Edward A. Doisy Department of
Biochemistry and Molecular Biology
Resources available in the Biochemistry department
  • Protein Facility
  • Genomics Facility
  • X-ray Facility
  • NMR Facility
  • Computer Resources
  • MicroTime 200
  • Olympus cellTIRF
  • Metabolomics Core
  • Bioinformatics Facility
  • Metabolic Screening Lab
  • Real-Time PCR
  • Specialized Instrumentation
  • Medical School Resources
Protein Core Facility

A shared-use facility that supports expression, purification, and analysis of research proteins by providing an array of instrumentation and consultation on strategies for protein production from small to large scale.

The Facility is managed by Dave Wood, Ph.D. (314-977-9220; dwood12@slu.edu).

For a complete description of all available services, please see the Protein Core website.

Genomics Core Facility

A full-service facility that provides investigators with a variety of options for whole genome analysis via microarrays, high-throughput screening, immunoprecipitation, and sequencing strategies.

The Facility is managed by Dale Dorsett, Ph.D. (314-977-9218; dorsettd@slu.edu) and Kathie Mihindukulasuriya, Ph.D. (314-977-9252; kkunz1@slu.edu).

For a complete description of all available services, please see the Genomics Core Facility website.
X-ray Crystallography Facility

A state-of-the-art X-ray facility is available to researchers in the department for the collection of high-resolution data on macromolecular samples. The facility has a 0.8 kW MM007 Rigaku generator with VHF optics interfaced to an R-Axis IV++ imaging plate system and a 1.2 kW MM007HF Rigaku generator with VHF optics double ported with two R-Axis IV++ imaging plate systems. A Phoenix robotic instrumentation from Art Robbins Instruments is available for the preparation, screening and imaging of crystals.

The Facility is managed by Sergey Korolev, Ph.D. (314-977-9261; korolevs@slu.edu).

Rigaku detectorPrethrombin-1

NMR Facility

The Department of Chemistry houses an NMR facility, which is available to all researchers at SLU. The facility has a multi-nuclear Bruker spectrometer with the field strength of 16.4 Tesla, as well as a newly-installed Bruker Avance HDTM 700MHz NMR spectrometer. These instruments can be used to determine the structures of organic molecules and biomolecules, and can also be used in other dynamic studies.

The Facility is located in Shannon Hall and is managed by the Department of Chemistry. See the NMR website for full details.


Computer Resources

The Department of Biochemistry and Molecular Biology maintains a wide variety of computing resources. These range from network and backup services to state-of-the-art high performance computing.

The most recent addition to the department is the Gemini Computing Cluster, a state-of-the-art, high performance computing cluster, leveraging modern technologies such as GPU computing capabilities.

Built in 2012, the Gemini computing cluster consists of 344 CPU cores, 80 GPUs and 1.3 TB of aggregate RAM, providing 135 TFLOPs peak computing power. Over 2.8 million CPU, and 750,000 GPU hours of processing time have been completed. Gemini can dock over 5.9 million compounds 1000x faster than a modern desktop workstation.

You can find out more information on the Gemini website.

Computational publications resulting from use of the Gemini Computing Cluster for some component of the work:

  • Pelc LA, Chen Z, Gohara DW, Vogt AD, Pozzi N, Di Cera E. Why Ser and not Thr brokers catalysis in the trypsin fold. Biochemistry. 2015 Feb 24;54(7):1457-64.
  • Moustafa IM, Korboukh VK, Arnold JJ, Smidansky ED, Marcotte LL, Gohara DW, Yang X, Sánchez-Farrán MA, Filman D, Maranas JK, Boehr DD, Hogle JM, Colina CM, Cameron CE. Structural Dynamics as a Contributor to Error-prone Replication by an RNA-dependent RNA Polymerase. J Biol Chem. 2014 Dec 26;289(52):36229-48.
  • Davis AR, Gohara DW, Yap MN. Sequence selectivity of macrolide-induced translational attenuation. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15379-84.
  • Heyduk, E., & Heyduk, T. (2014). Next generation sequencing-based parallel analysis of melting kinetics of 4096 variants of a bacterial promoter. Biochemistry, 53(2), 282–292.
  • Pozzi N, Chen Z, Gohara DW, Niu W, Heyduk T, Di Cera E. Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation. J Biol Chem. 2013 Aug 2; 288 (31) 22734-44.

Funding resulting from use of the Gemini Computing Cluster for some component of the work:

  • Development and Application of the AMOEBA Polarizable Force Field. National Science Foundation. Aug 2012 - Jul 2015. Award Number: 1152522
  • Ligand- and sequence-specific inhibition of protein synthesis by antibiotics. Edward J. Mallinckrodt Foundation. (PI: Frances Yap)
  • New Bioanalytical Methods Based on Next Generation Sequencing. National Institutes of Health. (PI: Tomasz Heyduk)
  • RNA-dependent RNA polymerase. National Institutes of Health. (PI: Craig Cameron, Subcontract: David Gohara)

MicroTime 200

The MicroTime 200 from Picoquant is a time-resolved confocal microscope with unique single molecule sensitivity. It includes an Olympus X71 inverted microscope-based system with 488, 532, and 640 nm picosecond pulsed lasers, four detection channels, and a piezo xyz scanner. Emission can be split according to color or polarization. Each collected photon is time-stamped both in nanoseconds timescale (from the laser pulse) and in seconds scale (from the beginning of the experiments), allowing flexible analyses of the collected data.

Typical uses of this instrument are for single molecule FRET, including Pulsed Interleaved Excitation (PIE) FRET. PIE interrogates each detected molecule with alternating donor and acceptor excitation with MHz speeds, allowing sorting of the molecules according the stoichiometry of donor and acceptor labels. FCS, FCCS, FLCS, TCSPC histogram, and photon-counting histogram (PCH) are examples of some additional analyses possible for freely diffusing molecules. Also, the following imaging measurement analyses are possible: Time-gated Fluorescence Intensity Imaging, Fluorescence Lifetime Imaging (FLIM), FLIM-FRET, Intensity FRET, and Anisotropy imaging.

The MicroTime 200 is managed by Nicola Pozzi, Ph.D. (314-977-9259; npozzi@slu.edu).

Olympus cellTIRF-4Line System

The Olympus cellTIRF-4Line system allows ultra-sensitive, simultaneous multicolor Total Internal Reflection (TIRF) using four laser channels with independent beam paths. This inverted microscope-based system with cellTIRF laser illumination (491 nm, 561nm, and 640 nm) allows through-objective TIRF with software control of the depth of evanescent field, allowing the user to produce high-contrast images with minimal background noise for cell surface and single molecule studies.

An Andor IXON Ultra897 EMCCD camera and QV2 four-channel image splitter allow simultaneous recording of up to four color images of immobilized single molecules at up to 52 frames per second. Fast (1 ms) switching between lasers allows interrogating immobilized molecules with alternating two excitation wavelengths.

The Olympus cellTIRF4-Line system is managed by
Tomasz Heyduk, Ph.D. (314-977-9238; heydukt@slu.edu).

Metabolomics Core
The Metabolomics Core Facility, operated by the Department of Biochemistry and Molecular Biology and the Center for Cardiovascular Research at Saint Louis University School of Medicine, is a University resource located in the Doisy Research Center. The Facility focuses on small molecule identification and quantification by mass spectrometry.

Instrumentation in this Core includes a Thermo Electron Surveyor LC and Quantum Ultra triple quadrupole electrospray ionization mass spectrometer, as well as two HP6890 gas chromatographs with FID detector and HP 5973 MS detector with both electron impact and chemical ionization sources.

The Facility is managed by Dave Ford, Ph.D. (314-977-9264; fordda@slu.edu).
Bioinformatics Facility

The Bioinformatics Facility offers complete analysis of high-throughput expression data, including gene ontology enrichment analysis. We also offer next-generation genomic sequence assembly and variant analysis. We maintain an in-house MASCOT database for peptide mass searches, NCBI BLAST for custom database searching, and HMMer for protein domain searches. Custom script development is available for automation of protein and DNA sequence analysis. We have access to a state-of-the-art high performance-computing cluster maintained by the Biochemistry HPC core.

The Facility is managed by Maureen Donlin, Ph.D. (314-977-8858; donlinmj@slu.edu).

Recent publications from data analyzed by the core:

  • Upadhya R., Campbell LT, Donlin MJ, Aurora R and Lodge JK. “Global transcriptome profile of Cryptococcus neoformans during exposure to hydrogen peroxide induced oxidative stress.” PLoS One, 2013; 8(1):e55110. PMID: 23383070
  • Alspach E, Flanagan KC, Huang H, Pazolli E, Donlin MJ and Stewart SA. “A p38MAPK-AUF1 post-transcriptional regulatory axis controls expression of the pro-tumorigenic senescence-associated secretory phenotype.” Cancer Discovery, 2014, 4:716-729. PMID: 24670723
  • Jackson SR, Yuan J, Berrien-Elliott MM, Chen CL, Meyer JM, Donlin MJ and Teague RM. “Inflammation programs self-reactive CD8+ T cells to acquire T-box-mediated effector function but does not prevent deletional tolerance.” J Leukoc Biol. 2014; 96(3):397-410. PMID: 24823810
  • Donlin MJ, Upadhya R, Gerik KJ, Lam W, VanArendonk LG, Specht CA, Sharma NK and Lodge JK. “Cross talk between the cell wall integrity and cAMP/protein kinase A pathways in Cryptococcus neoformans.” mBio, 2014; 5(4):e01573. PMID: 2511824
  • Berrien-Elliott MM, Yuan J, Swier LE, Jackson SR, Chen CL, Donlin MJ, Teague RM. “Checkpoint blockade immunotherapy relies on T-bet but not Eomes to induce effector function in tumor infiltrating CD8+ T cells.” Cancer Immunol Res. 2015 3(2):116-24. PMID: 25516478

William H. Elliott Mass Spectrometry Facility
In 1965, Dr. Elliott purchased one of the first commercially available mass spectrometers ever to be imported into the US. James Shoemaker, M.D., Ph.D., founded the Metabolic Screening Lab in 1989 to use gas chromatography-mass spectrometry to diagnose human metabolic disorders.

The facility now includes an Agilent 5973 Mass Selective Detector (Mass Spec) interfaced with a 6890 gas chromatograph accessed by a 7683 auto-injector, which is operated by an HP Compaq PC, and an Agilent 5975 inert Mass Selective Detector (Mass Spec) interfaced with a 6890 gas chromatograph accessed by a 7683 auto-injector, which is operated by an HP Compaq PC. The facility also houses a FISONS MD 800 benchtop GC-MS. Two Hewlett-Packard benchtop GC-MS instruments are also available for use by the department.

The Facility is managed by James Shoemaker, M.D. (314-977-9233; shoemajd@slu.edu) and Tony Thomas (314-977-9230; thomasag@slu.edu).
Real-Time PCR
The department has three "real-time" or kinetic PCR instruments.

  • MJ Research DNA Engine Opticon™ 2 Continuous Fluorescence Detection System: This instrument provides investigators with the ability to perform very sensitive, accurate, and reproducible measurements of levels of gene expression. In addition, this instrument can be used in other applications such as measuring viral load, performing allelic discrimination studies, and optimizing PCR conditions.

  • Bio-Rad Chromo4 Real-Time 4-color, 96-well PCR system: The Chromo4 is an interchangeable Alpha unit, bringing real-time quantitative PCR to a high-performance DNA Engine platform and allows upgrading to real-time PCR when coupled with an existing DNA Engine thermal cycler. Crosstalk is reduced by bringing fluorophore excitation and detection directly to each well.

  • Bio-Rad CFX96 Touch Real-Time 5-color, 96-well PCR Detection System: This six-channel system combines advanced optical technology with precise thermal control to deliver sensitive, reliable detection. Sample and reagent use are minimized using up to 5-target multiplexing with sample volumes as low as 10 µl. Reactions can be optimized in a single run using the thermal gradient feature and all run data can be visualized at once and exported in multiple formats.
Specialized Instrumentation
Laboratories within the department contain a variety of specialized instrumentation. These include a BioRad CHEF-DRIII pulsed field electrophoresis system for separation of extremely large molecules of DNA (up to 4 megabases), BioRad Biolistic particle delivery system for biolistic transformations of fungal, plant, and animal cells, multiple HPLC, FPLC, and chromatography systems, and an isolated perfused heart lab with Powerlab software for ventricular pressure and EKG monitoring. The department also has dynamic and static light scattering devices for analysis of macromolecular assemblies, standard gel documentation systems, and fluorescent plate readers and spectrophotometers.
Resources available within the Medical School
A 44,700-sq.-ft. animal care facility located within the Doisy Research Center is managed by the Department of Comparative Medicine. This facility is supervised by three veterinarians and has multiple technical staff who provide training, colony health surveillance, veterinary and technical support to investigators on a cost basis. They provide consultation and collaborative services to assist researchers in project planning and model development.
Flow Cytometry Research Core houses a FACSCallibur flow-cytometer with cell sorter, a Biosciences LSR II, capable of 10-color analyses, and a Biosciences FACSAria, capable of simultaneous sorting of 4 populations. The Flow Cytometry Research Core has two full-time staff and offers discounted rates to SLU researchers.
Animal Imaging Core Facility is located in the Molecular Microbiology and Immunology Department. They offer non-invasive, small animal imaging using an IVIS Spectrum instrument.
Research Microscopy and Histology Core, located in the Department of Pathology, provides a wide range of histological and microscopy services on a fee-for-service basis.
Saint Louis University maintains electronics and machine shops that are available to investigators. The electronics shop provides high-quality, in-house service for all standard laboratory equipment.