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SSRL Headlines Vol. 10, No. 9  March, 2010


Contents of this Issue:

  1. Science Highlight — Researchers Directly Observe Oxygen Signature from the Oxygen-evolving Complex of Photosynthesis
  2. Science Highlight — Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketides
  3. Researchers Rediscover the Structure of Water
  4. SSRL Scientific Advisory Committee Convened in March
  5. Joachim Stöhr to Deliver the 2010 Robert Hofstadter Memorial Lectures April 12-13
  6. The 5th Annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences: Theory and Application
  7. The 37th International Conference on Vacuum Ultraviolet and X-ray Physics (VUVX2010)
  8. Workshop Wrap-up on Exploring X-ray Effects on Biological Samples
  9. User Research Administration Update
  10. LCLS Proposal Deadline Extended to June 1

1.  Science Highlight — Researchers Directly Observe Oxygen Signature from the Oxygen-evolving Complex of Photosynthesis
       (contacts: J. Yano,; V. Yachandra,; U. Bergmann,

emission spectrometer
Schematic drawing of the setup for x-ray emission spectroscopy (right) and the 14-crystal analyzer (left).
The advent of photosynthesis gave life forms a new way to capture energy from the sun. The by-product of the success of photosynthesis, an abundance of dioxygen (O2) in our atmosphere allowed aerobic creatures, including humans, to evolve and prosper. This process transformed the history of life on Earth. The oxidation of water to O2 is catalyzed by the oxygen-evolving complex (Mn4OxCa cluster) in the membrane protein, photosystem II (PSII).

A team led by scientists from SLAC and Lawrence Berkeley National Laboratory used SSRL Beam Line 6-2 to directly observe the oxygen x-ray emission signal from the oxygen-evolving complex in PSII. They subjected concentrated spinach samples to x-ray emission spectroscopy (XES), and differentiated the signal of the few oxygen atoms bound to manganese in the oxygen-evolving complex versus the multitude of oxygen atoms in the surrounding protein. They observed changes to the bound-oxygen spectral signature depending on the type of binding using a series of model compounds.

In follow-up experiments, the researchers are trying to follow the water-splitting reaction using the x-ray emission of oxygen in the catalytic active site of PSII. This research was published in the January 18 issue of Angewandte Chemie.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketides
       (contact: S.-C. Tsai,

highlight figure
The PT dimer crystal structure.
UC Irvine researchers have unveiled the mystery behind one of the deadliest toxins that causes liver cancer. Aflatoxins are common contaminants of foods such as nuts and grains, which make up the staple diets of many developing countries. These toxins are produced by moldy fungi during food production, and are considered by the FDA to be an unavoidable food contaminant. Aflatoxin molecules are characterized by the presence of multiple aromatic rings. Chronic ingestion of aflatoxin B1 leads to liver tumors that are a major cause of death in Asia, Africa, and Central America. This toxin wreaks havoc of p53, an important gene in our body that prevents cancer. Without the protective effect of p53, then, aflatoxin further compromises immunity, interferes with our body metabolism, and causes severe malnutrition. It is urgently important to find inexpensive strategies that help protect the world population from aflatoxin food contamination.

A group led by researcher Sheryl Tsai of the University of California at Irvine, in collaboration with the Townsend lab of The Johns Hopkins University, used SSRL Beam Line 9-2 to solve two crystal structures of the "product template" (PT) domain that is crucial for aflatoxin formation in the molds. One structure shows a linear substrate analog bound in the active site, while the other shows an intermediate analog. When analyzed in light of the biochemical data, these aflatoxin-PT structures revealed, for the first time, how PT folds an incoming linear carbon chain called a polyketide to form two aflatoxin rings in an amazing feat of origami.

The researchers proposed that understanding how aflatoxin is made will lead to an understanding of how to prevent it and drastically reduce terminal illness in developing countries. The aflatoxin mechanism can also be applied to other moldy toxins. This research is published in the October 22, 2009 issue of Nature.

To learn more about this research see the full scientific highlight

3.   Researchers Rediscover the Structure of Water
       DOE Pulse

article image
A team of researchers at the Stanford Synchrotron Radiation Lightsource has found the molecular structure of water to be more complex than recently thought, suggesting that molecular models that went out of fashion decades ago may be in fact more accurate than recent ones.

By recording how SSRL's x-ray beam scattered off a flowing jet of water, lead author Ling Fu, a postdoc at the Centre National de la Recherche Scientifique in France, and SLAC colleagues Arthur Bienenstock and Sean Brennan were able to determine the distances between the water molecules in the jet. As recent models predicted, they saw molecules 0.28 and 0.45 nanometers apart. These measurements confirm the current commonly accepted model, which describes liquid water as a group of water molecules held together in tetrahedral shapes, with the molecule at the center of the tetrahedron separated from four others at the shorter distance and each of these four molecules separated from one another at the longer distance.

Yet the researchers saw some molecules at a third distance as well: 0.34 nanometers. The existence of this third separation length, though not included in the current model, was first seen in 1938. Additional experiments in the 1960s and 1970s first confirmed, but later rejected, that this length exists, concluding that its detection was due to shortcomings in the analysis. As a result, models including this intermediate distance fell out of favor—until now. Read more at:

4.   SSRL Scientific Advisory Committee Convened in March
       (contacts: P. Pianetta,; B. Hedman,

The SSRL Scientific Advisory Committee met March 29-30 to review and advise management on current and proposed programs at SSRL. The meeting began with a talk by SSRL Acting Director Piero Pianetta on operations and strategic planning. His overall facility update was followed by an overview of SSRL's Structural Molecular Biology program by Britt Hedman. Kelly Gaffney, Mike Toney, Tom Rabedeau, Aaron Lindenberg and Donghui Lu followed with in-depth talks on current and future developments in specific areas.

5.   Joachim Stöhr to deliver the 2010 Robert Hofstadter Memorial Lectures April 12-13
       Stanford Report

article image
Jo Stöhr
Joachim Stöhr, director of the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, will deliver the Department of Physics' 2010 Robert Hofstadter Memorial Lectures on April 12 and 13.

The lectures were established in memory of Nobel Prize-winning physicist Robert Hofstadter, who served on the physics faculty from 1950 until his death in 1990. Both talks are free and open to the public.

Stöhr joined Stanford and SLAC in January 2000 as a professor of Photon Science after spending nearly 15 years at the IBM Almaden Research Center. He was the director of the Stanford Synchrotron Radiation Lightsource at SLAC before becoming director of LCLS, which is the world's first x-ray laser. Read more about lecture schedule and topics at:

6.   The 5th Annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences: Theory and Application
       (organizers: M. Toney,; A. Mehta,; J. Bargar,

Registration is now open for the 5th Annual SSRL SRXAS School to be hosted by SSRL at SLAC June 1-3, 2010. This school will provide a practical users' guide to planning and conducting scattering measurements at SSRL beam lines. The school will cover important techniques, including surface and thin-film scattering, powder diffraction, in-situ x-ray scattering, and amorphous materials. It will cover topics that are not commonly addressed in text books or class lectures, but are typically obtained only through on-the-experiment training. Modern synchrotron-based x-ray scattering techniques offer the ability to probe nano- and atomic-scale structures and order/disorder relationships that critically govern the properties of advanced technological and environmental materials. Good planning and a working knowledge of beam lines, in addition to techniques, are keys to conducting successful SR-XRS measurements. The goal of the school is to provide this knowledge.

Register at:

See 2009 Meeting Report at:

7.   The 37th International Conference on Vacuum Ultraviolet and X-ray Physics (VUVX2010)       

VUVX2010 will take place at the University of British Columbia, Vancouver, BC, Canada from 11-16 July 2010. The abstract deadline is 16 April 2010 and early registration closes 14 May 2010.

This meeting will bring together scientists from countries all over the world developing new synchrotron, laser, or plasma-based sources of electromagnetic radiation in the vacuum ultraviolet (VUV), soft x-ray and hard x-ray regions, and exploring novel applications of these sources. First results from the new Linear Coherent Light Source (LCLS, Stanford) will be highlighted, along with results from the Canadian Light Source (CLS), Canada's third generation synchrotron. There will be an exciting program with outstanding plenary and invited speakers in 3rd and 4th generation synchrotron science (e.g. Alessandra Lanzara, John Rehr, Henry Chapman) and also in higher harmonic generation and attosecond laser science (Ferenc Krausz, Majed Chergui, Akiyoshi Hishikawa). In addition Paul Corkum will give a general interest lecture to the conference and the general public ("Catching Electrons with Light"). A special awards session will feature presentations from the winners of the newly inaugurated VUVX mid-career and student awards. PhD students may be interested in competing for the VUVX student award, which provides free registration, $1000 toward expenses, and a 20-minute podium talk. To be considered for the student award, the students MUST submit an extended abstract and other information to the awards chair, Chuck Fadley before April 16. Further details are available on the student prize page of the VUVX2010 web site.

There will also be a workshop (July 10-11): Quantitative Analysis of X-ray Absorption Spectra, and two satellite meetings New Science with Resonant Elastic and Inelastic X-ray Scattering at the University of Saskatchewan, Saskatoon, SK, Canada (July 8-9), chair: Alex Moewes and Ultrafast VUV and X-ray science at SLAC, Stanford, CA, USA (July 19-20), chair: John Bozek. For further information please see the conference web site at:

8.   Workshop Wrap-up on Exploring X-ray Effects on Biological Samples
       SLAC Today Article by Shawne Workman

Attendees of the Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples. (Photo by Natalie Cramar.)
More than 50 scientists from around the world came to SLAC for the Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, hosted by the Stanford Synchrotron Radiation Lightsource's Structural Molecular Biology group, or SMB. The March 11-13 workshop focused on sample damage during x-ray crystallography and similar techniques used to explore the structure of proteins and other biological molecules.

Proteins serve as the tiny gears-and also transport tubes, conveyor belts and more-that keep living cells ticking. This tiny machinery is too small to see with visible light, so researchers rely on the short wavelength of x-rays to catch a glimpse of protein shapes and, from that, their likely functions. As the x-rays ripple by, the sample molecules disturb, or diffract them, creating a pattern that reveals the molecules' shape. But it takes a bright beam to create a clear diffraction pattern. The exposure can damage samples and introduce noise into already subtle data.

"Radiation damage is really a serious problem when you use very intense x-ray beams on small and weakly diffracting samples, like protein crystals," said SLAC researcher Ana Gonzalez. Read more at:

9.   User Research Administration
       (contacts: C. Knotts,; L. Dunn,

Beam Time Requests for the June to July 26 macromolecular crystallography scheduling period are due April 20. Submit requests via the user portal at:

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. We plan to resume user operations in late November or the beginning of December 2010.

10.   LCLS Proposal Deadline Extended to June 1
       (contact: C. Knotts,

In this next call for proposals, the world's research community is invited to submit scientific proposals for experiments to be carried out ~March-June 2011. During this period, the AMO, SXR, XPP and CXI instruments will be operational. We have demonstrated FEL operations over the energy range 540 eV to 10 keV, and we expect to be able to offer an energy down to 520 eV with the LCLS fundamental for the Spring 2011 run. Typically, the LCLS delivers about 2 mJ per pulse in the fundamental. Further, LCLS will deliver photons up to 20 keV from a second harmonic afterburner but reduced by roughly an order of magnitude in photon number. The pulse length can be tuned from 70-300 fs. Additionally, shorter pulses (10-40 fs) with reduced pulse energy are also available. The maximum repetition rate of the x-ray flashes is expected to be 120 Hz. For more information, see:


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: 31 March 2010
Content Owner: L. Dunn
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