SSRL HEADLINES April 2003
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SSRL Headlines Vol. 3, No. 10  April, 2003

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Contents of This Issue:

  1. Science Highlight - Structure of the Specificity Domain of Bacterial
    RNase P
  2. 2003 SPEAR2 Run Ends on a Perfect Note
  3. Celebrating 30 Years of Synchrotron Science on SPEAR
  4. SPEAR3 Installation Begins
  5. SSRL/SLAC and IMSS/Photon Factory Sign Memorandum of Understanding
  6. Automated Sample Screening on BL11-1
  7. Recent Talks Explore Energy-Related Topics
  8. SSRLUO-EC Encourages Support of Light Sources
  9. Educating a New Class of Synchrotron Users
  10. Register by May 1 for Synchrotron Radiation Summer School



1.  Science Highlight - Structure of the Specificity Domain of Bacterial RNase P
      (contact: Alfonso Mondragˇn, Northwestern University)

One of the primary ways people find structure and coherence in the world is to identify fundamental characteristics common within and between apparently different classes - plants, humans, atoms, stars, etc. In the case of diverse biological life we know that RNA and/or DNA are common to them all. Thus, a deeper understanding of the architecture and interactions of RNA and DNA will lead to a greater understanding of the commonalities underlying all biological life. The intermediary between DNA and protein is RNA. RNA is the only known macromolecule that can encode genetic information and also act as a biocatalyst. In macromolecules like ribonucleases (RNAses), a protein and an RNA work together to form an enzyme that performs one of the fundamental tasks of constructing the protein-making machinery of the cell. Specifically, Rnase P plays a key role in the activation of tRNA and has a catalytic domain and a specificity (S) domain. The S domain alone can bind pre-tRNA directly with micromolar affinity. tRNA is the direct interface between the amino-acid sequence of a protein and the information in DNA. All tRNA's from all organisms have a similar structure. Indeed, a human tRNA can function in yeast cells. Thus, a greater understanding of the architecture and interactions of the S domain -and hence, tRNA - will lead to a better understanding of the process of transcription of genetic information.

Macromolecular crystallography experiments at SSRL and the APS have enabled researchers at Northwestern University to achieve a 3.15 ┼ resolution crystal structure of the 154-nucleotide S domain of Bacillus subtilis RNase P. The structure reveals the architecture of the S domain and provides a molecular framework for studying the interactions that must occur between tRNA and the ribozyme during pre-tRNA processing. The structure is consistent with the available biochemical data for bacterial RNase P RNA and extends our understanding of RNase P structure across all taxonomic kingdoms. Furthermore, as an important addition to the still limited number of large RNAs of known structure, it advances our knowledge of the general principles of RNA structure and packing. For more information on this work see:
http://www-ssrl.slac.stanford.edu/research/highlights_archive/rnase_P.html
or http://www-ssrl.slac.stanford.edu/research/highlights_archive/rnase_p.pdf


2.  2003 SPEAR2 Run Ends on a Perfect Note
      (contact: Piero Pianetta, SSRL)

Our most recent experimental run ended very successfully with SPEAR delivery of scheduled beam time to users at the 100% mark during the last week of operations. The up time average for the entire FY2003 run was 96.8%, tying it with an all time high delivery rate first achieved during the FY2000 run. Even though the FY2003 run was shortened by about 4 months due to the beginning of the SPEAR3 installation, a total of 813 users (including 221 "first-time" users) came to SSRL during the run to conduct experiments on 32 stations. Users were scheduled for 665 individual experimental starts over the 18 weeks of user operations. All in all, it was an excellent way to end the SPEAR2 era and move on to SPEAR3.


3.  Celebrating 30 Years of Synchrotron Science on SPEAR
      (contact: Cathy Knotts, SSRL)

SPEAR2 was turned off the morning of March 31. As users came offline, a few individuals gathered in the SPEAR control room at 7 am to witness the shutdown. Armin Busse, beam line development engineer, contributed to the sentiment of the moment by playing Auld Lange Syne on his bagpipes. Later that morning a larger event was held to commemorate the accomplishments of SPEAR2 with brief presentations by Burton Richter, SLAC Director Emeritus, and Keith Hodgson, SSRL Director. SPEAR has come a long way from the early days in 1974 with only one operational synchrotron beam line operated in "parasitic" mode. In 2003, our total user community has grown to approximately 2,000. Over the past 30 years, many scientists have utilized the facility and developed innovative synchrotron radiation (SR) techniques for wide application in the study of matter. Notable among these are photoemission spectroscopy for study of the electronic structure of materials; x-ray scattering methods including anomalous scattering approaches for the study of non-crystalline materials; development of x-ray absorption spectroscopy with numerous variations and applications from biology to materials; first application of SR for protein crystallography and demonstration of a novel approach to phasing called multiwavelength anomalous dispersion; first angiography studies on human patients using SR; establishing SR as a premier tool in molecular environmental science; developing methods for trace element detection on surfaces; and innovative angular resolved photoemission for study of materials like high Tc superconductors. Of course, all this has been possible only with the strong effort and support of a very talented and dedicated staff, and with the tremendous contributions of graduate students, postdocs, collaborators and users. see:
http://www-project.slac.stanford.edu/streaming-media/


4.  SPEAR3 Installation Begins
       (contacts: Richard Boyce, SSRL; Tom Elioff, SSRL; Bob Hettel, SSRL)

The SPEAR3 Installation Program began on schedule on March 31, 2003. The Installation Program involves 3 phases: demolition of SPEAR2, modification of the facilities to meet SPEAR3 needs, and finally the actual installation of SPEAR3 technical systems and components. Each phase is a complex procedure that is planned in great detail with overall completion projected by the end of October 2003. In phase one, the first week included the regimented shutdown process for electrical and vacuum systems together with radiation measurements within the tunnel followed by the removal of useful components of the ring. Power supply units were removed from Bldg. 118. The removal process of various cable systems for power, controls and monitoring was initiated. This overall effort was completed ahead of schedule thanks to the outstanding efforts of many SSRL staff members. During the second week, the cable cutting process inside the tunnel was completed. In the third week appropriate shielding blocks were removed such that the seven insertion devices could be removed and stored. This week initiated the removal of the eighteen main magnet girders. These 30-foot long concrete supports with installed magnets are being transported through the tunnel to a roof opening near the West straight section, removed by crane, and transported to a salvage area. The remaining work includes cable removal outside the tunnel, removal of beam line front-end components, and overall tunnel clean up and is scheduled for completion May 8, 2003 at which time phase two will begin.

Many SSRL users know that a SPEAR status report has been available on the web for some time, making it convenient to get up-to-the-minute information on energy, current and beam lines. A new feature, SPEAR CAM, has been added so that users and others interested in the SPEAR3 project can "watch" as the construction progresses. Visit:
http://www-ssrl.slac.stanford.edu/talk_display.html


5.  SSRL/SLAC and IMSS/Photon Factory Sign Memorandum of Understanding
       (contact: Keith Hodgson, SSRL)

A signing ceremony was held on Monday, April 14 at KEK in Tsukuba, Japan at which the SSRL Division of SLAC and the Photon Factory Division of the Institute of Material Structure Science (IMSS) at KEK agreed to collaborate in areas of mutual interest. An annex of the signed MOU provides the opportunity for users of SSRL and the PF to receive beam time at either facility in certain areas and under certain circumstances (such as the shutdown of one or the other facility for a major upgrade). This agreement will be of immediate benefit to SSRL users working in the area of small angle scattering and several groups will be soon scheduled for beam time at the PF under their SSRL proposals. We look forward to an expanding scientific and technical interaction with our colleagues at KEK as facilitated by this MOU. Additional opportunities for SAXS/D beam time may be available in the future, so please contact Cathy Knotts or Hiro Tsuruta if you are interested in pursuing this avenue.


6.  Automated Sample Screening on BL11-1
       (contacts: S. Michael Soltis, SSRL; Ashley Deacon, SSRL)

During the last month of the 2003 user run, the automated crystal screening system on BL11-1 was made available to the general macromolecular crystallography user community. This is the first complete automated screening system provided to general users for increasing experimental efficiency, data quality and throughput. The SSRL system is based on a small-scale commercial robot that mounts samples from high-capacity cassettes onto the experimental apparatus at liquid nitrogen temperature (the low temperature prevents chemical and radiation damage to the sample). Software was implemented as part of the standard control software package, Blu-Ice, which allows the user to select samples and to define a detailed screening procedure for each sample. Up to 285 crystals can be screened without opening the hutch door. Research groups were provided with a cassette kit comprised of a sample cassette, 95 Hampton-style mounting pins, a cassette handle, a magnetic wand and instructions on how to mount and ship their samples to SSRL. Six research groups used the system. They were all impressed by the efficient use of their beam time and they were very pleased with their results. In particular, Prof. Roger Kornberg's group (Structural Biology, Stanford) reported a major success. Kornberg's group has focused on transcription and transcription regulation, working with relatively large protein complexes (>0.5 MDa) such as polymerase II, which often form weakly diffracting crystals. Previously, the determination of a 3.0 ┼ resolution structure of polymerase II was significantly hampered due to the intensive screening effort required to identify suitable conditions that produced good diffracting crystals (Cramer, P. et al. Science 288, 640, 2000). Using the SSRL system, they were able to screen 130 crystals of polymerase complexes in about seven hours of beam time. In contrast, earlier in the year they manually screened 100 crystals in a 24-hour period and lost several crystals in the process. During their automated screening run they managed to find one crystal that diffracted to 0.6 ┼ resolution beyond anything observed to date. They then collected a complete data set from the best diffracting crystal, which they anticipate will lead to a better understanding of transcription and transcription regulation. Moreover, in-house staff members belonging to the Joint Center for Structural Genomics have used the system to screen over 3000 crystals during the last six months and during the last 18 hours of the SPEAR2 run they managed to screen 246 crystals from 21 different protein targets.

All the SSRL Macromolecular Crystallography beam lines will have the automated screening system in place when the beam lines become operational in the SPEAR3 era. In addition, the appropriate protocols are being implemented to allow remote operation of the entire system. In this mode, scientists will have the option of performing complete experiments (both screening and full data collection) from their home laboratories.


7.  Recent Talks Explore Energy-Related Topics

Fundamental challenges and research opportunities related to hydrogen energy technology were considered recently during a seminar given by Theanne Schiros of SSRL. Theanne is a Ph.D. student working with Prof. Anders Nilsson of SSRL. The exploration and development of new energy sources is one of the fundamental missions of the DOE. Within this broader framework hydrogen fuel, produced from renewable sources, has enormous potential to sustain global energy consumption within the regenerative capacity of the Earth. Theanne emphasized the challenges that remain in the production, storage, and distribution of hydrogen before it can be realized as a commercially viable energy carrier. She also pointed out how multidisciplinary efforts in basic science, especially x-ray research on interfacial processes, may be the key to making this technology an economically viable alternative. Additional information can be found at:
http://www2.slac.stanford.edu/tip/2003/mar21/hydrogen.htm

At a seminar on April 4, Jeff Terry (Illinois Inst. of Technology, Univ. of Notre Dame) discussed the topic of synchrotrons, XAS and energy related research. As many projects involve tailoring materials to provide better properties, probes that function on a nanoscale and that do not require perfect crystallinity can provide useful insight to these difficult properties. Synchrotron radiation and XAS is currently being used to probe impurity poisoning in solar cells, the structural stability of nuclear reactor walls, nanoscale magnetic devices, novel dielectric compounds, and nuclear technology spin-offs such as radiopharmaceutical design and characterization. Jeff addressed three specific areas, including: 1) results in the synthesis and characterization of novel aerogel dielectrics made up of conducting nanoparticle wires; 2) work on 99Tc radiopharmaceuticals, a spin-off technology of the nuclear industry; and 3) use of XAS to probe the electronic structure of small magnetic molecules.


8.  SSRLUO-EC Encourages Support of Light Sources
       (contacts: Uwe Bergmann, SSRL; Ben Bostick, Dartmouth College)

Uwe Bergmann and Ben Bostick (Chair and Vice Chair, SSRLUO-EC) joined their colleagues from the ALS, APS, and NSLS on a trip to Washington, DC on April 7-8. The group met with staff from the DOE, OMB, OSTP, House and Senate Energy and Water Appropriations Committees and the Committee on Natural Resources. Although most of the individuals that the group met with are already supportive of the mission of the four DOE light sources, these meetings help to maintain awareness of the importance of the scientific advances enabled by synchrotron radiation. The entire user community can help reinforce this message by sending congressional representatives correspondence illustrating the impact of SR studies in their own research. The Appropriation Committees meet towards the end of May, so it is a particularly good time to show some support for your light sources. For more information including the list of committee members and template letters visit the updated SSRLUO activism page:
http://www.dartmouth.edu/~ssrluo/

The SSRL Users' Organization Executive Committee will meet on Friday, May 9, from 1-3 pm in the Bldg. 137 3rd floor conference room. All users are welcome to attend. See the meeting agenda and minutes of previous meetings at:
http://www-ssrl.slac.stanford.edu/users/ssrluo/ssrluoec-mtgs.html


9.  Educating a New Class of Synchrotron Users
       (contact: Britt Hedman, SSRL)

Six graduate students, sponsored by the Alberta Synchrotron Institute, visited SSRL in March to gain first-hand experience with XAS studies. These students were participating in a course on "Structural Methods in Chemistry" taught by Dr. Farideh Jalilehvand (Asst. Prof. of Chemistry, Univ. of Calgary). After studying the principles of synchrotron-based XAS for several months, the students were able to participate in real experiments and data collection. Under the guidance of Prof. Magnus Sandstr÷m (Structural Chemistry, Univ. of Stockholm), they spent a few days learning about experimental set-ups for various types of EXAFS measurements, preparing samples and cells for solution and solid samples, and starting experimental scans. Dr. Jalilehvand reported, "After coming back from Stanford, these students were quite excited to begin data analyses on a few samples they measured while at SSRL, to share their experiences with their classmates by giving internal presentations about SLAC, what a synchrotron facility looks like, the discovery of subatomic particles in SLAC, and much more... This visit will definitely help us to promote synchrotron science and its applications among the graduate students in the University of Calgary, especially now when the Canadian synchrotron source is in its final stage of construction." The students look forward to applying synchrotron radiation to their own experiments.


10.  Register by May 1 for Synchrotron Radiation Summer School
       (contacts: Anders Nilsson, SSRL; David Attwood, UC-Berkeley/LBNL)

Students interested in participating in the June 9-13 Berkeley-Stanford summer school must submit their applications by May 1. This summer school program will provide basic lectures on the synchrotron radiation process, technologies and a broad range of scientific applications to ~40 students. Lectures will be presented by professors and scientists from the four sponsoring organizations (UC Berkeley, Stanford, LBNL and SSRL) and their user communities. David Attwood and Anders Nilsson are co-chairing the school. Cost of attendance is $625 for the course, including lectures, shared room, breakfast and lunch. Application forms and other details are available on the meeting website:
http://www.unex.berkeley.edu/eng/synchrotron


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 S ciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 31 MAR 2003
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