From Berkeley Lab: “Sweet Success”

Berkeley Lab

Berkeley Lab Researchers Find Way to Catalyze More Sugars from Biomass

April 07, 2013
Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

“Catalysis may initiate almost all modern industrial manufacturing processes, but catalytic activity on solid surfaces is poorly understood. This is especially true for the cellulase enzymes used to release fermentable sugars from cellulosic biomass for the production of advanced biofuels. Now, researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) through support from the Energy Biosciences Institute (EBI) have literally shed new light on cellulase catalysis.

PALM – for Photo-Activated Localization Microscopy – enables researchers to quantify how and where enzymes are binding to the surface of cellulose in heterogeneous surfaces, such as those in plant cell walls.

Using an ultrahigh-precision visible light microscopy technique called PALM – for Photo-Activated Localization Microscopy – the researchers have found a way to improve the collective catalytic activity of enzyme cocktails that can boost the yields of sugars for making fuels. Increasing the sugar yields from cellulosic biomass to help bring down biofuel production costs is essential for the widespread commercial adoption of these fuels.

From left, Jan Liphardt, Harvey Blanch and Doug Clark led the development of a way to improve the collective catalytic activity of enzyme cocktails that can boost the yields of sugars for making advanced biofuels. (Photo by Roy Kaltschmidt)

‘The enzymatic breakdown of cellulosic biomass into fermentable sugars has been the Achilles heel of biofuels, a key economic bottleneck,’ says chemical engineer Harvey Blanch, one of the leaders of this research. ‘Our research provides a new understanding of how multiple cellulase enzymes attack solid cellulose by working in concert, an action known as enzyme synergy, and explains why certain mixtures of cellulase enzymes work better together than each works individually.’”

See the full article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

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From Argonne APS: "Shedding Light on Chemistry with a Biological Twist"

News from Argonne National Laboratory

MARCH 14, 2013
David Bradley

“Many of life’s processes rely on light to trigger a chemical change. Photosynthesis, vision, the movement of light-seeking or light-avoiding bacteria, for instance, all exploit photochemistry. Discovering exactly how living things absorb and convert light energy into a form that can change the molecules involved in such processes would not only help scientists understand them but could lead to ways to mimic such processes for more efficient solar energy conversion, for instance. A clearer understanding of how light can drive biological processes has emerged from x-ray diffraction studies carried out on beamlines at the U.S. Department of Energy Office of Science’s Advanced Photon Source (APS) at Argonne, and the European Synchrotron Radiation Facility (ESRF). This work will help science shed a brighter light on some of life’s most critical processes.”

The isomerization of a small molecule caged inside a photoactive protein recorded by time-resolved x-ray crystallography reveals a detailed sequence of events (represented by dominos) composed of a short-lived intermediate (red) whose reaction trajectory bifurcates along bicycle-pedal (left) and hula-twist (right) pathways. No image credit.

See the full article here.

Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security.

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From Argonne Lab: “Breakthrough could lead to drugs that better combat ‘superbugs’ “

News from Argonne National Laboratory

February 28, 2013
Jen Salazar

“In the never-ending battle between antibiotic developers and the bacteria they fight, scientists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory have made a key breakthrough that could allow for the development of new drugs to more effectively combat antibiotic-resistant ‘superbugs’.

NDM-1, present in a number of pathogenic bacteria, including Klebsiella pneumonia and Escherichia coli, is able to defeat many of the world’s most widely used antibiotics, including penicillin derivatives, cephalosporins, monobactams and carbapenems.

An Argonne team led by Youngchang Kim of the Structural Biology Center, in collaboration with researchers from the Midwest Center for Structural Genomics, the University of Texas-Pan American and Texas A&M University, recently determined the structure of NDM-1, a harmful enzyme able to overcome several antibiotics. The team used a combination of X-ray crystallography at Argonne’s Advanced Photon Source (APS), biochemical assays, and computational modeling using resources at two Texas universities.

‘These kinds of enzymes can recognize many different targets,’ said Andrzej Joachimiak, head of Argonne’s Structural Biology Center and the Midwest Center for Structural Genomics.

‘The next step in the research is to look for inhibitors that we can create that would block the functioning of the enzyme,’ Joachimiak said. ‘If we can stop the enzyme from cutting the ring, the antibiotics stand a much better chance of staying effective.”

See the full article here.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

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From Berkeley Lab: “A Dual Look at Photosystem II Using the World’s Most Powerful X-Ray Laser”

Berkeley Lab

Berkeley Lab and SLAC Researchers Demonstrate Room Temperature Simultaneous Diffraction/Spectroscopy of Metalloenzymes

February 14, 2013
Lynn Yarris

“From providing living cells with energy, to nitrogen fixation, to the splitting of water molecules, the catalytic activities of metalloenzymes – proteins that contain a metal ion – are vital to life on Earth. A better understanding of the chemistry behind these catalytic activities could pave the way for exciting new technologies, most prominently artificial photosynthesis systems that would provide clean, green and renewable energy. Now, researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the SLAC National Accelerator Laboratory have taken a major step towards achieving this goal.

Green crystals, millionths of a millimeter in size, preserve the molecular structure and activity of photosystem II, the molecule that photoxidizes water into molecular oxygen. (Image courtesy of Jan Kern, Berkeley Lab)

Using ultrafast, intensely bright pulses of X-rays from SLAC’s Linac Coherent Light Source (LCLS), the world’s most powerful X-ray laser, the researchers were able to simultaneously image at room temperature the atomic and electronic structures of photosystem II, a metalloenzyme critical to photosynthesis.

Linac Coherent Light Source at SLAC

‘This is the first time that femtosecond X-ray pulses have been used for the simultaneous collection of both X-ray diffraction (XRD) and X-ray emission spectroscopy (XES) at room temperature of a metalloenzyme crystal,’ says Junko Yano, a chemist with Berkeley Lab’s Physical Biosciences Division who was one of the leaders of this research. ‘Collecting both diffraction and spectroscopy data from the same crystal under the same conditions is required for a detailed understanding of the mechanisms behind metalloenzyme catalysis.’”

See the full article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

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From Berkeley Lab: “New Details on the Molecular Machinery of Cancer”

Berkeley Lab

Berkeley Lab Researchers Resolve EGFR Activation Mystery

February 11, 2013
Lynn Yarris

“Researchers with Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have provided important new details into the activation of the epidermal growth factor receptor (EGFR), a cell surface protein that has been strongly linked to a large number of cancers and is a major target of cancer therapies.

A structural coupling that allows intracellular kinase domains to undergo dimerization is a key to EGFR activation. No image credit.

‘The more we understand about EGFR and the complex molecular machinery involved in the growth and proliferation of cells, the closer we will be to developing new and more effective ways to cure and treat the many different forms of cancer,’ says chemist Jay Groves, one of the leaders of this research. ‘Through a tour-de-force of quantitative biology techniques that included cutting edge time-resolved fluorescence spectroscopy in living cells, Nuclear Magnetic Resonance, and computational modeling, we’ve determined definitively how EGFR becomes activated through to its epidermal growth factor (EGF) ligand.

Jay Groves is a chemist who holds appointments with Berkeley Lab, UC Berkeley and HHMI. (Photo by Roy Kaltschmidt)

Groves, who holds joint appointments with Berkeley Lab’s Physical Biosciences Division and UC Berkeley’s Chemistry Department, and is also a Howard Hughes Medical Institute (HHMI) investigator is one of two corresponding authors of a paper in the journal Cell that describes this research. The paper is titled Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor. The other corresponding author is John Kuriyan, who also holds joint appointments with Berkeley Lab, UC Berkeley and HHMI.”

See the full article here.

A U.S. Department of Energy National Laboratory Operated by the University of California

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From Brookhaven: “Scientists Turn Toxic By-Product Into Biofuel Booster”

Brookhaven Lab

February 4, 2013
Karen McNulty Walsh
Peter Genzer

“Scientists studying an enzyme that naturally produces alkanes—long carbon-chain molecules that could be a direct replacement for the hydrocarbons in gasoline—have figured out why the natural reaction typically stops after three to five cycles. Armed with that knowledge, they’ve devised a strategy to keep the reaction going. The biochemical details—worked out at the U.S. Department of Energy’s Brookhaven National Laboratory and described in the Proceedings of the National Academy of Sciences the week of February 4, 2013—renew interest in using the enzyme in bacteria, algae, or plants to produce biofuels that need no further processing.

Chemical structure of methane, the simplest alkane

Brookhaven biochemist John Shanklin (left) and former postdoc Carl Andre. No image credit

‘Alkanes are very similar to the carbon-chain molecules in gasoline. They represent a potential renewable alternative to replace the petrochemical component of gasoline,’ said Brookhaven biochemist John Shanklin, who led the research, which was conducted in large part by former Brookhaven postdoc Carl Andre, now working at BASF Plant Science in North Carolina, and Xiaohong Yu of Brookhaven’s Biosciences Department. ‘Unlike the process of breaking down plant biomass to sugars and fermenting them to ethanol,’ Shanklin said, ‘biologically produced alkanes could be extracted and used directly as fuel.’”

See the full article here.

One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

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From Gizmodo: “This Wind Tunnel-Cooled Computer Is Helping Conquer Cancer”

World Community Grid

I got my first glimpse of the subject here at a WCG forum post. I followed the links and was blown away.
I was given permission to use this copyright protected material and I will do my best to honor that permission.

Jan 4, 2013
Andrew Tarantola

Distributed, crowd-sourced computing platforms—doesn’t matter if it’s Indigogo or SETI@home—are only as useful as the individual systems connected to them. And for IBM’s World Community Grid, a single system can do a lot, especially when it’s a purpose-built 4.5GHz calculation-crushing super computer.

Mike Schropp, the Total Geek behind the Total Geekdom website, built the Wind Tunnel Computer after grid computing piqued his interest in 2011. As Schropp describes:

‘The idea that I could build a computer, or use existing computer resources and donate their power so scientists and researchers could process medical and humanitarian research was extremely interesting. By donating computer processing time, you actively contribute towards a great cause. World Community Grid has numerous projects available; finding cures and treatments for cancer, AIDS, malaria, muscular dystrophy, etc.

In particular, Schropp was struck by IBM’s World Community Grid which combines the extra cycles of member machines into a virtual super computer. The organization has also recently begun implementing GPU- rather than CPU-based processes (such as the Help Conquer Cancer project) which is significantly faster when used in massive parallel applications—reducing computational times from hours to minutes.

The rig he built is composed of an Ivy Bridge 3770K CPU running at 4.5GHz, a pair of Radeon HD 7970 graphics cards, 8GB of 2133Mhz of RAM, and a Gigabyte Sniper M3 motherboard. With all these overclocked components running 24/7, heat generation is a major factor—but that’s where the wind tunnel comes in….”

And that is where you should go to the full Gizmodo article which is very instructive.

All we can say is Wow!

For a step-by-step photo review, visit Total Geeekdom’s article.

Thanks to Jesse for the permission to use this material.

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

Computing for Sustainable Water

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

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My BOINC

From Sandia Lab: “Engineering alternative fuel with cyanobacteria”

January 7, 2013
Sue Holmes

“Sandia National Laboratories Truman Fellow Anne Ruffing has engineered two strains of cyanobacteria to produce free fatty acids, a precursor to liquid fuels, but she has also found that the process cuts the bacteria’s production potential.

Sandia researchers are cultivating new algae strains to create algal biofuels.

Truman Fellow Anne Ruffing looks at a flask of cyanobacteria with precipitated fatty acid floating on top. She has engineered two strains of cyanobacteria to produce free fatty acids, a precursor to fuels, as she studies the direct conversion of carbon dioxide into biofuels by photosynthetic organisms. (Photo by Randy Montoya)

‘Even if algae are not the end-term solution, I think they can contribute to getting us there,’ Ruffing said. ‘Regardless of however you look at fossil fuels, they’re eventually going to run out. We have to start looking to the future now and doing research that we’ll need when the time comes.’

Ruffing favors cyanobacteria because fuel from engineered cyanobacteria is excreted outside the cell, in contrast to eukaryotic algae, in which fuel production occurs inside the cell.

Ruffing considers her studies as proof-of-concept work that demonstrates engineering cyanobacteria for free fatty acid (FFA) production and excretion. She wants to identify the best hydrocarbon targets for fuel production and the best model strain for genetic engineering, as well as gene targets to improve FFA production.”

See the full article here.

Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.

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From M.I.T. News: “Editing the genome with high precision”

New method allows scientists to insert multiple genes in specific locations, delete defective genes.

January 3, 2013
Anne Trafton

“Researchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and to develop new therapies, among other potential applications.

A new technique developed at MIT can edit DNA in precise locations. Graphic: Christine Daniloff/iMol

To create their new genome-editing technique, the researchers modified a set of bacterial proteins that normally defend against viral invaders. Using this system, scientists can alter several genome sites simultaneously and can achieve much greater control over where new genes are inserted, says Feng Zhang, an assistant professor of brain and cognitive sciences at MIT and leader of the research team.

‘Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,’ says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

Zhang and his colleagues describe the new technique in the Jan. 3 online edition of Science. Lead authors of the paper are graduate students Le Cong and Ann Ran.

This is really important applied research. See the full article here.

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From SLAC Today: “SSRL Yields Clues to Function of Vital Protein Family”

October 23, 2012
Lori Ann White

“A team of Stanford University researchers used the Stanford Synchrotron Radiation Lightsource. to gain a deeper understanding of a vital family of signaling proteins responsible for regulating an organism’s development and growth, as well as tissue regeneration and wound healing. The protein family, known by the collective name ‘Wnt,’ can cause havoc when their signals go astray; mistakes in Wnt signaling are associated with the development of many types of cancer, including colon cancer, breast cancer and melanoma, and degenerative diseases like multiple sclerosis, Alzheimer’s and type 2 diabetes.

Overview of signal transduction pathways. On the upper right hand side of the cell, a Wnt signaling protein is shown to bind to a frizzled receptor. Wikipedia

XWnt8, a member of the family of signaling proteins called “Wnt” proteins, has an unusual structure resembling a fist with an outstretched thumb and index finger. No image credit.

See the full article here.

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

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