Starting the
RNA assembly line
by Bruce Balfour
Protein crystallography images from the
ALS have helped researchers from Stanford University to analyze
the inner workings of RNA and its role in turning DNA's genetic
blueprint into working proteins. RNA polymerase II (Pol II)
is the protein complex responsible for all messenger RNA production.
TFIIB and TBP are transcription factors that interact with
Pol II to start the transcription assembly line. The researchers
determined the structure and function of Pol II-TFIIB complexes,
offering the first real understanding of the defining events
of DNA transcription. Full
story.
Publications about this research: D.A.
Bushnell, K.D. Westover, R.E. Davis, and R.D. Kornberg, "Structural
Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal
at 4.5 Angstroms," Science 303,
983 (2004); K.D. Westover, D.A. Bushnell, and R.D. Kornberg,
"Structural Basis of Transcription: Separation of RNA
from DNA by RNA Polymerase II," Science 303,
1014 (2004).
Contact: David Bushnell, bushnell@stanford.edu
Targeting proteins
to membranes
by Art Robinson
For the new protein emerging from a ribosome
amino acid by amino acid, the journey toward its final functional
state may involve integration into or secretion through a
membrane whenever the protein's polypeptide chain exhibits
a particular sequence (signal sequence). A signal recognition
particle (SRP) binds to the sequence and carries the ribosome–protein
complex to the membrane, where the SRP associates with its
membrane receptor (SR). The ribosome–protein complex
is then released and selectively attaches to the translocon,
a channel in the membrane. Guanine triphosphate (GTP) plays
an essential role, both in assembling the SRP–SR targeting
complex and, when hydrolyzed, in driving its dissociation.
The SRP and SR stimulate each other's activity as GTPases
to catalyze the GTP hydrolysis. Full
story.
Publication about this research: P.F.
Egea, S. Shan, J. Napetschnig, D.F. Savage, P. Walter, and
R.M. Stroud, "Substrate twinning activates the signal
recognition particle and its receptor," Nature
427, 215 (2004).
Contacts: Robert Stroud, stroud@msg.ucsf.edu
Pascal Egea, pascal@msg.ucsf.edu
Impact of top-off
injection
evaluated
As many of you know, there are plans
to upgrade the ALS to operate in a top-off injection mode.
In top-off mode, electrons will be frequently injected into
the storage ring (every half minute or so), keeping the storage-ring
current nearly constant, as opposed to our present operation
where the storage ring is filled only once every 8 hours.
Top-off operation has many advantages compared to our present
operational mode. We expect a twofold increase in the average
current (see Fig. 1 below). In addition, there will be further
increases in the brightness—due to reduction of the
beam size and the minimum gap of insertion devices—and
improvements in the thermal stability of the storage ring
and beamline components. Top-off operation is the standard
operational mode at a number of other light sources, including
the Advanced Photon Source, Swiss Light Source, and Spring-8.
Fig. 1. Sketch of the beam current
history
during one day before and after top-off.
One of the main concerns with top-off
is the impact of the injection process on the ALS users. In
top-off, the beamline shutters remain open during injection
and the injection process itself is not completely transparent
to all users. In particular, the injection magnets perturb
the stored beam during injection. At present, there is a fast
oscillation caused by nonclosure of the fast-pulsed injection
bump magnets (Fig.
2), as well as a slower closed-orbit distortion caused
by decaying eddy currents in the main septum magnet (Fig.
3).
This past year a number of measurements
were performed to evaluate the impact of the injection process
on users. During three accelerator physics shifts, experiments
were performed with representatives of various beamlines—1.4,
4.0.2, 5.3.2, 6.3.2, 7.0.1, 7.3.1, 8.3.1, 10.0.1, 10.3.2,
11.0.2, and 12.0. The measurements were taken with the injection
elements both on and off. The results were presented at several
meetings, including a spring Users' Executive Committee (UEC)
meeting, and are summarized in ALS Light Source Note LSBL-709.
The results of these studies showed that
most of the experiments did not see the injection transients.
However, microscopes with short integration times were affected.
By far the most sensitive technique was STXM, with transient
intensity fluctuations from 5% to 40%, depending on whether
the septum magnet was pulsing. In addition, the infrared beamline
could detect these injection transients. Gating seems to be
a requirement for these sensitive experiments and injection
timing pulses will be provided for this purpose. In addition,
Beamline 4.0.2 saw the effect of the septum magnet. We are
currently in the process of reducing the impact of the septum
on the beam transients. For additional information please
contact us or refer to the above mentioned note. The top-off
project will also be discussed in detail at a workshop at
the Users' Meeting in October.
Contacts:
David Robin, DSRobin@lbl.gov
Christoph Steier, CSteier@lbl.gov
Tony Warwick, T_Warwick@lbl.gov
Attention: Camshaft
and
bunch-gap users
In the ALS storage ring there are 328 rf "buckets"
that can be filled with electron bunches. Each of these buckets
is separated by 2 ns. In present operation, the filling pattern
in the storage ring typically is as follows: a train of buckets
1 through 276 and bucket 318 (the so-called camshaft bunch)
are filled with electrons. So between buckets 276 and 318
there is a gap of 84 ns and between buckets 318 and 1 there
is a gap of 22 ns.
If possible we would like to reduce these gaps for two reasons.
First, larger gaps reduce the beam lifetime. Second, with
the present gaps the longitudinal spacing between bunches
is not uniform and changes by more than the bunch length over
the course of a fill. This presents major challenges for laser
synchronization.
We would like to find out who is currently using the camshaft
bunch and/or the empty gaps and how large a gap is necessary.
Please send a brief summary of your requirements and their
rationale to Christoph Steier (CSteier@lbl.gov)
by September 15. Thank you very much.
Contacts: David Robin, DSRobin@lbl.gov
Christoph Steier, CSteier@lbl.gov
ALS users and
staff well represented
at VUV XIV
 The
center of gravity of the synchrotron world shifted down under
this summer (or is it winter?) as the Fourteenth International
Conference on Vacuum Ultraviolet Radiation Physics (VUV XIV)
was held July 19–23, 2004, in Cairns, Australia. This
was the first visit to the Southern Hemisphere in the 40-year
history of the VUV conference series, which began in Los Angeles
in 1962 and is now run triennially. The ALS hosted VUV XII
in 1998. The premier international conference covering research
in the vacuum ultraviolet and soft x-ray range, VUV XIV brought
together physicists, engineers, chemists, biologists, technologists,
and others concerned with the production and applications
of vacuum-ultraviolet and soft x-ray radiation over many subfields.
The ALS was well represented in the program,
with an impressive number of users and staff listed among
the event's invited speakers. Two of the five plenary speakers
were ALS users: Reinhard Doerner (Univ. of Frankfurt) spoke
to the entire conference on "Electrons from fixed-in-space
molecules and clusters" and Adam Hitchcock (McMaster
Univ.) addressed the assembly on "Soft x-ray spectromicroscopy
of biological and synthetic polymer systems." Invited
speakers with ALS ties include Elke Arenholz (ALS) on "Vectormagnetometry
studies of exchange biased systems using soft x-ray magnetic
dichroism;" Steve Kevan (Univ. of Oregon) on "Coherent
soft-X-ray magnetic scattering;" Carolyn Larabell (Berkeley
Lab, Life Sciences Div.) on "X-ray tomography: Cells
in 3-D at better than 50 nm resolution;" Norman Mannella
(Stanford Univ.) on "Electron localization, polarons
and clustered states in manganites;" Michael Martin (ALS)
on "Synchrotron infrared science: Physics, biology, environmental
science and coherence;" Francois Wuilleumier (Univ. Paris-Sud)
on "Photoionization of excited atoms and ions: Recent
progress and future prospects;" and Han Woong Yeom (Yonsei
Univ.) on "Electronic transitions of atomic wires on
surfaces."
A number of ALS users and staff also
gave 15-minute "Hot Topics" talks: Nora Berrah (Western
Michigan Univ.) on "Inner-shell dynamic studies in negative
ions," John Bozek (ALS) on "Spin resolved inner-shell
photoelectron spectroscopy of Xe clusters," Tony van
Buuren (Lawrence Livermore National Laboratory) on "X-ray
absorption and emission studies of diamond nanoparticles,"
Phil Heimann (ALS) on "Ultrafast x-ray absorption spectroscopy
of laser-excited materials," Daniel Rolles (Fritz-Haber-Institut)
on "Probing the degree of core hole localization in isotope
substituted N2 via photoelectron spectroscopy," and Eli
Rotenberg (ALS) on "Spin density wave phase diagram of
Cr(110) thin films." Look for the conference proceedings
to be published as a special issue of the peer-reviewed Journal
of Electron Spectroscopy and Related Phenomena. The next
conference, VUV XV, will be held in 2007 in Berlin, Germany.
Contact: Neville Smith, NVSmith@lbl.gov
Experts meet
for review of
photoemission at ALS
Several leading photoemission researchers
came to the ALS last month to participate in a crosscutting
review on the future of photoemission at the ALS. The two-day
meeting, held July 29–30 at Berkeley Lab, drew capacity
crowds. Neville Smith (ALS Division Deputy for Science) began
by stating the charge to the committee: To identify the elements
of a world-leading photoemission program at a facility like
the ALS with a ten-year horizon. In a slight departure from
past formats, this crosscutting review was conducted as a
workshop in which the reviewers themselves made presentations.
The first session, "Whither Photoemission?"
featured Stefan Hufner (Univ. des Saarlandes), who discussed
very high resolution photoemission experiments, and Ward Plummer
(Univ. of Tennessee), who addressed the question, Who needs
synchrotron radiation? Mike Norman (Argonne National Lab)
followed up by providing a theoretical perspective. The second
session dealt with correlated systems, and Z.X. Shen (Stanford
Univ.) gave a talk with the intriguing title, "The Holy
Grail." In a session on low dimensionality, Franz Himpsel
(Univ. of Wisconsin-Madison) talked about nanostructures,
and in a session on catalysis, Frank Ogletree (Berkeley Lab,
Materials Sciences Div.) discussed ambient-pressure photoemission.
Zahid Hussain (ALS Scientific Support Group Leader) rounded
out the presentations with a look at "Activity at the
ALS: Present and Future." Each of the sessions also included
time for "nuggets" (Steve Kevan's term for brief
presentations on highly focused topics) and open discussion
amongst attendees. Reports generated as a result of this workshop
will be used in future strategic planning efforts at the ALS.
Contact: Neville Smith, NVSmith@lbl.gov
Users' Meeting
update; call for
award nominations
 Each
year, the ALS UEC presents awards to scientists and staff
who have made significant contributions to the ALS scientific
and user support programs. This year, the UEC invites ALS
users and staff to submit nominations for any or all of the
following awards: the David A. Shirley Award for Outstanding
Scientific Achievement at the Advanced Light Source, the Klaus
Halbach Award for Innovative Instrumentation at the Advanced
Light Source, and the Tim Renner User Services Award. The
nominations may be for an individual or a group, and a brief
rationale for each nomination is required.
Past award winners, along with a representative
from the UEC and the ALS, will serve on the award selection
committee. To submit a nomination, go to the 2004 ALS Users'
Meeting Award Nominations Web page. The deadline for nominations
is Friday, October 1. The awards will be presented at the
ALS Users' Meeting dinner/buffet on Tuesday, October 19.
General information, deadlines, and online
registration for this year's ALS Users' Meeting is available
on the Users'
Meeting Web site. The early registration deadline is Friday,
October 1. The deadline for abstract submissions for oral
and poster presentations is Wednesday, September 15.
This year, ten workshops will follow
the end of the formal Users' Meeting program. For detailed
information about workshop agendas and speakers, you may contact
the workshop organizers directly at the Users'
Meeting Workshops Web page.
Contact: alsum@lbl.gov |
