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SSRL Headlines Vol. 8, No. 3  September, 2007

Contents of this Issue:

Science Highlight — Steps Toward Understanding Autism Nature Materials Includes SSRL Research in Most Influential Articles List User Research to be Highlighted at SSRL/LCLS Users' Meeting and Workshops, September 28-October 3 SSRL Faculty Updates - Name Change and New Faculty Appointments Users' Organization Activities Information Requested for Reports to SSRL Funding Agencies SSRL User Wins Scientific Award Low-Alpha Mode Increases Possibilities at SSRL 2007 Structural Molecular Biology Summer School Wrap-up Upcoming Proposal Deadlines

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1.  Science Highlight — Steps Toward Understanding Autism
       (contact: J. Trewhella, jtrewhella@usyd.edu.au)

Ribbon representation of the neuroligin-1/bb-neurexin Complex. View from the pre-synapse

Autism is considered among the most devastating neurological disorder conditions of early childhood. Now, researchers working in part at SSRL's Beam Line 4-2 have determined a three-dimensional structural model of a complex with the only two extracellular synaptic proteins implicated in autism spectrum disorders and mental retardation. Such a finding could deepen our understanding of this mysterious and debilitating type of disorder. The findings were published in the June 2007 edition of the journal Structure.

Many neurodevelopmental disorders involve abnormal synaptic function. Synapses provide essential connections between nerve cells in the brain that enable signals to be transmitted. Neurexin and neuroligins are proteins that associate in the extracellular space between synapses in the brain, and they appear to play a crucial role in maintaining the functionality of the brain's synaptic circuitry.

The research team combined small angle x-ray scattering data collected at SSRL with neutron solution scattering data to determine the molecular shapes of neuroligin and neurexin, which led to the creation of a model of the neurexin and neuroligin complex in the synaptic space. This new model provides an important structural framework for linking genetic information on mutated neurexins and neuroligins with neuro-developmental disorders.

To learn more about this research see the full scientific highlight at:
http://www-ssrl.slac.stanford.edu/research/highlights_archive/neuroligin_autism.html

2.   Nature Materials Includes SSRL Research in Most Influential Articles List

	Schematic of orientation of crystals within the film corresponding to the peak and background of the rocking curve of P3HT films.

To mark their fifth anniversary in September 2007, the editors at Nature Materials put together their highlights of the ten most influential articles that have appeared since 2002. Included in this short list was the work by SSRL users on development of plastic electronics, which was featured as an SSRL Science Highlight in August 2006. This work describes a new class of polymer semiconductors - liquid-crystalline polythiophenes - developed by using the appropriate synthetic building blocks to promote supramolecular organization of the conjugated polymers. The charge-carrier mobilities of the polymers, when used in field-effect transistors, are found to be on a par with those of amorphous silicon, and demonstrate real potential for applications.
http://www-ssrl.slac.stanford.edu/research/highlights_archive/p3ht.html
http://www.nature.com/nmat/5th_anniversary/

3.   User Research to be Highlighted at SSRL/LCLS Users' Meeting and Workshops, September 28-October 3
       (contact: C. Knotts, knotts@slac.stanford.edu)

There are several very exciting events planned for the upcoming SSRL/LCLS Users' Meeting, beginning with a special symposium on September 28-29 to look into the future of x-ray science. The main Users' Meeting, on October 1-2, will feature presentations on recent developments and new opportunities in structural biology, material and environmental science, and two dedicated sessions on early science opportunities with LCLS and the associated instrumentation. Over 60 users will share their research through poster presentations on Monday, October 1, 5-7 pm. New this year will be a "Data Blitz" to give users an opportunity to advertise their scientific posters at an open microphone session during lunch earlier that day. If you plan to present a poster and are interested in participating in the Data Blitz, please let us know before October 1.

	Roger Kornberg

We are honored that Nobel Laureate Professor Roger Kornberg has agreed to give the keynote presentation on Tuesday afternoon, October 2. Kornberg, professor of Structural Biology at the Stanford University School of Medicine, received the 2006 Nobel Prize in Chemistry for his work in understanding how DNA is converted into messenger RNA. Kornberg's studies have provided an understanding at the atomic level of how the process of transcription occurs and also how it is controlled. As transcriptional regulation underlies all aspects of cellular metabolism, his work also helps explain how the process sometimes goes awry, leading to birth defects, cancer and other diseases. Key to this understanding was the determination of the three-dimensional arrangement of the atoms in the RNA polymerase - in its "base" structure and caught in snapshots of it in action - through the use of synchrotron radiation-based macromolecular crystallography. Kornberg and his group carried out a significant part of this research at SSRL's macromolecular crystallography beam lines, starting as early as in 1991 but with the main work leading to the first published structure in the late 1990s. Some of the results have been previously highlighted in SSRL Headlines (2001 and again in 2004).
http://www-ssrl.slac.stanford.edu/research/highlights_archive/rna_polymerase.pdf
http://www-ssrl.slac.stanford.edu/research/highlights_archive/rna_polymerase_04.pdf

At SSRL/LCLS 2007, users also have the opportunity to learn about the latest research and state-of-the-art developments at several focused workshops including: Synchrotron Techniques (Sept. 30); Scientific Opportunities for Studying Laser Excited Dynamics at the LCLS (Oct. 3); Imaging and X-ray Microscopy (Oct. 3); Microfocusing (Oct. 3); and XANES Spectroscopy (Oct. 3). Program: http://www-conf.slac.stanford.edu/ssrl-lcls/2007/program.htm

4.   SSRL Faculty Updates - Name Change and New Faculty Appointments
       (contacts: P. Bucksbaum, phb@slac.stanford.edu; B. Hedman, hedman@ssrl.slac.stanford.edu)

The name of the SSRL Faculty has officially been changed to the Photon Science Faculty. This reflects the department's expansion into exciting new scientific areas at SLAC and Stanford. The change was approved by the Stanford University Provost and Advisory Board in the spring, and took effect September 1. The Photon Science name more clearly captures the strong synergy and overlap of the research activities at SSRL, the X-ray Laboratory for Advanced Materials (XLAM) and the Photon Ultrafast Laser Science and Engineering (PULSE) center, and provides the platform for further expansion into other areas within photon science, as LCLS becomes operational and other directions open. Many Photon Science Faculty appointments are joint with departments on Stanford's main campus, and this is expected to grow in the future. The chair and vice-chair remain the same, Phil Bucksbaum and Britt Hedman, respectively.

Wendy Mao

We are pleased to announce the addition of Wendy Mao to the Photon Science Faculty. She assumed an Assistant Professor position in August, joint with the Stanford Department of Geological & Environmental Sciences (GES). Wendy received her Ph.D. in 2005 in Geophysical Sciences from the University of Chicago and has since been a J.R. Oppenheimer Fellow at Los Alamos National Laboratory. Wendy is a mineral physicist interested in understanding the behavior of materials at extreme conditions using a suite of experimental techniques. With the aid of the 3rd generation SPEAR3 synchrotron facility and with laser facilities, Wendy will establish a new program in high pressure materials physics at SSRL, utilizing both SPEAR3 and the LCLS, to enrich our fundamental knowledge of Earth and planetary interiors, and to address important energy and environmental questions.

	Tom Devereaux

Thomas Devereaux joined the faculty as Professor on September 1. He earned a Ph.D. from the University of Oregon in 1991, has held research positions in the US, Germany, France and Canada, and left the faculty at the University of Waterloo in Ontario, Canada to accept this appointment, with focus on condensed matted physics theory. With the newly upgraded SPEAR3 and the soon-to-be completed LCLS, Stanford is excellently positioned to make breakthrough discoveries in the area of condensed matter physics. Tom's breadth, both as a theorist and a phenomenologist, his computational skills and his ability to put a complex problem into a realistic numerical simulation, will provide an ideal platform from which to build a strong theory group, working closely with experimentalists, in particular within XLAM.

5.   Users' Organization Activities
      (contacts: C. Kim, cskim@chapman.edu; R. Szilagyi, szilagyi@montana.edu; J. Hastings, jbh@slac.stanford.edu)

Voting to fill two open positions for representatives in environmental science and macromolecular crystallography on the SSRL Users' Organization Executive Committee (SSRLUOEC) is now underway. Having a full and engaged committee is essential, particularly during times of growth and change. Please take a few minutes if you haven't already done so to cast your ballot. SSRLUOEC representatives will be elected by the SSRL user community by majority vote, and the results will be announced on October 2. Vote at:
http://www-conf.slac.stanford.edu/ssrl-lcls/2007/voteform.asp
http://www-conf.slac.stanford.edu/ssrl-lcls/2007/nomination.htm

The next SSRL Users' Organization meeting on Tuesday, October 2, will begin at 2:30 pm in the Kavli Auditorium. Results from the 2007 user survey will be shared, and user input is encouraged for the 2008 survey to understand what issues are most important to users and how we can better meet user needs. Mike Lubell, American Physical Society, will share tips with users on communicating their science for the general public.
http://www-ssrl.slac.stanford.edu/users/ssrluo/ssrluoec-mtgs.html

After the SSRLUOEC meeting, there will be an open discussion aimed at forming a LCLS Users Organization and a discussion of user access policies aimed at early open access to the broad community. The instrument scientists that are responsible for the LCLS instruments as well as the associated scientific team leaders will be present, and they would appreciate your input to guide the LCLS to a successful launch of its experiment program in summer 2009 as well as your help to make this inaugural joint SSRL/LCLS Users' Meeting a success.

6.   Information Requested for Reports to SSRL Funding Agencies
      (contacts: C. Knotts, knotts@slac.stanford.edu; L. Dunn, lisa@slac.stanford.edu)

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.

In the near term we will be sending out a request for information for inclusion in our Annual NIH, NCRR/Biomedical Technology Program (BTP) Progress Report and in our response to the DOE's request for information for an upcoming peer review of our facility in January 2008. A direct request will be going out to our user community, but this information can also be submitted anytime via email message to Lisa Dunn or Cathy Knotts or via the reference submission form at:
http://smb.slac.stanford.edu/forms/reporting/form_publication.shtml

For publications lists and the proper acknowledgement statements see:
http://www-ssrl.slac.stanford.edu/pubs/

7.   SSRL User Wins Scientific Award

Junko Yano

Dr. Junko Yano, a researcher in the Physical Biosciences Division at Lawrence Berkley National Laboratory, received the Robin Hill Award, given by the International Society for Photosynthesis Research in July. The honor is given for outstanding investigations into physical aspects of the photosynthesis process. Recent research by Yano and collaborators have focused on structural studies of the photosystem II catalytic metal-cluster center, containing four manganese atoms and one calcium atom (Mn₄Ca), that drives the reaction which splits water molecules into protons, electrons and oxygen - the cornerstone of photosynthesis. Much of this work was performed using the DOE-BER and NIH-NCRR funded polarized single crystal x-ray absorption spectroscopy facility on SSRL's Beam Line 9-3 as published in Science and elsewhere.
(see http://www-ssrl.slac.stanford.edu/research/highlights_archive/psii-06.html)

8.   2007 Structural Molecular Biology Summer School Wrap-up
      (contact: S. DeBeer George, serena@slac.stanford.edu)

This year's Structural Molecular Biology (SMB) Summer School was held at SSRL during September 9-14. The Summer School was co-chaired by SSRL staff scientists Serena DeBeer George, Clyde Smith and Thomas Weiss, and focused on the application of x-ray absorption spectroscopy, small angle x-ray scattering and macromolecular crystallography to biological systems. The summer school consisted of three days of lectures, which provided a general introduction to the three techniques, as well as covering basic theory, experimental considerations, and applications. These lectures were followed by 3 days of rotating practical sessions, giving the students hands-on experience in data analysis in each of the methods. Led by a team of 20 tutors, 34 students, representing four different countries, attended this year. The Summer School is an integral part of the NIH NCRR and DOE BER funded SMB program with the next in the series planned for 2009.

9.   Low-Alpha Mode Increases Possibilities at SSRL
       - SLAC Today article by Ken Kingery

	A. Terebilo, J. Safranek and X. Huang

Since the Stanford Synchrotron Radiation Laboratory (SSRL) began experiments in 1973, it has proven to be a bottomless well of scientific discovery. Now, a team of SLAC accelerator physicists is working to add new functionality to the SPEAR synchrotron accelerator. The team, comprising James Safranek, Xiaobiao Huang and Andrei Terebilo has tested a new "low-alpha mode" for SPEAR that results in shorter x-ray pulses that could be advantageous for some users.

The path a particle travels around the 234-meter SPEAR ring can vary slightly because of minute differences in the energy of each electron in the beam. This causes accelerator magnets to create slightly different paths around the ring for each particle. Because the beam is actually 280 separate packets of particles-the length of which determines the length of pulses of x-rays created-the small variations in how far each particle travels-alpha-affects how short the pulses of x-rays can be made.

Shorter x-ray pulses allow scientists to study tiny processes in extremely short time frames, such as the movement of molecules of liquid water. In fact, short x-ray pulses are one of the defining characteristics of the Linac Coherent Light Source (LCLS) project currently under construction at SLAC. Although SPEAR's x-rays are longer than those that will be created by the LCLS, they are less powerful and won't damage fragile samples. Read more at:
http://today.slac.stanford.edu/feature/2007/low-alpha-mode.asp

10.   Upcoming Proposal Deadlines
      (contacts: C. Knotts, knotts@slac.stanford.edu; L. Dunn, lisa@slac.stanford.edu)

If your current proposal is getting close to its expiration date or if you plan additional experiments, please consider submitting new X-ray and VUV proposals by the November 1, 2007 deadline or a new Macromolecular Crystallography proposal by the December 1, 2007 deadline.
http://www-ssrl.slac.stanford.edu/users/user_admin/guide.html

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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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