SPM Applications in Biology
Viruses have been good targets for imaging with AFM especially in the early phase of its application to biology. Bacteriophage T4 is first imaged by Kolbe et al.  with a distinction of the head and tail. The result is soon improved by Ikai and his collaborators with a successful imaging of tail fibers of 2 nm in diameter. Zenhausern et al. and Imai et al. image the tobacco mosaic virus as well as bacteriophages .
According to Ikai et al.  the dimension of the T4 phage in air dried state is: the head (W = 140 nm, H = 50 - 60 nm); the tail (W = 40 nm, H = 17 - 20 nm), the tail-fiber (W = 7 - 8 nm, H = 1 - 2 nm). Occasionally phage particles with very low head height are observed corresponding to "empty" head particles that were devoid of DNA normally packed in the head. One advantage of AFM over other microscopic methods like electron microscopy is its ability to directly give information about the height of the specimen .
Tobacco Mosaic Virus (TMV or Satellite TMV) is the most popular object among other numerous mosaic viruses investigated so far [, ]. Colloidal solutions of TMV behave similarly to those of commonly known protein ones and can therefore be studied in the same way. TMV microcrystals fail to grow at low supersaturations. It is found that two-dimensional nuclei are the source of growth steps both at high and at rather low supersaturations. However, at higher supersaturations (typically used for TMV crystallization), three-dimensional nuclei provide the major source of growth steps [, , ]. Two other mosaic viruses studied recently are the icosahedral turnip yellow mosaic virus (TYMV) and the cucumber mosaic virus (CMV) . Growth of these crystals proceeds by two-dimensional (2D) nucleation. The authors present highly resolved AFM images of the hexameric and pentameric capsomers of the T = 3 capsids on the surface of the individual TYMV virions which are as small as 28 nm in diameter. According to data obtained by X-ray crystallography the capsid of TYMV is composed of 180 identical protein subunits, each of about 20 kDa, organized into 12 pentameric and 20 hexameric capsomers which project about 40 Å above the surface of the virion. The authors particularly emphasize that the difference between the highest and lowest points on the capsid surface mentioned above is accurately reflected by AFM. The CTM virus capsomer structure is much finer and cannot be resolved to appropriate quality as yet. Clear in situ AFM images of structural peculiarities of virus crystal surfaces obtained under various experimental conditions help to interpret X-ray crystallography data. A series of images with scan sizes of 300 x 300 nm reveals evolution of the surface layer of the (101) face of the TYMV crystals, when exposed to equilibrium conditions. Structural defects in crystal lattice such as vacancies, individual particles, dislocations and aggregates are excellently discernible.
Once a living biological specimen is under the AFM tip and in a favorable environment the system can be maintained and studied for hours. Thus, biological processes can be studied in real time. Haberle et al.  study the viral infection process of mammalian cells. Living monkey kidney cells are reproducibly imaged with resolution on the 10 nm scale and then a solution of pox viruses is added to the medium. In the first instance the cell membrane is observed to soften for a short period as the viral infection of the cell took place. Exocytosis events are then observed as viral proteins are expelled from the cell. Finally, the emergence of the progeny viruses is witnessed when large temporary protrusions of 200 - 300 nm cross section appear in the membrane leaving scars.
A notable paper that elegantly demonstrates how AFM's high resolution enables the relationship between structure and function to be drawn is that of Müller et al. . These researchers achiev subnanometer resolution of the f29 bacteriophage headtail connector to provide structural evidence that the connector and its movement play an important role in the packing of the viral DNA.
The promising AFM technique involving AFM cantilever tips functionalized with specific molecules can be easily extended to the sphere of virology. The prospects of this technique are outlined by R.d.S. Pereira . It is proposed that the use of the enzyme reverse transcriptase from the AIDS virus to modify AFM cantilever can make it a powerful tool to test new medications capable of inhibiting this enzyme and inactivating the action of the virus . In addition, immobilization of one virus particle on the tip of the AFM cantilever opens up the possibility of measuring the force necessary for this virus to infect a single cell . In this way, a test medication that could weaken these Van der Waals forces could be a potent anti-virus drug and could avoid virus infection.
Ohnesorge et al.  report observing exocytosis of a virus from an infected cell in real time. In spite of the low spatial resolution (scan sizes of 3.6 x 2.0 µm) time resolution is relatively high, reaching one image frame per second, so rearrangement of parts of the cytosceleton is discernible. The virus itself is also characterized with a much higher resolution of ~ 2 - 3 nm, enabling the identification of substructural elements on the surface.
The binding of influenza viruses to supported lipid membrane as well as the effect of the substrate-exposed lipid monolayer on defect structures in self-assembled, fully hydrated bilayers are studied in order to develop a novel biosensor capable of recognition of specific viruses and other macromolecules . The spherical particles are of about 200 nm in diameter and may be slightly elongated in the scanning direction due to partial deformation by the AFM tip. Later, extended study of influenza hemagglutinin is reported .
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