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ALSNews Vol. 304 Print
Wednesday, 25 November 2009 00:00

In This Issue

Proofreading RNA: Structure of RNA Polymerase II's Backtracked State

X-Ray Imaging of the Dynamic Magnetic Vortex Core Deformation

Call for General User Proposals: Deadline January 15

ALS Job Posting: Deputy Division Director, Operations

Light-Source Safety Officials Meet for Two-Day Workshop

UEC Corner: New Members for 2010, Survey Results

Welcome: Shauna Kanel and Clyde Lewis

Around the Ring: Science Cafe, High-Profile Visitors

Ring Status Notifications to Cell Phone

Operations



News Links

Meet a Postdoc: Shuyun Zhou (a Berkeley Lab video series)

Engineering Division Upgrades the ALS without Downsizing Safety

X-ray diffraction microscopy peers into tiny cells

Research: Tuning Bilayer Graphene to Create New Quanta

Microscopy: Cell close-up (Nature Research Highlight)

Alivisatos Named Director of Berkeley Lab

Atomic-level Snapshot Catches Protein Motor in Action



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Proofreading RNA: Structure of RNA Polymerase II's Backtracked State

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For genes to be expressed, a complementary strand of RNA must be produced from a DNA template. During this process of transcription, a special class of enzyme called RNA polymerase moves along the DNA template, reading the DNA and producing an RNA complement. This process operates with amazingly high fidelity—the error rate is as low as one mistake for every 100,000 DNA base pairs transcribed—thanks in part to error correction by an RNA polymerase known as pol II, which "backtracks," or reverses, along the transcript to remove misincorporated or damaged nucleotides. A group from the Stanford University School of Medicine has solved the structure of pol II in the backtracked state, providing structural insights about a key mechanism for ensuring accurate transcription. Read more...

Proofreading During Transcription

Publication about this research: D. Wang, D.A. Bushnell, X. Huang, K.D. Westover, M. Levitt, and R.D. Kornberg, "Structural basis of transcription: Backtracked RNA polymerase II at 3.4 angstrom resolution," Science 324, 5931 (2009).

X-Ray Imaging of the Dynamic Magnetic Vortex Core Deformation

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Magnetic thin-film nanostructures can exhibit a magnetic vortex state in which the magnetization vectors lie in the film plane and curl around in a closed loop. At the very center of the vortex, a small, stable core exists where the magnetization points either up or down out of the plane. Three years ago, the discovery of an easy core reversal mechanism at the ALS not only made the possibility of using such systems as magnetic memories much more realistic, it also initiated investigation of the core switching mechanism itself. Now, a Belgian–German–ALS collaboration has used high-resolution, time-resolved, magnetic x-ray microscopy to experimentally reveal the first step of the reversal process: the dynamic deformation of the vortex core. The group also measured a critical vortex velocity above which reversal occurs. Both these observations provide the first experimental support for the postulated reversal mechanism. Read more...

Reversing a Magnetic Vortex Core

Publication about this research: A. Vansteenkiste, K.W. Chou, M. Weigand, M. Curcic, V. Sackmann, H. Stoll, T. Tyliszczak, G. Woltersdorf, C.H. Back, G. Schuetz, B. Van Waeyenberge, "X-ray imaging of the dynamic magnetic vortex core deformation," Nature Phys. 5, 332 (2009).

Call for General User Proposals: Deadline January 15

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The User Services Office is accepting general user proposals from scientists who wish to conduct research at the ALS in the next cycle.

PROPOSAL SUBMISSION DEADLINE (physical sciences beamlines):
Cycle: July–December 2010
Deadline: January 15, 2010

PROPOSAL SUBMISSION DEADLINE (structural biology/biological SAXS):
Cycle: March–April 2010
Deadline: January 15, 2010

NEW PROPOSALS: To submit a new proposal, please complete the appropriate online form.

ACTIVE PROPOSALS: Proposals for physical sciences beamlines are considered active and may be renewed for up to three, six-month cycles after the initial submission. After a total of four cycles, a new proposal must be submitted. If you have an active proposal for which you would like to request beam time during the July–December 2010 cycle, please submit a Proposal Renewal Form.

The following resources have been recently updated and are available for further information:

General information on the proposal process

Advice on what to include in the scientific case

Beamline information

Proposal scores for the current cycle

The proposal form now includes a section on publications from previous ALS work. The publications will be pre-filled automatically from the ALS publication database by searching for the principal investigator's name. Please make sure your publications are entered into our database.

ALS Job Posting: Deputy Division Director, Operations

The ALS is accepting applications for a Division Deputy for Operations to serve as the Chief Operating Officer for the ALS. This critical position offers the challenge and opportunity to be a part of a world-renowned center for scientific research. The deputy's primary role is to manage the overall operation of the ALS. High-impact responsibilities include handling business, project, and facility management and long-range planning related to Berkeley Lab's mission. The deputy will also assume the day-to-day responsibilities of the division director, as needed. Required qualifications include substantial experience managing a scientific program/project and knowledge of a national scientific user facility; demonstrated ability to work effectively with multidisciplinary teams; demonstrated ability to recruit, retain, and develop staff; and experience with financial and budget oversight and development. Substantial knowledge of the synchrotron radiation community is highly preferred. Read the full job posting.

Light-Source Safety Officials Meet for Two-Day Workshop

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Workshop participants

Attending the meeting to discuss user experiment and safety issues were, from left: Ken Goldberg, Mike Martin (LBNL); Zoe Van Hoover, Matthew Padilla (SLAC); Nena Moonier (APS); Jim Floyd (LBNL); Cathy Knotts (SLAC); Sue Bailey (LBNL); Ian Evans (SLAC); Susan Strasser (APS); Deborah Smith, Liz Moxon (LBNL); Andrew Ackerman (NSLS); David Malone (LBNL); and Mohamed Benmerrouche(CLS).

Safety and User Services staff from the five Department of Energy light sources met at a workshop at the ALS on November 16–17. The purpose was to present each facility's user safety program and to identify best practices and potential areas of collaboration. In all, eleven different issues were found for further work. The most significant of these was to work towards a more common experiment review process. The eventual goal, where practical, is to have a consistent web tool for users such that similar work would have a consistent review and authorization process across all of the light sources. The meeting paved the way for staff at the ALS to overhaul the current paper-based Experiment Safety Sheet (ESS), replacing it with an electronic system based on the Advanced Photon Source's Experiment Safety Approval Form (ESAF).

UEC Corner: New Members for 2010, Survey Results

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I'm very pleased to announce the four new members of the ALS UEC, the next UEC chair, and the results of the user poll. 156 users voted. See results.

The new UEC members are Hendrik Bluhm, David Kilcoyne, and Brandy Toner.

UEC chart 1

The new student representative is Holly Barth.

UEC chart 2

Their terms begin January 1st, 2010.

David Osborn (Sandia National Laboratories) has been elected as the next UEC chair for 2010. Many thanks to Peter Fischer, Franz Himpsel, Anne Sakdinawat, and Hendrik Ohldag, who will all be rotating off the committee in 2010.

Thank you to everyone who participated in the Users' Meeting opinion poll and charter amendment vote. Here are the results.

UEC chart 3

Welcome: Shauna Kanel and Clyde Lewis

Shauna KanelShauna Kanel is excited to be joining the ALS communications team. She comes to us from the Stanford School of Medicine, where she was the communications coordinator in charge of marketing, Web design, and news for the Biomedical Informatics Research division and the National Center for Biomedical Ontology. Shauna did her undergraduate and graduate studies in molecular biology at the University of California, San Diego. She will be writing and editing ALSNews and science highlights, helping redesign the ALS Web site, and improving the ALS's social marketing strategies. "If you have any exciting research coming down the pike, contact us and we'll get the news out," Shauna said. You can reach her at This e-mail address is being protected from spambots. You need JavaScript enabled to view it and 510-486-6376. Her office is in Building 4, Room 210.

Clyde LewisThe User Services Office would like to welcome Clyde Lewis to the ALS. Clyde will be working as the ALS's proposal administrator. He recently completed a term as a writing instructor with Berekely Lab's Center for Science and Engineering Education, assisting undergraduates with internship writing requirements. Clyde's Masters Degree in Educational Administration and experience derived from creating a Center for Foreign Language Study at Keio University, Japan, will be an asset to the ALS. "I couldn't have asked for a better position; all the people I'm working with are phenomenal," Clyde said. His open and friendly personality will make him a great addition to the ALS support staff, where he hopes to build relationships and gain a better understanding of the Lab. You can contact Clyde at This e-mail address is being protected from spambots. You need JavaScript enabled to view it and 510-486-7692.

Around the Ring: Science Cafe, High-Profile Visitors

A second Science Cafe was held on Tuesday, November 10, again attracting an overflow crowd interested in hearing about energy-related research taking place on ALS beamlines. Speakers for this event included Simon Teat, who spoke about investigating molecular structures for gas sequestraion using small-molecule crystallography on Beamline 11.3.1; Martin Kunz, who presented recent lithium-ion battery research on Beamline 12.3.2, and who also proposed several ideas to develop new energy-research user communities at the ALS; and Jinghua Guo, who rounded out the program with his presentation about metal-oxide clusters as photocatalysts for water splitting. Division Director Roger Falcone moderated the discussions that followed each talk. The next Cafe will take place on Wednesday, January 20, 2010.

Representative Bill Foster, one of only three physicists in the U.S. Congress, spoke on "What It's Like to be a Scientist in the U.S. Congress" at Berkeley Lab on Monday, November 9. Foster, who represents the 14th District in Illinois, was a researcher at Fermilab for 22 years. While there, Foster helped discover the top quark, the heaviest known form of matter. Foster currently serves on the House Financial Services Committee. As part of his visit, Rep. Foster toured the ALS with Director Roger Falcone. The congressman was particularly interested in Alastair MacDowell's effort on measuring CO2 transport through rock on Beamline 8.3.2, in connection with the Lab's work on energy and climate change related to carbon sequestration. Foster was also interested in Berkeley Lab's proposed new x-ray free-electron laser source, and his knowledge of particle accelerators from his previous life's work at Fermilab led to some probing questions.

Bill Foster with Alastair MacDowell

Congressman Bill Foster (IL-14 with Alastair MacDowell (ALS).

Members of the Australian Parliament also toured the ALS with Roger on Monday, September 28. The delegation was led by Senator John Hogg, President of the Australian Senate (equivalent to the U.S. Speaker of the House). In addition to visiting the ALS, the delegation toured the National Center for Electron Microscopy (Uli Dahmen) and heard presentations on advanced biofuels development (Jay Keasling) and energy-efficient buildings (Arun Majumdar/Steve Selkowitz).

Ring Status Notifications to Cell Phone

You may now receive text message notifications to your cell phone of the ALS ring status. Send a text message from your phone to This e-mail address is being protected from spambots. You need JavaScript enabled to view it containing the letters "als" in the body of the text. You will get a response with the current status and, if the beam is down, it will send a follow-up text as soon as the beam is back. James Glossinger of the Berkeley Center for Structural Biology (BCSB) developed the application, with help from Eric Berryman of Engineering Division. Thanks to Leif Steinhour (also BCSB) for suggesting the project.

Operations

For the user runs from October 21 to November 15, the beam reliability [(time scheduled - time lost)/time scheduled)] was 92.6%. For this period, the mean time between failures (MTBF) was 29.6 hours, and the mean time to recovery (MTTR) was 143 minutes. A failure within the SR01C SD power supply November 3–4 resulted in a loss of over 14 hours of scheduled beam time (eight of those hours during a scheduled special operations shift.)

More detailed information on reliability is available on the ALS reliability bulletin board, which is located in the hallway between the ALS and the control room in Building 80. Questions about beam reliability should be directed to This e-mail address is being protected from spambots. You need JavaScript enabled to view it (x4376 ).

Long-term and weekly operations schedules are available here. Requests for special operations use of the "scrubbing" shift should be sent to Rick Bloemhard ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it , x4738) by 1:00 p.m. Friday. View the ring status in real time here.

 
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