Electron Microscopy

Overview

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annulate-lamellae-small2_opt
JEM-1400plus-small2
kidney-diseased_2-6457_small_opt
nanoparticle

The Electron Microscopy Core Laboratory is sponsored by the Health Sciences Center and the School of Biological Sciences.

Our techniques can help you understand structure and function.  Examples of questions we can help you answer (illustrated by six of the eight pictures above):

  1. What is the cellular structure of my sample?  Does genotype, disease, or different environmental conditions affect the structure?  (see picture of diseased kidney in upper right)
  2. What is the morphology of a biological macromolecule?  Does genetic mutation or different environmental conditions affect the morphology?  (see picture of phage particles, top row, second from left)
  3. What is the morphology of a macromolecule or macromolecular complex within a cell?  Does genetic mutation, disease, or different environmental conditions affect the morphology?  (see picture of dynein in human respiratory tract cilia, upper left, and annulate lamellae, second from right in top row)
  4. What is the three-dimensional structure of a biological macromolecule?  How does genetic mutation, interactions with other molecules, or different environmental conditions affect its morphology?  What residues (e.g. amino acids or nucleotides) interact in a macromolecular complex?  (see picture of virus-antibody complex in bottom left)
  5. What is the size and morphology of a nanoparticle or synthesized nanomachine?  How do different synthesis methods or environmental conditions affect the morphology?  (see picture of nanoparticles, bottom right)

To answer these questions, both transmission electron microscopy (TEM) and scanning electron microscopy (SEM) imaging and sample preparation are available.  For example, we a) process tissue from fixative through plastic embedding and thin-sectioning, b) perform immuno-labeling experiments, c) view particulate samples, d) prepare frozen-hydrated specimens, and e) compute three-dimensional reconstructions.

To make a reservation for use of our equipment or services, please go to the Batch Viewer login page.

Staff

Staff

David Belnap Ph.D., Director of the EM Core
Expertise: Macromolecular EM
801-585-1242
David.Belnap@utah.edu

Nancy Chandler,
Senior Laboratory Specialist
Expertise: Cellular & Tissue EM
801-585-1242
Nancy.Chandler@hsc.utah.edu

Linda Nikolova,
Senior Laboratory Specialist
Expertise: Cellular & Tissue EM
801-585-1242
lnikolova@genetics.utah.edu

Willisa Liou, Ph.D.
Senior Laboratory Specialist
Expertise: Cryoultramicrotomy & ImmunoEM
801-585-1242
willisa.liou@hsc.utah.edu

Oversight Committees

Whole Laboratory

Erik Jorgensen, Department of Biology
Patricia Revelo, Department of Pathology
Erhu Cao, Department of Biochemistry
Richard Rabbitt, Department of Bioengineering

Cryo-EM

Peter Shen, Department of Biochemistry
Heidi Schubert, Department of Biochemistry
Erhu Cao, Department of Biochemistry
Christopher Hill, Department of Biochemistry
Wesley Sundquist, Department of Biochemistry
Julia Brasch, Department of Biochemistry

Locations

Locations

Main Lab Location
Sorenson Molecular Biotechnology Building (SMBB) Room 2500
36 S. Wasatch Dr.
Salt Lake City, UT 84112
801-585-1242

Satellite Lab, including Arnold & Mabel Beckman Center for Cryo-EM
Crocker Science Center (CSC) Room 024
1390 Presidents Cir
Salt Lake City, UT 84112
801-587-0353

Electron Microscopes

To schedule microscopes listed below, please visit resource.cores.utah.edu or contact a member of the lab.

*Academic users outside the University of Utah are charged an additional 53.5% to cover Facilities and Administrative costs.

Transmission Electron Microscopes
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FEI Tecnai F20 Transmission Electron Microscope
(Cryo-capable)

Location: CSC Room 024
Academic Fee:*

  • Mon-Fri (8am-5pm): $47/hr
  • Evenings & weekends: $27/hr

Commercial Fee: $73/hr

TKg3
ThermoFisher Titan Krios G3
Transmission Electron Microscope
(Cryo-capable)

Location: CSC Room 024
Academic Fee:* $1400/day

Commercial Fee: $2750/day, $3000/day (after 1 Jul 2023)

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JEOL JEM-1400 Plus Transmission Electron Microscope (Cryo-capable)

Location: SMBB Room 2135
Academic Fee:*

  • Mon-Fri (8am-5pm): $47/hr
  • Evenings & weekends: $27/hr

Commercial Fee: $73/hr

Scanning Electron Microscopes
Zeiss GeminiSEM 300 Scanning Electron Microscope

Location: CSC Room 031
Academic Fee:*  $30/hr

Commercial Fee: $47/hr

COMING SOON!  ThermoFisher Aquilos 2 Cryo-Focus Ion Beam Scanning Electron Microscope

Location: SMBB Room 2137
Academic Fee:*  TBD

Commercial Fee: TBD

Microtomes, etc.

Microtomes & Other Equipment

To schedule microtomes or other equipment listed below, please visit resource.cores.utah.edu or contact David Belnap (1-801-585-1242).

*Academic users outside the University of Utah are charged an additional 52.5% to cover Facilities and Administrative costs.

Leica UC6 Ultramicrotome (3)

Location: SMBB Room 2128
Academic Fee:* $20/hr
Commercial Fee: $31/hr

Reserve for Use
Leica UCT Ultramicrotome

Location: SMBB Room 2128
Academic Fee:* $20/hr
Commercial Fee: $31/hr

Reserve for Use
Leica UC7 with Cryo-Attachment Ultramicrotome

Location: CSC Room 034
Academic Fee:* $25/hr + liquid nitrogen fee
Commercial Fee: $39/hr + liquid nitrogen fee

Reserve for Use
Other Specimen-Preparation Equipment (supplies, usage fees, and staff time charges may apply)
  • Sputter coater
  • Vacuum evaporator
  • High-pressure freezer (e.g. tissue or cells)
  • Vitrification robot (plunge freezing, Vitrobot)
  • Microscopy tissue processor
  • Laboratory microwave oven
  • Freeze substitution machine
  • Light microscope
  • Critical-point dryer
  • Rotary microtome

Services & Rates

Clinical EM

Transmission electron microscopy is used in the diagnosis of some diseases, particularly certain renal diseases. The EM Core Laboratory provides the technical component for clinical electron microscopy, or clinical EM. We process (fix, embed, and stain) submitted tissue samples. Once embedded in a plastic block, thin sections of the biopsy are cut on an ultramicrotome and then are imaged on one of our transmission electron microscopes. Images are then turned over to a pathologist for diagnosis. The EM Core Laboratory is certified by the College of American Pathologists (CAP).

Please contact a staff member of the EM Core Laboratory to arrange for this “technical only” service. Please note that we require submitted samples to have at least two identifying labels (e.g. patient name and accession number). If submitted samples are not compliant, we will contact the submitting institution. Samples should be sent in fixative solution. Please contact us for details on appropriate solutions.

Pricing is as follows. Note that prices may be reduced or increased for very simple or complex cases, respectively. For example, if a large amount of tissue is sent, then we are required to produce, cut, and image more blocks. We will increase pricing accordingly.

*Sending Samples to the EM Lab 

Clinical Service Price
Full Tissue Biopsy Thin Sectioning: process tissue sample (fix, embed, and stain); cut sections; record images $472.50/sample
Partial Tissue Biopsy Thin Sectioning: process and cut or cut and record images $236.25/sample
Partial Tissue Biopsy Thin Sectioning: stain and image sections $120/sample

As per CAP requirements, sample blocks and images are stored for at least 10 years.

Research Services
Service Academic Fee*# Commercial Fee*#
EM Core Staff Time (directors) $78/hour $120/hour
EM Core Staff Time (senior lab specialists and technicians) $40/hour $62/hour

*Supplies and equipment usage fees are additional costs.

#Academic users outside the University of Utah are charged an additional 53.5% to cover facilities and administrative costs.

Specific Tissue and Cellular Specimen Preparation Procedures Done by Core Staff

Procedure for observing tissue & cellular specimens Academic Cost# Commercial Cost
Epoxy Resin Embedding   contact lab.   contact lab.
L.R. White Embedding contact lab.   contact lab.
Immuno-Bed (for light microscopy only)   contact lab. contact lab.
Immuno-TEM Staining contact lab. contact lab.
Osmification and Storage (in buffer)   contact lab. contact lab.
Osmification, Dehydration (ethanol) & Drying (hexamethyldisalizane)   contact lab.   contact lab.
Other Procedures (costs vary depending on the time taken)*#
Negative Staining and Imaging
Metal Coating (sputter coating or vacuum evaporation)
Critical Point Drying
Cryogenic TEM
3D Reconstruction or Data Analysis

*Supplies, staff time, and equipment usage fees are costs.

#Academic users outside the University of Utah are charged an additional 53.5% above academic rates to cover facilities and administrative costs.

Supplies

Supplies
Supply Cost per unit*
Box for Light Microscope Slides at cost
Chucks for Light Microscopy (for Immuno-Bed) at cost
Embed 812 (for TEM sample preparation) at cost
Forceps (tweezers), Dumont #5 at cost
Immuno-Bed Filtrate at cost
Immuno-Bed Solution B at cost
Osmium tetroxide (for sample preparation) at cost
Saturated aqueous uranyl acetate at cost
TEM grids at cost
TEM grid box at cost
Tray of Molds (for light microscopy) at cost

(Not a complete list)

*Users outside the University of Utah are charged an additional 53.5% to cover facilities and administrative costs.

Referencing Us

If you are trained on the EM and use the EM Core for your research project, please acknowledge that use in the acknowledgement section of your publication. Here is one example: “Electron microscopy was performed by [EM Core researcher] at the University of Utah Electron Microscopy Core Laboratory.”

If a member of the EM Core Laboratory does research work for you, please consider him or her as a collaborator on your project. He or she wants to be part of your team. As appropriate, please have that person participate in group discussions of the project. At a minimum, please acknowledge that person and the University of Utah Electron Microscopy Core Laboratory in the acknowledgement section of your paper.

Data Retention Policy

The Electron Microscopy Core Laboratory is not responsible to keep copies of research data. That is the responsibility of each user of the facility. As a courtesy to our users (to keep a copy of images until the user has ample opportunity to copy data to another computer) and provided space exists, the EM Core Laboratory will retain copies of images stored on our computer hard drives for at least one month. Clinical data is retained for a significantly longer period. Please see the Clinical EM page. (updated May 14, 2014)

Training

EM training is a serious committment for the researcher and the EM Core.  The microscopes and microtomes are expensive and require great care and patience to use properly.  Misuse may result in significant downtime and expense to repair the device.  A new user will likely need many hours of practice on the EM instrument or microtome before he or she will be able to use the device properly and achieve high quality results.  He or she may need multiple sessions to properly fix and embed specimens.  Nevertheless, a new user can become proficient in a reasonable amount of time.Training in usage of microtomes and EM instruments, in tissue processing (for thin-sectioning), and in negative stain and other sample preparation techniques is available.  Contact the director or a staff member to make arrangements for training.  Training is usually done on an individual basis.  Small groups of two or three people can usually be accommodated.

Training for EMs and microtomes will consist of the following:

  1. An overview of how the EM instrument or microtome works
  2. Introduction to operation of the device
  3. Practice operating the device
  4. Demonstrating your proficiency with your own specimen

Steps 1 and 2 can be done on the first session, but steps 3 and 4 will require additional sessions unless the user has had previous experience. For example, for use of a TEM the training involves a 1-2 hour introductory session, a 1-2 hour training in focusing, a 1-2 hour instructions in alignments, and additional sessions as required for your sample. After the first two sessions, the user will spend time on his or her own practicing before the third session. After training is “completed”, members of the EM Core Laboratory are available to offer help and advice. Users who demonstrate proficiency will be allowed access to the equipment after normal business hours. Training in cryo-TEM will require proficiency first in “traditional” TEM. In other words, the user will need to demonstrate independence with dry samples:

  1. At least 30 hours of experience looking at samples.
  2. At least 30 vent-free specimen exchanges.
  3. Demonstrate the ability to align the TEM independently (direct alignments).
  4. Demonstrate the ability to use the low-dose procedure (search, focus, expose) with a non-cryo sample.
  5. Independently
    • At an appropriate magnification, take quality pictures of a negatively stained or dry (if stain is unnecessary) specimen you prepared.
    • At a magnification > 100,000x, take pictures of a specimen.
    • At a magnification > 40,000x but < 100,000x, take a focal series (underfocus, at focus, overfocus)
    • Images must not have astigmatism.
  6. Understand how to find the beam when it is “lost”.
  7. Understand how to handle problems with the T12 that may arise.

Usage of the ThermoFisher Tecnai F20 instrument will require extensive practice and proficiency first on the ThermoFisher Tecnai 12 instrument.

Training fees are user fees for the desired device plus cost of staff member doing the training.

Electron Microscopy