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Vol. 13, No. 6 - December 2012
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From Director


We've reached the end of another exciting year at SSRL and are getting ready for the winter break. The 2012 run was quite successful with an average uptime of 96.8% in spite of a site-wide power outage in April. We delivered 5,162 hours which was almost 400 hours more than the previous year enabling 1,597 users to conduct experiments. In the past year, we raised the SPEAR3 current to our new standard of 450 mA and finished insulating the accelerator tunnel which will provide for even more stable photon beams. I would like to offer my thanks to the outstanding SSRL staff for their hard work in continuing to keep SSRL at the forefront, and our users for performing such excellent science using our very diverse beam line facilities. Thanks also goes to our funding agencies for their support in enabling SSRL to serve the science community.

As we look forward to 2013, we will be laying the foundations for more exciting developments. For example, we have shown during accelerator studies that the emittance of SPEAR3 can be lowered 6 nm-rad which is 50% lower than our current operating point and a factor of 3 better than the original design value. Although this is still in the R&D stage, we are confident that the hardware improvements we have planned will bring this operating mode into reality. In addition to several new beam line projects, SSRL staff have been collaborating with users to create new programs in energy materials, catalysis and collaborations with LCLS on nanocrystallography.

Best wishes for a wonderful holiday filled with joy, peace and prosperity in the New Year.

Science Highlights

Enzyme Created in Test Tube Promises Biocatalysts for a Range of UsesBurckhard Seelig (University of Minnesota) and Ritimukta Sarangi (SSRL)

In recent years, enzymes have gained an important role in industry as cheap and environmentally friendly alternatives to traditional chemical catalysts. Learning to create such enzymes from scratch is necessary in order to provide biocatalysts for the wealth of non-natural reaction chemistries and substrates that have emerged over the last century.

Until now this has been achieved only when extensive knowledge of the mechanism of the reaction is available. Recently, however, researchers have used a clever in vitro strategy to synthesize an artificial RNA ligase enzyme capable of a previously unknown catalytic activity, and to do so they began with a protein not associated with catalysis. A team of scientists led by Burckhard Seelig of the University of Minnesota have now determined the unique structure of this novel biocatalyst using NMR and synchrotron-based Zn K-edge EXAFS at SSRL's Beam Line 9-3. As this new structure has not been subjected to the billions of years of natural evolution that shaped contemporary enzymes it can therefore be considered an early or primordial catalytic fold. In effect, the simplified environment of in vitro evolution allows the generation of model systems and the study of basic principles of complex natural evolution.  Read more...

Competing Phases Found in High-Temperature SuperconductorContacts: Inna Vishik and Z. X. Shen (Stanford University)

Although the behavior of conventional superconductors has been explained via the BCS theory, the mechanism of superconductivity in the cuprate high temperature superconductors remains unresolved. One approach to this problem is to explore the phases next to superconductivity on the temperature-doping phase diagram. The pseudogap phase above Tc has been a particular stumbling block because it is not a Fermi liquid as with conventional superconductors.

There has been increasing evidence that the pseudogap phase is distinct from superconductivity and persists below Tc, and not simply  a precursor to superconductivity.  In a study recently published in PNAS, researchers at SSRL Beam Line 5-4 and Stanford explored the full doping, temperature, and momentum dependence of spectral gaps in the superconducting state of Bi2Sr2CaCu2O8+δ (Bi-2212) with unprecedented precision and completeness. Read more...


Experiment Finds Ulcer Bug's Achilles' Heel: X-rays Pinpoint Drug Target for Bacteria that Affect Hundreds of Millions Worldwide
Excerpted from December 10, 2012 SLAC Press Release

Experiments at SLAC have revealed a potential new way to attack common stomach bacteria that cause ulcers and significantly increase the odds of developing stomach cancer.

The breakthrough, made using powerful x-rays from SSRL, was the culmination of five years Helicobacter pylori, which is so tough it can live in strong stomach acid. At least half the world's population carries H. pylori and hundreds of millions suffer health problems as a result; current treatments require a complicated regimen of stomach-acid inhibitors and antibiotics.

"We were looking for a means to disrupt H. pylori's own mechanism for protecting itself against stomach acid," said Hartmut "Hudel" Luecke, a researcher at the University of California, Irvine, and principal investigator on the paper, published online December 9 in Nature. With this study, he said, "We have deciphered the three-dimensional molecular structure of a very promising drug target."   Read more ...

Stanford Researchers Find Clues to the Baltic Crusades in Animal Bones, Horses and the Extinct Aurochs
December 6, 2012 Stanford Report article by Melissa Pandika

Stanford researchers have discovered that pagan villages plundered by medieval knights during the little-known Baltic Crusades had some problems in common with the modern-day global village.

Among them: deforestation, asymmetric warfare and species extinction.

According to a research paper published in Science, a project investigating the Baltic Crusades' profound environmental legacy could yield valuable insight into colonialism, cultural changes and ecological exploitation – relevant issues not only throughout history, but especially in today's increasingly globalized society.

The researchers, including professors at Stanford and in Europe, are drawing from disciplines as disparate as history and chemistry to analyze their findings, which they've already begun synthesizing into a database of unprecedented depth and scope. Read more...


Biological Small Angle X-ray Scattering Workshop – March 18-20, 2013 

The SSRL Structural Molecular Biology group will be hosting a comprehensive three-day workshop on the application and use of small angle x-ray scattering techniques in structural biology research. This workshop will include lectures on theoretical and experimental aspects of biological small angle scattering, hands-on experimental tutorials at the BioSAXS Beam Line 4-2, as well as software tutorial sessions on data analysis and modeling.  The workshop is planned for Monday-Wednesday, March 18-20, 2013. Additional information will be forthcoming on SSRL's website.


  • Holiday Site Closure – SLAC National Accelerator Laboratory and SSRL will close for a two-week holiday break starting at the end of the day on Friday, December 21, 2012. Although some pre-approved work will be underway during the shutdown, SSRL facility and buildings will not be available to users during the holiday closure. The Stanford Guest House will close at noon on Friday, December 21, 2012, and will re-open on Monday, January 7, 2013.

  • Macromolecular Crystallography Beam Time Requests due January 22 – Requests for beam time on macromolecular crystallography beam lines during March through May 2013 are due January 22, 2013. Please submit requests through our User Portal.


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 for the U.S. Department of Energy Office of Basic Energy Sciences by Stanford University. Additional support for the SSRL Structural Molecular Biology Program is provided by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences and the National Center for Research Resources. Additional information about SSRL and its operation and schedules is available from the SSRL web site.

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Questions? Comments? Contact Lisa Dunn