Biology Department Biology Department  

Scanning Transmission Electron Microscopy Facility

Overview and Historical Perspective

Overview    Biological specimens are difficult to see in the electron microscope because of their low contrast. Electron microscopy became useful to biology over the last 40 years as methods were developed to add high-contrast heavy atoms (osmium, tungsten, lead, uranium, etc) to biological specimens in a controlled way. However, the object being imaged was actually an "artifact" composed of heavy atoms surrounding features of interest. Careful controls and much trial and error gave rise to much of our present understanding of the structure of sub-cellular components. However, it has always been clear that detailed interpretation of small structures was ultimately limited by the indirect nature of this imaging process.
   Two approaches have been developed recently to circumvent the need for staining: use of image averaging of ordered arrays (pioneered by Unwin and Henderson, and not discussed further here) and dark-field imaging. The idea of dark-field microscopy is like observing stars in the night sky; dim stars are more visible in the dark background sky of the countryside rather than in the bright lights of the city. In electron microscopy, the background comes from electrons transmitted directly through the specimen as well as from electrons scattered by the substrate and surrounding structure. The STEM design removes the direct beam very efficiently and measures almost every scattered electron as it makes a flash of light upon hitting a detector. The conventional electron microscope is much less efficient for dark-field imaging and requires a dose at least ten times greater than the STEM to make an image of the same quality. Theoretically, molecules could be poised over holes to give a minimum background, but this is difficult and unreliable. A good compromise is a very thin substrate stretched across holes in a thicker film. In practice 2 nanometer (nm) thick carbon films are very easy to produce and handle, giving about 100 percent contrast for unstained DNA (also 2nm thick) on top of such a substrate. Single heavy atoms and heavy atom clusters also give high contrast in the STEM and can be used as labels.
   The high contrast in the dark field STEM images makes it easy to identify most problems in specimen preparation and outline candidate molecules. All images are acquired and stored digitally, so there is no data loss by using film for image processing. A simple computer program can measure the total mass of a particle minus the background within a contour to identify the number of subunits present and the variation from one object to another. This provides a direct link to biochemistry.
   Specific sites within complexes can be labeled with heavy atom clusters; much like putting pins in a map. The mass distribution shows the scaffolding while the bright spots delineate features of interest. A variety of reactivities, labels and chemistries are available.
Historical Perspective    The STEM concept was described by VonArdenne at about the same time Ruska developed the TEM (Transmission Electron Microscope) in the late 1930's. However, the STEM did not develop at that time due to lack of electronics and adequate electron sources. In the 1960's interest in the STEM was revived by Crewe and coworkers with the development of the cold field emission electron source and optimization of electronics and electron-optical components, culminating in the first visualization of single heavy atoms in the electron microscope in 1971.
  This work was continued at Brookhaven in 1971 constructing STEM1, with NSF, NIH, and DOE support. STEM 1 was completed in October 1977 and has operated as a User Facility continually since then, mainly with NIH and DOE Support. Significant early results include demonstration that:
  1. native and reconstituted nucleosomes had the expected mass (Woodcock et al. 1979, 1980)
  2. tri-nodular fibrinogen molecules had the mass of monomers rather than trimers (Mosesson et al. 1981)
  3. there were various size classes of intermediate filaments (Steven et al. 1982, 1983)
  4. undecagold clusters could be visualized (Safer, et al. 1982)
  5. dynein has a "bouquet" structure (Johnson et al. 1983).
STEM1 (left) continues to operate as a User Facility with support from the US Department of Energy, Office of Health and Environmental Research (DOE-OHER).
References Johnson K.A., and Wall J.S.
Structure and molecular weight of the dynein ATPase.
J. Cell Biol., 96:669-678 (1983).
Mosseson M.W., Hainfeld J., Haschmeyer R.H., and Wall J.S.
Identification and mass analysis of human fibrinogen molecules and their domains by scanning transmission electron microscopy (STEM).
J. Mol. Biol., 153:695-718 (1981).
Safer D., Hainfeld J.F., Wall J.S., and Riordan J.
Biospecific labeling with undecagold: visualization of the biotin binding sites on avidin.
Science, 218:290-291 (1982).
Steven A.C., Hainfeld J.F., Trus B.L., Wall J.S., and Steinert P.M.
The distribution of mass in heteropolymer intermediate filaments assembled in vitro: STEM analysis of vimentin/desmin and bovine epidermal keratin.
J. Biol. Chem., 258:8323-8329 (1983).
Steven A.C., Hainfeld J.F., Trus B.L., Wall J.S., and Steinert P.M.
Epidermal keratin filaments assembled in vitro have masses-per-unit-length that scale according to subunit mass: structural basis for homologous packing of subunits in intermediate filaments.
J. Cell Biol., 97:1939-1944 (1983).
Steven A.C., Wall J.S., Hainfeld J.F., and Steinert P.M.
The structure of fibroblastic intermediate filaments: analysis by scanning transmission electron microscopy.
Proc. Natl. Acad. Sci. USA, 79:3101-3105 (1982).
Woodcock C.L.F., Frado L.L.Y., and Wall J.S.
Direct molecular weight determination of chromatin particles by STEM.
J. Cell Biol., 83:156a (1979).
Woodcock C.L.F., Frado L.L.Y., and Wall, J.S.
Composition of native and reconstituted chromatin particles: direct mass determination by scanning transmission electron microscopy.
Proc. Natl. Acad. Sci. USA, 77:4818-4822 (1980).


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Last Modified: June 12, 2009
Please forward all questions about this site to: Kathy Folkers

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