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SSRL Headlines Vol. 4, No. 2  August, 2003


Contents of this Issue:

  1. Science Highlight — Protecting against Cocaine, Heroin, and Sarin Gas
  2. X-ray Absorption Spectroscopy Catches the Chemical Form of Mercury in Fish
  3. Final Phase of SPEAR3 Installation on Schedule
  4. Registration Extended for SSRL SMB Summer School
  5. Call for Nominations for 6th Annual Lytle Award
  6. Nominations for the SSRLUO-EC
  7. Several Workshops Planned for October 8, 2003
  8. 30th Annual SSRL Users' Meeting — October 9-10, 2003

1.  Science Highlight — Protecting against Cocaine, Heroin, and Sarin Gas
      (contact: Matthew Redinbo, University of North Carolina at Chapel Hill)

SSRL has played an important role in characterizing a family of enzymes that detoxify heroin and cocaine, and have the potential to metabolically eliminate the nerve poisons sarin, soman, and tabun, which have claimed thousands of lives. Using x-ray crystallographic data, the Redinbo group at the University of North Carolina at Chapel Hill has uncovered the specific and general ways the carboxylesterase enzymes bind to those dangerous substances. This new understanding of the structure-function relationships will be of very significant value in designing drugs to combat overdoses, terrorist attacks and chemical warfare. Redinbo's group is working on developing more specific and faster versions of the human form of the enzyme (hCE1) to inject into people who have overdosed on heroin and cocaine and into soldiers potentially facing nerve gas attacks.

Carboxylesterases in mammals are responsible for breaking down a wide variety of human-made drugs and foreign chemicals, and may have evolved to safely process the chemicals many plants use to protect themselves. The first crystallographic study of hCE1 bound to cocaine- and heroin-like compounds revealed important molecular details about how the drugs are metabolized and how the enzyme can recognize such structurally diverse compounds. Redinbo's group found that the hCE1 active site contains both a specific compartment (that binds with specific features of a compound, the way Lego pieces fit together), and a promiscuous compartment (that can bind with many shapes, the way gum sticks to many surfaces). These features enable the enzyme to act on structurally distinct chemicals like dangerous narcotics and weaponized nerve agents.

For more information on this work see:
or http://www-ssrl.slac.stanford.edu/research/highlights_archive/hce1.pdf

2.  X-ray Absorption Spectroscopy Catches the Chemical Form of Mercury in Fish - SSRL Scientists Reveal New Findings in Science Article
       (contact: Graham George)

The presence of "methyl mercury" in fish is well-known, but until now the detailed chemical identity of the mercury has remained a mystery. In an x-ray absorption spectroscopy study published in the August 29 issue of Science (Science 301, 2003: 1203; http://sciencenow.sciencemag.org/cgi/content/full/2003/828/3), SSRL scientists report that the chemical form of mercury involves a sulfur atom (most likely in a so-called aliphatic form). The study presents significant new knowledge - because the toxic properties of mercury (or any element) are critically dependent upon its chemical form - and represents an important milestone in developing an understanding of how harmful mercury in fish might actually be. The study was carried out by SSRL staff scientists Ingrid Pickering and Graham George and postdoctoral fellow Hugh Harris using SSRL's structural molecular biology beam line 9-3. The very high flux, excellent beam stability and state-of-the-art detector technology allowed the team to measure samples of fish containing micromolar levels of mercury, much lower than had previously been possible. Funding for this research was provided by the U.S. Department of Energy, Office of Biological and Environmental Research and by the NIH National Center for Research Resources, Biomedical Technology Program. (Ingrid Pickering and Graham George have recently relocated to the University of Saskatchewan and Hugh Harris to the University of Sydney).

3.  Final Phase of the SPEAR3 Installation on Schedule
       (contact: Tom Elioff)

The final installation phase of the SPEAR3 project continues on schedule -- only 2 months remain for planned project completion. The final magnet/vacuum raft assembly was installed on August 27 at 15:30, completing the magnetic lattice for SPEAR3. Due to the hard work of many staff and external contract workers, the 54 raft assemblies (weighing more then 1,250,000 lbs) were successfully rolled into SPEAR and placed onto precision pins over a period of only 13 working days beginning August 11. In addition, the majority of the new power supplies have been tested and installed, the new beam line front-ends are in place (except for BL10), the RF klystron power supply, loads, and waveguides are installed, all 4 new RF cavities have been received and checked-out, the bellows and vacuum straight section components are nearing completion, and injection system components are complete. Remaining work in the coming months includes final low conductivity water (LCW) connections to the magnet rafts, LCW piping and connection to the RF system, AC power connections to power supplies, DC connections to power supplies and to magnet rafts in the tunnel, Klystron installation and check-out, RF cavity installation in the ring and installation and testing of remaining instrumentation and control system components. The work should be complete and the ring closed down by early November at which time accelerator and vacuum commissioning will commence. Those interested can view time lapsed video clips of the SPEAR3 installation process by visiting the SSRL home page at: http://www-ssrl.slac.stanford.edu/ and clicking on the video links. SPEAR3 is indeed on schedule to begin to deliver its significant benefits to users in early 2004.

4.  Registration Extended for SSRL SMB Summer School
       (contacts: Hiro Tsuruta; Serena George; Ana Gonzalez)

The application deadline for the lecture portion only of SSRL's 2003 Structural Molecular Biology Summer School has been extended until September 3. This track 1 of the Summer School, which will be held September 16-17, will include presentations from experts aimed at the graduate student level, but will also be appropriate for more experienced researchers entering the field. Sessions will focus on the use and applications of three synchrotron x-ray techniques in studying biological systems including: small angle x-ray scattering, x-ray absorption spectroscopy, and macromolecular crystallography. For more information visit the website:
http://smb.slac.stanford. edu/SR-School/SMB2003/

5.  Call for Nominations for 6th Annual Lytle Award
       (contact: Cathy Knotts)

Users are encouraged to submit nominations for the 2003 Farrel W. Lytle Award, which consists of a $1,000 award and a plaque that is displayed in the User Research Administration Office at SSRL. This award was established by the SSRL Users' Organization Executive Committee (SSRLUO-EC) to promote technical or scientific accomplishments in synchrotron radiation-based science and to foster collaboration and efficient use of beam time among users and staff at SSRL. Previous awardees include: Farrel W. Lytle, Tom Hostetler, Roger Prince, Britt Hedman, and Paul Phizackerley. Nominations should be sent to Cathy Knotts, SSRL User Research Administration Manager, by September 8, 2003.

6.  Nominations for the SSRLUO-EC
       (contact: Cathy Knotts)

The September 15 deadline for nominating SSRL users for the 2004 Users' Organization Executive Committee is fast approaching. Nominations are needed for vacant positions in materials/chemistry, environmental/geosciences, structural molecular biology, and macromolecular crystallography. Nominations are also needed for a graduate student member of the committee (in any of the disciplines listed). The final voting will be held at SSRL's Annual Users' Meeting. http://www-ssrl.slac.stanford.edu/conferences/ssrl30/ ssrluoec_nominations.html

7.  Several Workshops Planned for October 8, 2003
       (contact: Cathy Knotts)

  • Crystallography Beam Line Automation: Work Smarter Not Harder
    (Aina Cohen, SSRL)

    New technologies for high-throughput crystallography at SSRL, ALS and other synchrotron facilities will be introduced focusing on the benefits and concerns of general users. For more information please see the following website: http://smb.slac.stanford.edu/public/research/automation_workshop
  • Synchrotron Techniques for Environmental Microbiology and Biogeochemistry
    (John Bargar, SSRL; Scott Fendorf, Stanford University; David Shuh, LBNL)
    Environmental microbiology and geomicrobiology have emerged as vibrant scientific fields with cross-cutting research themes emphasizing the interplay and energy flow between microbial communities, inorganic and organic contaminants, (bio)minerals, groundwater, and other solutions. Synchrotron (SR)-based techniques are beginning to play important roles in these research areas because of the utility of SR methods for characterizing metal ion and organic molecule speciation under in-situ conditions in complex environmental materials. The purpose of this meeting is to bring together scientists from the environmental microbiology, biogeochemistry, and synchrotron communities to share ideas. Topics to be discussed include mechanisms of metal binding by bacteria, microbially mediated redox cycling of metals in the environment and their application to bioremediation, biomineral structures, compositions, and formation mechanisms, and competitive sequestration of metals by inorganic sinks (oxide, sulfide surfaces, solids) and bacteria. (Co-sponsored by SSRL, ALS and the DOE (Natural and Accelerated Bioremediation Research (NABIR) Program). For more program information see:
  • Probing Mechanical Deformation and Failure via Synchrotron X-rays
    (Apurva Mehta, SSRL; Nobumichi Tamura, ALS)

    This workshop will involve scientists interested in investigating mechanical properties of materials via synchrotrons. Sessions will focus on salient issues in mechanical deformation and failures, such as crystal plasticity models, fatigue, crack propagation, etc. A brief survey of relevant synchrotron methods including parallel beam geometry for mesodiffraction, microdiffraction, and phase contrast imaging, as well as talks on actual experiments done at synchrotrons will also be included. At the end of the day, we plan to brainstorm future projects and developments.
  • Sub-eV Inelastic X-ray Scattering Facility with SPEAR3
    (Uwe Bergmann, Anders Nilsson, SSRL)

    SSRL is planning to build a dedicated facility for sub-eV inelastic x-ray scattering in the 5-15 keV range at SPEAR3. The techniques will include non-resonant and resonant x-ray Raman scattering, selective x-ray absorption and x-ray emission spectroscopy. In this workshop we will discuss scientific problems that can be addressed at this facility and the resulting beam line and x-ray optics parameters. The topics will include the study of low Z systems under ambient and extreme conditions and the study of 3d transition metal compounds.
  • Recent Advances in Soft- and Hard X-ray Microscopy
    (Greg Denbeaux, ALS; Gary Mitchell, Dow; Katharina Lüning, Piero Pianetta, SSRL)
    In recent years there have been many advances in scanning and full field x-ray imaging techniques such as improved spatial resolution, more stable instruments for spectromicroscopy and time resolved microscopy, phase contrast imaging techniques as well as high resolution tomographic capabilities in absorption and phase contrast. These techniques enable novel nanoscale research in various fields of materials science, environmental science and biology. This workshop, hosted jointly by the ALS and SSRL, is to discuss these new capabilities and to identify the scientific direction for soft- and hard x-ray microscopy at both light sources. Time will be given for open discussion with feedback on possible future directions from workshop attendees. Please see the ALS Users' Meeting website to register for this workshop: http://www-als.lbl.gov/als/usermtg/

8.  30th Annual SSRL Users' Meeting — October 9-10, 2003
       (contact: Cathy Knotts)

If you haven't already done so, register for SSRL's Annual Users' Meeting by September 29 to take advantage of early registration discounts ($75 regular; $25 students). Held on October 9-10, this meeting will focus on a variety of synchrotron-based techniques of interest to the broad scientific community of synchrotron users. Meeting sessions will focus on interdisciplinary applications of small angle x-ray scattering, macromolecular crystallography, microspectroscopy and diffraction, and surface spectroscopy. The Users' Meeting provides a forum for the presentation and discussion of research activities from SSRL and the synchrotron community. New data and developments will be shared through invited talks and poster presentations. Find registration and additional information on the meeting website:

Call for Posters and Graduate Student Poster Competition: Abstracts for the poster session can be submitted through September 22 for inclusion in the program material. Poster presentations will be displayed throughout the Users' Meeting and will be highlighted during a poster session on October 9. Graduate students are encouraged to submit posters of their work and are eligible to compete for poster prizes. Graduate students who wish to participate in this competition must be registered to attend the Users' Meeting, and must indicate that they are participants in the graduate student poster competition on the poster abstract submission form. Prizes include a monetary award and a ribbon. Poster instructions are available on the website:

Special Session to Honor Iran Thomas: In tribute to the late Iran Thomas of the U.S. Department of Energy's Office of Science, a special session at the Users' Meeting has been organized to honor Thomas' interest in education and diversity. Thomas, who passed away on February 28, was a long-time director in the Office of Basic Energy Sciences who supported and enabled the development of new and innovative research programs, including the University of Texas El Paso (UTEP) and SSRL Gateway program. This special session, PERSPECTIVES ON THE UTEP-SSRL GATEWAY PROGRAM, will be held on Thursday, October 9, and will include several presentations from students in the Gateway program.


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 S ciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 29 AUG 2003
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