she presented some of her findings from the multi-omics analysis of the gene knockouts conducted at EMSL. The researchers analyzed several knockout mutants of ADTs, including single, double, triple and quadruple knockout mutants, with each mutant strain producing varying degrees of lignin reduction. They found that knocking out multiple ADTs and specific ADTs leads to a measured reduction of lignin in the plants.

By knocking out different combinations of the ADT-related genes, the researchers produced plants with various levels of lignin. In the most extreme case where they knocked out four ADT-related genes, the plant was unable to hold its own weight and became vine-like.

“We knew there were a lot of changes going on in this plant, but we didn’t know at the molecular level what those changes were,” says Hixson. “The questions about what pathways are being changed and what potential points of regulation are being up-regulated or repressed are precisely what transcriptomics coupled with proteomics can answer.”

Other findings from Hixson’s research showed knocking out ADT genes alters the photosynthesis machinery and pathways in the mutant plants. For reasons not completely understood, knocking out ADT genes causes the mutant plant systems to produce more photosynthetic machinery, potentially fixing more carbon, but an overall increase in plant mass was not observed. Using transcriptomics and proteomics techniques at EMSL, the researchers were able to look at the other pathways and genes that were changed in the mutant plants. They found the photorespiration pathways were also up-regulated. While more carbon was potentially being fixed, more of it was likely being lost or released back into the atmosphere through the photorespiration pathways.

“This is potentially a very useful discovery,” says Hixson. “In future bioengineering attempts we may need to incorporate strategies to counteract carbon loss via photorespiration which would potentially improve the rates of biomass growth in ADT-altered plants used for biofuels or biochemicals.”

Applying Their Findings to Poplars

Researchers collect samples of mutant poplars to undergo multi-omics analysis to determine if the genetic changes affect other pathways and functions in the tree.
The research has developed several lines of mutant Arabidopsis by altering the composition of the ADT genes, which ultimately decreases the amount of lignin these plants produce. Questions arise about how much ADT can be lessened and thus how much lignin can be reduced before a plant in a real world setting shows detrimental growth affects. Additionally it is important to understand how these changes alter other pathways and other systems within the plant, and how the changes are altering the plant system as a whole.

“These are really important questions, not so much in Arabidopsis, which is just a little weed,” says Hixson. “But we’ve started to incorporate some of the same knockouts into poplar trees, which show good potential as a biofuel feedstock.”

Poplar trees are native to the Pacific Northwest and widely used as a feedstock in the paper industry. The Department of Energy is interested in the poplar as a biofuel. Within the missions of EMSL and the DOE Office of Biological and Environmental Research is a charge to reduce the United States’ dependence on foreign oil and to develop technology for alternative fuel and chemical options.

Hixson hopes the manipulations in the Arabidopsis translate to other plants, such as poplars. Poplar has a larger and more complex genome than Arabidopsis. She will test the altered poplars at EMSL with multi-omics analysis to see how the transcriptome and proteome changes and if she sees the same types of response in the tree as she saw in the Arabidopsis.

“I expect a lot of things are going to be similar between the two plants,” Hixson says. “But they are different systems and it will be interesting to see the changes in the poplar compared to the Arabidopsis at the molecular level.”

The researchers have incorporated the ADT knockouts into poplar trees to test if the amount of lignin can be reduced and how far it can be reduced without damaging effects to the tree as a whole. Hixson recently collected samples of the mutant poplars from a test plot and greenhouse in western Washington. She will use EMSL’s multi-omics capabilities to determine if a change to one pathway affects other pathways and functions in the tree. According to Hixson, proteomics and transcriptomics identify what genes are being affected, either positively or negatively. This information will be useful when bioengineering poplars as a feedstock. The data will also be incorporated into her dissertation for her doctorate in molecular plant sciences from WSU.

Other Proposals: Where few Have Gone Before

The study with the poplar trees is an approved EMSL user project. Lewis is the principal investigator and Hixson is a collaborator. Lewis is also Hixson’s faculty advisor.

Hixson and Lewis have several research proposals they are hoping get approved. In collaboration with Mary Lipton, an integrative omics scientist at Pacific Northwest National Laboratory, and other scientists, they submitted a proposal to NASA. In this study several of the mutant Arabidopsis would be sent into outer space to test what happens to reduced-lignin plants in a microgravity environment.

“I really hope NASA approves it,” Hixson says. “The findings could be very interesting.”

In another submission, this one in response to an EMSL internal call, Hixson and Lewis are proposing to study red alder trees as an ideal biofuel source. A red alder grows almost as fast and dense as a poplar, but it forms specialized symbiotic relationships in its root system. These symbiotic relationships produce root nodules which can fix nitrogen, allowing red alders to thrive without added fertilizer and grow on marginal lands. Hixson believes red alder has the potential to be a highly valuable source for biomass feedstock or other wood-based materials.

For this study, they will apply what they learned from the Arabidopsis and poplar research. The proposal includes a full genetic characterization of the red alder and a multi-omics study of the tree’s association with two ubiquitous root symbionts.

“Our end goal is to gather enough information throughout multi-omics evaluations to be able to bioengineer the ideal biofuel and biochemical feedstock,” says Hixson. “We’re not there yet, but we’re working on it.”

See the full article here.

EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

ScienceSprings relies on technology from

MAINGEAR computers

Lenovo

Dell

From EMSL: “Improving catalysts”

Environmental Molecular Sciences Laboratory (EMSL)

No Date
No Writer Credit

Better bimetallic catalysts for fuel and chemical industries

The Science

Nanocatalysts consisting of two metals can offer superior performance compared with those made up of only one metal, so they are widely used for industrial processes that generate fuels and chemicals from natural gas, coal or plant biomass. However, complex interactions between the two metals during catalytic reactions can lower catalytic efficiency. This study addresses this issue by directly observing the changes of platinum-cobalt nanoparticles in operating conditions. Such particles are used as catalysts to convert carbon dioxide and hydrogen into long-chain carbon fuels and are important to the operation of low-temperature fuel cells.

No image credit

The Impact

The new insights on the transformations of multiple component catalysts will allow researchers to optimally design similar catalysts to improve their performance, extend their lifetime, and reduce their environmental impact. Moreover, this research could guide efforts to minimize the use of precious metal components such as platinum and therefore reduce the cost of catalysts and lead to a more economical product for consumers.

Summary

In a multi-national lab effort led by Haimei Zheng from Lawrence Berkeley National Laboratory, researchers from DOE’s Pacific Northwest National Laboratory and collaborators examined real-time changes in the atomic structure of nanoparticles consisting of platinum and cobalt during reactions with oxygen and hydrogen using environmental transmission electron microscopy (ETEM), a specialized instrument housed in the Quiet Wing at the Environmental Molecular Sciences Laboratory (EMSL), a DOE national scientific user facility. The work was supported by the Chemical Imaging Initiative at PNNL.

During oxidation in an oxygen gas environment, cobalt migrated to the nanoparticle surface, where it formed a cobalt oxide film that covered the platinum. Within ten seconds, this oxide film broke apart to form distinct islands and created voids in the interior of the particle, which can impair catalyst performance. This process was reversed during reduction in a hydrogen gas environment, which caused the cobalt oxide patches to decrease and the cobalt to migrate back to the bulk of the particle. Reduction with hydrogen also caused a layer of platinum to form on the particle surface, which is expected to improve catalyst performance.

These new insights into the atomic scale behavior of nanoparticles consisting of multiple metals in reactive environments pave the way for a deeper understanding of the properties of multi-component catalysts and will guide efforts to improve their performance. In particular, the findings can be used to design multi-component catalysts that do not form oxide islands on the nanoparticle surface, but rather retain the material with higher catalytic performance on the nanoparticle surface during catalytic reactions.

Funding

This research was supported by DOE’s Office of Science and the Office of Basic Energy Sciences’ Chemical Science Division, as well as the Chemical Imaging Initiative at PNNL through the

Laboratory Directed Research and Development Programs at PNNL and LBNL.

See the full article here.

EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

ScienceSprings relies on technology from

MAINGEAR computers

Lenovo

Dell