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SSRL Headlines Vol. 10, No. 11  May, 2010


Contents of this Issue:

  1. Science Highlight — Archaeopteryx Feathers and Bone Chemistry Fully Revealed via Synchrotron Imaging
  2. Science Highlight — Structural Basis for Senior Immunity to the Current H1N1 Flu
  3. Science Highlight — Suspected Copper Chelator Binds not just Copper but Copper-Protein Trimer Complexes
  4. From the Acting Director of SSRL: Where Do We Go from Here?
  5. SPEAR3 Increased Current and Frequent Fill Update
  6. ARRA Funded Facility Upgrade Project
  7. First Bio-Imaging Results from LCLS: Henry Chapman Presents June 7 SLAC Colloquium
  8. LCLS/SSRL Users' Conference and Workshops, October 17-21, 2010
  9. Fomer SSRL Director Named to the Royal Swedish Academy of Engineering Sciences
  10. Web-based Proposal Submission Process Launched
  11. SSUN Energy Summer School 2010 Deadline Extended to June 7
  12. 1st North American Core Shell Spectroscopy Conference

1.  Science Highlight — Archaeopteryx Feathers and Bone Chemistry Fully Revealed via Synchrotron Imaging
       (contacts: U. Bergmann,; R. Wogelius,

False colour SRS-XRF map of Archaeopteryx.
Archaeopteryx, the half-reptilian, half-avian creature that lived 150 million years ago is famous as the fossil record's link between dinosaurs and birds. The discovery of the first Archaeopteryx fossil, which coincided with the publication of Charles Darwin's On the Origin of Species, provided strong evidence of the theory of evolution. Because Archaeopteryx fossils are important and rare, no samples have been taken for standard chemical analysis, which is a destructive process.

A research team including scientists from SLAC, the University of Manchester, and the Black Hills Institute of Geological Research used SSRL Beam Line 6-2 to analyze the chemical composition of a well-preserved Archaeopteryx fossil. They used the non-destructive technique Synchrotron Rapid Scanning- X-ray Fluorescence (SRS-XRF) imaging to analyze the presence of trace elements in the fossilized bone compared to the surrounding rock. They found that the zinc and copper levels in the fossilized bone are similar to those found in living bird species. Using a novel form of the SRS-XRF technique, the researchers were able to visualize phosphorous and sulfur in the feather shaft impressions in the fossil, showing that, contrary to expectations, some of the chemistry of the soft-tissue has been preserved.

The researchers point to the power of the SRS-XRF technique to find evidence of ancient biochemistry. The technique could be used on other fossils that have not been removed from the surrounding rock. This work was published online by the Proceedings of the National Academy of Sciences on May 11, 2010.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Structural Basis for Senior Immunity to the Current H1N1 Flu
       (contacts: R. Xu,; I.A. Wilson,

h1n1 figure
This image, from the Scripps Research Wilson lab, shows part of the 1918 Spanish flu virus in complex with an antibody that also neutralizes the 2009 "swine flu" virus.
An unusual property of the last year's H1N1 "swine flu" virus pandemic is that it disproportionately affected the young. People over the age of around 65 showed much less vulnerability than to more typical flu strains, suggesting that they might have been exposed to a similar virus over three decades ago. Another atypical property of the 2009 H1N1 strain is that its hemagglutinin (HA) subunit is the same subtype as the regular seasonal strains, whereas most pandemics are caused by viruses with novel HA domains. The HA protein extends out of the virus surface and is responsible for binding the virus to the cell it will infect. Because it is located on the surface of the virus, HA is often targeted by antibodies.

A group of researchers led by Prof. Ian Wilson of The Scripps Research Institute has found structural similarity between last year's H1N1 strain and the 1918 influenza virus that also caused a pandemic. They used SSRL Beam Line 9-2 to solve the 3D structure of the HA subunit of the 2009 H1N1 virus to 2.6 Å resolution. They compared their structure of HA of historic H1 flu strains from 1918 to the present. Their analysis shows a striking similarity between the surface residues in their HA structure and those of the 1918 virus, with decreasing similarity of viruses in subsequent years and a significant drop in similarity around 1940. The researchers also solved a 2.8 Å crystal structure of the 1918 HA bound to an antibody, which shows that the region that is conserved between the 2009 and 1918 strains matches the area recognized by the immune system.

The authors conclude that the resistance of older people to the current H1N1 virus is likely due to antibodies they acquired from flu strains in the early 20th century.

To learn more about this research see the full scientific highlight

3.  Science Highlight — Suspected Copper Chelator Binds not just Copper but Copper-Protein Trimer Complexes
       (contact: T.V. O'Halloran,

Cu and Mo K-edge extended x-ray absorption fine structure (EXAFS) Fourier transforms phase-shift overlay (experimental data) for [TM][(Cu)(Cu-Atx1) 3], and a kidney sample extracted from LPP rats treated with TM.
Cells need copper to function, but too much copper can be toxic, leading to liver damage and neurological problems, as happens in disorders such as Wilson disease. The inorganic small molecule tetrathiomolybdate (TM), assumed to be a copper chelator, is commonly used to treat Wilson disease. TM may also be an effective treatment of some cancers by starving the cancer cells of the copper they need to grow. Despite its common use, its molecular mechanism was unknown.

A team of researchers led by Profs. Thomas O'Halloran and Alfonso Mondragón of Northwestern University and Jim Penner-Hahn of University of Michigan used SSRL Beam Line 9-3 to solve the solution electronic and geometric structure (XAS) and SBC-CAT and IMCA-CAT at APS to determine the three-dimensional crystal structure of TM bound to copper and its chaperone protein. They were surprised to find that TM does not simply sequester copper from Atx1, the copper chaperone, but binds to a copper-protein trimer complex in a nest-like structure, completely disrupting the copper transport system. The TM binds to the copper atoms that are bound to the cysteine sulfurs of chaperone proteins.

Understanding the way TM can shut down the copper ferrying system could lead to treatments for some cancers, since growing cancers require a supply of copper. TM may also be useful for treating other diseases, such as familial amyotrophic lateral sclerosis (ALS), Parkinson's disease, multiple sclerosis, Alzheimer's disease, and some disorders associated type II diabetes. The research was published in the January 15 issue of Science.

To learn more about this research see the full scientific highlight

4.   From the Acting Director of SSRL: Where Do We Go from Here?
       SLAC Today Article by Piero Pianetta

P. Pianetta
P. Pianetta
As with other scientific facilities, SSRL faces an ever-changing landscape of experimental requirements, as a result of changing national needs and discoveries that direct the focus of its extensive user communities into new directions. These new research directions give rise to opportunities as well as challenges to further develop SSRL's capabilities. These challenges are met by the technical staff throughout SLAC who push the accelerator and beam lines to new performance levels. As is often the case in science, these new technical capabilities will in turn push scientific users to come up with new experimental ideas.

Since its commissioning in 2004 as a third-generation synchrotron facility, SSRL has been undergoing a process of continuous improvements, with reductions in emittance, increases in current as well as upgrades of all of its beam lines with higher performance monochromators, state-of-the-art detectors and new types of end stations too numerous to mention in a short article. In spite of all these advancements, the question that never goes away is: where do we go from here? To answer this question, we in SSRL management have been developing a strategic plan that looks forward at least five years to guide our thinking. Read more at:

5.   SPEAR3 Increased Current and Frequent Fill Update
       (contact: J. Schmerge,

SPEAR3 was designed to operate at 500 mA with frequent injections with stoppers open. The goal is to keep the current constant to better than 1% in order to maintain nearly constant power on the optics to maximize the photon beam stability. Earlier this year we received final approval to operate all beam lines in top-off mode (beam line shutters open while injecting), and now we are nearly ready to start frequent injections to maintain the current to approximately 1%. We plan to implement the frequent injection phase in the next few weeks. The number of injections will accordingly increase from 3 per day (every 8 hours) to 144 per day (every 10 minutes) to maintain 1% current stability.

After frequent injection has been thoroughly established and once the beam lines are approved for higher current, the SPEAR3 current will be gradually increased from 200 mA to 350 mA. Eventually the current will be raised to 500 mA.

6.   ARRA Funded Facility Upgrade Project
       (contacts: T. Rabedeau,; B. Choi,

Starting this spring and continuing through our regular late-summer shutdown which begins July 26, an upgrade project funded by the American Recovery and Reinvestment Act (ARRA) will address two SSRL infrastructure issues related to Liquid Nitrogen (LN)-cooled crystal monochromators which are key optical elements in hard x-ray insertion device beam lines at third generation light sources. The SSRL monochromator design utilizes internally cooled crystals for optimal thermal performance under power loads approaching a kW when SPEAR3 operates at its full 500-mA design current. This combination of high power loading and internal cooling poses two challenges: (a) the monochromators consume a lot of liquid nitrogen (~7000 liters/day for the 11 installed monochromators with SPEAR3 operating at 500 mA) and (b) the vacuum tight seals between the monochromator crystals and the LN manifolds are extremely sensitive to thermal cycling owing to power outages.

The first upgrade will install a new 13,000 gallon LN storage tank and associated plumbing next to the existing 3,000 gallon LN storage tank on the hill above Building 120 (B120). This significant increase in LN storage capacity is essential to ensure a reliable, adequate supply of LN as increased SPEAR3 current results in greater LN consumption by the monochromators as well as to provide capacity for future expansion of beam lines and experimental equipment. The installation of the new foundation for the new tank commenced early this month, and the new tank will be installed in the middle of July. A new trench covered with removable steel plates will also be installed from the new tank to the existing liquid nitrogen distribution system. Part of the B120 parking lot has been blocked off for staging.

The second infrastructure upgrade involves the installation of a pair of 50 KW, diesel-fueled backup generators strategically placed at two locations near the SPEAR3 ring and B131. These generators and the associated power distribution network will be used to provide backup power to the monochromator LN pumps and heat exchanger units as well as a limited number of other essential systems such as the house oxygen deficiency monitoring system. Once installed, the backup power system will eliminate sustained power outages as a source for LN-cooled monochromator thermal cycling and associated crystal seal failures. Given the roughly six person weeks required to rebuild a failed crystal seal, this represents a significant operational enhancement to beam line reliability. The generator and associated power distribution installation is scheduled to commence in early August and be completed in mid September.

SSRL user operations will resume after the shutdown with full integration of these infrastructure enhancements to our facility.

7.   First Bio-Imaging Results from LCLS: Henry Chapman Presents June 7 SLAC Colloquium       

Henry Chapman from the Centre for Free Electron Laser Science at Hamburg/DESY will talk about the first results on coherent imaging of nano crystals using LCLS on June 7 at 4:15 pm in the SLAC Panofsky Auditorium. This form of protein nanocrystallography may open a new avenue for high-throughput membrane protein crystallography. A new frontier is being opened. Come share in the excitement!

8.   LCLS/SSRL Users' Conference and Workshops, October 17-21, 2010
       (contact: C. Knotts,

Make plans to attend our upcoming 2010 LCLS/SSRL Users' Conference and Workshops, October 17-21, 2010. It's a very exciting time here with new capabilities at SSRL and LCLS. The ultrafast experiments which are now possible with the LCLS x-ray laser will push our understanding and technology and will promote key innovations in such diverse areas as energy science, environmental science, chemistry, biology and material science.

We welcome your ideas and suggestions for topics and speakers that would be of interest to the light source user community. The meeting will have plenary talks, a joint poster session, workshops, and vendor exhibits. This year Thomas Earnest (, Garth Williams (gjwillms@SLAC.Stanford.EDU) for LCLS, and Beth Wurzburg ( and Stefan Mannsfeld ( for SSRL, are co-chairing the conference.

9.   Fomer SSRL Director Named to the Royal Swedish Academy of Engineering Sciences       
A. Bienenstock
A. Bienenstock
At its General Meeting on March 24, 2010, The Royal Swedish Academy of Engineering Sciences, (IVA) elected Prof. Arthur Bienenstock Foreign Member of the Academy. The Royal Swedish Academy of Engineering Sciences, which was founded in 1919, is a learned society composed of elected members active in the technological and economic sciences or in areas where these are applied. The task of the Academy is to the benefit society by promoting the engineering and economic sciences and the advancement of business and industry. Persons who are permanent residents in a country other than Sweden who have performed outstanding work in the Academy's field of activities, and in the Academy's spirit "for the benefit of society", and who have evinced a particular interest in developing contacts with Swedish research and the Swedish industrial and business community, may be appointed foreign members. See full SLAC Today article at:

10.   Web-based Proposal Submission Process Launched
       (contact: C. Knotts,

We recently migrated to a new platform for users to submit proposals. From the joint SSRL and LCLS User Portal, users can update their account and contact information, submit an End of Run Summary after each experiment, and submit new proposals. Proposal spokespersons and their authorized lead contacts can also view their active proposals and beam time allocations as well as submit requests related to experiments.

Stay tuned as additional features are implemented through the portal to continue to enhance your user facility experience. We welcome your feedback and suggestions.

REMINDER: New proposals can be submitted three times each year: Submit new X-ray/VUV proposals by June 1, September 1, December 1; submit new Macromolecular Crystallography proposals by July 1, December 1, April 1.

LCLS proposals for AMO, SXR, XPP and CXI experiments are due by June 15.

11.   SSUN Energy Summer School 2010 Deadline Extended to June 7       

The deadline to register for the SSUN (SLAC-Stanford University-NREL) Energy Summer School has been extended to June 7—just a week away.

The summer school, set to take place August 9-20 at Stanford University, will provide an overview of current issues and sustainable technologies in the energy cycle from generation through collection, storage, distribution and utilization. This year's sessions will focus specifically on the challenges of modernizing electric grid infrastructure to develop power systems that are intelligent, efficient, robust and secure.

For full details and registration, see the SSUN Energy Summer School Web site.

12.   1st North American Core Shell Spectroscopy Conference       

The 1st North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-ray Conference August 2-6, 2010 at the Denver Marriott Tech Center Hotel in Denver, CO.

Abstract submissions for oral presentations in areas related to core shell spectroscopy are being accepted until Thursday, June 10

The conference will feature a special Symposium and Dinner honoring Prof. Edward A. Stern's contributions to the field of XAFS.


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: 28 May 2010
Content Owner: L. Dunn
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