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SSRL Headlines Vol. 9, No. 6  December, 2008


Contents of this Issue:

  1. Science Highlight — A Golden Ruler Used to Measure the Stretching Rigidity of Short-length Scale DNA
  2. Darwin's Dinobird Fossil Analyzed at SSRL
  3. Holiday Greetings from the SSRL Director
  4. First Electrons Stream Through the LCLS
  5. From the SLAC Director: The SPC Visits Again
  6. Popular Microprobe on Beam Line 2-3 Moves to Full-time
  7. Call for Publications

1.  Science Highlight — A Golden Ruler Used to Measure the Stretching Rigidity of Short-length Scale DNA
       (contacts: R. Mathew-Fenn,; P.A.B. Harbury,

Molecular Ruler figure
Probability distance distribution curves
DNA is softer and stretchier than previously believed, at least on the short length scales of up to 20 base pairs. This finding is the result of a recent study conducted in part at SSRL's biological small-angle x-ray scattering Beam Line 4-2 by a team of researchers from Stanford University. The results were published in the October 17 edition of the journal Science.

In a cell nucleus, enzymes constantly pull, twist and bend DNA molecules in order to transmit and express genetic information. Therefore, the bending, twisting and stretching rigidity of DNA affect how it wraps around histones to form chromosomes, supercoils during replication, bends and stretches upon interactions with proteins and packs into the confined space within a virus particle. Understanding these mechanical properties could deepen our understanding of how it functions in cells. Until now, however, measuring the stretching rigidity of DNA has been difficult on short length scales.

The team of Stanford researchers, led by Pehr Harbury, solved the problem using specially prepared nanocrystals that contain 75 gold atoms. The nanocrystals were attached to modified sections of DNA of various lengths - from 3 to 35 base pairs - and used as reference points. Using small-angle x-ray scattering interference between the nanocrystals for this series of DNA double helices in solution, the team found that, for short duplexes up to 20 base pairs in length, DNA is far "softer" and more elastic than previously thought by an order of magnitude. Although the research is ongoing, the team believes this cooperative stretching behavior could underlie a mechanism of molecular communication between neighboring strands of DNA during transcription and other key processes.

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

2.  Darwin's Dinobird Fossil Analyzed at SSRL

A keystone of evolutionary history, the Thermopolis Archaeopteryx fossil, arrived at SSRL in December to undergo a revolutionary type of analysis for fossil studies. Using intense x-ray beams, scientists search for spatially distributed chemical characteristics of the "dinobird" that have eluded all previous scientific analyses.

A team of researchers attempted to uncover secrets of the Archaeopteryx hidden from view since the creature sank to the bottom of a shallow lagoon and became entombed in limestone some 150 million years ago. Only ten Archaeopteryx fossils have been found and studied. These specimens have undergone extensive visual analyses and even CT scans in the past, but never anything as comprehensive as the element-specific x-ray fluorescence imaging technique being utilized at SSRL on BL6-2. Here, researchers made the first maps of the chemical elements hidden within one of the best preserved specimens, possibly including remnants of soft tissue-not just bone. Approximately 16 by 16 inches (40 by 40 centimeters) in size, the Thermopolis specimen was originally discovered near Solnhofen, Germany, and is now owned by the Wyoming Dinosaur Center, located in Thermopolis, Wyoming. Read the full press release at:

Archaeopteryx at the Beam Line
Archaeopteryx Fossil at BL6-2 (Photo by Nikola Stojanovic)

3.   Holiday Greetings from the SSRL Director

SSRL Director Jo Stohr 
Jo Stöhr
Dear Users, Colleagues and Friends of SSRL,

As we near the end of 2008, I would like to take a moment to send you my best wishes for a happy holiday and to reflect back on many high points from the past year.

During the FY2008 run (November 2007-August 2008), SPEAR3 continued to provide very stable beam for >97% of the scheduled time. Over >2,000 researchers benefitted from 5,027 hours of beam which were delivered on our 28 experimental stations for a total of 91,717 hours delivered to users. Also during the past three scheduling periods, >1,200 experiments were conducted on 391 different proposals. Users consistently rated their overall scientific experience at SSRL very highly (96% ranked their experience as excellent or very good).

The FY2009 run has started off well. You may recall that we opened a new Beam Line 13 last year. In November 2008 we opened a newly rebuilt Beam Line 4. We project 5,100 hours for users in the current run, contingent on the final operating budget we receive when the continuing resolution ends in March 2009.

SSRL continues to provide valuable scientific training experience for the future workforce, indicated by the large number of on-site users who are undergraduate students, graduate students, or postdoctoral fellows (>60%). Since SSRL began user operations in 1974, users have reported approximately 8,600 scientific publications based on research conducted at SSRL. In the last three years alone, users published >1,000 papers including >95 student theses (reported to date). I encourage you to inform us of your SSRL-related publications, awards, and invited lectures as this information provides an important metric for our funding agencies. The current list of publications that have been reported to SSRL to date can be found at Please forward information on your updated publications to Lisa Dunn,, or use the web form at:

At a ceremony at SLAC on October 15, Dr. Patricia Dehmer, Deputy Director for Science Programs at the DOE Office of Science, and SLAC Director Persis Drell announced SLAC's new name, the SLAC National Accelerator Laboratory. Since it is customary for National Laboratories to have only one "Laboratory" on site, SSRL became the Stanford Synchrotron Radiation Lightsource. We will continue to use the SLAC and SSRL abbreviations that are so well-known throughout the world-wide scientific community.

Approximately 315 individuals participated in the various activities of the second joint LCLS/SSRL Users' Meeting held October 15-18, 2008. The four-day event began with an LCLS-themed science and development session held concurrently with two SSRL-related workshops: Advanced Topics in EXAFS Analysis and Applications; Crystallography Made Easy through Automation. The next full-day plenary session was devoted to a joint LCLS/SSRL session including LCLS and SSRL overview talks, updates from Washington, science highlights, a keynote speech by SLAC Director Persis Drell on the future of photon sciences at SLAC (see and ended with the user scientific poster session, reception and dinner. Activities resumed on Friday with an SSRL session devoted to science and technical developments as well as two concurrent LCLS workshops: Application of Coherent X-rays at the LCLS; Atomic, Molecular & Optical Physics with the LCLS. The final event was an all-day joint SSRL/LCLS/ALS workshop on Soft X-ray Beam Line for Material and Energy Science at the LCLS. We have already started planning the next Users' Conference, so mark your calendar and plan to participate October 19-21, 2009.

We offer our congratulations to the recipients of awards for outstanding scientific and technical achievement in synchrotron radiation-based science, including prizes for Outstanding Student Scientific Posters: Rebecca Fenn (Stanford University), Reassessing the Mechanical Properties of DNA; Sarah Hayes (University of Arizona), Characterization of Mine Tailings Using Complimentary Synchrotron Techniques; Thomas Lohmiller (UC Berkeley), What is the Role of Ca in Photosynthetic Water Oxidation: Polarized X-ray Absorption Spectroscopy of the Ca-depleted Oxygen Evolving Complex of Photosystem II; Jasquelin Pena (UC Berkeley), Zinc Surface Speciation on Biogenic Manganese (IV) Oxides: Influence of pH and Surface Coverage; Ming Yi (Stanford University), Angle-resolved Photoemission Spectroscopy on the New Iron-based High Temperature Superconductors; Diling Zhu (Stanford University), Beyond Fourier Transform Holography: Reference Guided Phase Retrieval. The William Spicer Young Investigator Award was presented to R. Joseph Kline, a staff scientist at the National Institute of Standards and Technology (NIST) in Gaithersburg, MD. Ajay Virkar, a graduate student in the Department of Chemical Engineering at Stanford University, received the Melvin P. Klein Professional Development Award. And, the SSRL Users' Organization Executive Committee presented the 2008 Farrel W. Lytle Award to Robert A. Scott in recognition of his contributions to synchrotron radiation research.

In 2009 we anticipate implementing top-off as well as higher current operations pending reviews and approvals. We have also started to prepare for the more distant future of SSRL. You can read about the potential new x-ray source PEP-X on our website, and we have also posted a document put together by SLAC and Berkeley scientists on future scientific opportunities with x-rays. We are now working with Berkeley, Argonne and Brookhaven on a document that makes the case for future US investments in x-ray science and technologies, and we hope to be able to share this with you early in 2009.

I want to thank everyone who provided feedback and suggestions to us through the 2008 users' survey, the end-of-run surveys, and especially those individuals who serve on SSRL's advisory committees - the SSRL Scientific Advisory Committee (SAC), Proposal Review Panel (PRP), the SMB Advisory Committee (SMBAC) and the SSRL Users' Organization Executive Committee. Guidance from these groups is extremely important to help us plan and move forward in the wisest and most effective ways. We continue to be grateful to our funding agencies - the Department of Energy's Office of Basic Energy Sciences for providing the core operations funding and support for materials research and the DOE Office of Biological and Environmental Research and the National Institutes of Health NIGMS and NCRR Programs for support of the structural biology program. Without their effective support, we would not be able to push the scientific forefront and effectively serve our diverse and growing user community. I urge you to continue to let us know your opinions and ideas - it helps us to serve you better, to improve our operations and to plan for our future.

In closing, on behalf of SSRL and its staff, let me extend our very best wishes to all of you for this holiday season and for 2009!

—Jo Stöhr, SSRL Director

4.   First Electrons Stream Through the LCLS
       December 15, 2008 SLAC Today Article by Kelen Tuttle

LCLS Control Room
Teams of physicists and technicians worked throughout the day on Saturday, December 15, to take the first beams of electrons all the way through the LCLS to the beam dump. (Photo by Brad Plummer)
On Saturday, December 13, a series of electron beams zipped down the full length of the Linac Coherent Light Source for the first time. In an exciting round of first-ever tests, bunches of electrons traveling very close to the speed of light traveled from the injector, down the final third of SLAC's linac into the beam transport hall and through the undulator hall, ending their journey in the electron beam dump.

The first shot of electrons tripped an improperly configured shut-off monitor in the beam transport hall and caused a five-hour delay. But once the situation was rectified, subsequent attempts to reach the beginning of the undulator section took only 10 minutes. Once final preparations were made to complete the test and send the beam into and through the undulator hall, the beam reached its target in only two shots, confirming the predictions of Paul Emma, head of the LCLS accelerator physics group. The control room erupted in cheers.

"This is a major milestone, and one that we've been working toward for quite some time," said SLAC Director Persis Drell. "Congratulations to everyone who made this test a success. I'm looking forward to the start of LCLS operations next year!" Read more...

5.   From the SLAC Director: The SPC Visits Again       

On December 5 and 6, lab management hosted the semi-annual visit of our Scientific Policy Committee. The SPC is now one of four subcommittees of our Board of Overseers, which is chaired by Stanford Vice President for SLAC Bill Madia. This fall, for the first time, all subcommittees completed meetings, and a full board meeting will take place on December 19. The new system of Stanford University oversight is in place and seems to be working well.

The SPC is now firmly focused on oversight of our science programs. Highpoints of this visit were Linac Coherent Light Source progress, plans for early science and the light source strategy developments led by Jo Stöhr and Lawrence Berkeley National Laboratory's Roger Falcone. The SPC was interested to hear about the future Particle Physics and Astrophysics programs and developments with SLAC participation in the ATLAS experiment at the Large Hadron Collider. Tor Raubenheimer gave an excellent talk on the laboratory's accelerator science strategy. There was also a series of talks about some of the science currently going on at the lab, including lovely talks on recent experiments at FLASH and early results from the Fermi Gamma-ray Space Telescope.

This meeting was the final meeting for Professor Doug Rees of the California Institute of Technology, who has chaired the SPC for the past two years through a time of great change. We owe Doug thanks for his dedication, wise advice and unwavering support during a trying time for the laboratory. At the May 2009 meeting, Professor Graham Fleming from University of California at Berkeley will take over as chair and the board membership will rotate. The new membership will be posted on the director's Web page once the invitations to the new members have been finalized.

6.   Popular Microprobe on Beam Line 2-3 Moves to Full-time
       December 8, 2008 SLAC Today Article by Michael Torrice

BL2-3 Microprobe
BL2-3 microprobe studies chemical details of environmental, biological and archaeological samples. (Photo by Sam Webb)
Metal-tipped spider fangs, ancient Roman pottery shards and arsenic-sipping ferns have one thing in common. They've all been studied by the x-ray microprobe on Beam Line 2-3.

For the past two years, the microprobe has been available part-time for SSRL users to map specific locations of chemicals on their samples. The probe was originally designed for environmental scientists to study chemical contamination, but now users include biologists and archaeologists. Due to this growing popularity, the microprobe became a permanent fixture at SSRL in early December.

"Beam Line 2-3 went from being one of the least popular beam lines to being one of the top five requested, most oversubscribed beam lines," said Sam Webb (, the SSRL scientist in charge of the microprobe. "Users from many fields have seen how useful the microprobe is and are eager to use it in their experiments."

The device is one of only a handful of x-ray microprobes in the nation. The other comparable microprobe on the West Coast is installed at the Lawrence Berkeley National Laboratory's Advanced Light Source. Read more...

7.   Call for Publications       

You've read this above in our Director's message and we'll say it again because we cannot overstate the importance of users not only informing us about SSRL-related publications, but also acknowledging SSRL and our funding agencies in each publication. We need your ongoing help in keeping 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: 17 DEC 2008
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