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SSRL Headlines Vol. 7, No. 6  December, 2006


Contents of this Issue:

  1. Science Highlight — SSRL Examines Stardust
  2. Science Highlight — High Resolution Structural Study of a Modular Polyketide Synthase Didomain
  3. Science Highlight — The Structural Basis of Transcription
  4. Holiday Greetings from the Director
  5. SLAC Policy Committee Fall Meeting
  6. Michael Casassa, DOE-BES, Visits Ultrafast Facilities at SLAC and Stanford
  7. Piero Pianetta Awarded APS Fellowship
  8. Test Groups Commission Macromolecular Crystallography Uni-Puck at SSRL
  9. Photon Science Job Opportunities

1.  Science Highlight — Stardust Examines Stardust
       (contacts: H. Ishii,; S. Brennan,

An international collaboration that included researchers at SSRL has used x-ray scanning microprobe fluorescence techniques at BL6-2 to characterize the elemental chemistry of samples from comet 81P/Wild-2 brought back aboard the Stardust spacecraft last January. Twenty-three aerogel samples containing cometary particles were analyzed by the 175-member Preliminary Examination Team, and five of those samples were studied at SSRL. This collaboration provided the first look at the Stardust samples after the return, and results are presented in several publications in the December 15 issue of Science.

Optical microscope images of two of the five Stardust comet dust impact tracks in aerogel keystones analyzed by micro-SXRF at SSRL
Until 1974, comet 81P/Wild 2 orbited beyond Jupiter, but a gravitational kick from that planet altered its orbit transforming it into a short-period comet in the inner solar system. This allowed NASA's solar-powered Stardust spacecraft to intercept the comet's tail within the orbit of Mars. The fly-by was completed at a relative speed of 6.1 km/s passing through the coma of the comet. Microscopic dust grains were captured in low-density silica aerogel tiles and aluminum foils, and these samples were returned successfully to Earth in January 2006. These Stardust samples are unique among extraterrestrial materials on Earth as the first samples returned from an identified parent body originating in the Kuiper belt beyond the gas giants. Due to the very recent orbit change, dust from Comet Wild 2 provides a means of inferring conditions in the Kuiper belt, and thus, theoretically, the origins of the solar system. First order, fundamental research involves understanding the elemental and isotopic chemistry, the astronomical signatures, the organics and mineralogy of these samples.

The mean elemental composition of the Stardust Comet 81P/Wild 2 dust measured is generally consistent with the CI meteorite composition, believed to be representative of the overall composition of the solar system. A few elements, Cu, Zn and Ga, are enriched suggesting that the CI meteorites may not be entirely representative of the solar system composition for these moderately volatile elements.

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

2.  Science Highlight — High Resolution Structural Study of a Modular Polyketide Synthase Didomain
      (contacts: Y. Tang,; C. Khosla,

Structure of the KS-AT didomain from DEBS module 5.
Researchers have obtained the highest-resolution image of a didomain structure in a modular polyketide synthase (PKS), revealing new structural features. PKS enzymes catalyze the synthesis of polyketides, which include a number of antibiotics, anticancer agents, antiparasitics, and immunosuppressants. The researchers solved the x-ray crystal structure of a didomain of 6-deoxyerythronolide B synthase (DEBS), a model PKS using data measured at SSRL Structural Molecular Biology Beam Line 11-1. They imaged a 194-kDA fragment of module 5 of the enzyme with multiwavelength anomalous dispersion (MAD). The fragment contained full-length ketosythase (KS) and acyl transferase (AT) domains, and the linkers that are part of the polyketide chain elongation process. With 40,908 atoms (582 kDa) per asymmetric unit, this structure represents the largest unique crystal structure to be solved using MAD. The 2.7-Å resolution image showed that the active site residues of the KS and AT domains, Cys199 and Ser642, respectively, were more than 80 Å apart. The distance is too large to be traversed by the long arm of a statically positioned acyl carrier protein, needed to ferry growing polyketides along the synthase backbone. The unexpected feature suggests substantial domain reorganization may be needed for the synthase module to function. The didomain structure also revealed a novel protein fold for the KS-to-AT linker.

Principal investigator Chaitan Khosla of Stanford University was recently elected a fellow to the American Association for the Advancement of Science for his contributions to the field of metabolic chemistry and engineering, particularly to the biosynthesis of polyketide antibiotics.

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

3.  Science Highlight — The Structural Basis of Transcription
      (contacts: D. Wang,; D. Bushnell,; R. Kornberg,

 Cell Cover
Life as we know it depends on turning on and off the proper genes at the correct time. This process of gene expression starts when an RNA message is copied from DNA. Scientists have long known that an enzyme called RNA polymerase II plays the central role in this delicate transcription process. But the exact mechanism by which RNA polymerase II selects specific nucleotides and catalyzes the reaction that incorporates them into a growing RNA strand has not been well understood.

In a new study published in the December 1, 2006 issue of Cell, the 2006 Chemistry Nobel Prize Laureate, Roger Kornberg, and his research group at Stanford University performed x-ray studies at SSRL Beam Lines 11-1 and 9-2 and at the Advanced Light Source at Berkeley to investigate the molecular structure of this enzyme in action. The study revealed that a structural element of the enzyme called the trigger loop is involved in both nucleotide recognition and catalysis.

To ensure the accuracy of the transcription process, RNA polymerase II must distinguish between ribonucleotides (nucleotides that make up RNA) and deoxyribonucleotides (nucleotides that make up DNA) in the cell. It also must distinguish between different types of ribonucleotides and add to the RNA strand the one that is complimentary to the deoxyribonucleotide in the DNA template. When such a "correct" ribonucleotide is present, it fits together with an extensive network consisting of the trigger loop, a structural element known as the bridge helix, and other nearby polymerase residues, which all fit together like pieces of a puzzle. Additionally, when a correct ribonucleotide is present, the interactions between these puzzle pieces cause the trigger loop to then swing into position beneath the nucleotide and seal off the active site. This move puts the ribonucleotide into the right position to be added to the growing RNA strand, and the interaction between the side chain of trigger loop and nucleotide phosphate thus acts as a trigger for the catalytic reaction. The trigger loop's role in both selection and catalysis therefore ensures the accuracy of the transcription process, without which cells would have inefficient transcription and become unhealthy or die. This finding promises to inform future efforts to manipulate the transcription process for therapeutic and other purposes.

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

4.  Holiday Greetings from the Director

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

As we near the end of 2006, 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 FY2006 run (November 2005-August 2006), SPEAR3 provided very stable beam for 96.2% of the scheduled time and a total of 64,585 hours of beam were delivered on our 25 experimental stations. The significant over-demand for SSRL facilities is reflected by the fact that only half of the requested time could be accommodated. Of the approximately 500 active proposals, 345 different proposals received beam time at SSRL during the FY2006 run with >1,000 experimental starts involving ~1,700 researchers. Users consistently rate their overall scientific experience at SSRL very highly (92% ranked their experience as excellent or very good).

The FY2007 run got off to a good start in November 2006 and will run through August 6, 2007. The average uptime to date is ~96%, with 100% uptime for users during the last week alone.

SSRL continues to provide valuable scientific training experience for the future workforce, indicated by the large number of users who are undergraduate students, graduate students, or postdoctoral fellows (>57%). Since SSRL began user operation in 1974, users have reported 7,736 scientific publications based on research conducted at SSRL, including 790 student theses. In 2005 and in 2006 alone, users reported >650 publications, including so far 43 theses.

One exceptional achievement in 2006 was the announcement of the Nobel Prize in Chemistry awarded to Roger Kornberg, Professor of Structural Biology at the Stanford University School of Medicine, for his work in understanding how DNA is converted into RNA. 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 action snapshots - 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 1991 but with the main work leading to the first published structure in the late 1990s.

During 2006, SSRL's Sub-Picosecond Pulse Source (SPPS) experiments concluded, as its home - the Final Focus Test Beam (FFTB) - was dismantled to make way for the Linac Coherent Light Source (LCLS), the world's first x-ray free-electron laser. Several significant new discoveries and publications resulted from this pioneering endeavor. Two researchers working on the SPPS experiment jointly received the 2006 W. E. Spicer Young Investigator Award: Adrian Cavalieri (Max Planck Institute for Quantum Optics) and David Fritz (SSRL). We also congratulate Mike Soltis and Bill Schlotter, recipients of the 2006 Farrel W. Lytle Award and the 2006 Melvin P. Klein Scientific Development Award, respectively. These awards were presented at the 33rd Annual SSRL Users' Meeting in October (SSRL33), which had approximately 300 participants. As I mentioned in my Meeting talk and also at the ensuing SSRL Users' Organization meeting, I encourage your input and suggestions to identify and prioritize future scientific opportunities for SSRL. A number of workshops to focus on scientific facilities will be held over the next several months; most recently a workshop was held in early December to discuss new directions in x-ray scattering.

An official ground breaking ceremony for the LCLS was held in October, with nearly 1,000 attendees including DOE Under Secretary of Science Raymond L. Orbach who noted during his keynote address that the LCLS "will drive understanding and opportunity as no facility has ever done before." The LCLS remains on track for first light in 2008.

I thank those who serve on SSRL's advisory committees - the SSRL Scientific Advisory Committee (SAC), Proposal Review Panel (PRP), the SMB Advisory Committee and the SSRL Users' Organization Executive Committee for their tireless work and advice. 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 large and growing user community.

I urge you to continue to let us know your opinions and ideas - it helps us serve you better, improve our operations and plan for the 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 2007!

—Jo Stöhr, SSRL Director

5.   SLAC Policy Committee Fall Meeting
      (contact: K.O. Hodgson,

The fall meeting of the SLAC Policy Committee (SPC) was held December 1-2. The SPC is the highest level oversight committee for SLAC. The group meets twice yearly and reports to the Stanford University President. At this meeting, the SPC considered a range of topics that included LCLS Construction and loss of the CLOC building, plans for accommodating the space needs resulting from the loss of the CLOC, and programmatic topics for Photon Science (PS) and Particle and Particle Astrophysics (PPA). They heard reports on progress in developing a strategy for scientific computing and accelerator science. The ES&H program was also discussed. The PS and PPA faculties presented their faculty development plans. Recommendations were made in a closeout with Stanford Provost Etchemendy, Vice Provost for Research Ann Arvin and Assistant Dean of Research, John Brauman. The advice of such a distinguished committee of outside scientists is a central and key component of both near and long term strategic planning and I thank the SPC members for their time and effort in such valuable service of SLAC and Stanford. Thanks also to all the faculty and staff who prepared material and made presentations during the meeting. The SPC will meet again next May.

6.  Casassa, DOE-BES, Visits Ultrafast Facilities at SLAC and Stanford

      (contact: P. Bucksbaum,

Michael Casassa of the Department of Energy, Office of Basic Energy Sciences Chemical Sciences, Geosciences and Biosciences Division visited SLAC and Stanford on Wednesday, December 13, for a briefing on the ultrafast science program. Keith Hodgson welcomed Dr. Casassa with an overview talk on the Linac Coherent Light Source (LCLS) project and the closely tied LCLS Ultrafast Science Instruments project. Phil Bucksbaum followed with an overview of PULSE (Photon Ultrafast Laser Science and Engineering). The morning session continued with talks by Aaron Lindenberg, David Fritz, John Bozek, Yves Acremann and Jerry Hastings as well as a tour of the new ultrafast center facilities in Bldg. 130 and Central Labs Bldg. 40. Markus Guehr and Peter Hommelhoff made presentations to start off the afternoon session on the Stanford central campus followed by a tour of the PULSE research carried out in laboratories of Bucksbaum and Kasevich, and a tour of the microfabrication facilities used by Yves Acremann for PULSE research.

Dr. Casassa was very impressed by both the quality and level of ultrafast activities in PULSE, and particularly enjoyed the opportunity to meet and speak to the postdocs and students involved in the research, both on the SLAC campus and on the central Stanford campus.

Piero Pianetta
Piero Pianetta
7.  Piero Pianetta Awarded APS Fellowship
           —excerpted from 12/7/06 edition of the SLAC Today

The American Physical Society has awarded fellowships since its inception in 1899. The Society currently awards fellowships to approximately 200 members a year, about one half of one percent of their total membership. To receive a fellowship, APS members are nominated and elected by APS fellowship committees and the APS Council. Fellowship is an honor signifying recognition by one's professional peers. SSRL Deputy Director Piero Pianetta was recently awarded a fellowship for his pioneering contributions to the synchrotron based photoelectron spectroscopy study of electronic structure of surfaces and interfaces. Nominated By: Condensed Matter Physics (DCMP).

8.  Test Groups Commission Macromolecular Crystallography Uni-Puck at SSRL
      (contacts: A. Cohen,; S.M. Soltis,

SSRL Uni Puck
SSRL Uni-Puck
The Uni-Puck device, a storage container for macromolecular crystal samples, compatible with the automated robotic sample mounting systems currently in use in the US and with many of the systems used abroad, was initiated at SSRL and developed in collaboration with the ALS, the APS SBC-CAT, CHESS, NSLS, and Rigaku-MSC. Previously there were three main sample storage containers in use at synchrotron stations in the US: the SSRL cassette, the ALS puck, and the MSC magazine. The costs to purchase these containers and associated cryo-tools and the inconvenience of their non-interchangeability had become a significant impediment to user groups seeking to take advantage of more than one of these facilities.

The design and initial testing of the Uni-Puck was a collaborative effort and the first version (V1 Uni-Puck) was released in October 2006. The puck is currently available for use at several beam lines that use the ALS robot system; at SSRL the Uni-Puck is being commissioned by several test user groups and it is expected to be released to general users in February 2007. The puck should also be available for general users at the APS SBC-CAT in early 2007. Additionally, a joint SSRL/ALS macromolecular crystallography workshop was held on October 10-11 in conjunction with the ALS and SSRL Users' Meetings to introduce the Uni-Puck and to train the user community, in particular those users who collect data at both facilities.

9.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


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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