1. Techniques in Cell and Molecular Biology
CHAPTER 18
Techniques in Cell and Molecular Biology

2. Introduction
Research in cell biology requires complex instrumentation and techniques.
Understanding the technology helps in understanding the cell.

3. 18.1 The Light Microscope (1)
The light microscope uses the refraction of light rays to magnify an object.
A condenser directs light toward the specimen.
The objective lens collects light from the specimen.
The ocular lens forms an enlarged, virtual image.

4. The paths taken by light rays to form an image

5. The Light Microscope (2)
Resolution
Resolution is the ability to see two nearby points as distinct images.
The numerical aperture is a measure of the light-gathering qualities of a lens.
The limit of resolution depends on the wavelength of light.
Optical flaws, or aberrations, affect resolving power.

6. Resolution

7. The Light Microscope (3)
Visibility
Visibility deals with factors that allow an object to be observed.
It requires that the specimen and the background have different refractive indexes.
Translucent specimens are stained with dyes.
A bright-field microscope a light that illuminates the specimen is seen as a bright background; it is suited for specimens of high contrast such as stained sections of tissues.

8. The Feulgen stain

9. The Light Microscope (4)
Preparation of Specimens for Bright-Field Light Microscopy
A whole mount is an intact object, either living of dead.
A section is a very thin slice of an object.
To prepare a section, cells are immersed in a chemical called a fixative.
The rest of the procedures minimize alteration from the living state.

10. The Light Microscope (5)
Phase-Contrast Microscopy
The phase-contrast microscope makes highly transparent objects more visible by converting differences in the refractive index of some parts of the specimen into differences in light intensity.
Differential interference contrast (DIC) optics gives a three-dimensional quality to the image.

11. A comparison of cells seen with different types of light microscopes

12. The Light Microscope (6)
Fluorescence Microscopy (and Related Fluorescence-Based Techniques)
Fluorescence microscopy has made possible advances in live-cell imaging.
Fluorochromes are compounds that release visible light upon absorption of UV rays.
Fluorochrome stains cause cell components to glow, a phenomenon called fluorescence.

13. The Light Microscope (7)
Fluorescence microscopy (continued)
Fluorochrome-conjugated antibodies are used to locate specific cellular structures (immunofluorescence).
The gene for green fluorescent protein (GFP) from jellyfish can be recombined with genes of interest in model organisms.
GFP is expressed with the host gene of interest.
GFP is used to follow a gene of interest.

14. Use of GFP variants to follow the dynamic interactions between neurons and target cells in vivo

15. The Light Microscope (8)
Fluorescence microscopy (continued)
A GFP variant is called fluorescence resonance energy transfer (FRET), which uses fluorochromes to measure changes in distance between labeled cellular components.

16. The Light Microscope (9)
Video Microscopy and Image Processing
Video microscopy is used to observe living cells.
Video cameras offer several advantages for viewing specimens.
They can detect and amplify very small differences in contrast.
Images produced by video cameras can be converted to digital electronic images and processed by a computer.

17. The Light Microscope (10)
Laser Scanning Confocal Microscopy
A laser scanning confocal microscope produces an image of a thin plane located within a much thicker specimen.
A laser beam is used to examine planes at different depths in a specimen.

18. Laser scanning confocal fluorescence microscopy

19. The Light Microscope (11)
Super-Resolution Fluorescence Microscopy
STORM (stochastic optical reconstruction microscopy) allows the localization of a single fluorescent molecule within a resolution of <20 nm.
Fluorescent images can be positioned with greater accuracy.

20. Breaking the light microscope limit of resolution

21. 18.2 Transmission Electron Microscope (1)
Transmission electron microscopes (TEMs) use electrons instead of light to form images.
The limit of resolution is about Å.

22. Transmission Electron Microscope (2)
The components of an electron microscope:
An electron beam from a tungsten filament accelerated by high voltage, and focused with a magnetic field.
A condenser lens is placed between the electron source and the specimen.
Differential scattering of electrons by the specimen creates the image.
Proportional to the thickness of the specimen.
Tissues are stained with heavy metals for contrast.

23. A comparison of the lens system of a light and electron microscope

24. Transmission Electron Microscope (3)
Specimen Preparation for Electron Microscopy
Specimens must be fixed, embedded, and sectioned thinly.
Glutaraldehyde and osmium tetroxide are common fixatives.
Specimens are dehydrated prior to embedding.
Epon or Araldite are common embedding resins.
Thin sections cut with glass or diamond knives are collected on grids.

25. Preparation of a specimen for observation in the electron microscope

26. Transmission Electron Microscope (4)
Specimen preparation (continued)
Chemicals used may cause an artifact, which may be disproved by using other techniques.
In negative staining, heavy metal diffuses into spaces between specimen molecules.
Shadow casting coats a specimen with metal to produce a three-dimensional effect.

27. Examples of negatively stained and metal-shadowed specimens

28. The procedure used for shadow casting

29. Transmission Electron Microscope (5)
Freeze-Fracture Replication and Freeze-Etching
In freeze-fracture replication, frozen tissue is fractured with a knife.
A heavy-metal layer is deposited on fractured surface.
A cast of the surface is formed with carbon.
The metal-carbon replica is viewed in the TEM.
In freeze-etching, a layer of ice is evaporated from the surface of the specimen prior to coating it with heavy metal.

30. Procedure for the formation of freeze-fracture replicas

31. Freeze-fracture and freeze-etching

32. 18.3 Scanning Electron Atomic Force Microscopy (1)
Scanning electron microscopes (SEMs) form images from electrons that have bounced off the surface of a specimen.
Specimens for SEM are dehydrated by critical-point drying.
Specimens are coated with a layer of carbon, then gold.
The image in SEM is indirect.
SEM has a wide range of magnification and focus.

33. Scanning electron microscopy

34. Scanning Electron Atomic Force Microscopy (2)
The atomic force microscope (AFM) is a high-resolution scanning instrument.
AFM provides an image of each individual molecule as it is oriented in the field.

35. 18.4 The Use of Radioisotopes (1)
Radioisotopes can be easily detected and quantified.
Properties of radioisotopes:
An isotope refers to atoms that differ in the number of neutrons.
Isotopes with an unstable combination of protons and neutrons are radioactive.
The half-life of a radioisotope measures its instability; half of the radioactive material disintegrates in a given amount of time.

36. Properties of a variety of radioisotopes

37. The Use of Radioisotopes (2)
Liquid scintillation spectrometry
Scintillants absorb the energy of an emitted particle and release it in the form of light.
Radiation of a tracer in a sample can be detected by measuring light emitted by a scintillant.

38. The Use of Radioisotopes (3)
Autoradiography is a technique to where a particular isotope is located.
A particle emitted from a radioactive atom activates a photographic emulsion.
The location of the radioisotope in the specimen is determined by the positions of the overlying silver grains in a photographic emulsion.

39. Preparation of light microscopic autoradiograph

40. Examples of autoradioagraphs

41. 18.5 Cell Culture (1)
Most of the study of cells is carried out using cell culture.
Cells can be obtained in large quantities.
Most culture contain a single type of cell.
Many different types of cells can be grown in culture.
Cell differentiation can be studied in a cell culture.
Cells in a culture require media that includes hormones and growth factors.

42. Cell Culture (2)
A primary culture is when cells are obtained directly from the organism.
A secondary culture is derived from a previous culture.
A cell line refers to cells with genetic modifications that allow them to grow indefinitely.
Many types of plant cells can be grown in culture.

43. Cell Culture (3)
A two-dimensional culture system is when cells are grown on the flat surface of a dish.
Labs are moving to three-dimensional cultures in which cells are grown in a 3D matrix consisting of extracellular materials.
3D cultures are better suited to study cell-cell interactions.

44. A comparison of cell morphology of cells growing in 2D versus 3D cultures

45. 18.6 The Fractionation of a Cell’s Contents by Differential Centrifugation
Differential centrifugation facilitates the isolation of particular organelles in bulk quantity.
Prior to centrifugation, cells are broken by mechanic disruption in a buffer solution.
The homogenate is subjected to a series of sequential centrifugations.
Organelles isolated can be used in a cell-free system to study cellular activities