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Microbes Online

The MicrobesOnline genome database contains over 700 prokaryotic genomes. All genomes are analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, SwissProt, COG) and protein domains (InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes, predict operon structures and regulon networks.

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Metacyc

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,600 pathways from more than 2,000 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.

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KEGG

KEGG: Kyoto Encyclopedia of Genes and Genomes. A grand challenge in the post-genomic era is a complete computer representation of the cell, organism, ecosystem, and biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end, a bioinformatics resource named KEGG was developed as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.

Auer Lab

The Auer Lab shares a high resolution cryo-EM facility with two additional cryo-EM groups at Lawrence Berkeley National Laboratory (LBNL). Sample preparation is carried out in the UC Berkeley EM facility, directed by Dr. Kent McDonald. LBL-Donner lab features several state-of-the-art electron microscopes, including a Philips CM200FEG, JEOL 4000, JEOL-3100FEF, Tecnai F20, and JEOL-1200, as well as associated equipment including PDS, Leafscan and Nikon scanning microdensitometers. We have ready access to a Nikon TE2000 and Olympus IX71 inverted fluorescence microscopes.

 

The Auer laboratory is located in the Donner building of LBNL, where the following equipment is available:

 
Electron Microscopes
  • JEOL 4000, with two Gatan cryo-holders, anticontaminator, external PC control, 2kx2k slow-scan CCD camera.
  • JEOL-3100FEF equipped with an FEG operating at 300 kV; side entry goniometer (+/-70 degree tilt), liquid helium cooled stage; Gatan 2k CCD camera; and, in-column energy filter.
  • Philips CM-200FEG with Gatan Ultrascan CCD camera.
  • Tecnai F20 with Gatan Ultrascan CCD camera.
  • JEOL 1200 with Gatan BioScan CCD camera. Used for routine survey of specimen materials.
 
Image Processing
  • Nikon Coolscan-8000 film digitizers and automated film handling robot.
  • Perkin-Elmer PDS 1010M scanning microdensitometer controlled by a PC.
  • Leafscan 45 film digitizing systems.
 
Electron Microscopy Preparation and Analysis
  • Denton vacuum evaporator.
  • Balzers 301 freeze-fracture system.
  • Home-built specimen plunge-freezing apparatus.
  • Gatan specimen freezing system.
  • 2 Leica Ultramicrotome UC6 on isolation table.s
  • 2 Leica Automated MIcrowave Processors AMW.
  • Leica Trimmer.
  • 8 diamond knives.
 
Fluorescence Light Microscope
  • Nikon TE 2000S epifluorescence microscope - This epifluorescence microscope is located in our laboratory and we have ready access to it. The microscope is equipped with a cooled highsensitivity Photometrix CH350 CCD camera that is able to detect faint fluorescence signals.
  • Olympus IX71 DIC with an Andor IXON+ electron multiplying CCD camera.

 

We have access to the Electron Microscope Laboratory (EML), which is directed by Dr. Kent McDonald and is located in 26 Giannini Hall in the North basement at UC Berkeley. EML features the following equipment:

 
Sample Preparation for EM
  • RMC MTX, Reichert Ultracut E.
  • RMC MT6000 microtome.
  • High Pressure Freezer Balzers HPM 010 designed to freeze non-cryoprotected samples up to 0.5mm in thickness without significant ice crystal damage.
  • Balzers High Vacuum Freeze Etch Unit BAF 301 is designed for the MOOR Freeze-etch technique and other high vacuum specimen preparation work for electron microscopy (C-support films, shadowing, replicas, coating temperature sensitive specimens, freeze drying, etc).
  • Tousimis AutoSamdri 815, Series A, Critical Point Drying Aparatus.
  • MED 020 Bal-tec Modular High Vacuum Coating System.
  • The MED 020 coating system currently supports high resolution sputter coating of specimens with Au,Pt, Au/Pd, and Cr metals.
  • BIO-RAD E5400 Sputter Coater is a DC diode sputter coater with magnetic deflection for coating SEM specimens with an ultrafine metallic coating.
 
Electron Microscopes
  • Scanning electron microscope Hitachi S-5000 is a high resolution, cold field emission SEM.
  • The Philips XL-30 ESEM is a flexible scanning electron microscope with a large chamber.
  • Environmental Scanning Electron Microscope Electroscan E3
  • ISI DS-130 SEM.
  • Philips/FEI XL30 W TMP SEM.
  • Tecnai T12 with Gatan Ultrascan CCD camera.
DOE BioEnergy Research Centers