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SSRL Headlines Vol. 7, No. 4  October, 2006


Contents of this Issue:

  1. Science Highlight — Uranium-Hungry Bacteria Lead to Safer Water Supply
  2. Science Highlight — Uranium Trapped in Bacteriogenic Manganese Oxide Tunnels
  3. Roger Kornberg Wins the 2006 Chemistry Nobel Prize
  4. Another Successful Users' Meeting
  5. SSRL Awards Honor Mike Soltis and Bill Schlotter
  6. SSRL Users' Organization Executive Committee Update
  7. Ground Breaking New Science
  8. NIH-NCRR Officials Visit SSRL
  9. SESAME to Open: Particle Accelerator Spurs Middle East Science Partnership
  10. Beam Time Requests for X-ray/VUV Beam Lines and Macromolecular Crystallography Proposals Due December 1
  11. Photon Science Job Opportunities

1.  Science Highlight — Uranium-Hungry Bacteria Lead to Safer Water Supply
      (contact: C. Criddle,

Uranium(VI) reduction diagram
Uranium (U) contamination of ground and surface water is a serious problem in many parts of the world. Agricultural practices, mining, and nuclear weapons production have resulted in elevated levels of this heavy metal at a variety of locations, which threatens human health by seeping into groundwater and dispersing over large areas. Researchers at Stanford University and Oak Ridge National Laboratory (ORNL) have now shown that several common types of bacteria may be used to convert an unstable form of U into a stable form that greatly reduces the environmental and health threat of contamination.

In groundwater, U is most commonly found in the hexavalent oxidation state, U(VI)—a highly soluble, mobile and therefore troublesome form. U(VI) bonds readily with minerals suspended in water and can spread easily over large areas. However, the tetravalent state, U(IV), resists combining with minerals and is highly stable and immobile. Several common types of bacteria are known to convert U(VI) into U(IV), which then precipitates as an insoluble oxide, uraninite, and researchers have successfully tested a pilot program designed to exploit this natural process. Until 1983, millions of gallons of waste containing U and nitric acid were discharged into unlined ponds at ORNL. Starting in 2001, researchers began injecting ethanol into the subsurface environment to stimulate microbial activity, and the results were dramatic—concentrations of U(VI) began falling rapidly. Research at SSRL using x-ray absorption near-edge structure (XANES) on SSRL's BL11-2 has verified that those reductions were indeed the result of stimulated microbial action. Current studies aim to monitor the long-term stability of biologically reduced U and the viability of biostimulation as a remediation technique.

To learn more about this research see the full technical highlight at:

2.  Science Highlight — Science Highlight - Uranium Trapped in Bacteriogenic Manganese Oxide Tunnels
      (contacts: J.R. Bargar,; S.Webb,

Manganese oxides precipitated around a spore (cell) of the marine Mn(II)-oxidizing bacterium, Bacillus sp., strain SG-1.
Uranium contamination is a major concern at Department of Energy sites and decommissioned mining and ore processing facilities around the U.S. Migration of uranium has contaminated ground water in several locations, and the threat remains for further contamination unless costly measures are taken to isolate the contaminates and stop their spread. A major obstacle to efficient clean-up of uranium contamination is the great depth and extensive areas over which they are dispersed. Subsurface remediation techniques must therefore take advantage of naturally occurring, environmentally stable agents to stop the spread.

Manganese (Mn) oxides produced by bacteria have been shown to naturally remove large amounts of heavy metal contaminants from water. These oxides commonly form coatings on mineral grains within soils and streambeds. Now, researchers are one step closer to understanding how this process may be harnessed to clean up uranium contamination. Using two complementary synchrotron-based techniques (x-ray absorption spectroscopy and in-situ x-ray diffraction), collaborators from SSRL and Oregon Health and Science University have characterized how bacteriogenic Mn oxides sequester the highly soluble hexavalent uranium (U(VI)).

The collaborators found that in high concentrations, as U(VI) is incorporated into Mn oxides, a stable mineral is formed within which the U(VI) is trapped inside a three-dimensional matrix of "tunnels." Because the U(VI) is structurally bound within the bacteriogenic oxides, much larger amounts of contaminant can be removed from water than with techniques relying on sorption onto particle surfaces. This research could lead to improved techniques suitable for long-term stabilization of subsurface U(VI) contamination. To learn more about this research see the full technical highlight at:

3.  Roger Kornberg Wins the 2006 Chemistry Nobel Prize

L. Cicero
R. Kornberg
Roger Kornberg, professor of Structural Biology at the Stanford University School of Medicine, is the recipient of the 2006 Nobel Prize in Chemistry for his work in understanding how DNA is converted into RNA, a process known as transcription. A key step in gene expression is the transcription of the DNA sequences, comprising the genes, into a message that can be read by the ribosome to produce proteins. Transcription is the first step and a key control point in this process, with RNA polymerase at the heart of the molecular transcription mechanism. Kornberg's studies have provided an understanding at the atomic level of how the process of transcription occurs and also how it is controlled. As transcriptional regulation underlies all aspects of cellular metabolism, his work also helps explain how the process sometimes goes awry, leading to birth defects, cancer and other diseases.

Key to this understanding has been the determination of the three-dimensional arrangement of the atoms in the RNA polymerase - in its "base" structure and caught in snapshots of it in action - through the use of synchrotron radiation-based macromolecular crystallography. Kornberg and his group carried out a significant part of this research at SSRL's macromolecular crystallography beam lines, starting as early as in 1991 but with the main work leading to the first published structure in the late 1990s. Some of the results have been previously highlighted in SSRL Headlines (2001 and again in 2004).

The SSRL Structural Molecular Biology Program and the beam lines on which much of the crystallography work was performed are supported by the Department of Energy, Office of Biological and Environmental Research and by the National Institutes of Health, National Center for Research Resources and National Institutes of General Medical Sciences. SSRL operations are supported by the Department of Energy, Office of Basic Energy Science. Read the full press release from the Royal Swedish Academy of Sciences.

4.  Another Successful Users' Meeting
      (SSRL33 Co-Chairs: C. Kim,;
          A. Lindenberg,

SSRL33 featured excellent science, friendly camaraderie, delicious refreshments, and entertainment. Approximately 300 people participated in this 33rd Annual SSRL Users' Meeting, with workshops and social events October 11-13, 2006. In the opening session, SLAC Deputy Director Keith Hodgson welcomed users and gave introductory remarks. Jo Stöhr, SSRL Director, gave an update on current and future plans for SPEAR3 as well as an update on plans for 500 mA and top-off injection tests during the 2007 run. SSRLUOEC Chair Joy Andrews discussed recent activities of the SSRL Users' Organization, including coordinated activities with representatives from other DOE facilities. Pedro Montano, Director of Scientific User Facilities, DOE Office of Basic Energy Sciences, gave an update from the perspective of the DOE Office of Science. In a special keynote presentation, Z.X. Shen gave a presentation reflecting on the contributions of Bill Oosterhuis: A Legacy and Vision for the Future.

D. Rogers
Spicer Awardees
from left: D. Fritz, A. Cavalieri and J. Stöhr
The scientific sessions of SSRL33 focused on user scientific highlights over the past year, new opportunities for microfocusing and high resolution imaging, structural biology, ultrafast science and new scientific opportunities for SPEAR3. During the young investigators session, recipients of the W. E. Spicer Award, Adrian Cavalieri (Max Planck Institute of Quantum Optics) and David Fritz (SSRL), gave presentations on their respective projects: Clocking Femtosecond X-rays (A. Cavalieri) and Mapping the Excited State Potential Energy Surface of Bismuth (D. Fritz).

Over 50 users presented their research activities during the poster session on October 12, and prizes were awarded to four students for their outstanding posters:
Christopher Lentini (Chapman University), Sorption and Structural Incorporation of Hg(II) and Zn(II) onto Nanoscale Iron Oxyhydroxides

Wei-Sheng Lee (Stanford University), Is One Mode Enough? The Existence of Multiple Bosonic Modes Coupling in Bi2Sr2CaCu2O8

Alexandra Zidovska (UC Santa Barbara), A Two-Dimensional Columnar Phase of Cationic Liposome-DNA Complexes for Gene Delivery: Hexagonally Ordered Cylindrical Micelles Embedded within a DNA Honeycomb Lattice

Cori Demmelmaier (UC Santa Barbara), XAS Investigation of the Precursor to the Phillips Catalyst
D. Rogers
2006 poster winners Poster award winners from left:C. Lentini, W.-S. Lee, A. Zidovska, C. Demmelmaier
Several joint SSRL/ALS workshops were held to give users the opportunity to explore techniques in more depth and, in some cases, to gain hands-on experience and training in using beam line equipment and software.

Overall, SSRL33 was a great success, and we look forward to SSRL34 - Mark your calendars now and plan to attend the 34th Annual SSRL Users' Meeting and Workshops on October 1-3, 2007!

5.  SSRL Awards Honor Mike Soltis and Bill Schlotter
       —J. Yauck, SLAC Today

Congratulations to scientist Mike Soltis and graduate student Bill Schlotter, recipients of the Farrel W. Lytle Award and the Melvin P. Klein Scientific Development Award, respectively. The two awards were presented at the 33rd Annual Stanford Synchrotron Radiation Laboratory (SSRL) Users' Meeting on October 12.

D. Rogers
M. Soltis and B. Schlotter
The Lytle Award, given annually since 1998, recognizes technical or scientific achievements in synchrotron radiation-based science as well as efforts to promote collaboration and efficiency at SSRL. Soltis received the honor for his leadership in developing and implementing advanced robotics and remote-access systems at SSRL's crystallography beam lines, and for developing many now-common techniques for cryo-cooling of crystals. Soltis, who has led the SSRL Macromolecular Crystallography Group since 1999, was also recognized for his role in establishing a world-renowned user-support program at SSRL. "Mike Soltis represents perfectly what the Lytle Award represents," says Linda Brinen, a structural biologist on the faculty at UC-San Francisco and an SSRL user. "His dedication to making top-notch science succeed is constant, as is his unfailing ability to work with both staff and users. He is a true professional."

The Klein Award, presented for the first time this year, recognizes outstanding scientific work performed at SSRL by a graduate or undergraduate student. Bill Schlotter received the award for conceiving and developing a technique that improves the quality of x-ray microscopy images without using longer exposure times or higher illumination intensities, which can damage samples. The technique averages multiple holographic reference images of a sample, taken simultaneously and at relatively low x-ray intensities, into a single final image. According to Jo Stöhr, SSRL Director and Schlotter's research advisor, the technique will have applications in research performed at the future Linac Coherent Light Source, the world's first x-ray laser. "I believe Mel Klein, who I knew quite well and for whom the award is named, would have liked Bill's clever idea and its implementation," he says.

6.  SSRL Users' Organization Executive Committee Update
       (2007 SSRLUOEC Chair: C. Kim, SSRLUOEC Vice-Chair,;
          2006 SSRLUOEC Chair: J. Andrews, SSRLUOEC Chair,

D. Rogers
C. Kim
2007 SSRLUOEC Chair
At the October 13 SSRL Users' Organization Executive Committee (SSRLUOEC) meeting we welcomed the five newly elected user representatives: Wayne Lukens (LBNL), Art Nelson (LLNL), Karen McFarlane Holman (Willamette University), Monika Sommerhalter (Cal State East Bay) and Becky Fenn (Stanford University, graduate student). Jo Stöhr led a discussion encouraging users to provide input on their thoughts regarding the future of SSRL so that it can be folded into planning efforts. In addition to working with SSRL management to determine priorities and strategies, the SSRLUOEC also participates in meetings of the SLAC and SSRL advisory panels and coordinates activities with representatives from other DOE user facilities to promote and sustain support for basic sciences. User input is vital, and we urge you to become more engaged in these activities or to contact us to share your views so that we can best represent the interests of the entire SSRL user community.

7.  Ground Breaking New Science
       —B. Plummer and R. Courtland SLAC Today

D. Rogers
from left: J. Dorfan, J. Etchemendy, R. Orbach, A. Eshoo and Z. Lofgren
On Friday, October 20, SLAC officially broke ground for the Linac Coherent Light Source (LCLS), the world's first x-ray free-electron laser. Scheduled for completion in 2009, the LCLS will produce ultra-fast, ultra-short pulses of x-rays a billion times brighter than any other source on earth. The LCLS "will drive understanding and opportunity as no facility has ever done before," said DOE Under Secretary of Science Raymond L. Orbach, who delivered the keynote address during the ceremony. "What you'll have here is what we all hope for, a window into the future, one that we think we will understand, but where conventional wisdom can be turned on its head."

Nearly 1,000 attendees looked on as Orbach and other dignitaries including Congresswomen Anna Eshoo and Zoe Lofgren, Congressman Mike Honda, Stanford University Provost John Etchemendy, and SLAC Director Jonathan Dorfan ceremonially shoveled the first spades of earth at the start of the event. The audience then cheered as an excavator scooped the first bucket of dirt from the site of the LCLS Near Experimental Hall. Read more...

8.  NIH-NCRR Officials Visit SSRL
      (contacts: K.O. Hodgson,; B. Hedman,

Drs. Barbara Alving, Acting Director, and Amy Swain, Health Sciences Administrator of the National Institutes of Health National Center for Research Resources (NIH-NCRR), visited Stanford and SLAC on Tuesday, October 10. After spending the morning at the Stanford Medical School the agenda for the afternoon was focused on the NCRR Synchrotron Radiation Structural Biology Resource program at SSRL.

Keith Hodgson and Britt Hedman led a tour of the SSRL experimental hall and the SPEAR3 ring, stopping at several structural biology beam lines where users and staff gave brief presentations on the beam line facilities and the research they conduct there. Our thanks to David Bushnell (Stanford), Sarah Hymowitz (Genentech), Kelly Lee (Scripps), Martina Ralle (OHSU), Vittal Yachandra (LBNL) and Alexandra Zidovska (UC Santa Barbara) for their time and effort in helping put together a successful demonstration of the research enabled by the NIH NCRR's continued support of SSRL's structural molecular biology program.

9.   SESAME to Open: Particle Accelerator Spurs Middle East Science Partnership
      —Clara Moskowitz, Stanford Report

Herman Winick
H. Winick
When Stanford physicist Herman Winick heard that Germany was planning to throw out an old particle accelerator, he thought, why not donate it to the Middle East? This idea has sparked plans to build a new state-of-the-art research facility in Jordan using pieces of the old German equipment. The lab will speed up electrons in a circle to produce high-energy light called synchrotron radiation, which is useful for a host of experiments. The project's leaders hope that the new facility will help solve important scientific questions and bring together researchers from different parts of the region.

"My main motivation is to help create a project in which people can work constructively and collectively," Winick said. "There will be collaborations between Israeli and Arab scientists, in particular. This is reasonably unusual." Previous cooperation has been bilateral (between just Israel and Palestine, for example). This is the first time that scientists from many different Arab nations, along with Israel, will all work together, he explained. Read more in the Stanford Report...

10.   Beam Time Request for X-ray/VUV and Macromolecular Crystallography Proposals Due December 1
      (contacts: C. Knotts,; L. Dunn,

The SPEAR operating schedule and user schedule by beam line for the first scheduling period (which begins this week) is posted on the web

X-ray/VUV Beam time requests for the second scheduling period in 2007 (Feb-May) need to be submitted by Friday, December 1:

The next proposal deadline for macromolecular crystallography proposals is also December 1. Proposals submitted for this deadline will be eligible for beam time beginning in March 2007. Spokespersons with expiring proposals will be reminded via direct email in early November.

11.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


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.


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Last Updated: 31 OCT 2006
Content Owner: L. Dunn
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