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SSRL Headlines Vol. 10, No. 5  November, 2009


Contents of this Issue:

  1. Science Highlight — Researchers Define the Structures of Prion Amyloid Variants
  2. Science Highlight — New Data from Beam Line 12-2 Reveals how Macromolecular Structural Distortions Impact Function
  3. Stanford-led Research Helps Overcome Barrier for Organic Electronics
  4. Nobel Laureate Did Landmark Work at SSRL
  5. Keith Hodgson Serving as SLAC CRO
  6. Ian Evans Brings Together SSRL and LCLS User Safety
  7. Users and the Flu Season
  8. December 1 Beam Time Proposal Deadline

1.  Science Highlight — Researchers Define the structures of prion amyloid variants
       (contact: G. Stubbs, Vanderbilt University)

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While the normal function of human prion protein (PrP) remains a mystery, the results of abnormal PrP are quite well known. Misfolded PrP (denoted PrPSc) leads to diseases such as Creutzfeldt-Jakob disease, mad cow disease, and scrapie in sheep. In these diseases, the protein acts like an infectious agent, recruiting other PrP to become PrPSc without requiring any involvement from nucleic acids or any other molecules. Many PrPSc molecules can bind together to form amyloid structures, similar to those that contribute to a wide variety of diseases including Alzheimer's and Parkinson's.

A research group led by Prof. Gerald Stubbs from Vanderbilt University used SSRL's Beam Line 4-2 to collect fiber diffraction data from hamster and mouse PrPSc amyloids. Results of their measurements were consistent with a beta-helical structure, which had been previously hypothesized from other methods. They also looked at a recombinant PrPSc amyloid that is less infectious than the wild type. The recombinant amyloid structure formed stacked beta-sheets, quite different from the natural amyloid structure. Yet they found that a recombinant PrPSc amyloid isolated from an in vivo system formed the beta-helical structure found in the native amyloid.

The researchers propose that there could be a link between structure and infectivity, but more research must be done to find the basis of the connection. This work was published in the October 6 issue of the Proceedings of the National Academy of Sciences.

To learn more about this research see the full scientific highlight

2.  Science Highlight — New Data from Beam Line 12-2 Reveals how Macromolecular Structural Distortions Impact Function
       (contacts: P. Dervan and W. Clemons, Caltech)

Biological macromolecules, like proteins and nucleic acids, are good examples of the form follows function paradigm; and, in the case of these molecules, deformation follows function as well. Flexibility in proteins and nucleic acids allows for the recognition of targets, the binding of complexes, and the adoption of functional configurations. Recent research at SSRL Beam Line 12-2
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see: Dervan_12-2_DNA.html

has revealed how distortion in macromolecular structure is linked to function. BL12-2 is the high-intensity, state-of-the-art undulator beam line for advanced macromolecular crystallographic studies funded by The Gordon and Betty Moore Foundation in cooperation with the California Institute of Technology.

Research by a group led by Prof. Peter Dervan from California Institute of Technology shows how a small molecule compresses DNA's major groove upon binding to its minor groove. This structural distortion interrupts the recognition and binding of transcription factors, affecting gene expression. This work was published in the August 11, 2009, issue of the Proceedings of the National Academy of Sciences.

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Another team, led by Bil Clemons from Caltech, solved several crystal structures of complexes of a transport protein (Get3). Get3 is responsible for delivering tail-anchored (TA) proteins to their proper locations after translation by the ribosome. Their data suggest a model in which both the binding of ATP and ATP hydrolysis cause dramatic conformational changes in Get3 that allow the binding and release of the TA-proteins. This work was published in the September 1, 2009, issue of the Proceedings of the National Academy of Sciences.

see: Clemons_12-2_Get3.html

3.   Stanford-led Research Helps Overcome Barrier for Organic Electronics
       Stanford Report Article by David Orenstein

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Providing insight into a frustrating inconsistency in the performance of electronics made with organic materials, Stanford researchers have shown that the way boundaries between individual crystals in a film are aligned can make a 70-fold difference in how easily current, or electrical charges, can move through transistors. The research, which could help engineers design better digital displays and other devices, was published online Nov. 8 in the journal Nature Materials, and was based partly on x-ray scattering measurements at SSRL.

Organic semiconductors have a lot to offer in electronics. They are cheap and flexible, and the production process is much simpler than for traditional silicon chips. Applications such as computer display screens, digital signs or magazines made of "electronic paper" have been possibilities for more than a decade, but their full potential seems always just around the corner. A persistent problem is that performance from transistor to transistor varies much more than can be allowed in commercially viable devices.

"You can make a single device that has high 'charge mobility,' but you really need to make thousands of them," said Alberto Salleo, an assistant professor of materials science and engineering at Stanford and a senior co-author of the paper. "Most research groups report a high variation in that mobility. What we did here is try to understand what causes the variation."

Read more at:

see the related Science Highlight at:

4.   Nobel Laureate Did Landmark Work at SSRL
       SLAC Today article by Calla Cofield

Yonath image
Ada Yonath
Last month, Ada Yonath became the fourth woman in history to win a Nobel Prize in Chemistry, which she shared with Thomas Steitz and Venkatraman Ramakrishnan for "studies of the structure and function of the ribosome." As many of her colleagues will attest, it wasn't always clear that Yonath was headed for great success following this research avenue. For more than a decade, her passionate, unwavering study of the ribosome looked to many like a dead end. A major breakthrough in her work, and a turning point in the opinion of her peers, happened in 1987 at SSRL.

It was polar bears that got Yonath interested in the human ribosome: she read a book about polar bears, and wondered what kind of mechanism would preserve the bears' ribosome so they wouldn't fall apart or be degraded during hibernation. The Ribosome is perhaps the most essential structure within our cells. They read the plans carried in DNA through its intermediary, messenger RNA, to build the proteins necessary for life. The delicate ribosome was easily destroyed under examination, but knowing that nature had its own method of preserving it made Yonath believe that there must be a way to crystallize and study it. Read more at:

5.   Keith Hodgson Serving as SLAC CRO
       SLAC Today Article by Keith Hodgson

Hodgson Image
Keith Hodgson
So just what is a "CRO"? In the corporate world, CRO can have many meanings-Chief Risk Officer, Chief Restructuring Officer, Chief Revenue Officer and Chief Research Officer among them. It is this latter definition that fortunately for me defines the role of a CRO at SLAC and typically at the other Department of Energy national laboratories. I was appointed SLAC's Chief Research Officer by SLAC Director Persis Drell in September and it is a real privilege and opportunity for me to serve in this capacity (in addition to my continuing role as SLAC Associate Laboratory Director for Photon Science).

In this brief article, I want to talk about the nature of this new job, both in the context of SLAC and in the broader DOE National Laboratory system.

The CRO is another of the O's that are a central element of the laboratory's management structure. Under the leadership of Persis (who has a role analogous to a Chief Executive Officer in the corporate sense), SLAC's Chief Operating Officer Sandy Merola, Chief Financial Officer Susan Calandra, Chief Information Officer Don Lemma, Chief Safety Officer Craig Ferguson and the Chief Research Officer (myself) have roles and responsibilities that support, coordinate and represent important activities cutting across many areas of the laboratory.

At SLAC, some of my own specific roles and responsibilities as CRO include coordination with the lab director and COO on topics of mutual concern that relate to SLAC's research agenda. I am also responsible for coordinating the science and technology component of the Annual DOE Laboratory Plan and for the annual PEMP science and technology goals. Another area of responsibility is in coordinating the development of international agreements and Memoranda of Understanding in scientific areas relevant to the lab's mission. I will also coordinate the annual Laboratory Directed Research and Development process, interfacing with others who expertly manage aspects such as the external peer review. Read more at:

6.   Ian Evans Brings Together SSRL and LCLS User Safety
       SLAC Today Article by Lauren Knoche

Evans Image
Ian Evans
He's back! Environment, Safety & Health Program Manager Ian Evans has returned to SLAC after three years developing the user safety program at the Spallation Neutron Science and High Flux Isotope Reactor research facility at Oak Ridge National Laboratory in Tennessee. Prior to working at Oak Ridge, Evans managed the ES&H program at SSRL for over a decade. In his new position Ian will provide management of the effort to develop and implement the LCLS safety program, ensure that the SSRL safety programs continue to develop to meet programmatic needs and integrate these efforts across both facilities.

"SSRL is an established, mature facility, whereas LCLS is young and in the process of developing a program from a user's standpoint," Evans said. "The end goal is that, from the user perspective, the systems you see would be equitable at SSRL and LCLS."

To help SLAC offer world-class user programs in addition to world-class facilities, Evans will work to combine safety and operations programs so that users will see congruency between the two user facilities. Users will see consistency between SSRL and LCLS programs during the proposal review process, throughout a unified training program, and when interacting with support staff who will have similar roles and responsibilities at each facility. These commonalities will enable smoother transition for users who may have worked at SSRL in the past and are starting experiments at LCLS. Read more at:

Also of interest, safety officials and administrators recently met at the ALS to discuss a similar effort to develop review and authorization processes and web tools geared to provide a consistent user safety program across all of the light sources - where practical.

7.   Users and the Flu Season

With user operations at both SSRL and LCLS coinciding with the current flu season (and added concerns about the risk of the H1N1 "swine" flu), we want to send a brief reminder about influenza symptoms to be on the watch for, how it is spread, and how you can protect yourself and others. This is particularly important at an international user facility like ours that attracts researchers who travel from a wide variety of locations and work long hours in close quarters.

Flu Symptoms include fever, cough, sore throat, runny or stuffy nose, body aches, headache, chills and fatigue. Some people may have vomiting and diarrhea. People may be infected with the flu, including 2009 H1N1, and have respiratory symptoms without a fever. Flu viruses are spread mainly from person to person through coughing or sneezing or by touching their mouth or nose after having contact with a surface or object with flu viruses on it.

The U.S. Centers for Disease Control (CDC) recommends taking these everyday steps to protect your health:

  • Cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it.
  • Wash your hands often with soap and water. If soap and water are not available, use an alcohol-based hand sanitizer (sanitizers have been placed around the beam lines).
  • Avoid touching your eyes, nose or mouth.
  • Try to avoid close contact with sick people
If you are sick with flu-like illness, stay home and avoid contact with others for at least 24 hours after you are free of fever (100F / 38C) or signs of fever (chills, flushed appearance, sweating), without the use of fever-reducing medications.

If a large-scale flu outbreak or any other emergency situation were to occur at SLAC, emergency information can be found on the SLAC Emergency Status telephone line (877-447-7522) and on the SLAC Emergency Web page

For additional information, see:

For SSRL science highlights related to pandemic flu see:

8.   December 1 Beam Time Proposal Deadline
       (contacts: C. Knotts,; L. Dunn,

December 1 is the next deadline for submitting new X-ray, VUV and Macromolecular Crystallography standard proposals. For more information on proposal deadlines, instructions, and forms see:

If you miss the December 1 deadline for submitting standard proposals, April 1 is the next deadline for macromolecular crystallography proposals and June 1 for X-ray/VUV proposals.

Additionally, time is reserved on many beam lines for rapid access proposals. A full listing of the Rapid Access applications is available at:


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 November 2009
Content Owner: L. Dunn
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