Previous Editions__________________________________________________________________________SSRL Headlines Vol. 11, No. 12 June, 2011__________________________________________________________________________
Contents of this Issue:
The SAC also approved the new SSRL user access policy, in particular the
collaborative access proposal, a new mechanism for the user community to
partner with SSRL. The policy will be published shortly. In addition, the SAC
heard a progress report on the new strategic plan, and offered some excellent
guidance on each scientific research area. They also championed the need for
us to get feedback from the user community. We are now writing up the
plan-taking into account the SAC's initial feedback-and, as I have mentioned in
previous columns, we will soon ask for your input.
In the few weeks since the review, we have received funding from DOE for the
procurement of an in-vacuum undulator to begin the construction of a new beam
line. In addition, we've just been informed that additional funds will be made
available to us to implement the proposed upgrades to stabilize the temperature
of the SPEAR3 tunnel. This project, which will begin later this year, will
reduce the thermal motion of the accelerator to reduce the photon beam motion
at the beam lines. Preliminary tests indicate that the motion can be reduced
by a factor of 7 with insulation. Both projects are critically important for
SSRL to take full advantage of the brightness enhancement from the SPEAR3
upgrade.
In the meantime, we have already increased the SPEAR3 running current from 300
to 350 mA. As expected given the small increment in current, we haven't seen
any negative impacts on beam line performance. Tests are also underway during
accelerator physics time this week toward decreasing the interval between
fills. SSRL employs a frequent fill schedule to maintain the SPEAR3 current
constant to approximately 1%. At present, the interval is 10 minutes but, if
these tests go well, it may decrease to as low as 5-7 minutes beginning in
early July. We will keep users informed about this progress by e-mail.
In all, it's been a very exciting month and SSRL's future is looking brighter
than ever.
—Chi-Chang Kao
A recent XAFS study conducted at SSRL Beam Line 4-3 by a team of researchers
from KEMA and the University of Twente in the Netherlands and the University of
Kentucky in the U.S. sought to determine how the chromium in fly-ash-which is
often stored in isolated surface piles or in impoundments-behaves both during
coal combustion and in ash disposal situations. Their work determined that
Cr(VI) as a percentage of the total Cr was less than 10% in fly-ash when
derived from commercial pulverized combustion of bituminous coals. However, it
was significantly higher (up to 30%) in ash from combustion of subbituminous
and other lower-rank coals and also from coal and wood co-firing.
The results indicate that the combustion conditions, particularly the air/fuel
ratio, are important in determining the percentage of chromium as Cr(VI), and
that leachable Cr(VI) contents in the ash could be minimized by better control
on the excess air present during combustion and possibly by additives that
promote the formation of insoluble chromate species.
This work was published in Environmental Science & Technology.
To learn more about this research see the full scientific highlight
For decades, people have been using penicillium mold and molecules produced by
soil bacteria as a means of fighting off harmful bacteria and treat infection.
But resistance to these chemicals is now becoming commonplace. Today many
infections are resistant to not only penicillin but also other b-lactam
antibiotics, some of which are classified as "last line of defense" drugs for
E. coli and Klebsiella pneumoniae.
Experiments at SSRL Beam Line 12-2 revealed that a previously unknown bacterial
strain (Oceanobacillus iheyensis) found in deep ocean sediment (a place
where it is highly unlikely that the bacteria would have ever encountered
man-made penicillin) has a very active b-lactamase
enzyme with a three-dimensional structure almost identical to the known
b-lactamases in common bacteria. This work reveals
that the development of this enzyme cannot be due solely to exposure to
clinically-derived b-lactam
antibiotics. This work suggests that the enzyme's evolution took place prior to
the use of penicillin and b-lactam antibiotics.
Work conducted at SSRL has also revealed that b-lactamase enzymes have
developed the ability to break down the carbapenems-"last resort" b-lactam
antibiotics-including the Guiana extended-spectrum b-lactamases (GES).
Fortunately, the GES enzymes can be stopped in their tracks by known
ß-lactamase inhibitors, something recently demonstrated with the high
resolution structure of GES-2 with tazobactam, using data collected at SSRL
Beam Line 12-2.
Nonetheless it appears that, overall, the GES family of enzymes is evolving the
ability to break down carbapenems which, while alarming, is not unexpected
given the "pressure" that we are applying to the environment with respect to
the use, overuse and misuse of antibiotics which will naturally result in
mutation, adaption and evolution of resistance mechanisms. To stay one step
ahead of the bacteria, we will need to continue to study bacterial enzymes and
design drugs that remain effective despite enzyme mutation.
This work was published in Acta Crystallographica and the Journal of
Biological Chemistry.
To learn more about this research see the full scientific highlight
SSRL's newest macromolecular crystallography beam line, 12-2, is providing
outstanding capabilities for study of exceptionally challenging biological
systems. The technical aspects of the beam line are described briefly below,
and science enabled by this undulator beam line is further illustrated by the
results described in the science highlights linked to at the bottom of this
overview.
The Beam Line 12-2 undulator beam line, funded by the Gordon and Betty Moore
Foundation in collaboration with Caltech, is optimized for microfocus
experiments (down to 5 micron beam size) but can easily accommodate more
conventional macromolecular crystallography beam-size projects through a
flexible optics and collimation approach. The state-of-the-art Beam Line 12-2
DECTRIS PILATUS 6M Pixel Array Detector (PAD), with its high dynamic range,
very fast readout and low point spread function, enables a rapid, shutterless
fine-phi-slicing mode of data collection where complete data sets are typically
collected in 2-3 minutes. Capabilities are further enhanced by the higher
operating current of the SPEAR3 storage ring, currently 350 mA. Enhanced
computer infrastructure keeps up with data transfer and reduction in real time.
The robotic Stanford Auto-Mounter (SAM) is fully integrated into the beam line
control system and has been used in the screening of nearly 30,000 crystals on
Beam Line 12-2 to date. Around 95% of the user groups collect data in full
remote-access mode, running the experiment from their home lab. Beam Line 12-2
is in full operation, with the following three papers illustrating new and
complex structures based on recent data collections from challenging crystals:
The pigment, eumelanin, is one of the coloring agents responsible for brown
eyes and dark hair in many modern species, including humans. It would have
been one of the factors that determined the birds' color patterns, along with
structural properties of the birds' feathers and other pigments they ingested
as part of their diets.
The discovery, reported June 30 in Science Express, will help give textbook
illustrators, diorama makers and Hollywood special-effects artists a more
realistic palette for their depictions of ancient animals. Understanding these
pigment patterns is important for science, too, since they play a role in a
wide range of behaviors that are important in evolution such as camouflage,
communication and selecting mates.
Read the full press release.
Pixel and Microstrip Detectors for Current and Future Synchrotron Light
Sources, July 1 - On Friday, July 1, Christian Broennimann of DECTRIS will
present a talk entitled "Pixel and Microstrip Detectors for Current and Future
Synchrotron Light Sources" at 1:00 p.m. in SLAC's Kavli Auditorium. The talk
will cover current development plans for these state-of-the-art detectors.
11th International Workshop on X-ray Spectroscopy of Magnetic Solids,
October 21-22 - The 2011 X-ray Spectroscopy of Magnetic Solids (XRMS)
meeting will take place October 21-22 at SLAC. These annual meetings have
proved as a fruitful forum for informal discussion of recent results and future
projects of synchrotron radiation based research on magnetism and magnetic
materials. They also serve for the formation of new collaborations. Learn more
on the XRMS website.
Annual Users' Conference, October 24-26 - Plans are underway for the
Annual SSRL/LCLS Users' Meeting and Workshops, October 24-26, 2011. Mark your
calendar and plan to participate to learn about new developments and share
exciting user research at both LCLS and SSRL. It is also a great time to
interact with other scientists, potential colleagues, and vendors of light
source-related products and services. Check back later for more details and
registration. The draft program and registration details will be posted
shortly. You can also reserve lodging for the meeting by contacting the
Stanford Guest
House. Specify SSRL/LCLS/SLAC to take advantage of discounted
rates.
Please take a few moments to consider nominating your colleagues or students
for the annual Klein and Spicer awards, which will be presented at the joint
SSRL and LCLS Users' Meeting, October 24-26:
Last year's Klein Award winner, Diling Zhu, developed a new experimental
technique to carry out x-ray holography, something that usually requires
significant computing power and can lead to false conclusions. In his thesis,
Zhu described two new methods to more accurately and reliably reconstruct the
two-dimensional image of the object from the interference pattern. "The
importance of Diling's work is increased reliability in obtaining real space
images from the obscure x-ray scattering patterns," said Jo Stöhr,
director of the Linac Coherent Light Source and Zhu's thesis advisor. "We now
have two robust methods which give us robust and reliable pictures of
nanostructures. These methods will be used at both SSRL and LCLS and at other
x-ray facilities around the world."
Jeffrey Lee received the 2010 Spicer Award for his studies of the
Ebolavirus,
which causes an untreatable disease that kills 50 to 90 percent of people who
contract it. Using SSRL and other U.S. synchrotrons, Lee was able to uncover
the structure of the Ebolavirus glycoprotein, which initiates the attachment
and fusion of the virus and the host membranes, when it was bound to an
antibody from a human survivor of the virus. The methods Lee and his team
developed are applicable for other groups and will likely streamline the
structure determination process for glycoproteins in other viruses.
Submit your 2011 nominations to Cathy Knotts (knotts@slac.stanford.edu) by
August 1.
In addition, award donations are now being accepted card to ensure that the
awards will continue in perpetuity as memorials to Spicer and Klein. These can
be sent by check, made payable to "Stanford University" (noting "Spicer Award"
or "Klein Award" on the memo line), to SSRL c/o Cathy Knotts, SLAC National
Accelerator Laboratory, 2575 Sand Hill Road MS 99, Menlo Park, CA 94025.
Alternatively, if you would like to make a gift by credit card, please phone
866-543-0243 (toll free) Monday - Friday, 8 a.m. to 5 p.m. PST to reach a
customer service representative. Please specify that your gift is designated
for "The Spicer Award" or "The Klein Award." Callers from outside the US,
please phone 650-724-0627 (not toll free).
The painting is a gift from the artist, Carey Phelps. A recent graduate of the
Castilleja School in Palo Alto, Phelps painted the piece after seeing two SLAC
scientists discuss the intersections of art and physics at her Introduction to
the Arts class. Linac Coherent Light Source Deputy Directory Uwe Bergmann spoke
about uncovering the ancient writings of
Archimedes at SSRL, while SSRL Staff
Scientist Apurva Mehta explained how the science of today can be used to help
understand and preserve the art of the past, from better understanding the
origins and properties of unusual
pigments to explaining the methods used to
produce specific finishes on
pottery.
"The scientists from SLAC talked about science and art," Phelps said. "I wanted
to make the connection between art and science."
Increased Current to 350mA
SPEAR3 Top-Off Injection
Brochures and Information
Hagström was a pioneer in electron spectroscopy for chemical analysis in
the 1960s, and was a noted expert in surface sciences and thin-film deposition
processes. His work had a major impact on scientific understanding of surface
chemistry and physics. He and his collaborators developed "soft X-rays" for
use in studying oxidation of aluminum and he was among the first to use
synchrotron radiation in spectroscopy.
"It was Hagström, in 1968, who suggested to Stanford Professor William
Spicer that synchrotron radiation offered great possibilities for
condensed-matter science, leading to the creation of what would become the
Stanford Synchrotron Radiation Lightsource," said friend and fellow Stanford
Professor Emeritus Arthur Bienenstock. "Stig had tremendous impact on Stanford,
the nation and the world." Read more in Stanford Report.
Images of Fossil Birds Show Ancient Pigments
New Glimpse of the Color Palette of Long-Extinct Creatures
Bird Fossils Reveal Life's Colourful Chemistry
Dinosaur-era Feather Colors Revealed
Concerns about Arsenic-Laden Bacterium Aired
Pledges of Support Keep Mideast SESAME Project on Track
__________________________________________________________________________
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 National Institute of General Medical
Sciences. Additional information about
SSRL and its operation and schedules is available from the SSRL WWW
site.
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