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ALSNews Vol. 303 Print
Wednesday, 28 October 2009 00:00

In This Issue

ALS Users' Meeting 2009: Haiku, Top-Off, Nobel, Oh My!

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

Robust, High-Throughput Analysis of Protein Structures

Thomas Steitz to Share 2009 Chemistry Nobel Prize

More UEC Corner Haiku, by Ken Goldberg

Guest House Welcomes First User Groups

New X-Ray Data Booklet/Spectrum Published

ALS Supplier, Boyd Technologies, to Close


News Links

Scientists decipher missing piece of first-responder DNA repair machine

"Promiscuous" protein interactions found in the nuclear pore complex

First direct information about the prion's molecular structure reported

Small (and Big) Talk at FIO

Accelerators for America's future: An exercise in integration

Researchers find new route to nanotechnology self-assembly

Team led by Scripps Research and UC San Diego scientists reveals secrets of drought resistance

The Energy Challenge (video of Secretary Chu's talk at Berkeley Lab, 10/26/09)

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ALS Users' Meeting 2009: Haiku, Top-Off, Nobel, Oh My!

The 2009 ALS Users' Meeting was another successful joint effort between the ALS and the Molecular Foundry. After the 2007 Joint Users' Meeting, this year’s co-chairs David Osborn and Yayoi Takamura wanted to bring ALS and Foundry users together again to continue improving scientific collaboration. The Users' Executive Committee Chairs for the ALS and the Foundry, Ken Goldberg and Oscar Dubon, welcomed attendees to the opening session with some clever haikus: "Autumn in Berkeley; ALS users converge; jointly with Foundry."

ALS Division Director Roger Falcone gave an opening address covering stimulus project progress, new safety efforts, and Thomas Steitz's 2009 Nobel Prize for Chemistry. Falcone then introduced Robert Schoenlein, ALS's new Deputy Director for Science, and shared some details of the Lab's biggest upcoming initiative: the Next Generation Light Source. The NGLS will be "an array of soft x-ray lasers, for 3D imaging, with chemical selectivity, to measure structure at the nano-scale." Foundry Director Carolyn Bertozzi then gave an overview of the facility's science, progress, and future plans, followed by Basic Energy Sciences Associate Director Harriet Kung, who showed how a large portion of BES's stimulus funds will be invested in light sources and nanoscale science research centers.

Bill BrinkmanKeynote addresses rounded out the morning. William Brinkman, the new Office of Science Director, opened by presenting energy research being done at synchrotron radiation facilities. "X-ray light sources are revolutionizing biology," Brinkman said. Synchrotrons have contributed to the discovery of 70% of the 50,000 protein structures in the Protein Data Bank, with the ALS alone contributing over 2700 entries. Berkeley Lab Interim Director Paul Alivisatos then gave his keynote speech on the Carbon Cycle Research Program, artificial photosynthesis, and energy storage. He focused on nanoscale materials for solar fuel generation, and multi-component nanoparticle systems for light-induced hydrogen production from water.

Sessions resumed after lunch with science highlight talks. Mark Le Gros (National Center for X-ray Tomography) presented biological applications of soft x-ray tomography, which he called an "unmatched imaging tool for precision structural phenotyping ... created for biologists, by biologists." Jim DeYoreo (TMF) spoke about unconventional pathways during protein self-assembly and template-directed nucleation. Pupa Gilbert (University of Wisconsin, Madison) gave an animated presentation on biominerals, specifically self-sharpening sea urchin teeth and abalone nacre. Marissa Caldwell (Stanford University) rounded out the session with a talk about optical phase change memory and its use in modern memory storage devices, like DVDs and Blu-Ray discs. Attendees then had a chance to explore the 130+ posters displayed on the ALS patio.

Poster session

Students explain their posters to other students and to judges of the student poster competition.

Friday, users were treated to talks given by this year's award winners. The Halbach award for innovative instrumentation went to all 30+ members of the ALS top-off team. The Shirley award for outstanding scientific achievement was awarded to M. Zahid Hasan (Princeton University) for the discovery of topological order in solid state samples and quantum Hall-like behavior without magnetic fields. The Renner award recipient, Bruce Rude, was announced at Friday's dinner banquet. Student poster competition winner Samantha Ying (Stanford University) delivered an engaging presentation on the testing of and proposed controls for arsenic fate, despite having beam time all Thursday night.

Award winners

This year’s award winners (from left to right): M. Zahid Hasan (Shirley award); David Robin and Christoph Steier, representing the top-off team (Halbach award); Bruce Rude (Renner award); Funda Aksoy (second place, student poster); and Holly Barth (honorable mention, student poster). Not pictured: Samantha Ying (winner, student poster).

The user services session opened with a dialogue between users and the proposal study panel. Sue Bailey gave an update on the newly opened guest house, the user satisfaction survey, and the streamlining of the ALS-TMF joint proposal process. Bailey also highlighted the upcoming ALS Web site redesign, and encouraged Users to become more involved with ALS Science Briefs, Science Highlights and Science Cafés. Christoph Steier and Jim Floyd gave short operations and safety updates, followed by an ALS town hall meeting. Workshops preceded the awards banquet Friday, and continued Saturday. A full agenda is posted on the meeting Web site.

Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has remained unknown. To address this mystery, a British-American team lead by researchers at the Scripps Research Institute recently applied a combination of x-ray structural, biochemical, and genetic studies to ATLs in the yeast Schizosaccharomyces pombe without and with damaged DNA. By showing how a process called non-enzymatic nucleotide flipping activates ATL-initiated DNA repair, their results may improve our understanding of genomic integrity and responses to DNA damage relevant to pathogens and cancer development. Read more...

Repairing DNA

Publication about this research: J.L. Tubbs, V. Latypov, S. Kanugula, A. Butt, M. Melikishvili, R. Kraehenbuehl, O. Fleck, A. Marriott, A.J. Watson, B. Verbeek, G. McGown, M. Thorncroft, M.F. Santibanez-Koref, C. Millington, A.S. Arvai, M.D. Kroeger, L.A. Peterson, D.M. Williams, M.G. Fried, G.P. Margison, A.E. Pegg, and J.A. Tainer, "Flipping of alkylated DNA damage bridges base and nucleotide excision repair," Nature 459, 808 (2009).

Robust, High-Throughput Analysis of Protein Structures

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Scientists have developed a fast and efficient way to determine the structure of proteins, shortening a process that often takes years into a matter of days. The Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the ALS has implemented the world's highest-throughput biological-solution x-ray scattering beamline enabling genomic-scale protein-structure characterization. Coupling brilliant x rays from one of the superconducting bend magnets at the ALS to liquid-handling robotics has enabled the collection of 96 samples in 4 hours. Importantly, the sample format and the amount of material required are practical for most biological problems. The beamline's high-throughput capability is set to have a large impact on many fields that require genomic-scale information, such as Berkeley Lab's bioenergy efforts and cancer biology studies. Read more...

SIBYLS Steps Up the Pace

Publication about this research: G.L. Hura, A.L. Menon, M. Hammel, R.P. Rambo, F.L. Poole II, S.E. Tsutakawa, F.E. Jenney Jr, S. Classen, K.A. Frankel, R.C. Hopkins, S.-J. Yang, J.W. Scott, B.D. Dillard, M.W.W. Adams, and J.A. Tainer, "Robust, high-throughput solution structural analyses by small angle x-ray scattering (SAXS)," Nat. Methods 6, 606 (2009).

Thomas Steitz to Share 2009 Chemistry Nobel Prize

SteitzThomas Steitz (Yale University and Howard Hughes Medical Institute), a regular user of structural biology Beamlines 8.2.1 and 8.2.2 at the ALS, received the 2009 Nobel Prize for Chemistry (with Venki Ramakrishnan and Ana Yonath) for studies of the structure and function of the ribosome. Ribosomes are RNA-based protein factories found in all living cells, responsible for translating the genetic information encoded in messenger RNA (mRNA) into proteins. Research in this area may lead to novel antibiotics targeting bacterial ribosomes that have developed resistance to current drugs. At the ALS, Steitz has performed crystallographic experiments at Beamline 8.2.2 to understand the mechanism of antibiotic resistance by eubacterial ribosomes, resulting in the publication of "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance," D. Tu, G. Blaha, P.B. Moore, and T.A. Steitz, Cell 121, 257 (2005). In addition, each Nobel announcement includes supporting documentation outlining the case that the Nobel committee considered in coming to their conclusion. Two of our users, Jamie Cate (University of California, Berkeley) and Harry Noller (University of California, Santa Cruz) were widely cited for their pioneering structural work on the ribosome, including the first solution of the intact ribosome structure to atomic resolution.

UEC Corner: In Haiku, by Ken Goldberg

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Great users' meeting!
Kudos to all who helped, and
thanks to The Foundry!

Ken GoldbergSo many posters
the joint meeting overflowed.
Next time elbow room.
(Mark your calendar: October 14–16, 2010)

A tiny Z stage,
a quieter roughing pump...
Vendors spring for drinks

UEC voting
and meeting opinion poll
open now! Please vote.

More time for workshops?
B.B.Q. is not for you?
We care what you think.
email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
or any UEC member

Guest House Welcomes First User Groups

Since officially opening last month, the Berkeley Lab Guest House has been quite busy with visitors coming in for the ALS Users' Meeting and other conferences being hosted by Berkeley Lab this fall. Even before that, however, one of the first ALS user groups to take advantage of the brand-new accommodations was a group of six geoscientists from Germany and Mexico who were working at Beamline 12.2.2 on chemical reactions in materials at high temperatures and pressures. The group's research and week-long stay at the Guest House were sponsored by COMPRES (Consortium for Materials Properties Research in Earth Sciences), which is in turn supported by the Division of Earth Sciences of the National Science Foundation. During previous visits, the group would stay at the "ALS apartments," a block of off-site rental apartments in downtown Berkeley that was reserved for ALS users. According to members the group, the Guest House is "much more comfortable and makes life very convenient." Others mentioned how nice it is to stumble out of bed and go work just a few steps away, especially when dealing with jet lag. The consensus was that it was about time that Berkeley Lab built a guest house, and they "absolutely recommend" it to other users.


COMPRES group in Guest House Lobby. From left: Florian Schröder, Jasmin Biehler, Björn Winkler, Alexandra Friedrich, Erick Juarez-Arellano, Lkhamsuren Bayarjagal.

New X-Ray Data Booklet/Spectrum Published

CoversNew editions of the CXRO/ALS X-Ray Data Booklet and ALS Spectrum newsletter were handed out to attendees of the ALS Users' Meeting earlier this month. Now in its third edition, the X-Ray Data Booklet contains a few minor revisions and has been reprinted to replenish the supply of this highly sought-after pocket reference. The ALS will be working with other light sources regarding further production and distribution of the booklet (the ALS will not be mailing them out at this time). ALS Spectrum is an annual publication that reviews the past year's major science highlights and facility developments in a short, readable, newsletter-like format. This year, featured on the front page are stories about the ALS's successful transition to top-off mode and high-profile science involving the study of working catalysts. Contents also include a round-up of other science highlights, brief reports from ALS staff and user groups, articles about ALS people and events, and facility updates. A PDF version can be downloaded from the General ALS Publications Web page.

ALS Supplier, Boyd Technologies, to Close

We recently learned the sad news that Peter Boyd, owner of Boyd Technologies, passed away last month. His friends and family will miss him greatly. Through his company, Peter supplied a diverse community of ALS users with equipment for synchrotron x-ray scattering experiments, especially protein crystallography. With Peter's passing, Boyd Technologies will close its doors, and his former clients will need to seek new vendors for products his company formerly supplied.


For the user runs from October 6 to 18, the beam reliability [(time scheduled - time lost)/time scheduled)] was 93.5%. For this period, the mean time between failures (MTBF) was 22.4 hours, and the mean time to recovery (MTTR) was 94 minutes. There were no significant interruptions.

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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