[3dem] 4 of 4 positions at Lawrence Berkeley Lab (Auer Group) & group description

Manfred Auer mauer at lbl.gov
Mon Apr 14 14:05:05 PDT 2008

4. Postdoc
Decription: Electron tomography and correlative Raman microscopy of  
plant cell walls in the context of the UC Berkeley Energy Biosciences  
Institute (EBI; www.energybiosciencesinstitute.org)
The successful postdoctoral researcher will employ cryo and RT  
electron tomography of high-pressure frozen, freeze-substituted and  
resin-embedded plant samples, microwave processed plant samples, as  
well as high-pressure frozen and cryo-sectioned plant samples (as part  
of a collaborative effort with Kent McDonald and Ken Downing). The  
goal of this project, lead by the Auer group, is to obtain a realistic  
model of plant cell walls via direct 3D ultrastructural imaging as  
well as correlative Raman microscopy (in close collaborattion with the  
Liphardt group), which will allow to determine the chemical  
composition. Imaging information will be mined by advanced automated  
segmentation and image analysis procedures in collaboration with a  
computational science group  (Parvin group). Apart from its scientific  
merit, this project offers the opportunity to become part of  a  
multiscale, multimodal correlative imaging effort and work with world  
experts in cryo-sample preparation, (cryo)-EM 3D imaging, correlative  
Raman and PALM imaging and image analysis and modeling.

Apart from the specific project described above, this team serves as  
the sole TEM sample preparation and TEM imaging program for the entire  
EBI, and over its time course is likely to engage in a number of  
interesting collaborative projects, including plant-pathogen  
interactions and enzymatic degradation. The EBI is a unique  
environment: while being an academic center with a focus on basic  
sciences, there exists close interactions with the oil company BP,  
which adds a different dimension to this research and is highly  
educational, as the work carried out by EBI has the potential to  
directly impact the global energy market.

·  Ph.D. in Physics, Biophysics, Plant Biology, Biophysical Chemistry  
or a related field of science.

·  Experience with electron microscopic sample preparation and  
imaging. Experience with high-pressure freezing, immuno-affinity or  
tag-based labeling would be a plus, but is not essential.

·  Strong written and oral communication skills, and a high degree of  
organization would be desirable, but highly creative (and less  
organized) candidates would also be welcome.

·  Demonstrated ability to work autonomously and obtain results.

·  Ability to work in a team environment and effectively interact with  
a broad range of colleagues.

The Auer Team:
The successful candidates will join an enthusiastic group consisting  
of three undergraduate students, three graduate students, one postdoc,  
two project scientists, and two senior research associates (senior  
technicians). The team enjoys conducting a broad agenda of bioimaging  
research with a focus on high-end electron microscopy on a variety of  
disease-, bioremediation- and bioenergy/biofuel-relevant projects,  
ranging from the molecular understanding of hearing, over breast  
cancer model systems to microbial communities (biofilms) and plants/ 
plant cell walls, with an emphasis on lignocellulosic biofuels.

The Auer lab conducts research in the field of modern electron  
microscopy, including cryo-electron tomography, tomography of resin- 
embedded samples, 2D and 3D imaging of high-pressure frozen samples,  
as well as novel tag-based labeling approaches and correlative  
multiscale multimodal imaging. While 2D and 3D electron microscopy of  
high-pressure-frozen, freeze-substituted and resin-embedded samples  
remains our methodological priorities, we also have active projects on  
cryo-tomography of frozen-hydrated samples, on biochemistry (including  
mass spectrometry), cell biology and related fields. We are also  
conducting SEM experiments and are exploring the potential of dual- 
beam FIB|/SEM to study the 3D organization of resin-embedded samples.

We are increasingly interested in performing correlative optical and  
electron microscopy studies, and are currently trying to carry out  
correlative 16S rRNA FISH/EM studies of microbial communities as well  
as a combination of superresolution light microscopy (PALM) and Raman  
Microscopy with electron microscopy. Some of our efforts are in close  
collaboration with the Liphardt group at UC Berkeley, who has  
substantial experience and expertise in optical imaging.

The Auer group is involved in the Department of Energy - Gemomes to  
Life (DOE-GTL) PCAP and VIMMS programs on bioremediation  
(pcap.lbl.gov) where the focus lies on the visualization of microbial  
biofilms and the development of SNAP-based labeling approaches. In  
addition, the Auer group oversees all imaging and biophysical  
characterization efforts of the Joint BioEnergy Institute  
(www.jbei.org), and all sophisticated sample preparation and electron  
microscopy efforts of the BP-sponsored UC Berkeley/UIUC/LBNL's Energy  
Biosciences Institutes  (EBI) (www.energybiosciencesinstitute.org).  
JBEI is one of three DOE-sponsored BioEnergy Research Centers, and the  
only one with a significant imaging component. Its overall mission is  
to reduce the United States' dependence on foreign oil by overcoming  
significant hurdles of economic ethanol/biofuel production from plant  
biomass (not food crops) such as the recalcitrance of lignocellulosic  

The UC Berkeley EBI is a academic research institute with a goal  
similar to JBEI. Our group leads an effort by 5 groups (Auer, Downing,  
Liphardt, McDonald, Parvin) to come up with a realistic model of the  
plant cell wall, based on correlative Raman/EM tomography imaging and  
sophisticated image analysis.

The Auer group - in close collaboration with the Liphardy lab - is  
leading Lawrence Berkeley Lab's initiative of a multiscale, multimodal  
integrated imaging center. The establishment of such a center has  
become the top priority of LBNL as part of its 10-year strategic  
vision for DOE.  The Auer and Liphardt labs have received seeds funds  
for this endeavor and expect continuous growth of this activity in the  
upcoming years.

Please send e-mail with a brief description of interests and relevant  
work experience and a resume to Manfred Auer at mauer at lbl.gov. We look  
forward to hearing from you.

best wishes


Manfred Auer, Ph.D.
Lawrence Berkeley National Laboratory
1 Cyclotron Road, Mail Stop Donner
Berkeley, CA 94720
phone:          +1-510-486-7702
facsimile:        +1-510-486-6488
mauer at lbl.gov

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