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SSRL Headlines Vol. 11, No. 12  June, 2011


Contents of this Issue:

  1. From the Director of SSRL: Looking Ahead
  2. Science Highlight — Estimating Cr(VI) in Coal-Derived Fly-Ash
  3. Science Highlight — Staying One Step Ahead of Antibiotic Resistance
  4. Science Highlight — SSRL's Microfocus Macromolecular Crystallography Beam Line 12-2
  5. First SSRL Pump-Probe Experiments Under Way
  6. SSRL X-rays Reveal Patterns in the Plumage of the First Birds
  7. Upcoming SSRL Events: Detectors, XRMS, 2011 Users' Conference
  8. Call for Nominations for Spicer and Klein Awards
  9. New SSRL Artwork Inspired by Science Talk
  10. User Administration Update
  11. Stig Hagström, Spectroscopy Pioneer, Dies at 78
  12. In the News: Birds, Bacteria, SESAME

1.   From the Director of SSRL: Looking Ahead

Chi-Chang Kao
Chi-Chang Kao
Although the written report is not yet in, it's safe to say that we had a very successful SSRL Scientific Advisory Committee (SAC) meeting earlier this month. The review, which took place on June 2 and 3, was led by Glenn Waychunas from Lawrence Berkeley National Laboratory. Glenn and the eleven other members of the committee reviewed all aspects of the SSRL science program and operations, including studies on lowering the machine's emittance, first results from low-alpha experiments, accelerator operations and user support.

The SAC also approved the new SSRL user access policy, in particular the collaborative access proposal, a new mechanism for the user community to partner with SSRL. The policy will be published shortly. In addition, the SAC heard a progress report on the new strategic plan, and offered some excellent guidance on each scientific research area. They also championed the need for us to get feedback from the user community. We are now writing up the plan-taking into account the SAC's initial feedback-and, as I have mentioned in previous columns, we will soon ask for your input.

In the few weeks since the review, we have received funding from DOE for the procurement of an in-vacuum undulator to begin the construction of a new beam line. In addition, we've just been informed that additional funds will be made available to us to implement the proposed upgrades to stabilize the temperature of the SPEAR3 tunnel. This project, which will begin later this year, will reduce the thermal motion of the accelerator to reduce the photon beam motion at the beam lines. Preliminary tests indicate that the motion can be reduced by a factor of 7 with insulation. Both projects are critically important for SSRL to take full advantage of the brightness enhancement from the SPEAR3 upgrade.

In the meantime, we have already increased the SPEAR3 running current from 300 to 350 mA. As expected given the small increment in current, we haven't seen any negative impacts on beam line performance. Tests are also underway during accelerator physics time this week toward decreasing the interval between fills. SSRL employs a frequent fill schedule to maintain the SPEAR3 current constant to approximately 1%. At present, the interval is 10 minutes but, if these tests go well, it may decrease to as low as 5-7 minutes beginning in early July. We will keep users informed about this progress by e-mail.

In all, it's been a very exciting month and SSRL's future is looking brighter than ever.

—Chi-Chang Kao

2.  Science Highlight — Estimating Cr(VI) in Coal-Derived Fly-Ash
       (contact: F. Huggins,

Cr(VI) figure
Chromium forms in coal and wood and their converted forms in fly-ash, the major product of coal and coal/wood combustion. (Image courtesy F. Huggins et al.)
The element chromium is found in the environment in two common forms: Cr(VI), which is easily adsorbed by the human body, and Cr(III), which is not. The first of these in the form of chromates can have severe adverse effects on the human body, including cancerous tumor formation and gene damage. Normally Cr(VI) forms are not present in the approximately one billion tons of coal used annually for electricity generation in the U.S., however, a fraction of the Cr(III) in coal can become oxidized during coal combustion ending up as a Cr(VI) component in fly-ash, the major waste product from coal combustion.

A recent XAFS study conducted at SSRL Beam Line 4-3 by a team of researchers from KEMA and the University of Twente in the Netherlands and the University of Kentucky in the U.S. sought to determine how the chromium in fly-ash-which is often stored in isolated surface piles or in impoundments-behaves both during coal combustion and in ash disposal situations. Their work determined that Cr(VI) as a percentage of the total Cr was less than 10% in fly-ash when derived from commercial pulverized combustion of bituminous coals. However, it was significantly higher (up to 30%) in ash from combustion of subbituminous and other lower-rank coals and also from coal and wood co-firing.

The results indicate that the combustion conditions, particularly the air/fuel ratio, are important in determining the percentage of chromium as Cr(VI), and that leachable Cr(VI) contents in the ash could be minimized by better control on the excess air present during combustion and possibly by additives that promote the formation of insoluble chromate species.

This work was published in Environmental Science & Technology.

To learn more about this research see the full scientific highlight

3.  Science Highlight — Science Highlight: Staying One Step Ahead of Antibiotic Resistance
       (contact: C. Smith,

For decades, people have been using penicillium mold and molecules produced by soil bacteria as a means of fighting off harmful bacteria and treat infection. But resistance to these chemicals is now becoming commonplace. Today many infections are resistant to not only penicillin but also other b-lactam antibiotics, some of which are classified as "last line of defense" drugs for E. coli and Klebsiella pneumoniae.

Experiments at SSRL Beam Line 12-2 revealed that a previously unknown bacterial strain (Oceanobacillus iheyensis) found in deep ocean sediment (a place where it is highly unlikely that the bacteria would have ever encountered man-made penicillin) has a very active b-lactamase enzyme with a three-dimensional structure almost identical to the known b-lactamases in common bacteria. This work reveals that the development of this enzyme cannot be due solely to exposure to clinically-derived b-lactam antibiotics. This work suggests that the enzyme's evolution took place prior to the use of penicillin and b-lactam antibiotics.

Work conducted at SSRL has also revealed that b-lactamase enzymes have developed the ability to break down the carbapenems-"last resort" b-lactam antibiotics-including the Guiana extended-spectrum b-lactamases (GES). Fortunately, the GES enzymes can be stopped in their tracks by known -lactamase inhibitors, something recently demonstrated with the high resolution structure of GES-2 with tazobactam, using data collected at SSRL Beam Line 12-2.

Nonetheless it appears that, overall, the GES family of enzymes is evolving the ability to break down carbapenems which, while alarming, is not unexpected given the "pressure" that we are applying to the environment with respect to the use, overuse and misuse of antibiotics which will naturally result in mutation, adaption and evolution of resistance mechanisms. To stay one step ahead of the bacteria, we will need to continue to study bacterial enzymes and design drugs that remain effective despite enzyme mutation.

This work was published in Acta Crystallographica and the Journal of Biological Chemistry.

Antiobiotic Resistance image

To learn more about this research see the full scientific highlight

4.  Science Highlight — SSRL's Microfocus Macromolecular Crystallography
Beam Line 12-2

       (contact: M. Soltis,

SSRL's newest macromolecular crystallography beam line, 12-2, is providing outstanding capabilities for study of exceptionally challenging biological systems. The technical aspects of the beam line are described briefly below, and science enabled by this undulator beam line is further illustrated by the results described in the science highlights linked to at the bottom of this overview.

The Beam Line 12-2 undulator beam line, funded by the Gordon and Betty Moore Foundation in collaboration with Caltech, is optimized for microfocus experiments (down to 5 micron beam size) but can easily accommodate more conventional macromolecular crystallography beam-size projects through a flexible optics and collimation approach. The state-of-the-art Beam Line 12-2 DECTRIS PILATUS 6M Pixel Array Detector (PAD), with its high dynamic range, very fast readout and low point spread function, enables a rapid, shutterless fine-phi-slicing mode of data collection where complete data sets are typically collected in 2-3 minutes. Capabilities are further enhanced by the higher operating current of the SPEAR3 storage ring, currently 350 mA. Enhanced computer infrastructure keeps up with data transfer and reduction in real time. The robotic Stanford Auto-Mounter (SAM) is fully integrated into the beam line control system and has been used in the screening of nearly 30,000 crystals on Beam Line 12-2 to date. Around 95% of the user groups collect data in full remote-access mode, running the experiment from their home lab. Beam Line 12-2 is in full operation, with the following three papers illustrating new and complex structures based on recent data collections from challenging crystals:

BL12-2 Rees
"Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase" (Rees, Ribbe, et al., Science, 331, 91, 2011) describes the structure of NifEN, an essential protein in the biosynthetic pathway to form nitrogenase, the complex enzyme responsible for biological nitrogen fixation. The ability to screen many crystals robotically (more than 200), together with the ability to vary the beam size and the high x-ray flux were crucial for the successful completion of this project. The precursor-bound NifEN crystals had high levels of growth defects. However, it was possible to focus the beam on several small volumes of the crystals, enabling measurement in areas that were more homogenous, providing higher quality data overall. Model building and interpretation was performed using ~20 datasets collected at 3 wavelengths from 4 selected (through screening) high quality crystals. To learn more about this research see the highlight at: full scientific highlight

BL12-2 Kornberg
"Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism" (Kornberg et al., Science, 327, 206, 2010) reveals the structure of RNA polymerase II-general transcription factor TFIIB complex at 3.8 Å and proposes a mechanism for the transcription initiation process. The high brightness available at Beam Line 12-2 coupled with the PAD detector allowed the researchers to collect the data to the highest resolution possible. To learn more about this research see the highlight at: full scientific highlight

BL12-2 Noller
"Crystal Structures of Complexes Containing Domains from Two Viral Internal Ribosome Entry Site RNAs Bound to the 70S Ribosome" (Noller, Kieft, et al., PNAS, 108, 1839, 2011) addresses the structural basis of ribosome entry. More than 1,000 crystals were pre-screened utilizing the SAM system and the high x-ray brightness on Beam Line 12-2. Final x-ray diffraction datasets were collected for the 70S-CrPV complex (one of the structures reported in the paper) on Beam Line 12-2. To learn more about this research see the highlight at:
full scientific highlight

5.   First SSRL Pump-Probe Experiments Under Way
       (by Lori Ann White, SLAC Today)

pump probe
From the left: Apurva Mehta, Aaron Lindenberg, and Mariano Trigo, from Lindenberg's team, on Beamline 10-2, site of SSRL's first pump-probe experiment. (Photo by Lori Ann White.)
Both the Linac Coherent Light Source and SSRL take advantage of the ways x-rays can peer at, into and through materials in an effort to learn how matter behaves biologically, chemically or electronically. However, the LCLS, in operation since 2009, has a head start on the nearly 40-year-old SSRL in exploiting one area-ultrafast atomic and molecular processes. That head start gives the LCLS an edge on some vital areas of research, such as catalysis. Now, SSRL is moving in this direction as well as researchers use pump-probe experiments to create movies that answer some basic questions-why are certain substances better at trapping the sun's energy than others? What happens to the molecules that have their electrons stolen away to carry current? Learn more about this research in SLAC Today

6.   SSRL X-rays Reveal Patterns in the Plumage of the First Birds
       (SLAC Press Release

C. sanctus
Synchrotron rapid scanning x-ray fluorescence image of the calcium distribution in a fossil specimen of Confuciusornis sanctus, an ~120 million year old avian species, the oldest documented to. (Image created by Gregory Stewart, SLAC)
Scientists report today that they have taken a big step in determining what the first birds looked like more than 100 million years ago, when their relatives, the dinosaurs, still ruled the Earth. At the Department of Energy's SLAC National Accelerator Laboratory, they discovered chemical traces of a pigment, an important component of color, that once formed patterns in the feathers of the fossilized birds.

The pigment, eumelanin, is one of the coloring agents responsible for brown eyes and dark hair in many modern species, including humans. It would have been one of the factors that determined the birds' color patterns, along with structural properties of the birds' feathers and other pigments they ingested as part of their diets.

The discovery, reported June 30 in Science Express, will help give textbook illustrators, diorama makers and Hollywood special-effects artists a more realistic palette for their depictions of ancient animals. Understanding these pigment patterns is important for science, too, since they play a role in a wide range of behaviors that are important in evolution such as camouflage, communication and selecting mates.

Read the full press release.

7.   Upcoming SSRL Events: Detectors, XRMS, Users' Conference

Pixel and Microstrip Detectors for Current and Future Synchrotron Light Sources, July 1 - On Friday, July 1, Christian Broennimann of DECTRIS will present a talk entitled "Pixel and Microstrip Detectors for Current and Future Synchrotron Light Sources" at 1:00 p.m. in SLAC's Kavli Auditorium. The talk will cover current development plans for these state-of-the-art detectors.

11th International Workshop on X-ray Spectroscopy of Magnetic Solids, October 21-22 - The 2011 X-ray Spectroscopy of Magnetic Solids (XRMS) meeting will take place October 21-22 at SLAC. These annual meetings have proved as a fruitful forum for informal discussion of recent results and future projects of synchrotron radiation based research on magnetism and magnetic materials. They also serve for the formation of new collaborations. Learn more on the XRMS website.

Annual Users' Conference, October 24-26 - Plans are underway for the Annual SSRL/LCLS Users' Meeting and Workshops, October 24-26, 2011. Mark your calendar and plan to participate to learn about new developments and share exciting user research at both LCLS and SSRL. It is also a great time to interact with other scientists, potential colleagues, and vendors of light source-related products and services. Check back later for more details and registration. The draft program and registration details will be posted shortly. You can also reserve lodging for the meeting by contacting the Stanford Guest House. Specify SSRL/LCLS/SLAC to take advantage of discounted rates.

8.   Call for Nominations for Spicer and Klein Awards
       (contact: C. Knotts,

Please take a few moments to consider nominating your colleagues or students for the annual Klein and Spicer awards, which will be presented at the joint SSRL and LCLS Users' Meeting, October 24-26:

Last year's Klein Award winner, Diling Zhu, developed a new experimental technique to carry out x-ray holography, something that usually requires significant computing power and can lead to false conclusions. In his thesis, Zhu described two new methods to more accurately and reliably reconstruct the two-dimensional image of the object from the interference pattern. "The importance of Diling's work is increased reliability in obtaining real space images from the obscure x-ray scattering patterns," said Jo Stöhr, director of the Linac Coherent Light Source and Zhu's thesis advisor. "We now have two robust methods which give us robust and reliable pictures of nanostructures. These methods will be used at both SSRL and LCLS and at other x-ray facilities around the world."

Jeffrey Lee received the 2010 Spicer Award for his studies of the Ebolavirus, which causes an untreatable disease that kills 50 to 90 percent of people who contract it. Using SSRL and other U.S. synchrotrons, Lee was able to uncover the structure of the Ebolavirus glycoprotein, which initiates the attachment and fusion of the virus and the host membranes, when it was bound to an antibody from a human survivor of the virus. The methods Lee and his team developed are applicable for other groups and will likely streamline the structure determination process for glycoproteins in other viruses.

Submit your 2011 nominations to Cathy Knotts ( by August 1.

In addition, award donations are now being accepted card to ensure that the awards will continue in perpetuity as memorials to Spicer and Klein. These can be sent by check, made payable to "Stanford University" (noting "Spicer Award" or "Klein Award" on the memo line), to SSRL c/o Cathy Knotts, SLAC National Accelerator Laboratory, 2575 Sand Hill Road MS 99, Menlo Park, CA 94025. Alternatively, if you would like to make a gift by credit card, please phone 866-543-0243 (toll free) Monday - Friday, 8 a.m. to 5 p.m. PST to reach a customer service representative. Please specify that your gift is designated for "The Spicer Award" or "The Klein Award." Callers from outside the US, please phone 650-724-0627 (not toll free).

9.   New SSRL Artwork Inspired by Science Talk

Student Inspired by SLAC Donates Painting (Photo by Lori Ann White.)
Hanging in an SSRL user lounge is a new painting in acrylics of the SLAC linear accelerator at sunset, overlaid with a giant sun-like detector and the ghostly outline of a scientist. It's not only a lovely painting, it's also a beautiful reminder of the way science can inform art, and, in turn, art can capture science.

The painting is a gift from the artist, Carey Phelps. A recent graduate of the Castilleja School in Palo Alto, Phelps painted the piece after seeing two SLAC scientists discuss the intersections of art and physics at her Introduction to the Arts class. Linac Coherent Light Source Deputy Directory Uwe Bergmann spoke about uncovering the ancient writings of Archimedes at SSRL, while SSRL Staff Scientist Apurva Mehta explained how the science of today can be used to help understand and preserve the art of the past, from better understanding the origins and properties of unusual pigments to explaining the methods used to produce specific finishes on pottery.

"The scientists from SLAC talked about science and art," Phelps said. "I wanted to make the connection between art and science."

10.   User Administration Update
       (contacts: Cathy Knotts,; Lisa Dunn,

Increased Current to 350mA
SSRL increased the SPEAR3 running current from 300 to 350 mA on June 15. Given the small increment in current, we do not expect any negative impacts on beam line performance.

SPEAR3 Top-Off Injection
SSRL employs a frequent fill schedule to maintain the SPEAR3 current constant to approximately 1%. At present, the interval is 10 minutes but it may decrease to as low as 5-7 minutes. Tests at shorter fill patterns are planned for this week. If everything works out, the shorter fill patterns (~every 5-7 minutes) could begin the first week in July. Contact the beam line scientists/engineers if you have any questions or to discuss how these changes may impact your planned experiments.

Brochures and Information
Next time you're at SSRL, be sure to stop by the Beam Line 1 area to see the new "info stop." This area now houses a monitor that publicizes upcoming seminars and events, user science highlights and recent publications, as well as a brochure rack full of the latest brochures and fact sheets.

11.   Stig Hagström, Spectroscopy Pioneer, Dies at 78
       (by Andrew Myers, Stanford Report)

Stig Hagstr&oouml;m
Stig Hagström, who helped found the Stanford Synchrotron Radiation Lightsource, died May 28 at Stanford Medical Center; he was 78.

Hagström was a pioneer in electron spectroscopy for chemical analysis in the 1960s, and was a noted expert in surface sciences and thin-film deposition processes. His work had a major impact on scientific understanding of surface chemistry and physics. He and his collaborators developed "soft X-rays" for use in studying oxidation of aluminum and he was among the first to use synchrotron radiation in spectroscopy.

"It was Hagström, in 1968, who suggested to Stanford Professor William Spicer that synchrotron radiation offered great possibilities for condensed-matter science, leading to the creation of what would become the Stanford Synchrotron Radiation Lightsource," said friend and fellow Stanford Professor Emeritus Arthur Bienenstock. "Stig had tremendous impact on Stanford, the nation and the world." Read more in Stanford Report.

12.   In the News: Birds, Bacteria, SESAME

Images of Fossil Birds Show Ancient Pigments
New York Times

New Glimpse of the Color Palette of Long-Extinct Creatures
National Geographic

Bird Fossils Reveal Life's Colourful Chemistry

Dinosaur-era Feather Colors Revealed
USA Today

Concerns about Arsenic-Laden Bacterium Aired
Science News and Analysis

Pledges of Support Keep Mideast SESAME Project on Track


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 National Institute of 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 June 2011
Headlines Editor: K. Tuttle