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SSRL Headlines Vol. 8, No. 1  July, 2007


Contents of this Issue:

  1. Science Highlight — Discovering the Many Sides of Cells
  2. Science Highlight — Floppy Hairs and Sound Waves
  3. Science Highlight — A Surprising Behavior of Yttrium Impurities
  4. Taking Aim at 500 mA
  5. Pottery Shards Reveal Clues about the Rise and Fall of the Roman Empire
  6. Apply Now for SSRL Structural Molecular Biology Summer School
  7. Register for 2007 SSRL/LCLS Users' Meeting and Workshops
  8. Workshop on STXM and X-ray Nanoprobe Capabilities and Needs for
    Geo-, Environmental, and Biological Sciences Held in July
  9. SSRL Users' Organization Update
  10. User Administration Update
  11. Photon Science Job Opportunities

1.  Science Highlight — Discovering the Many Sides of Cells
       (contacts: D.A. Hattendorf,; W.I. Weis,

Sro7 Figure
Model for how Sro7 may coordinate release of the SNARE Sec9 with arrival of a secretory vesicle.
[larger view]
The mechanics of a basic cellular process found in most living organisms, including humans, is less of a mystery, thanks to work done by Douglas Hattendorf and collaborators, in part at the Stanford Synchrotron Radiation Laboratory (SSRL). The team of researchers, led by Prof. Bill Weis of the Stanford University School of Medicine and of SSRL, solved the structure of a protein that assists in the developmental process of cellular polarization, which gives cells the ability to perform specific biological functions.

Polarization occurs in most living cells, and is a feature whereby different sides of individual cells are made up of membranes of differing composition that perform different functions. Epithelial cells in the lining of the gut, for example, possess membranes that absorb nutrients on one side and membranes that connect to other cells on the other side. Special surface proteins determine the composition and function of these differing membranes. The current study sheds light on how these surface proteins find their way to the proper membrane of a cell.

Within a cell, pockets called vesicles deliver proteins to the various surface membranes, fusing with the membrane to deliver its cargo. The mechanism behind how vesicles discriminate between the membranes-fusing with some but not with others-has been mostly a mystery.

Using SSRL Beam Line 11-1, Hattendorf and colleagues solved the crystal structure of a yeast cell protein key to the process of polarization, called Sro7p, which is also found widely in other organisms. It is known that the Sro7p protein is involved in vesicle-membrane fusion. This protein consists of two barrel shaped structures and an additional, unexpected feature— a "tail" consisting of 60 amino acids that is bound to the bottom surface of one of the barrels. The researchers found that this tail is responsible for regulating how Sro7p interacts with other proteins that are important for vesicle fusion. It is this property that may give vesicles the ability to preferentially fuse with some membranes and not others, allowing them to deliver proteins to the correct locations on the cell surface to establish cellular polarity.

To learn more about this research, recently published in the journal Nature, see the full scientific highlight at:

2.  Science Highlight — Floppy Hairs and Sound Waves
       (contact: G.C.L. Wong,

Scientists exploring the physics of hearing have found an underlying molecular cause for one form of deafness. The team, led by Gerard Wong, Professor of Materials Science and Engineering, of Physics, and of Bioengineering at the University of Illinois at Urbana-Champaign, report their findings in the February 2007 issue of the journal Physical Review Letters.

actin-espin system figure
(a) Diffraction from partially oriented F-actin-espin bundles shows many hexagonally coordinated peaks. The reconstructed 3D bundle structure is approximated in (b). (c) Diffraction from F-actin complexed with mutant espin. The diffraction pattern only shows a "bow-tie" pattern which is indicative of a liquid crystalline nematic phase, like that shown in (d). The mutant espins only weakly crosslink the actin filaments, but the normal espins arrange the actin into tight crystalline bundles.
Filamentous actin (F-actin) is a rod-like protein that provides structural framework in living cells. F-actin is organized into bundles by actin binding proteins, such as espin, a linker protein found in sensory cells, including hair cells in the cochlea of the inner ear. Within the cochlea, sound waves stimulate the hair cells and trigger nerve impulses that are transmitted to the brain.

Using small-angle x-ray scattering experiments at SSRL's Beam Line 4-2 and at APS, Wong's team solved the structure of various espin-actin bundles. The team learned that mutations in espin can cause actin in the bundles to 'melt' into a liquid crystal (the kind of molecular organization in a liquid crystal laptop screen), thereby making these bundles of protein filaments within the cochlear hair cells much floppier, impairing the passage of vibrations and resulting in deafness.

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

3.  Science Highlight — A Surprising Behavior of Yttrium Impurities
       (contacts: B. Chen,; J. Banfield,

Experimental Setup
The EXAFS experimental setup.
Structurally incorporated impurities have been shown to have systematic effects on the rate of the thermally driven transformations in titania nanoparticles. For example, the anatase-to-rutile transformation is slowed when anatase nanoparticles are doped with a cation of valence > +4, but favored when the valence < +4. Based on these observations, Y3+ dopants should promote the anatase-to-rutile transformation. However, prior studies showed that the transformation is actually inhibited by such impurities. So far these observations have remained unexplained.

Recently, scientists from University of California Berkeley and Lawrence Berkeley National Laboratory, in collaboration with SSRL beam line scientists at BLs 10-2 and 11-2, used extended x-ray absorption fine structure (EXAFS) experiments on yttrium-doped titania nanoparticles to determine the local structural environment of Y3+ impurities.

Results indicate that yttrium impurities are mostly present as individual, oxygen-coordinated atoms at the titania surface (i.e., as YO6 groups) and about 15% of the surface oxygen sites are bound to Y. Together with the observation of the structural modification and phase transformation retardation in complementary wide-angle x-ray scattering experiments for the study, the researchers found that the low concentrations of yttrium surface impurities on nano-anatase reduce surface energy and inhibit nanoparticle growth over a large temperature range. The findings demonstrate the effectiveness of surface bound impurities of stabilizing nanoparticle size and phase, an issue of great importance for retaining the materials properties of nanoscale catalysts that operate at high temperatures.

To learn more about this research, recently published in the journal, Physical Review Letters, see the full scientific highlight at:

4.   Taking Aim at 500 mA

       —Brad Plummer, SLAC Today, July 12, 2007

John Schmerge in the SPEAR3 injector vault with the laser setup and cathode gun used to test a new method of generating electrons.
Last month a small team of SLAC physicists conquered another challenge in the quest to take the SPEAR3 synchrotron permanently up to its full operational capability of 500 milliamperes (mA). Using the existing electron gun and accelerator, the team demonstrated that a laser can be used to create a large pulse of electrons, which will aid rapid injection of beam into the ring.

As it now operates, SPEAR3's electron gun produces electron pulses as the gun's cathode is heated to nearly 2,000 degrees Fahrenheit (1,050 Celsius). This configuration allows only minimal control over the timing and the amount of power in each pulse because the hot cathode continually emits a pulsed stream of a few thousand electron bunches, of which only five or six are useable for injection into the SPEAR3 storage ring. Using a brief laser pulse to stimulate a burst of electrons eliminates limitations associated with a hot cathode, producing a single, precise electron microbunch with much higher charge.

"This is a first step," said physicist John Schmerge who worked on the project. "Basically what we've done is turn off the heater and put in a laser."

The Linac Coherent Light Source (LCLS) injector gun already in operation also uses a laser to produce electrons. In fact, the laser used by Schmerge and colleagues is the same one used to test the LCLS prototype electron gun.

SPEAR3 is designed to operate at a current of 500 mA, but at the moment the synchrotron is limited to 100 mA until the upgrade of a few systems to accommodate the higher power is completed and required safety reviews have been performed and approaches approved. Running at 500 mA, the present scheme of refilling the ring three times a day would cause a large variation of beam power on delicate x-ray optics between fills, reducing beam stability and data quality. Upgrading the electron gun to operate by laser will enable SPEAR3's operators to inject new current into the ring, not only much more quickly, but more frequently and in shorter intervals to reduce the variation of stored current between injection cycles—a process called "top off injection." This rapid mode of injection will minimize the thermal strain on delicate optics and will even out disruption to the users as the storage ring current is maintained at a nearly constant level.

5.   Pottery Shards Reveal Clues about the Rise and Fall of the Roman Empire

       —Brad Plummer, SLAC Today, July 25, 2007

Phillipe Goudeau (left) and Phillipe Sciau visited SSRL in early July to study fragments of ancient pottery. Here, Sciau holds a replica of the clay pots.
Call it old-school outsourcing - more than 2,000 years ago, the Roman Empire exploited the labor of artisans in southern Gaul (modern-day France) to mass-produce a particular style of Italian pottery craved by the Roman populace. Now, synchrotron light is helping to detail the particulars of how this pottery was produced and how the method of production and quality of the ware reflects the rise and fall of the Roman Empire.

"This pottery and how it is made—how the technology developed and declined—gives us clues about the end of the Roman Empire," says Philippe Sciau, one of two visiting researchers from the National Center for Scientific Research (CNRS) in France.

The design of the pottery originated in Northern Italy, but as demand rose, factory ovens for mass production were built in southern Gaul. The Romans conscripted Gaulish workers to fire as many as 30,000 pieces at a time in these enormous ovens. Read more at:

6.   Apply Now for SSRL Structural Molecular Biology Summer School
       (contact: S. DeBeer George,

The 2007 Structural Molecular Biology (SMB) Summer School, co-chaired by Serena DeBeer George, Clyde Smith, and Thomas Weiss, will be held September 9-14, 2007 at SSRL. The SMB Summer School will highlight the use and application of x-ray absorption spectroscopy, macromolecular crystallography, and small angle x-ray scattering. Presentations from experts in the fields will be aimed at the graduate student level, but will also be appropriate for researchers with more
2007 SMB
School image
For more information and to apply, see:
extensive experience in one of these techniques with an interest in using other complementary methods to further the scope of their research.

The six-day school will consist of three days of lectures from experts in the field, followed by three days of hands-on practical sessions. Enrollment will be limited, so prospective participants should apply by the August 15, 2007 deadline.

7.   Register for 2007 SSRL/LCLS Users' Meeting and Workshops

      (contact: C. Knotts,

Users mtg logo
There are several very exciting events planned for the upcoming SSRL/LCLS Users' Meeting, beginning with a special symposium on September 28-29 to look into the future of x-ray science.

A joint SSRL/ALS Workshop on Synchrotron Techniques will follow on Sunday, September 30. The workshop will provide a tutorial-style basic introduction to the various experimental techniques available at synchrotron facilities, with the goal of helping users make the most out of their beam time.

The main Users' Meeting, on October 1-2, will feature presentations on recent developments and new opportunities in structural biology and spectroscopy, material and environmental science, ultrafast science and LCLS instrumentation. A special keynote presentation will be given by Nobel Laureate Professor Roger Kornberg. Share your recent research results at the Users' Meeting by submitting an abstract for oral or poster presentation, due August 15 and September 4, respectively. Don't forget that the 2007 SSRL/LCLS dinner is free for students who submit an abstract! (send abstracts to

Awards for outstanding technical and scientific accomplishments in synchrotron radiation-based science will be presented the evening of Tuesday, October 2, immediately preceding the meeting dinner. Please take a few minutes to recognize your colleagues' outstanding contributions by nominating them for the following awards:

Several concurrent workshops will be offered on October 3: XANES Spectroscopy (Data Collection, Analysis, and Simulation); Microfocusing; Imaging and X-ray Microscopy; and Research Opportunities at the X-ray Pump-Probe Facility at the LCLS.

More information and registration for all of these events can be found at:

8.   Workshop on STXM and X-ray Nanoprobe Capabilities and Needs for Geo-, Environmental, and Biological Sciences Held in July
      (organizers: S. DeBeer George,; J. Bargar,; H. Ohldag,

A two-day workshop on STXM and x-ray nanoprobe geo-, environmental, and biological science was hosted by SSRL at the Bechtel International Center, Stanford Campus, on July 9-10, 2007. The workshop brought together 49 leading international STXM experts and scientists from three continents to explore future possibilities, challenges and needs for STXM in these scientific areas. The keynote talk was given by Harald Ade (NCSU). Subjects explored in detail included scientific drivers, optics and beam design, end station instrumentation and detectors. An extensive review of STXM and nanoprobe facilities in Europe and North America was presented by members of the respective facility teams. Key conclusions from the workshop include the finding that there is overwhelming demand for beam time at high-resolution spectromicroscopy facilities, that the present spatial resolution limit of 20 to 40 nm provides critical capabilities for a wide range of scientific problems, but that 5 to 10 nm resolution (expected in the next few years) will open exploration of new types of scientific problems, that the ability to quickly measure K-edge spectra from C and elements up through S, Ca, and Fe (~250 through 7200 eV) is of paramount importance, but that there is no existing single facility that provides such capability.

The workshop was supported by DOE offices of Basic Energy Science and Biological and Environmental Research.

A workshop report will be available at:

9.   SSRL Users' Organization Update

      (contacts: C.S. Kim (SSRLUOEC Chair),; C. Knotts,

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on Friday, July 20. Plans for the September 28-October 3 Special Symposium, SSRL/LCLS Users' Meeting, and Workshops were discussed.

Other topics included undergraduate research and user suggestions from the user survey which was conducted in January 2007 and completed by 370 users. Results comprising users' opinions on scientific areas, proposed facilities and initiatives, SSRL operations, and user resources were presented at the February 2007 meeting of the SSRL Scientific Advisory Committee (SAC). The presentation itself can be found on the SSRLUOEC website at:

Hendrik Ohldag joined the meeting to summarize the July 9-10 Workshop on STXM and X-ray Nanoprobe Capabilities and Needs for Geo-, Environmental, and Biological Sciences. And, Apurva Mehta gave a presentation on the New Directions in X-ray Scattering Workshop held last December.

Notes from SSRLUOEC meetings are posted on the web at:

The SSRLUOEC is currently seeking nominations to fill two SSRLUOEC positions later this year (environmental sciences and macromolecular crystallography).

Ballots will be distributed in September, and candidates will be elected by the SSRL user community by majority vote. Election results will be announced during the annual Users' Meeting. The next SSRLUOEC meeting will be held on the afternoon of Tuesday, October 2.

10.   User Administration Update

      (contacts: C. Knotts,; L. Dunn,

SSRL's current experimental run ends at 6:00 am on Monday, August 6; user operations will resume on most beam lines in early November 2007. The FY2008 SPEAR3 preliminary operating schedule which includes information on scheduled maintenance and accelerator physics studies is available at:

Spokespersons with active proposals who are interested in requesting beam time on X-ray/VUV beam lines for the next scheduling period (November 2007-January 2008) must submit beam time request by the August 17 deadline.

A message will be sent to Macromolecular Crystallography spokespersons in August regarding Beam Time Requests for the first scheduling period in the FY2008 experimental run.

11.   Photon Science Job Opportunities

A number of positions are currently available at SSRL and LUSI. 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: 30 JUL 2007
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