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SSRL Headlines Vol. 2, No. 10  April, 2002


Contents of This Issue:

  1. Science Highlight - Towards Understanding Anthrax: Structural Basis of Target Recognition by Anthrax Lethal Factor
  2. LCLS Lehman Review
  3. New Opportunities in Ultrafast Science Using X-rays
  4. JCSG 2nd Annual Meeting
  5. Materials Science - Update on the Seminar Series
  6. 2002 Stanford-Berkeley SR Summer School
  7. Beam Line 1-5 is Up and Running Again
  8. SSRL in the News
  9. SLAC Celebrates 40 Years of Research
  10. Positive Contributions by SLAC/SSRL Employees Recognized
  11. Upcoming Events at SSRL and Elsewhere
  12. User Research Administration Announcements

1.  Science Highlight - Towards Understanding Anthrax: Structural Basis of Target Recognition by Anthrax Lethal Factor
    (contact: Thiang Yian Wong, tywong@burnham.org)

The disease Anthrax kills via a deadly toxin produced by the bacterium Bacillus anthracis and secreted directly into the host's bloodstream. The result is septic shock and subsequent death of the infected victim. While antibiotics can be used to kill the bacteria, diagnosis of Anthrax infection often does not take place quickly enough for this to be curative. Once a high level of toxin is reached in the bloodstream, removing the bacteria from the host is not sufficient to prevent fatality. Therefore, the design of anti-toxins offers the prospect of treatment in the advanced stages of infection. A group led by R. Liddington, Burnham Institute, in collaboration with researchers at NIH and Harvard Medical School, are working on studying the structures at atomic resolution of the several components of the Anthrax Toxin and their complexes, which include peptido-mimetics that suggest clues to the design of potential therapeutics. Macromolecular crystallography data measured at SSRL's Beam Lines 7-1 and 9-1, as well as at other synchrotrons, have been key to the advances made so far and are expected to play an important role in the future.

The group recently reported the crystal structure of one of the three proteins of the toxin, the Lethal Factor (LF), both in its native form and in a complex with an amino acid residue representing part of its natural substrate. The three-dimensional structure of LF shows an intricate four-domain arrangement that reveals clues of the protein's evolutionary process. The structure of LF is also the first known example of a protease complexed to its uncleaved naturally occurring substrate and essentially provides an atomic-level snapshot of molecular recognition. A noteworthy feature illustrated in one of the complex structures of LF is an extended substrate-binding pocket. Understanding the structural and sequence qualities of this pocket will be key in the creation of effective anti-toxins that inhibit LF activity.

More information regarding this research, including the reference to the recent publication in Nature can be found at:

2.  LCLS Lehman Review
    (contact: John Galayda, galayda@slac.stanford.edu)

On April 23-25, the LCLS Project was reviewed by the DOE Office of Science. The reviewers determined that the LCLS Project is ready to begin project design activities in FY2003.

The review was chaired by Dan Lehman, head of the DOE-SC Construction Management Division. The purpose of the review was to judge the feasibility of the conceptual design and the validity of the cost estimate. Approval of these items by the review committee is a prerequisite for Critical Decision 1, which is in turn a prerequisite for authority to spend the $6M Project Engineering Design funds that the LCLS should receive in October. Members of the LCLS Collaboration from SLAC, Argonne and Livermore made 55 presentations to the committee over the three-day review. The committee was particularly impressed with the Conceptual Design Report, which is now available electronically at the LCLS website: http://www-ssrl.slac.stanford.edu/lcls/CDR/

3.  New Opportunities in Ultrafast Science Using X-rays
    (contact: John Arthur, arthur@ssrl.slac.stanford.edu)

The Workshop on New Opportunities in Ultrafast Science using X-rays was held April 14-17 in Napa, CA. Sponsored by the Advanced Light Source, SSRL, the Swiss Light Source, the DOE Office of Basic Energy Sciences, and BioCARS-NIH, the workshop brought together more than 100 scientists from the ultrafast optical community and the emerging ultrafast x-ray community. Since the development of ultrafast optical laser systems has revolutionized the study of many problems in the biological, chemical, and physical sciences, and since new ultrafast x-ray sources offer the possibility for extending optical studies to include x-ray techniques such as x-ray absorption spectroscopy and x-ray diffraction, the workshop was convened in order to define scientific highlights and directions for the use of the x-ray techniques, to promote cross fertilization of ideas, and to define the source characteristics required for ultrafast x-ray experiments. For this workshop, "ultrafast" described the femtosecond- picosecond time regime.

The workshop was organized around morning and evening lecture sessions, with extended afternoon discussion periods. After preliminary tutorial talks on x-ray methods and new ultrafast x-ray sources, the lectures offered presentations on both x-ray and optical laser techniques for studying structural dynamics, magnetism, chemical dynamics, biological dynamics, and high-energy-density dynamics. The lectures highlighted the different, complementary strengths of optical photons and x-rays as probes, as well as the level of sophistication with which these probes are used today. With expectations that the next few years will see vast improvement in ultrafast x-ray sources, and many more facilities that combine laser and x-ray capability, it is clear that ultrafast science will blossom. (for specifics see workshop program)

4.  JCSG 2nd Annual Meeting
    (contact: Linda Brinen, brinen@slac.stanford.edu)

The Second Annual Meeting of the Joint Center for Structural Genomics (JCSG) was held April 22-23 at SLAC. Members of all three core groups of the consortium, BioInformatics, Crystallomics, and Structure Determination, were in attendance. Representatives from each of the Cores gave overview talks and updates on key developments made over the past year. Invited talks were given by David Stuart (Wellcome Trust Center for Human Genetics, Oxford, UK), Soichi Wakatsuki (KEK Photon Factory, Tsukuba, Japan) and Helen Berman (Protein Data Bank, Rutgers University). Also in attendance were Judith Greenberg, Acting Director of the NIH NIGMS; John Norvell, Director of the NIGMS Protein Structure Initiative; as well as members of the JCSG Science Advisory Board, Carl-Ivar Brändén (Karolinska Institute), Elbert Branscomb (DOE Joint Genome Institute), Stephen Cusack (EMBL, Grenoble) and Erkki Ruoslahti (The Burnham Institute). Attendees were able to witness in person many of the robotic and software developments made at JCSG's Structure Determination Core, centered at SSRL during tours that were given of SSRL's macromolecular crystallography beam lines. Particular focus was given to the automated crystal mounting system that is under development at BL11-1. (see JCSG Home Page)

5.  Materials Science - Update on the Seminar Series
    (contact Jo Stohr, stohr@ssrl.slac.stanford.edu)

Building on the strength of the materials research programs at SSRL and Stanford, SSRL has begun a new seminar series in Chemical and Materials Science to bring together interested people at SSRL and the Stanford campus. The seminars are part of a plan to create an X-Ray Laboratory for Advanced Materials (XLAM) at SSRL that is closely linked to the Geballe Laboratory for Advanced Materials (GLAM) at Stanford University. Artie Bienenstock will take over as Director of GLAM in September, 2002. The first seminars are being given by SSRL and Stanford scientists in order to learn more about each other's research activities. The seminars will be held every second Wednesday at 4 p.m. in the SSRL LOS (Building 137) 3rd floor conference room. Cookies and coffee will be served! During the first round of seminars, the speakers are encouraged to give an overview of their research program addressing the big picture, i.e. motivation for the work, why the work is important, who cares about the work (e.g. specific scientific community, industry, the government, society as a whole) and why x-rays are crucial to solving the problem. Talks will be about envisioned experiments as well as completed ones. We welcome and encourage user participation in this initiative.

6.  2002 Stanford-Berkeley SR Summer School

Building upon last year's successful program (held at Berkeley), this year's joint Stanford-Berkeley Synchrotron Summer School, to be held July 7-13, 2002, will be hosted by Stanford and offers participants a choice between a physical science program and a life science program. Joint lectures, evening discussions, and visits to synchrotron light sources will provide an interdisciplinary and intellectually stimulating training ground for new and experienced researchers alike. Students, postdocs, and independent scientists who have ongoing research projects are encouraged to participate.

The physical sciences course will cover the fundamentals of synchrotron radiation, including the use of spectroscopy and diffraction in physics, chemistry, and materials science. The life sciences course, in addition to introducing the fundamentals of synchrotron radiation, will provide intensive training in x-ray diffraction, data collection, and crystal structure determination. More detailed information and applications for the week-long residential program are available online at http://smb.slac.stanford.edu/SR-School/. The program is limited to approximately 40 students per course, and prospective applicants are encouraged to apply early (by May 10). Applicants will be informed in writing regarding their application status by May 31.

The summer school is sponsored jointly by Stanford University, the University of California, Berkeley, Lawrence Berkeley National Laboratory, and the Stanford Synchrotron Radiation Laboratory, with additional funding support from the U.S. Department of Energy, the National Institutes of Health, and corporate sponsors. David Attwood (attwood@eecs.berkeley.edu) and Anders Nilsson (nilsson@ssrl.slac.stanford.edu) are the directors for the physical science program, and Peter Kuhn (pkuhn@stanford.edu) and John Kuriyan (kuriyan@uclink.berkeley.edu) are the directors for the life science program.

7.  Beam Line 1-5 is Up and Running Again
    (contact: Michael Soltis, soltis@ssrl.slac.stanford.edu)

The Macromolecular Crystallography group announces that the BL1-5 upgrade has recently been completed and that BL1-5 is now fully available to the general user community for MAD and other crystallographic experiments. This bending magnet beam line was one of first beam lines in the world dedicated to macromolecular crystallography, where pioneering MAD experiments were first performed. Recently, the beam line hutch and experimental equipment were completely replaced with the state-of-the-art instrumentation and the instrument control system that is available on the other macromolecular crystallography beam lines (9-1, 9-2, and 11-1). The setup includes the experimental control environment Blu-Ice/DCS and all of the related subcomponents, as well as the fully integrated suite of instrumentation for automated MAD and other crystallographic experiments. The beam line is currently equipped with an ADSC Quantum-4 CCD. The timely availability of this beam line will offset some of the current large overdemand on BL9-2. Under SPEAR2, BL1-5 has a 20-fold lower flux than BL9-2 but offers the same experimental capabilities in the energy range 5.9 - 16 keV. After the optics have been rebuilt for SPEAR3 operations, this bending magnet line will exhibit the same performance as the current BL9-2 (while of course BL9-2 will experience a significant gain).

8.  SSRL in the News

"X-rays to the Rescue", TechTV's The Screensavers: For Technology's Biggest Fans, April 10, 2002. Interview with Pat Frank on the Vasa and other research at SSRL including TXRF and the LCLS.

9.  SLAC Celebrates 40 Years of Research
    (contact: Herman Winick, winick@ssrl.slac.stanford.edu)

In April 1962, a contract was signed between Stanford University and the Atomic Energy Commission, five years to the month after the two-mile linear accelerator project was first formally proposed to the government. That same month, a lease was signed between Stanford University and the Atomic Energy Commission for use of "a parcel of land available for the location of the linear accelerator complex." A decade later in April 1972, the first colliding beams were obtained at SPEAR, and the Stanford Synchrotron Radiation Project officially began the following year. A number of activities will take place this fall to celebrate these significant milestones. More information will be forthcoming as the details become known.

(see article in Cern Courier or SLAC Highlights and Milestones for more information on SLAC's current research and historical achievements)

10.  Positive Contributions by SLAC/SSRL Employees Recognized

Forty-four SLAC employees were recently announced as recipients of the 2002 Employee Recognition Awards. The recipients were selected for their contributions towards maintaining a positive work environment at SLAC in a variety of ways, including consistently going out of their way to help others. Four SSRL staff members were selected for the award including: Daphne Mitchell and Michelle Steger, the first staff users meet upon checking in for beam time at User Research Administration and who spend a lot of behind-the-scenes effort ensuring that user experiments will run smoothly from an administrative standpoint; Ann Trautwein, a designer who is currently working on the SPEAR3 project and played a large role in the Beam Line 10 wiggler repair last year; and Teresa Troxel, group leader for Beam Line Electronics and an individual who enthusiastically promotes activities geared towards making young people aware of the opportunities available to them in a research environment. Honorees will be receive a "globe" award during a ceremony and luncheon with SLAC Director, Jonathan Dorfan, in early May.

11.  Upcoming Events at SSRL and Elsewhere

12.   User Research Administration Announcements
       (contacts: Cathy Knotts, knotts@ssrl.slac.stanford.edu,
                        Lisa Dunn, lisa@ssrl.slac.stanford.edu)

  • All SSRL proposals that will lose beam time during the SPEAR3 shutdown (April 2003-January 2004) have been granted an additional one-year of eligibility. Also due to SPEAR3, new X-ray/VUV proposals will only be accepted once this year; the deadline is May 1, 2002. (see: Proposal Submittal and Scheduling Procedures for Research at SSRL)

  • The parking lot between Buildings 120, 277, 274 and 219 has been reopened and parking within Gate 17 has improved. A parking space has also been designated near the entrance of Building 120 to allow equipment to be quickly and easily dropped off and picked up (this parking spot has a 30-minute maximum). However, as construction activities for the long-awaited user lodging building ramp up, parking and traffic flow outside of Gate 17 will be impacted, primarily during the hours of 7:00 a.m. to 4:00 p.m., Monday through Friday.

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: http://www-ssrl.slac.stanford.edu/

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Last Updated: 29 APR 2002
Content Owner: L. Dunn
Page Editor: L. Dunn