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SSRL Headlines Vol. 5, No. 12 June, 2005


Contents of this Issue:

  1. Science Highlight — Geological and Anthropogenic Factors Influencing Mercury Speciation in Mine Wastes
  2. Science Highlight — Super Oxidized Iron
  3. SPEAR3 Reaches 500 mA
  4. Director of the DOE Office of Science Addresses SLAC Staff
  5. User Input Encouraged at Next SSRLUOEC Meeting, July 11
  6. New Rapid Access Proposal Mechanism for Structural Biology SAXS
  7. SSRL Structural Molecular Biology Summer School in September 2005 - Open for Registration
  8. SSRL Receives NIH/NIBIB Funding for a High Resolution Hard X-ray Microscopy Facility for Bio-imaging
  9. SSRL Affiliated Faculty Member Awarded GM's Sloan Prize
  10. User Administration Update

1.  Science Highlight — Geological and Anthropogenic Factors Influencing Mercury Speciation in Mine Wastes
      (contact: Christopher S. Kim,

Hg figure
Chris Kim collects a mine waste sample from the Oat Hill mercury mine in Northern California.
Mercury (Hg) is a naturally occurring element that poses considerable health risks to humans, with high exposure levels resulting in damage to the brain, heart, kidneys, lungs, and immune system. Young children and unborn babies are particularly vulnerable to mercury, which can affect their nervous systems and impair their neurological development. As a result, mercury is one of the most strictly regulated pollutants by the Environmental Protection Agency (EPA), which controls mercury emissions from coal-fired power plants and issues consumption advisory warnings for various types of fish, the primary route of mercury exposure to humans.

Environmental mercury contamination is widespread due both to point sources and the transport/distribution of mercury on regional and global scales. Since mercury compounds possess a wide range of solubilities in water, understanding the specific forms of mercury present in a contaminated sample and the factors that influence what forms are likely to be present is critical to predicting the mobility, reactivity, and potential bioavailability of mercury in the environment. Research at SSRL by Dr. Christopher Kim of Chapman University and colleagues has resulted in the development of a sensitive technique which uses EXAFS spectroscopy to identify and quantify the proportions of different mercury species present in mercury-bearing samples; as applied to mine wastes from selected mercury and gold mine regions in California and Nevada, this represents the first in situ, non-destructive method by which to identify mercury speciation in heterogeneous samples.

The results of this research, conducted at SSRL Beam Lines 4-3 and 11-2, reveal that geological environment plays an important role in which mercury species are likely to appear, with hot-spring hydrothermal systems containing larger proportions of soluble (and potentially more toxic) mercury chloride species. The roasting of mercury-bearing ore at temperatures approaching 600C was found to have the effect of converting cinnabar (HgS, hex.) to the more soluble metacinnabar (HgS, cub.) species. Also, total mercury concentrations were found to increase dramatically with decreasing particle size in a heterogeneous mine waste, sometimes by nearly an order of magnitude. While this raises concern due to the higher transport potential for smaller particles, EXAFS analysis also determined that the mercury associated with these small particles is more likely to be present as relatively insoluble mercury sulfides rather than soluble mercury chlorides and oxides. This type of information will provide a higher degree of sophistication in assessing and prioritizing mine sites for remediation by agencies such as the EPA and Bureau of Land Management.

To learn more about this research see:

2.  Science Highlight — Super Oxidized Iron
      (contacts: Frank Neese,; Serena DeBeer George,

Fe K-edge XAS spectra of the Fe(III)-azide precursor and the Fe(V)-nitrido complex.
Iron metals oxidize to rust, losing electrons and gaining positive charge. Iron metals typically exist in an oxidation state of +2 or +3 (2 or 3 electrons less than a neutral iron atom). However, chemists have long thought that iron compounds with even higher oxidation states play important roles in enabling chemical reactions in metal-containing proteins. In recent years, scientists have been able to synthesize and characterize numerous iron +4 compounds [written Fe(IV)], but knew little about iron +5, Fe(V), compounds. Now researchers, using facilities at SSRL, have characterized a genuine Fe(V) species, which is even more oxidized and more positively charged than the iron in rust [Fe(III)] or Fe(IV).

Frank Neese (Muelheim), Karl Wieghardt (Muelheim), Serena DeBeer George (SSRL) and co-workers, used x-ray absorption spectroscopy (XAS), combined with other spectroscopic and computational results, to study the properties of the compound. Tuned to be sensitive to iron, XAS can provide direct information about the charge of the iron atom. The XAS "K-edge" corresponds to the excitation of the most tightly bound electrons in the iron atom. As the iron atom becomes more oxidized, the energy position of the K-edge increases, providing a signature for Fe(V). This study represents the first characterization of an Fe(V) species by XAS and serves as an important experimental marker for characterization of other Fe(V) species.

To learn more about this research see:

3.   SPEAR3 Reaches 500 mA
      (contact: Robert Hettel,

SPEAR3 500 mA Team
Initial tests for 500 mA operations in SPEAR3 began on Monday, June 20. At 11:08 pm, we reached 500 mA in SPEAR3 for the first time. No significant problems were encountered. Vacuum pressure remained low, and the maximum temperature that was monitored on any component was an acceptable 64C (on the BL 11 chamber upstream bellows). Other bellows temperatures were within expected ranges, but will be reduced with fans in the future. The lifetime at 500 mA was initially an unexpectedly high 15 hours. The high lifetime was attributed to vertical beam instability due to chamber impedance and ions. This instability was reduced substantially, and the lifetime reduced to the expected 8.5 hours, by increasing the vertical chromaticity. Although longitudinal oscillations were also seen, we believe it may be possible to attenuate them with the RF low level control system. More studies on beam instabilities and cures were conducted on Tuesday evening, June 21. This initial test follows the Accelerator Readiness Review (ARR) which was held on June 7, 2005. The final ARR report is expected to be completed in July. With the concurrence of the DOE and with the oversight of the SLAC safety representatives, tests to reach higher current in SPEAR were begun and will continue during the evening shifts of the next scheduled Accelerator Physics periods (July 5, 18, 19). This is an important milestone that will enable SPEAR3 to be run at its performance potential. Many thanks and congratulations to the SSRL, SPEAR3, SLAC, Radiation Protection, ES&H and DOE SSO staff who worked very hard to enable this landmark test of SPEAR3 operation.

4.   Director of the DOE Office of Science Addresses SLAC Staff
      (contact: Keith Hodgson,

Raymond Orbach and John Hennessey
Dr. Raymond L. Orbach, Director of the DOE Office of Science, spent the day at SLAC on Thursday, June 23. In addition to briefings with DOE site management and the SLAC Directorate, Dr. Orbach met with a group of SSRL users (Glenn Waychunas, Aaron Lindenberg, Meredith Murr) and HEP users (Gregory Dubois-Felsmann, David MacFarlane, Chandrashekhar Joshi) during lunch and toured the site of the future LCLS facility in the early afternoon. With a warm welcome by Stanford President John Hennessey, the highlight of Dr. Orbach's visit was a special address to the SLAC staff assembled on the Green. Dr. Orbach complimented the staff on the innovative science that has come out of SLAC over the past 40 years, citing specific papers and awards that involved SLAC scientists. He went on to comment that given such a rich history and a talented staff he anticipates that SLAC will continue to be at the leading edge of global scientific discovery well into the future - building upon initiatives like the LCLS. Dr. Orbach also acknowledged the recent achievement of 500 mA in SPEAR3 and remarked on the outstanding effort by the staff in achieving this maximum design performance.

5.   User Input Encouraged at Next SSRLUOEC Meeting, July 11
      (contact: Glenn Waychunas,

The SSRL Users' Organization Executive Committee (SSRLUOEC) will meet on Monday, July 11, at 12 noon in the SSRL Bldg. 137 3rd Floor Conference room. Several items on the agenda require user input, including top up and pulsed beam. Currently shutters are closed and there is no beam during 3 daily SPEAR3 fills at 6 am, 2 pm and 10 pm (it takes about 5 minutes to deliver beam). An alternative is top off injection which means that the shutters would remain open and fills would be transparent to users as beam is topped up at regularly scheduled intervals. User input is desired to determine how frequently top offs might be scheduled and the impact of this mode of operation on user experiments. The other topic, pulsed beam for time structure experiments, would represent a change from the current mode where electrons travel in the ring in bunches or buckets. An alternative involves a pulsed beam that would allow time-resolved studies. User input is requested to consider the desirable properties for a pulsed beam, how often, what types of experiments would benefit and the impact on other types of experiments. All interested users and staff are encouraged to participate in these discussions.

6.   New Rapid Access Proposal Mechanism for Structural Biology SAXS
      (contacts: Hiro Tsuruta,; Cathy Knotts,

Building on the success of the rapid access mechanism for macromolecular crystallography (, SSRL is now offering a similar mechanism for small angle x-ray scattering (SAXS) for structural biology studies on SSRL BL4-2. During normal user operations, at least 1 block of 2-3 shifts will be set aside each month for SAXS rapid access. Applications submitted by the first of the month will be peer reviewed for feasibility and scientific merit. Spokespersons will be contacted within 2 weeks so that beam time can be arranged for the rapid access application(s) that are accepted and score highest. Ideally, the entire process will be completed in less than 1 month, and at least 1 rapid access proposal will be scheduled each month. For the current scheduling period, applications are due by Friday, July 1, for the block of time set aside in late July. Additional instructions and restrictions for this rapid access mechanism can be found at:

7.   SSRL Structural Molecular Biology Summer School in September 2005 - Open for Registration
      (contacts: Serena DeBeer George,; Clyde Smith,

Students interested in participating in the SSRL Structural Molecular Biology Summer School on September 12-15, 2005 should apply well before the August 1, 2005 deadline, as space is limited. This year the School will highlight the use and applications of two synchrotron x-ray techniques in the study of biological systems: X-ray Absorption Spectroscopy (XAS) and Macromolecular Crystallography (MC). Presentations from experts in the fields will be aimed at the graduate student level, but will also be appropriate for more experienced researchers entering the field. Lectures will be followed by interactive practical sessions giving participants the opportunity to learn data collection and analysis techniques first hand. Details can be found at:

Additional educational opportunities, covering all aspects of synchrotron-related research, are available over the next several months in the US and Europe. An up-to-date listing of the courses and facilities participating is available at

8.   SSRL Receives NIH/NIBIB Funding for a High Resolution Hard X-ray Microscopy Facility for Bio-imaging
      (contacts: Katharina Luening,; Piero Pianetta,

Scientists from SSRL, NASA Ames Research Center, Cornell University, and Xradia Inc. received $2.44 million from NIH/NIBIB over 4 years for developing a high resolution full field transmission hard x-ray microscope at SSRL. This instrument will use a powerful wiggler x-ray source at SSRL and is based on zone plate optics from Xradia Inc. which will provide an unprecedented spatial resolution of 20 nm for 2D and 3D imaging. This facility will provide important and currently unavailable capabilities for the study of biological systems, in-situ by exploiting various contrast mechanisms as well as the ability to image elemental distributions within single cells or tissues. The full field microscope will operate using photon energies between 5-14 keV and will exploit the advantages of hard x-rays for 2D and 3D microscopy such as large penetration depth, a large depth of focus, analytical sensitivity and compatibility with wet specimens. Taken together, these capabilities will enable high resolution, in-situ imaging, tomography and spectro-microscopy without extensive sample preparation. The instrument will be commissioned in the fall of 2006 and will be open for general users during 2007.

This program is supported by the National Institutes of Health, National Institute for Biomedical Imaging and Bioengineering, grant number EB004321.

9.   SSRL Affiliated Faculty Member Awarded GM's Sloan Prize

Kornberg thumbnail
Roger Kornberg
Stanford Professor of Structural Biology and SSRL Affiliated Faculty member Roger Kornberg was awarded the General Motors Alfred P. Sloan, Jr. Prize on June 15 in Washington, D.C. General Motors has long been committed to furthering cancer research and this year marked the 27th anniversary of the General Motors Cancer Research Awards (GMCRA) program. Dr. Kornberg received his $250,000 award for his groundbreaking research on transcription - the process of copying DNA into RNA. His work, which has in part been enabled by synchrotron radiation-based studies done at the DOE light sources, has led to a better understanding of how a gene can mutate and cause cancer, thus providing a more comprehensive foundation for cancer researchers to build upon. According to Dr. Kornberg, "You can't understand a machine if you don't know the place of all the pieces, and our discoveries have helped locate the parts of the machine that make RNA."

Dr. Kornberg's research on RNA polymerase II was the subject of SSRL's first posted science highlight in April 2001 and a second highlight in February 2004. For links to these science highlights and the Kornberg Lab see:

10.   User Administration Update
        (contact: Cathy Knotts,

The current user run ends on August 1, 2005. Significant beam line development and construction activities are planned during the summer shutdown, including upgrades to BL10, BL9 and BL7. These beam lines will be available for users after upgrades and commissioning are completed. For BL10-1, BL10-2 and BL9-3, this is expected by mid December; BL9-1 and BL9-2 by January 2006. BL7-3 is expected to be available for users by February 2006, with BL7-1 and 7-2 a bit later in early 2006. A preliminary copy of 2006 user operations schedule, which is expected to resume around November 28, 2005 and continue through July 31, 2006, can be found at:

As a reminder, all spokespersons and collaborators planning to be on-site for scheduled experiments are required to inform the User Administration Office in advance. Several documents are required, including: a User Information form, a Safety Agreement, and a Hutch Authorization Agreement. Once the documentation and other training are completed, users will be issued - and must wear at all times while at SSRL - an ID badge and dosimeter. Any visitors, collaborators or other users who have not completed training and received their own SLAC ID badge, may get a temporary escort-required badge from Security (also inform the User Administration Office when this happens so that we can add these people to the appropriate proposal and ensure that relevant safety requirements are met). Anyone who signs as an escort must: 1) take full responsibility for the safety of their visitor, 2) go only to designated areas (for SSRL users, this is Bldg. 120 and 131) and 3) remain within 'visual contact' of their visitor at all times (this means that visitors will only be permitted through Security Gates 17 or 30 if their escort is with them).


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: 01 JULY 2005
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