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Vol. 13, No. 3 - September 2012
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From Director Chi-Chang Kao

As SSRL Director - I extend my invitation for you to attend our SSRL/LCLS joint Annual Users’ Meeting in the first week of October.  This annual event is the highlight of the year, and a valuable opportunity to hear from the Office of Science about their plans for the lightsources, for us to disseminate and our user community to learn about the latest plans, new developments and exciting research at SSRL and LCLS.  It is also a great time to interact with other scientists, potential colleagues, and vendors of light source related products and services.

This year, the meeting officially begins on October 4, but there are several events before and after that provide a full week of science - consisting of workshops, a conference and a symposium, as described later in this Newsletter.

We will also honor awardees for their outstanding science and roles in the community - and enjoy a poster blitz that will showcase our role in enabling young scientists to emerge.  We look forward to your participation.

While the Users’ Meeting takes place, we continue to move forward on our shutdown work with installations of new hardware, upgrades and a range of projects.  For the SPEAR3 accelerator, most of the ring exposed to the sun has now been covered with insulation to prevent temperature gradients across the ring shielding blocks from moving the tunnel floor and thus the beam by 10s of microns per day.  Last year a short section around BL7 and BL10 was insulated and we saw an order of magnitude reduction in vertical floor motion.  We expect a similar improvement around the rest of the ring as a result of the continuation of this work.  We are also focusing on continued efforts to further improve reliability and to study ways to reduce the beam emittance during the shutdown period.  Scheduling for the first run period in FY13 is underway and we look forward to resuming the buzzing user activity on the SSRL experimental floor soon. 


Science Highlights

The Elements of Stroke  Contacts: Sam Webb (SSRL) and Helen Nichol (University of Saskatchewan)

Correlation between XRF iron maps and MR imaging.
Ischemic lesions are outlined.

Rapid diagnosis and treatment is essential to limiting stroke damage.  Yet, despite decades of research into the causes and effects of this devastating disease, stroke is still the fourth leading cause of death in the United States and drains the national economy of more than 50 billion dollars per year. Now the Synchrotron Medical Imaging Team, a group of Canadian, US, and European scientists (including scientists from the Stanford Synchrotron Radiation Lightsource) are using SSRL’s x-ray facilities as well as the Canadian Light Source to answer key questions that affect the health and recovery of stroke patients.

There are actually two major categories of stroke: hemorrhagic, caused by a broken artery or vein leaking blood into the brain tissue, and ischemic, in which a blockage in a blood vessel starves part of the brain of oxygen. Clinical imaging of the brain is an important tool in diagnosing both types of stroke and following changes in the damaged area over time. For example, the collaborators used SSRL’s x-ray fluorescence (XRF) rapid scanning Beam Line 10-2 in parallel with magnetic resonance imaging (MRI) at Wayne State University to map and quantify iron and calcium on the same slices of human brain, thus confirming which MR sequences could best distinguish the excess iron associated with small hemorrhages  Read more

Structural Basis of Wnt Recognition by Frizzled Contacts: Claudia Janda and Christopher Garcia (Stanford University)

XWnt8 has an unusual two-domain structure.

Wnts are a family of signaling proteins that regulate the development and growth of an organism, as well as tissue regeneration and wound healing. Misregulated Wnt signaling is associated with the development of many types of cancers, including colon cancer, breast cancer and melanoma, and degenerative diseases like multiple sclerosis, Alzheimer's and Type 2 diabetes. Understanding of how Wnt proteins bind and activate Frizzled receptors is important for the development of effective anti-Wnt and anti-Frizzled drugs for the treatment of Wnt-related disease.

To understand how Wnts function, a team of researchers from Stanford University led by Prof. Christopher Garcia set out to determine the first 3D image of an isolated Wnt-Frizzled complex using macromolecular crystallography. However, Wnt proteins present a number of challenges due to lipid modifications and very poor expression. The biochemical studies showed that the cysteine-rich domain (CRD) of Frizzled, the primary Wnt binding domain, is able to solubilize Wnts in aqueous solution. They were able to grow crystals of Xenopus Wnt8 (XWnt8) bound to Frizzled 8-CRD and to determine the 3D structure of this complex using SSRL’s Beam Line 11-1. Read more

Closing in on a Means to Inhibit FDTS Enzymes Contacts: Irimpan Mathews (SSRL) and Amnon Kohen (University of Iowa)

The Active site view of the FDTS enzyme in complex
with FAD, dUMP and folate derivatives. Flavin-dependant thymidylate synthases (FDTSs) are a recently identified family of thymidylate synthases that employ a novel mechanism for the thymidylate synthase reaction.  These enzymes convert 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymine-5'-monophosphate (dTMP), a reaction crucial for the survival of the organism. Since FDTS enzymes are mainly found in very pathogenic microbes, including the pathogens causing leprosy, botulism, diarrhea, anthrax, pneumonia, syphilis, and more, the FDTS enzyme is an attractive target for antibiotic drugs, but until recently researchers had not been able to successfully characterize any crystal structures with folates, due to difficulties in crystallizing a complex containing methylenetetrahydrofolate. This limited understanding of the molecular mechanism and the scope of drug design for these enzymes.

A team of researchers from SSRL and the University of Iowa used SSRL's Beam Lines 9-2 and 12-2 to uncover the folate binding site in FDTS. Read more ..

See related article in SLAC Today



Tim MillerSIMES/PULSE Researcher to be Honored for Advancing Ultrafast X-ray Experimental Capabilities

Tim Miller, a graduate-student member of the SIMES and Stanford PULSE institutes, joint SLAC-Stanford programs, will receive the 2012 Melvin P. Klein Scientific Development Award for his leadership and ingenuity in establishing a new type of experimental capability that enables ultrafast x-ray experiments at SSRL.

Instead of taking a static snapshot of a sample using SSRL's x-rays, these “pump-probe” studies involve hitting the material first with a pump pulse – typically a laser – to cause a change in the material, such as a rearrangement of the atoms. Then the x-rays probe the material to see how it reacts over time, which gives the technique its other name: time resolution study.

With this technique, scientists can see the movements of atoms in materials and the forming and breaking of chemical bonds. Read More … 

James CryanJames Cryan to Receive 2012 Spicer Young-Investigator Award

James Cryan will receive the 2012 William E. and Diane M. Spicer Young Investigator Award for his innovative contributions to the development and execution of the first “pump-probe” experiments at LCLS.

Cryan was a Stanford physics department graduate student working in the Stanford PULSE Institute under the direction of Prof. Phil Bucksbaum when he played a central role in experiments that demonstrated the power of using two synchronized laser pulses to create and analyze fleeting atomic and molecular phenomena.

In those experiments, Cryan worked with Ryan Coffee of LCLS, fellow graduate student James Glownia and colleagues to use pulses of polarized infrared laser light to align rotating molecules of nitrogen gas. At the instant the molecules were perfectly aligned, the researchers hit the molecules with an intense pulse of x-rays from LCLS and recorded the trajectories of energetic electrons emitted during this process. Read more

SSRL Users’ Organization Update

Vote for SSRL Users' Organization Executive Committee Membership
Having a full and engaged Users' Organization committee is essential, particularly during times of growth and change. Please take a few minutes to cast your ballots between now and October 3 to fill open positions on the Stanford Synchrotron Radiation Lightsource Users' Organization Executive Committee. The results will be announced during the Users' Meeting on October 4.  VOTE

Participate in User Science Outreach and Advocacy Workshop, October 5

If average American citizens know little of the benefits they have derived from science–apart from medicine–it is the fault of the science community for not expending more effort to provide the narrative. That must change
—Mike Lubell, APS

Join UEC members to discuss ideas to increase engagement and mobilization of the scientific communities, including new forms of social media and networking, to promote the importance of science as well as the capabilities and science made possible by national user facilities in the session, Mobilizing the User Community for Outreach.

Learn how to translate your science for the public in the session that offers practical tips, training, and practice for scientists to communicate their science to the general public. Learn how to hone skills, develop ‘elevator talks’ and deliver key messages about your research as well as science in general and why it is important.  Register


  • Demystifying the Lightsource Experience, October 3
    Attend this workshop to expand your research 'toolkit'. Learn more about capabilities and techniques available at SSRL to the broad scientific community: Extended X-ray Absorption Spectroscopy Fine Structure (EXAFS), Near-Edge X-ray Absorption Spectroscopy (NEXAFS), nano-scale x-ray imaging with elemental/chemical sensitivity, x-ray scattering and small angle scattering. Learn more and register

  • Science with High Energy X-rays, October 3
    Explore the science case for high energy x-rays at SSRL and participate in discussions. Should SSRL build a high energy beam line? If yes, why? and what desired energy range (20-50 keV or 50-100 keV). Learn more and register

  • Opportunities for Nanoscale Spectromicroscopy, October 3
    The ability to obtain element specific spectroscopic information from nano-sized objects using high resolution x-ray microscopes has become one of the most popular applications of synchrotron facilities. Modern x-ray microscopes and x-ray beam lines provide the stability and reproducibility that is required to detect small changes in elemental distribution or electronic structure. This allows researchers from a wide variety of fields to understand chemical and electronic processes that occur e.g. in real battery, catalytic, electronic or magnetic devices. SSRL currently hosts two microscopes that are able to address such phenomena, the hard x-ray transmission microscope at Beam Line 6-2 and the soft x-ray scanning transmission microscope at Beam Line 13-1. The goal of this workshop is to give current users of these facilities an opportunity to present their research, propose future experiments, and to discuss the current status and capabilities of the facility to determine the needs for future development. Learn more and register

  • Mesoscale Science Workshop, October 5-6
    In February 2012, the DOE Office of Science charged the Basic Energy Sciences Advisory Committee with preparing a report on mesoscale science. The resulting report entitled “From Quanta to the Continuum: Opportunities for Mesoscale Science” will be released soon.  To engage the user community in this exciting new research direction, a workshop focusing on these opportunities is held October 5-6.  Learn more and register

  • Register for LCLS/SSRL Users' Meeting & Workshops, October 3-6, 2012
    There is still time to register and submit abstracts for poster presentations at the LCLS/SSRL Annual Users' Meeting and Workshops, October 3-6, 2012. It is a very exciting time with new opportunities for photon sciences, new capabilities, and exciting research results. We hope that you will join us for the following:

    Future Opportunities with Mesoscale, Terahertz, and XFEL Science

    • George Crabtree, ANL - Mesoscale Science and Opportunities for X-rays
    • Helmut Dosch, DESY - Future Opportunities with XFELs
    • ZX Shen, SLAC - Frontiers of THz Workshop Summary

     User Science Session Discussions

    • Environmental Science
    • Materials Sciences
    • Chemical and Biological Catalysis
    • Atomic, Molecular & Optical Physics/Matter in Extreme Conditions

     Workshops (as described above)

    • Demystifying the Lightsource Experience (Introduction to SR & XFEL Techniques)
    • Opportunities for Nanoscale Spectromicroscopy
    • Science with High Energy X-rays
    • Toward Controlled Excitations: Ultrafast Mechanisms of Lattice and Electron Dynamics
    • Mesoscale Science
    • Science Outreach and Advocacy/Translating Your Science for the Public
    • LCLS-II Instrument Workshop

    Light Source Products and Services Exhibits

    Deadlines for early registration and poster abstract submission have been extended to September 26 (late 'walk in registration' after September 26 with late registration fee).  Website

    For more information, contact meeting organizers: Sarah Hayes (U. Alaska), Jan Lüning (UPMC), Bill Schlotter (LCLS), Tsu-Chien Weng (SSRL) or Cathy Knotts (SSRL).

  • Herman Winick Register for Instruments of Discovery - Past and Future of Synchrotron Light Sources. A Symposium to Honor Herman Winick
    This one-day symposium honoring Herman Winick's many contributions to synchrotron source development since the early 1970s will be held on October 2, 2012 at the Quadrus Conference Center across Sand Hill Road from SLAC. The symposium will run 9 am – 5 pm with an open mike at the last session and followed by a dinner. Although there is no fee for the symposium, registration is required. There will be a cost for the dinner and registrants will be given the opportunity to sign up for the dinner. Register for the symposium

  • Register for Pittsburgh Diffraction Conference
    Registration is open for the 70th annual Pittsburgh Diffraction Conference, to take place from September 30 to October 2 at SLAC, immediately prior to the 2012 LCLS/SSRL Users' Meeting and Workshops (October 3-6). Organized by the Pittsburgh Diffraction Society, the three-day event is billed as the "oldest diffraction-related conference in North America.  Read more ...


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