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Vol. 13, No. 7 - January 2013
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From Director


We have begun the new year with a flurry of activities, and it promises to be a busy few months. The run started on schedule after the well-deserved holiday break for the staff, and the science activities began immediately as SPEAR3 was ramped to 450 mA current and the beam lines rapidly opened up. We were pleased with the announcement of the Stanford-DOE Management and Operations Contract extension, ensuring a seamless continuation of SSRL's user program. Last week the SSRL Scientific Advisory Committee met (as it does twice a year) and we presented our progress in science, beam lines and accelerator performance as well as our future plans, all of which was well received. We are now moving vigorously to prepare for an operations review that the Department of Energy, Basic Energy Sciences is performing for all user facilities this year. Our turn arrives in April -this is a very important review for SSRL - and we intend to do well! On a different note - we welcome Soichi Wakatsuki back to SSRL and SLAC and look forward to working with him on future program developments.

Science Highlights

Structural Basis for Iron Piracy by Pathogenic NeisseriaContact: Susan Buchanan, NIDDK, NIH

Of the 11 species of Neisseria bacteria that colonize humans, 9 of them coexist peacefully with us. However, two can cause serious diseases N. gonorrhoeae, responsible for the sexually transmitted disease gonorrhea, and N. meningitidis, which causes septicemia and meningitis.  Commercially available vaccines exist for four of the five known disease-causing serogroups of N. meningitidis (A, B, C, Y, W135) but no vaccine exists to combat serogroup B (menB); nor is there a vaccine available against N. gonorrhoeae. One target for vaccine development against menB and N. gonorrhoeae is the iron transporters found on the pathogens’ surfaces.  Cut off their access to iron and these pathogens cannot survive. Read more...

The Lassa Virus Nucleoprotein Appears to Exhibit Conformational Control of Genome BindingContacts: Kathryn Hastie and Erica Ollmann Saphire, The Scripps Research Institute

Lassa virus is endemic in Western Africa, and is the most common cause of viral hemorrhagic fever, infecting an estimated 300,000-500,000 people annually. It is also the hemorrhagic fever most frequently transported out of Africa to the United States and Europe. Understanding the key proteins of Lassa virus and any Achilles’ Heels written into their protein structures will enable development of therapeutics for medical defense. Recent analysis of the crystal structure of the virus’ RNA binding domain done at SSRL may have revealed one promising area of vulnerability.

This study revealed significant differences in the replication process of Lassa virus as compared to other negative-strand viruses as Ebola and measles, which also encode some or all of their genes in the negative direction. Read more...

News around the Site

Soichi Wakatsuki Joins the SLAC Photon Science Faculty
January 22, 2013 SLAC Today Article by Glennda Chui

One of SLAC's newest faculty members, Soichi Wakatsuki, says it was not any one thing that drew him here to help build and lead the lab's biosciences program. Rather it was many things: SLAC's cutting-edge X-ray facilities, the LCLS and SSRL; the future potential for developing the world's most powerful synchrotron, PEP-X, on site; and the prospect of forging strong collaborations with researchers at Stanford University, where Soichi holds a joint appointment at the School of Medicine.

"This combination of things, nobody else can match," he said last week. "I'm really enjoying it."

Soichi arrived on campus in early January from the High Energy Accelerator Research Organization (KEK) in Japan, where he directed the Photon Factory, an x-ray science facility similar to SLAC's SSRL. He is a professor of Photon Science at SLAC and of Structural Biology in the Stanford School of Medicine. Read more ...

Ludo Frevel Crystallography Scholarship Awarded to SSRL User Yezhou Shi

The Ludo Frevel Crystallography Scholarship is awarded annually by the International Center for Diffraction Data (ICDD) to graduate students who perform crystallography-oriented research. In the scholarship award, Yezhou proposed to study the surface of catalytically active oxide materials using synchrotron radiation surface x-ray diffraction in an experimental environment that is realistic for catalysis. These surfaces are important for solid-oxide fuel cells (SOFCs). The project is built upon the close collaboration between SLAC and Stanford and capitalizes on the expertise by both the x-ray scattering community and the materials science community. With the awarded scholarship, Yezhou will travel to more conferences and present the results from his thesis work. See also SLAC Today article.

Stanford University and the DOE Sign Extension of SLAC Operating Contract
Excerpted from January 29, 2013 SLAC Today Article

Stanford University and the U.S. Department of Energy (DOE) have signed a five-year contract to extend the University’s management and operation of SLAC National Accelerator Laboratory through September 2017.

The contract defines Stanford University's responsibilities on behalf of the DOE in the day-to-day operations of SLAC, which is one of 10 DOE Office of Science laboratories.

“The contract extension recognizes the outstanding work Stanford University has accomplished at SLAC,” said Paul Golan, SLAC's DOE Site Office manager, “and it provides a platform for Stanford to continue to innovate and tackle difficult scientific challenges that face our nation.”

William Madia, Stanford's vice president for SLAC, said, "Stanford is very pleased to continue our long collaboration with DOE with regard to the management of SLAC. The laboratory just celebrated 50 years of tremendous scientific accomplishments last year, and its future looks just as bright." Read more ...


Jo Stohr Stepping Down as LCLS Director

Jo Stohr, Associate Lab Director for the LCLS, and previously for SSRL, announced that he plans to step down from his position at the end of April to return to research, writing and mentoring the next generation of scientists who will take SLAC into the future. See his announcement.


  • 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. Registration will be open soon at the workshop website.

  • SSRL/LCLS Annual Users' Meeting & Workshops – October 2-4, 2013

    Meeting co-organizers Colleen Hansel (Woods Hole Oceanographic Institution), Christian Bressler (European XFEL), Jun-Sik Lee (SSRL) and Hae Ja Lee (LCLS), together with Cathy Knotts, will begin planning for our Annual Meeting soon. Your ideas for speakers, research and development to focus on and workshop topics are welcome. Please contact Cathy Knotts and/or the other co-organizers. Contact information can be found at the SSRL and LCLS UOEC websites.

SSRL-Related Science in the News

Prehistoric Ghosts Revealing New Details: Synchrotron Helps Identify Previously Unseen Anatomy Preserved in Fossils

Researchers from the Palaeontology Research Group at University of Manchester used Synchrotron Rapid Screening X-ray Fluorescence at SSRL to map the chemical make-up of a rare fossil lizard skin. Read More ...

Scientists Use SSRL to Study High-density Water on Crystal Surface at Supercool Temperatures

A research team has observed an unexpectedly dense form of water at supercool temperatures in experiments conducted, in part, at SSRL’s Beam Line 13-2.  Read more ...


  • X-ray/VUV Beam Time Requests due February 15 – Requests for beam time on X-ray/VUV lines May-August 2013 are due February 15, 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