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SSRL Headlines Vol. 10, No. 2  August, 2009


Contents of this Issue:

  1. Science Highlight — Riboswitch Crystal Structure May Lead to New Antibiotic Targets
  2. Science Highlight — Understanding Charge Transport in Plastic Electronics
  3. From the Acting Director of SSRL
  4. BL12-2 Microbeam Capability Established and Commissioned
  5. Register for the SSRL/LCLS Users' Conference - October 18-21, 2009
  6. Users Needed to Serve on the SSRL and LCLS Users' Organization Executive Committees
  7. Abstracts for User Science Posters Due October 9
  8. Please Report SSRL-Related Papers, Invited Talks, and Awards
  9. Recent Awards to Photon Science Faculty
  10. Ultrafast X-ray Summer School Held June 2009
  11. Macromolecular Crystallography Beam Time Requests Due September 15

1.  Science Highlight — Riboswitch Crystal Structure May Lead to New Antibiotic Targets
       (contact: J.E. Wedekind,

highlight figure
Crystal structure of the preQ1 riboswitch aptamer domain from Thermoanaerobacter tengcongensis See JBC article.
Like a busy city street needing stoplights to control chaos, cells need constant feedback to govern biochemical pathways. Most organisms engage in a balancing act to control the production of proteins, including the enzymes that produce metabolite molecules necessary for life. Like traffic signals reacting to the amount of traffic, cells can "switch" on or off biosynthetic enzymes depending on the cellular abundance of metabolites. In the past decade, researchers have discovered an elegant control mechanism that involves an unusual switch comprised of ribonucleic acid (RNA). Such 'riboswitches' are present in bacteria as well as some plants and fungi. They are unusual because they exist as segments in messenger (m)RNA, which has traditionally been perceived as only a passive carrier of genetic information connecting the DNA genes to ribosomes, the protein synthesis factories of the cell. When cellular abundance of a specific metabolite is high, the riboswitch region forms a pocket that harbors the metabolite, causing structural changes in the mRNA that physically block sequences critical for mRNA decoding by the ribosome. This causes the amount of the encoded enzyme to decrease and thus the amount of metabolite production to decrease until the metabolite concentration is too low for riboswitch binding. The mRNA is then unblocked and enzyme production begins again.

A research team led by Joseph Wedekind at the University of Rochester Medical Center (NY) crystallized the smallest naturally occurring riboswitch known, preQ1, from the hot spring bacterium Thermoanaerobacter tengcongensis. They solved the structure using MAD phasing at SSRL Beam Line 7-1. The researchers observed that the RNA sequence forms a compact structure with most of the RNA residues making multiple contacts to neighboring bases. Such visualization accounted for the strong binding affinity of the riboswitch to its metabolite and the conservation of specific bases in the RNA sequence.

Because riboswitches regulate the production of as many as 4% of bacterial genes, understanding their form and function relationships may lead to a new way to combat disease-causing bacteria that are resistant to current antibiotics. The researchers will continue to investigate this riboswitch from other bacterial species to determine if this method of metabolite binding and gene regulation is conserved. This work was published in April 24 issue of the Journal of Biological Chemistry.

To learn more about this research see the full scientific highlight.

2.  Science Highlight — Understanding Charge Transport in Plastic Electronics
       (contacts: L. Jimison,; M.F. Toney,; A. Salleo, Stanford University)

highlight figure
Phase mode AFM image of directionally crystallized P3HT, revealing the unique grain structure.
Recent advances in materials research are setting the stage for macroelectronics to have a disruptive effect on everyday technology. While microelectronics focuses of the miniaturization of electronic devices (think of the shrinking iPod), macroelectronics is the replication and integration of microelectronic devices onto large areas such as display backplanes (big screen TVs and electronic billboards), large-area photovoltaics (flexible solar cells) and radio frequency ID tags. One class of materials that has demonstrated great promise as the semiconducting layer in these macroelectronics devices is polymer semiconductors, which allow for potentially inexpensive manufacturing from solutions.

Often, thin films of these polymer semiconductors are semicrystalline, consisting of small regions or grains where the molecules are ordered; these grains are separated by grain boundary regions where molecules are amorphous or disordered. It is believed that charges can easily traverse the crystalline grains, but are hindered by the disrupted structure at the grain boundaries. By understanding exactly how the grain boundaries slow charge transport, the polymer film microstructure can be engineered for improved performance.

Researchers at Stanford University, including graduate student Leslie Jimison and Prof. Alberto Salleo, collaborated with SSRL staff scientist Mike Toney to perform x-ray diffraction experiments at SSRL Beam Lines 11-3 and 7-2. The researchers investigated the properties of unique, aligned thin films of semicrystalline poly(3-hexylthiophene) (P3HT). Diffraction data gave insight into film microstructure, including orientation of chains within grains and possible grain boundary structure. In one direction of the anisotropic film, there is the potential for polymer chains in adjacent crystallites to cross the grain boundaries, which may make these grain boundaries less detrimental to transport. Electrical measurements of thin film transistors confirmed that charge transport is indeed more efficient in directions where this is more likely to occur.

Results in this work help strengthen the understanding of the relationship between polymer film microstructure and semiconductor performance by giving insight into how crystalline orientation, which defines grain boundary structure, can be optimized for efficient charge transport in electronic devices. This work was published in the April 27 issue of the journal Advanced Materials.

To learn more about this research see the full scientific highlight.

3.   From the Acting Director of SSRL
       August 7, 2009 SLAC Today Article by Piero Pianetta

P. Pianetta
P. Pianetta
With the growth of photon science at SLAC, I thought it would be interesting to discuss the Stanford Synchrotron Radiation Lightsource's research portfolio and how it has been changing over the past several years. However, first I would like to give a short review of the past year. 2009 has been a great year for SSRL with an average uptime of 99 percent and excellent user satisfaction. This level of uptime and user satisfaction always amazes me when I reflect that this is a 24/7 operation. Not only must the accelerator operate flawlessly, the beam lines must be made ready on a daily basis for the rapidly changing sets of users that cycle through the lab. In many respects, this is much like a production line where dedicated support staff are critical to the smooth operation of the program, whether it is making sure that the SPEAR3 storage ring runs day in and day out, setting up for a new experiment or replacing a failed piece of equipment on short notice. Although the SSRL annual shutdown started on August 10, everyone will be busy in a different ways with maintenance and upgrade activities for the next few months until the user run cycle starts again for another nine months.

Other milestones we have met this year include the finishing of the SPEAR3 beam line upgrade project, with the completion of three stations on Beam Line 4 and successful routine user operation at 200 mA in top-off mode. This mode of operation was the result of hard work from the accelerator, beam line and Radiation Physics Department staff in close cooperation with the Department of Energy Site Office. Ultimately, this mode of operation will allow us to deliver stable beams at nearly constant current at up to 500 mA. Finally, DOE has come through this year with almost 10 million dollars to enable SSRL to undertake badly needed infrastructure and beam line upgrade projects.

As I mentioned at the beginning of this article, I wanted to discuss the changing experimental portfolio at SSRL. Early in SSRL's history, the high profile areas were in the development of x-ray absorption spectroscopy, surface diffraction and core level photoelectron spectroscopy. These techniques are now mature and are as strong as ever, being applied to real world applications ranging from understanding photosynthesis to understanding how advanced batteries work to the development of gate dielectrics for the integrated circuits used in the PlayStation3. With the high brightness of SPEAR3, new techniques are being developed and added to the capabilities being made available to users. One of the new research areas is microscopy over a wide range of length scales. Focused beams at the micron scale are being used at Beam Line 2-3 to study how and where metals accumulate in plants and fish in the environment. In addition, improvements in the focusing capabilities at Beam Line 12-2 have allowed protein crystals as small as 5 microns to be studied. A microscope employing zone plates to focus the beam is under development and will soon provide 30 nm beams to study properties of magnetic domains at Beam Line 13-1. Not only can x-rays be focused to probe materials in a small spot, but they are being used in an actual x-ray microscope, at Beam Line 6-2, that provides 2- and 3-dimensional images in real space at 30 nm resolution, showing objects ranging from biomaterials such as bones and teeth to advanced fuel cell materials and nanostructures. Rounding out SSRL's imaging capabilities is the lensless imaging station at Beam Line 13-3, which uses the two-dimensional pattern of soft x-rays scattered from the sample to image nanostructures at resolutions better than 30 nm. The extreme capabilities of the Linac Coherent Light Source will make it possible to use this technique to image objects at Ångström resolution. Finally, the advent of the LCLS has also resulted in a renewed interest in time-resolved studies at SPEAR3. This has been made practical through the development of the low-alpha mode to give shorter pulses and special fill patterns, for specific high intensity bunches in SPEAR3 that can be synchronized with a pulsed laser at the beam line experiment.

In this short article, I have been able to give only an incomplete summary of research at SSRL, but I encourage you to scan through the SSRL Science Highlights for a more complete picture of the exciting results that are coming out every week.

-Piero Pianetta

4.   BL12-2 Microbeam Capability Established and Commissioned
       (contact: S.M. Soltis,

BL12-2 is the high-intensity, state-of-the-art undulator beam line for advanced macromolecular crystallographic studies funded through The Gordon and Betty Moore Foundation in cooperation with the California Institute of Technology. The successful implementation of microbeam capability for studying microcrystals and higher quality portions of larger crystals was recently completed.

A precision goniometer, constructed in-house, based on a rotary air bearing capable of exceeding speeds of 360 degrees/s and with a demonstrated a sphere of confusion of ~1 mm was installed, and it includes x, y and z stages for precise sample positioning. In addition, a new in-line camera for viewing micron-sized samples along the beam axis was commissioned. The in-line camera system, procured from Accel, was originally developed on the ESRF microfocus Beam Line ID13. A new automated collimation system, designed in-house, was also commissioned and collimates the focused beam to yield smaller beams (20, 10 and 5 microns FWHM). Microcrystals of the virus-free recombinant form of the polyhedra cypovirus (kindly supplied by Prof. P. Metcalf [Metcalf et al., Nature 446, 97, 2007]) were used in the initial commissioning studies. These crystals are typically 5 x 5 x 5 mm3 in size and could be easily aligned with the precision goniometer and in-line camera. A data set to 1.65 Å was recorded in less than 7 minutes, marking a significant milestone for the advanced capabilities of BL12-2.

5.   Register for the SSRL/LCLS Users' Conference - October 18-21, 2009
       (contact: C. Knotts,
User Mtg banner

October 9 is the early registration deadline for the Annual SSRL/LCLS Users' Conference and Workshops which will be held October 18-21, 2009. The event kicks off on October 18 with a special symposium celebrating 35 years of outstanding science at the Stanford Synchrotron Radiation Lightsource. In addition to reviewing technical accomplishments and research highlights, future scientific and technical opportunities for SSRL will be discussed.

LCLS/SSRL 2009 officially begins on October 19 with a joint plenary session featuring updates from SLAC and DOE, a preview of the workshops, a user science poster session, and a keynote presentation. The Spicer Young Investigator Award, Klein Professional Development Award, Lytle Award, and the Outstanding Student Poster Session Awards will be presented on this day.

On October 20, concurrent sessions will focus on SSRL and LCLS facility development, instrumentation, and user science, followed by meetings of the respective SSRL and LCLS Users' Organizations.

On October 21, several concurrent workshops will be held including Microimaging; Nanoscale Imaging with the SSRL STXM; Macromolecular Crystallography; Soft X-ray Beam Line Experiment Preparation; and X-ray Pump Probe Experiment Preparation. Register for all events at:

6.   Users Needed to Serve on the SSRL and LCLS Users' Organization Executive Committees
       (contact: C. Knotts,

The SSRL and LCLS Users' Organization Executive Committees need scientists to represent their entire user community and interact with management to help determine potential opportunities and strategic plans for the future.

With the exception of the chairs, elected members serve a three-year term. Chairpersons, currently Wayne Lukens for the SSRL UOEC and Linda Young for the LCLS UOEC, will serve on the committee for two additional years to facilitate continuity of activities.

If this sounds like something that interests you, or perhaps a colleague, submit your nomination(s) by September 29. See the following links for current committee membership and the positions that need to be filled:


7.   Abstracts for User Science Posters Due October 9

We invite you to share your research during the Poster Session of the Annual Users' Meeting on October 19. We welcome posters on all photon science-related research and development at SLAC and students, in particular, are encouraged to present posters for the student poster competition. Representatives of the Users' Organization will judge student posters and prizes (including $100.00 award) for the most outstanding posters will be presented during the meeting. Additionally, students presenting posters are eligible to receive a free dinner - just sign up and indicate this when you register.

Submit abstract:

Poster session instructions:

8.   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:

9.   Recent Awards to Photon Science Faculty

B. Hedman
IXAS Award to Britt Hedman. The International X-ray Absorption Society (IXAS) announced its 2009 Awards for achievement in the field of XAFS. Professor Britt Hedman, a member of the SLAC Photon Science faculty and Deputy Director of SSRL, was named as co-recipient of the IXAS Outstanding Achievement Award. The Award is shared with Professor Frank de Groot, Utrecht University, Netherlands. This is the highest award of the International XAFS Society and is given every three years for outstanding accomplishments across all x-ray absorption spectroscopy disciplinary areas, including experimental and theoretical studies. The award, formally named the IXAS Edward Stern Outstanding Achievement Award, recognizes the contributions of Britt in the development of technology and methodologies for low- and hard- energy XAFS and extensive applications to the study of metalloprotein active sites. Britt's research has been carried out primarily at SSRL, within its Structural Molecular Biology program, which is funded by DOE-BER and NIH-NCRR.

E. Solomon
Professor Edward I. Solomon, Departments of Chemistry and Photon Science, has been awarded the honor of being chosen to the first class of American Chemical Society Fellows for excellence in chemistry. The honor is given to members who "share a common set of accomplishments, namely true excellence in their contributions to the chemical enterprise coupled with distinctive service to ACS or to the broader world of chemistry," says Immediate Past-President Bruce E. Bursten, who championed the creation of the program.

10.   Ultrafast X-ray Summer School Held June 2009

The Third Annual Ultrafast X-ray Summer School (UXSS 2009) was held from June 15-19, 2009 at the SLAC National Accelerator Laboratory and sponsored by the PULSE Institute for Ultrafast Energy Science. The summer school was a weeklong residential event that brought together about 100 students, post-doctoral researchers and other young and established scientists from diverse backgrounds. Particular emphasis was given to new scientific opportunities enabled by the world's first hard x-ray free electron laser, the Linac Coherent Light Source (LCLS) which underwent a spectacular turn on only months before. This year's school offered pedagogical lectures by world leading experts in free electron laser and accelerator science, atomic molecular and optical physics, condensed matter physics, physical chemistry and coherent imaging covering both experiment and theory. In addition, a day of research talks highlighted recent experimental advances. A special session was devoted to possibilities for future light sources, and there was a historical perspective of 35 years of photon science at SLAC. The summer students enjoyed a packed schedule that included tours of the LCLS and SSRL as well as a trip to the California Academy of Sciences; however, the highlight of the summer school may well have been the competition for the best mock beam time proposal for LCLS in which the students worked with LCLS and PULSE scientists to learn how to propose a compelling and technologically sound proposal.

About PULSE: The PULSE Institute for Ultrafast Energy Science at SLAC and Stanford University is jointly funded by the Department of Energy, Office of Science Basic Energy Sciences division of Material Science and Engineering and Chemical Sciences. More information on PULSE, the UXSS series and the LCLS can be found respectively at:

11.   Macromolecular Crystallography Beam Time Requests Due September 15
       (contact: L. Dunn,

If you are interested in requesting beam time on macromolecular beam lines during the first scheduling period (Nov 2009 - Feb 2010) of our 2010 experimental run, submit your request(s) by September 15. For reference, the 2010 operating schedule including maintenance days, holiday shutdown periods, etc., is available at:

Submit beam time requests by logging into the SSRL User Portal at:

Enter your email address and your password or click on 'request a password'. Remember to submit a SEPARATE request for each beam time allotment requested. We have tried to make the process to submit multiple requests easier by adding a feature that allows you to clone a previous request.

If you would like beam time during this first scheduling period, but do not have an active proposal, please submit a Rapid Access Request by September 15.


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: 3` August 2009
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