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SSRL Headlines Vol. 11, No. 5  November, 2010


Contents of this Issue:

  1. Science Highlight — Iron a Limited Barrier to Arsenic Contamination in Rice
  2. Science Highlight/Press Release — X-rays Offer First Detailed Look at Hotspots for Calcium-related Disease
  3. SSRL Starts the 2010-2011 Run
  4. SPEAR3 Injector Beefed Up for Frequent Injection Regimen
  5. SPEAR3 Computer Network Reorganization Underway
  6. Call for 2008-2010 Publications, Awards and Invited Talks
  7. USA Science & Engineering Festival
  8. SSRL Beam Time Requests and Proposals Due December 1
  9. LCLS Call for Proposals — Due January 11, 2011
  10. SSRL/LCLS T-shirts for Sale

1.  Science Highlight — Iron a Limited Barrier to Arsenic Contamination in Rice
       (contacts: A. Seyfferth,; S. Webb,; J. Andrews Hayter,

As-uptake image
Rice, the grain that provides more than one-fifth of the world population's calories, can become a health hazard if contaminated with arsenic. Such contamination, a surprisingly widespread occurrence, takes place in areas where soil or irrigation water is tainted by naturally occurring arsenic—including broad swaths of south and southeastern Asia. Studies have suggested that the natural iron coating around the roots of rice plants may serve as an important barrier to arsenic uptake because arsenic in its oxidized form has an affinity for iron. A team of Stanford and SSRL researchers recently sought to learn just how significant a barrier iron provides.

The team, which included Stanford post doctoral researcher Angelia Seyfferth, SSRL staff scientists Samuel Webb and Joy Andrews, and Stanford Professor Scott Fendorf, used SSRL Beam Lines 10-2 and 6-2 to view the distribution of iron and arsenic on rice roots, revealing that the iron coating varies across roots, affecting arsenic's entry into the plant. The researchers also found that many young roots and younger portions of mature roots are not yet naturally coated with iron and so allow arsenic to enter the root's cellular structure. This suggests that overall, iron coatings may not be an effective barrier to arsenic uptake by rice roots.

This work was published in the October issue of Environmental Science and Technology.

To learn more about this research see the full scientific highlight

2.  Science Highlight/Press Release — X-rays Offer First Detailed Look at Hotspots for Calcium-related Disease
       (contact: F. Van Petegem,

RyR structure
Calcium regulates many critical processes within the body, including muscle contraction, the heartbeat, and the release of hormones. But too much calcium can be a bad thing. In excess, it can lead to a host of diseases, such as severe muscle weakness, a fatal reaction to anesthesia or sudden cardiac death.

Using intense x-rays from SSRL's Beam Line 9-2 at the Department of Energy's SLAC National Accelerator Laboratory, researchers have determined the detailed structure of a key part of the ryanodine receptor, a protein associated with calcium-related disease. Their results, which combine data from SSRL and the Canadian Light Source, pinpoint the locations of more than 50 mutations that cluster in disease "hotspots" along the receptor.

The ryanodine receptor controls the release of calcium ions from a storehouse within skeletal-muscle and heart-muscle cells as needed to perform critical functions. Previous studies at lower resolution indicated that mutations cluster in three regions along the receptor, but without more detailed information it remained unclear exactly how they contributed to disease.

In a study recently published in Nature, Van Petegem and his group describe the structure of one of these hotspots in extremely fine detail and predict how the mutations might cause the receptor to malfunction and release calcium too soon. Read more at:

To learn more about this research see the full scientific highlight

3.   SSRL Starts the 2010-2011 Run
       (contacts: J. Schmerge,; T. Rabedeau,

SSRL's 2010-2011 user run started the week of November 15. The run is scheduled to last until July 25, 2011, with an estimated 1500 users coming to SLAC over the course of the run to perform research using SSRL's x-ray beam lines.

The original plan was to begin the run at an operating current of 350 mA, however, SPEAR3 vacuum problems resulting in frequent beam dumps have necessitated scaling back to 300 mA. The accelerator physics period this week has been used to troubleshoot the vacuum problems. Specifically, a new pump on a RGA near the rf cavities has been installed and the RGA vacuum system is being baked out. This will allow use of the RGA during the regularly scheduled maintenance day on Monday December 6. In addition a vacuum leak check was performed near the BL13 ID and a small leak found and hopefully repaired. The vacuum pressure in this region will be monitored frequently over the next few days to determine if the repair was successful and if additional repairs are necessary. Additional AP time was used to minimize the possibility of the vacuum leak causing SPEAR3 beam losses and making recovery even quicker. The SPEAR3 current will remain at 300 mA while we evaluate the effectiveness of the vacuum repair and other mitigations.

4.   SPEAR3 Injector Beefed Up for Frequent Injection Regimen
       SLAC Today article by Lori Ann White

Work at the SPEAR3 storage ring during the annual downtime involved projects both large and small to support the continued use of frequent-injection mode. Frequent injection is necessary to support SPEAR3's goal of reaching its full design current of 500 mA-and improved data collection for researchers using SSRL's bright x-rays. But frequent injection has challenges of its own. Read more at:

5.   SPEAR3 Computer Network Reorganization Under Way
       SLAC Today article by Lori Ann White

A multi-year project to reorganize the computer network for the SPEAR3 accelerator and beam lines is bearing fruit, according to Clemens Wermelskirchen, manager of the SPEAR3 control system and network, and his counterpart for the SPEAR3 beam lines, Martin George. The goal is to improve network performance and reliability-as vital to the performance of the accelerator and beam lines as mechanical upgrades and maintenance, Wermelskirchen said. "The SPEAR3 control system can never go down," he stated. "If we lose a significant network component, we lose the accelerator." However, the previous organization of the network coupled with the growth of SSRL made the network increasingly difficult to support. Read more at:

6.   Call for 2008-2010 Publications, Awards and Invited Talks
       (contacts: C. Knotts,; L. Dunn,

We are gathering data to compile for our 2008-2010 upcoming February 2011 review by the U.S. Department of Energy's Office of Basic Energy Sciences. Metrics of productivity and peer recognition resulting from work done at SSRL are crucial components of the review. Please take a few minutes now to send us your updated list of SSRL related publications, awards and invited talks. Thank you in advance for your assistance with collecting this important information.

SSRL Publications:

7.   USA Science & Engineering Festival
       (contact: C. Knotts,

The inaugural USA Science & Engineering Festival was held recently in Washington and included participation from many DOE laboratories, including LCLS Deputy Director Uwe Bergmann who gave a presentation on 'X-ray Vision: Revealing Ancient Secrets with New Technology' in one of the AAAS Meet the Scientists sessions. The National User Facility Organization (NUFO) also conducted hands-on demonstrations at their exhibit booth to stimulate interest and make science fun for the 5,000 students, parents and teachers who participated in this festival. Read more about this most recent outreach and education event and other NUFO news at and

8.   SSRL Beam Time Requests and Proposals Due December 1       

X-ray/VUV Beam Time Requests for February through May 2011 beam time are due Wednesday, December 1. Please submit your requests via our user portal:

December 1 is also the next deadline for submitting new X-ray, VUV and Macromolecular Crystallography proposals. New proposals should be submitted through our user portal as well.

9.   LCLS Call for Proposals — Due January 11, 2011       

Researchers are invited to submit scientific proposals for soft and hard x-rays at the LCLS AMO, SXR, XPP, CXI, XCS, and MEC (with limited capability) instruments. Proposals submitted by January 11 will be eligible for beam time ~October 2011-February 2012. Learn more about the latest developments by contacting LCLS staff scientists and reviewing detailed instrument descriptions available on the LCLS web site at:

New capabilities available to users for this call include a ~100 nm focus in CXI and the first time availability of the XCS and MEC instruments. LCLS has demonstrated FEL operations over the energy range 480 eV to 10 keV using the fundamental with pulse energies of 1-3 mJ depending on the pulse duration. Further, LCLS will deliver photons up to 20 keV from a second harmonic afterburner with a flux reduced by roughly an order of magnitude. The pulse length can be varied over 70-300 fs for hard x-rays, while for soft x-rays, the range is extended to 70-500 fs. Shorter pulses (<10 fs) with reduced pulse energy (number of photons per pulse) can also be provided by returning the injector to run at lower charge. The maximum repetition rate of the LCLS is expected to be 120 Hz during this run.

Submit proposals at: (note: spokespersons must be registered and approved as users to submit a proposal)

10.   SSRL/LCLS T-shirts for Sale
       (contact: M. Steger,

We have SSRL/LCLS long sleeve & short sleeve t-shirts for sale. Please stop by User Research Administration, SSRL Bldg. 120, if you are interested. Sizes available include M, L, XL, XXL & XXXL in the short sleeve and L, XL, XXL & XXXL in the long sleeve version. These t-shirts make great gifts!


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: 30 November 2010
Content Owner: L. Dunn
Page Editor: L. Dunn