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SSRL Headlines Vol. 10, No. 8  February, 2010


Contents of this Issue:

  1. Science Highlight — Researchers Discover an Unexpected Source of Energy for Deep-sea Microbial Communities
  2. Science Highlight — Researchers Find a New Type of Copper-Protein Binding Site
  3. From the Acting Director of SSRL: Deliberate, Stepwise Progress to 500 mA
  4. Anders Nilsson Receives Humboldt Research Award
  5. Herman Winick Accepts Sakharov Prize at APS Meeting
  6. Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
  7. SSRL Proposal Review Panel Meeting
  8. User Research Administration Update
  9. Traffic and Vehicular Safety at SLAC

1.  Science Highlight — Researchers Discover an Unexpected Source of Energy for Deep-sea Microbial Communities
       (contact: A.S. Templeton,

seafloor biofilms image
Pillow basalts from from inside the Pisces V.
New rock formed by deep undersea volcanoes does not stay bare long. Microbes quickly move onto these basalts to form communities in the form of biofilms. As these biofilms grow and develop, they change the geology of their environment, forming mineral deposits. Since many of these communities are deep in the cold ocean waters, where sunlight does not reach, they must use alternative sources of energy. What these might be is unknown, but a common theory posits that the microbes may be obtaining energy using materials from the rock itself.

To test this theory, that the microbes are dissolving the basalts for energy, a group of researchers led by Alexis Templeton and students at the University of Colorado in Boulder investigated the microbial communities near the Big Island of Hawaii. They used deep-sea submersibles to collect recently formed basalt samples to determine if the associated microbes catalyze the release of specific elements such as iron and manganese. They solved the problem of detecting chemical changes in minute quantities of these metals by using SSRL Beam Lines 2-3 and 11-2 to collect synchrotron-based x-ray fluorescence microprobe mapping and x-ray absorption spectroscopy data. They compared these spectroscopic results with electron microscopic imaging to reveal where certain elements were concentrated.

The researchers were surprised at their results that suggest that the microbes are not gaining their energy from dissolution of the basalts. Instead, the data suggest that the microbes are dependent on materials from hydrothermal vents that diffuse in the deep ocean. Additionally, the researchers found that these microbial communities are forming the precursors to ferromanganese crusts, which are widespread on the ocean floor but are of previously unknown origin. This research was published in the December 2009 issue of Nature Geoscience.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Researchers Find a New Type of Copper-Protein Binding Site
       (contacts: K.M. Lancaster,; H.B. Gray,

highlight figure
Distorted tetrahedral active site of Copper(II) C112D/M121L azurin from 2.1 Å crystal structure.
Copper is an essential ingredient for animal and plant life. Some proteins specifically bind copper for both structural and catalytic purposes. Up until now, mononuclear copper(II) ion binding sites fit into two categories, type 1 and type 2, defined by both their functional roles, structures, and the physical properties of the interactions.

Using a combination of spectroscopic and structure determination techniques and Cu K-edge XAS, Kyle M. Lancaster and Professors Harry B. Gray and John H. Richards of the California Institute of Technology found a novel copper-protein interaction and named the site "type zero." A specific mutation of a type 1 protein that uses copper for an electron transfer function results in the type 0 site. When initial analyses suggested that this copper site does not fit into either the type 1 or type 2 groups, the researchers solved high-resolution crystal structures of the protein. These revealed structural details that were unlike those found in either known type, in particular a distorted tetrahedral site with a very short copper-oxygen bond. To confirm their results and conclusions, they used SSRL Beam Line 7-3 for a copper-K edge and EXAFS study, in collaboration with Dr. Serena DeBeer George.

The researchers conclude that they have found a novel type of copper-protein interaction. They will continue to use SSRL to further characterize the properties of the type zero site and investigate its potential use as a catalyst in fuel cells. This research was published in the December 2009 issue of Nature Chemistry.

To learn more about this research see the full scientific highlight

3.   From the Acting Director of SSRL: Deliberate, Stepwise Progress to 500 mA
       SLAC Today Article by Piero Pianetta

Piero Pianetta
Piero Pianetta
At the time I wrote my last article for SLAC Today, the Stanford Synchrotron Radiation Lightsource was just starting to come out of the summer shutdown having completed improvements that would enable the SPEAR3 storage ring to run with top-off injection at 500 mA. I am happy to report that in spite of rainstorms, the power outage and a water leak in a beam line mask, we have made excellent progress toward that goal over the past four months. Read more at:

4.   Anders Nilsson Receives Humboldt Research Award
       Based on SLAC Today Article by Julie Karceski

Anders Nilsson, SLAC Photon Science Faculty and Deputy Director of the Stanford Institute for Materials & Energy Science (SIMES), was both honored and a little amused when he recently received the Humboldt Research Award. The award, he noted, was for a "senior U.S. scientist."

"I was a little shocked because I'm still a Swedish citizen," Nilsson joked.

Anders Nilsson
Anders Nilsson
He was nominated by scientists in Germany with whom he will collaborate at the University of Hamburg and the Fritz Haber Institute of the Max Planck Society in Berlin. The Humboldt Research award funds scientists for up to one year of scientific research based in Germany. Nilsson, who studies chemical processes on surfaces and water chemistry, looks forward to gathering new ideas on how to better use the Linac Coherent Light Source here at SLAC.

Much of Nilsson's research has focused on understanding chemical bonds, especially bonds on the surfaces of materials. He uses x-rays to examine them at the atomic level. More recently, Nilsson also began studying the structure of water in its liquid phase, entering a debate on the fundamental properties of perhaps Earth's most essential molecule. These two rather different fields within chemistry converge in research methods, as they both rely on x-rays and can benefit from the LCLS's extraordinarily bright, short pulses of x-ray laser light. Read more at:

Sakharov Prize Recipients
Herman Winick (right) and Morris Pripstein, at the APS April Meeting in Washington, DC. (Photo by Calla Cofield.)
5.   Herman Winick Accepts Sakharov Prize

As mentioned in our October edition of the Headlines, Herman Winick has been awarded the Andrei Sakharov Prize for Upholding Human Rights. At the April 2010 Meeting of the American Physical Society held in Washington DC earlier this month, Herman, along with other recipients, Joseph Birman of the City College of New York and City University of New York and Morris Pripstein of the National Science Foundation, accepted the Prize. Read more at:

6.   Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
       (contact: A. Gonzalez,

SSRL will host the Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples to be held March 11-13, 2010 here at SLAC. This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by x-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionizing radiation to examine biological structures at the molecular and cellular level.

The organizers are Ana Gonzales, Elspeth Garman, Colin Nave, Sean McSweeney, Raimond Ravelli, Gerd Rosenbaum, Soichi Wakatsuki and Martin Weik. For more information see:

7.   SSRL Proposal Review Panel Meeting
       (contact: C. Knotts,

The SSRL Proposal Review Panel met January 29-30 to review new proposals and extension requests submitted for the December 1, 2009 deadline. SSRL Acting Director Piero Pianetta started off the meeting by welcoming new committee members Rachel Segalman (UC Berkeley), Paul Fenter (ANL), and Gerard Wong (UCLA) and giving an overview talk. Cathy Knotts, User Research Administration Manager, followed with a presentation outlining SSRL's current proposal process as a segue for a panel discussion on ways to make the process and the form itself more user friendly as we move toward a web-based submission.

8.   User Research Administration
       (contact: C. Knotts,

The next opportunity to submit new macromolecular crystallography proposals is April 1 for beam time eligibility beginning June 2010. New X-ray/VUV proposals are due June 1 for beam time starting in fall 2010. Please note that our current experimental run ends July 26, 2010. There are many projects planned over the summer shutdown which will be longer than usual this year. We plan to resume user operations in late November or the beginning of December 2010. X-ray/VUV Beam time requests for this scheduling cycle will be due in September 2010.

For more information on proposal submittal see:

See the SPEAR3 operating schedule at:

9.   Traffic and Vehicular Safety at SLAC       

Getting safely from point A to point B around the SLAC site via car, bike, cart or foot takes year-round vigilance, but with construction along the Loop Road continuing into the spring, now is an especially good time for added focus on safely navigating SLAC's busy roadways. SLAC launched the current focus on traffic and vehicular safety in January with an article in the SLAC Today ( Additionally, a series of video clips targeting particular areas of concern has been posted.

Traffic in the parking lot and roadways around SSRL's experimental facilities housed in Buildings 120, 130 and 131 can be particularly busy with passenger vehicles, government vehicles, delivery trucks and pedestrians converging from multiple directions. The speed limit in these areas is 10 mph. Please observe it!


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 26 February 2010
Content Owner: L. Dunn
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