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SSRL Headlines Vol. 10, No. 6  December, 2009


Contents of this Issue:

  1. Science Highlight — Imaging Mercury in the Rhizosphere of Wetland Plants
  2. Science Highlight — A tRNA Synthetase Domain Couples Aminoacylation and Editing Activities
  3. Researchers Uncover Chemical Basis for Extra "Quality Control" in Protein Production
  4. Holiday Greetings from Piero Pianetta
  5. Zhi-Xun Shen Receives 2009 E.O. Lawrence Award
  6. New User-friendly Sample Prep Labs Website
  7. Planned System Outages over Winter Break
  8. User Research Admin Updates
  9. Please Report SSRL-Related Papers, Invited Talks, and Awards

1.  Science Highlight — Imaging Mercury in the Rhizosphere of Wetland Plants
       (contacts: C. Patty, J. Andrews Hayter & P. Pianetta, SSRL)

mercury methylation figure
Transmission X-ray Microscope (SSRL BL6-2) mosaic image of S. foliosa roots.
High levels of mercury in our diets can have adverse effects on our health, and fish are a major source of dietary mercury. Because of a process called biomagnification, mercury levels in fish can build up to be at a much higher concentration than in the surrounding water. The mercury that accumulates in the tissue of fish is in the form of methylmercury, but this is not necessarily the chemical form that pollutes the water. Microorganisms living in the rhizosphere, or root zone, of plants are responsible for much of the methylation of mercury.

A team of researchers led by Joy Andrews of SSRL studied mercury uptake and methylation in the rhizospheres of two common plant species in the San Francisco Bay. They used a combination of experiments to piece together the story of methylmercury formation. Using data collected at SSRL Beam Lines 9-3 and 10-2, they used Hg L3 x-ray absorption edge spectroscopy (XANES) to determine what species of mercury were present in the root systems. They used Beam Line 2-3 to perform scanning x-ray fluorescence (XRF) and micro-XANES experiments to map the location of mercury species within the roots of the plants. Additionally, they performed transmission x-ray microscopy (TXM) experiments using Beam Line 6-2c, which showed that the mercury seen in the roots was most concentrated on the outside of microorganisms.

The researchers conclude that much of the mercury is binding to sulfur in the plant roots and microbes' cell walls, and about 10% of the total mercury is likely to be methylated. Because these plants dominate the San Francisco Bay environment, their rhizospheres could be a significant source of methylated mercury in this estuary ecosystem. This work was published in the September issue of Environmental Science & Technology.

To learn more about this research see the full scientific highlight

2.  Science Highlight — A tRNA Synthetase Domain Couples Aminoacylation and Editing Activities
       (contacts: M. Guo, X.-L. Yang & P. Schimmel, The Scripps Research Institute)

highlight figure
Structure of the C-Ala domain of Aquifex aeolicus.
The information encoded in genes is only useful if the decoder is accurate. The complicated process of translating information from nucleic acid to proteins incorporates systems that ensure accuracy and systems that edit inaccuracies. The ribosome has mechanisms to make certain that the codon on the messenger RNA matches the aniticodon on the transfer RNA before it adds the amino acid to the growing polypeptide chain. But it is just as critical that the tRNA is properly charged with the amino acid dictated by the genetic code. The synthetases that are responsible for placing amino acids on tRNAs have an editing feature that double-checks the match.

The synthetase that charges alanine tRNA has a structural domain that places the amino acid, a domain that removes the wrong amino acid, and a third domain with a previously unknown role. A group led by Professors Paul Schimmel and Xiang-Lei Yang at The Scripps Research Institute solved the crystal structure of this third domain of the alanine tRNA synthetase. They used SSRL Beam Line 11-1 to collect data and determined the structure at 1.85 angstroms using single anomalous diffraction. The structure revealed a known nucleic acid binding fold. This domain was shown through biochemical experiments to contact the elbow region of the tRNA.

The researchers propose that this domain promotes the coupling of the activities of the aminoacylation and the editing domains of alanine tRNA synthetase. Because phylogenic data shows that this domain has an ancient origin, it could have been the first bridge between these activities, ensuring that the tRNA bears the correct amino acid. This work was published in the August 7 issue of Science.

To learn more about this research see the full scientific highlight

3.   Researchers Uncover Chemical Basis for Extra "Quality Control" in Protein Production
       Scripps News & Views Article by Mika Ono

"To me, it's amazing that a single chemical feature [illustrated above] can determine the fate of almost every organism on earth," says Research Associate Min Guo, an author of the new Nature paper.
Even small errors made by cells during protein production can have profound disease effects, and nature has developed ways to uncover these mistakes and correct them. Though in the case of one essential protein building block-the amino acid alanine-nature has been extra careful, developing not one, but two checkpoints in her effort to make sure that this component is used correctly.

Now, scientists at The Scripps Research Institute have discovered the chemical basis for why these extraordinary efforts are necessary. The work was published in the December 10, 2009 issue of the prestigious journal Nature. Several data sets from SSRL are included in the paper.

"What is shown here with the 'serine paradox' is just the tip of the iceberg," said senior author Paul Schimmel, who is the Ernest and Jean Hahn Professor and Chair of Molecular Biology and Chemistry and a member of The Skaggs Institute for Chemical Biology at Scripps Research. "In the coming years, there will be an increasing awareness of the role of mistranslation in human diseases and of how nature has struggled to find solutions to attenuate mistranslation and its consequences." Read more at:

4.   Holiday Greetings from Piero Pianetta

P. Pianetta
P. Pianetta
Dear Users, Colleagues and Friends of SSRL,

It's that time of year again, with another successful year of innovative science, operations, and outstanding customer service winding down. We ended the 2008-09 user run year with a record average uptime of 99%. In the past year, we ran SPEAR3 routinely at 200 mA, added several new beam lines and experienced an almost 19% increase in the number of users that we serve (1,361 on-site and remote access users). Users and staff have published over 9,000 scientific papers, books, and theses since SSRL began in 1974, with 2009 marking SSRL's 35th anniversary!

As I look forward to 2010, I see a many exciting developments on the horizon including continuing on our path to 500 mA and the bringing of two new beam lines into operation. I also look forward to working with all of you to develop both short- and long-term plans for SSRL that will keep our capabilities at the forefront for a long time to come.

Over the upcoming holiday shutdown, I encourage you all to take time out to breathe, to appreciate how much we have accomplished as a team, and to relax with family and friends. We look forward to coming back in 2010 ready and eager to begin again. Best wishes for a wonderful holiday filled with joy, peace and prosperity in the New Year.
    —Piero Pianetta, Acting Director for SSRL

5.   Zhi-Xun Shen Receives 2009 E.O. Lawrence Award
       Based on SLAC Press Release

Z.-X. shen
Z.-X. Shen
Zhi-Xun Shen, Professor of Photon Science, SLAC, and the Paul Pigott Professor in Physical Sciences at Stanford University, and Director of the Stanford Institute for Materials and Energy Science, or SIMES, a joint institute of the Department of Energy's SLAC National Accelerator Laboratory and Stanford University, has been awarded the Ernest Orlando Lawrence Award by the U.S. Department of Energy. Shen, who received the prize for his pioneering work in materials science, is among six other distinguished awardees, announced on December 16, 2009.

"The contributions made by these researchers to advance the national, economic and energy security of the United States are wide-ranging and meaningful," said Secretary of Energy Steven Chu. "I congratulate the winners and look forward to their discoveries still to come."

One of the highest scientific honors that is bestowed by the U.S. Government, recipients of the E.O. Lawrence Award receive citations signed by the Secretary, a gold medal bearing the likeness of the award's namesake, Ernest Orlando Lawrence, and a $50,000 honorarium.

Shen's citation reads, "For his ground breaking discoveries and pioneering use of high resolution angle-resolved photoemission to advance understanding of strongly correlated electron systems including high-transition temperature superconductors and other complex oxides."

"Z.-X.'s accomplishments truly fit the spirit of this award," said SLAC Director Persis Drell. "In addition to providing leadership in the fields of materials and energy research, Z.-X. is also tirelessly dedicated to the encouragement of young scientists. We are privileged to have him on our faculty." Read more at:

6.   New User-friendly Sample Prep Labs Website
       (contact: C. Patty,

The sample preparation labs at SSRL have a new user-friendly web-based interface. Here, old friends and new scientists coming to SSRL can request laboratory access and easily link to resource pages for help in coordinating beam time arrangements. Descriptions of the different sample preparation labs and their special capabilities can be surveyed before you arrive. Information about lab training, available laboratory equipment and supplies, and chemicals is readily available.

We are continuing to build on this existing site to provide more sophisticated search and database capabilities and scheduling features; your input in the development of this website is greatly appreciated. Please feel free to contact Cynthia Patty ( and Nik Stojanovic ( with any comments or suggestions.

For access to the full SSRL User Resources page, see:

7.   Planned System Outages over Winter Break

System upgrades are scheduled December 21-23, and sporadic outages or difficulty connecting to our website and/or user portal are likely during this time. Please note that SLAC operations are shut down from December 19-January 3. We hope you have a great holiday! Please check back with us after January 4.

8.   User Research Admin Updates
       (contact: C. Knotts,

  • X-ray/VUV Beam Time Requests due February 15
    The X-ray/VUV beam line schedule for February through mid May is currently being drafted and will be distributed by late January. If you are interested in requesting additional beam time in the next scheduling period, May-July, please submit your request by Monday, February 15.

    As you prepare for your upcoming beam time, please check the SPEAR operating schedule to note holidays, accelerator physics and maintenance days.

  • Fresh Food Options Coming Soon to SSRL Building 120
    In response to your requests, in January the SLAC Café will stock a new deli-style refrigerator located in the Building 120 kitchen each afternoon (Monday-Friday). The Café will offer a wide a selection of fresh entrees, salads, sandwiches, etc. The Café will add a collection box to collect payments for these fresh food items on the honor system. We hope that you will participate in and enjoy this pilot program so that we can continue to provide fresh food options to users and staff.
  • Coyote Alert
    Over the past month, there have been several sightings of a single coyote as well as a pair of coyotes along the Dish hiking trail. At different times, a single coyote has come within feet of different people, exhibiting little or no fear of humans. According to Santa Clara County Vector Control District, coyotes that are not afraid of humans are displaying unusual behavior and could be dangerous. Report all incidents to the officer at the Visitor Information Center located at the Stanford Avenue gate and telephone county Vector Control at (408) 918-4770. If you witness a coyote attack, dial 9-1-1. See the Stanford Community Crime Alerts website at:

9.   Please Report SSRL-Related Papers, Invited Talks, and Awards
       (contacts: C. Knotts,; L. Dunn,

It is extremely important that users not only inform us whenever work conducted at SSRL results in a publication, but also acknowledge SSRL and our funding agencies in each publication. User help is needed to keep current records on publications including refereed journal papers, conference proceedings, book chapters and theses, invited lectures and major awards and patents based at least in part on work conducted at SSRL. This information allows SSRL to demonstrate scientific achievements and productivity when responding to requests sent out by the Department of Energy and the National Institutes of Health.

This information can be submitted anytime via email message to Lisa Dunn or Cathy Knotts or via the reference submission form at:

For recent publications lists and the proper acknowledgement statements see:


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: 18 December 2009
Content Owner: L. Dunn
Page Editor: L. Dunn