1. Microscopy techniques

2. Units of Measurement

3. Scientists use metric units of measurement that are simpler than English units and are standardized throughout the world. The metric system is a decimal system in which each unit is one tenth the size of the next largest unit. The basic unit of length in the metric system is the meter (m), which is slightly longer than an English yard. One thousandth of a meter is a millimeter (mm), about the thickness of a dime, and one-thousandth of a millimeter is a micrometer (μm), which is small enough to be useful in measuring the size of cells. One thousandth of a micrometer is a nanometer (nm), which is one billionth of a meter and is used to measure the smallest cellular organelles and viruses.

4. Microscopy Refers to the use of light or electrons to magnify objects.

5. General Principles of Microscopy The same general principles guide both light and electron microscopy.

6. Wavelength of Radiation Various forms of radiation differ in wavelength, which is the distance between two corresponding parts of a wave. The human eye distinguishes different wavelengths of light as different colors. In addition to light, moving electrons act as waves with wavelengths dependent upon the voltage of an electron beam. Electron wavelengths are much smaller than those of visible light, and thus their use results in enhanced microscopy.

7. Magnification Magnification is the apparent increase in size of an object and is indicated by a number followed by an “×” which is read “times.” Magnification results when a beam of radiation refracts (bends) as it passes through a lens.

8. Resolution Resolution (also called resolving power) is the ability to distinguish between objects that are close together. The better the resolution, the better the ability to distinguish two objects that are close to one another. Modern microscopes can distinguish between objects as close as 0.2 μm.

9. A principle of microscopy is that resolution distance is dependent on – the wavelength of the electromagnetic radiation and – the numerical aperture of the lens, which is its ability to gather light. Immersion oil is used to fill the space between the specimen and a lens to reduce light refraction and thus increase the numerical aperture and resolution.

11. Contrast Contrast refers to differences in intensity between two objects, or between an object and its background. Since most microorganisms are colorless, they are stained to increase contrast. Polarized light may also be used to enhance contrast.

12. Light Microscopy Several classes of microscopes use various types of light to examine specimens.

13. Bright-Field Microscopes The most common microscopes are bright-field microscopes, in which the background (or field) is illuminated. There are two basic types: Simple microscopes – contain a single magnifying lens and are similar to a magnifying glass. Compound microscopes – use a series of lenses for magnification.

14. Light rays pass through a specimen and into an objective lens immediately above the object being magnified. The objective lens is really a series of lenses, and several objective lenses are mounted on a revolving nosepiece. The lenses closest to the eyes are ocular lenses, whereas condenser lenses lie beneath the stage of the microscope and direct light through the slide.

15. The total magnification of a compound microscope is determined by multiplying the magnification of the objective lens by that of the ocular lens. The limit of useful magnification for light microscopes is 2000× because they are restricted by the wavelength of visible light. A photograph of a microscopic image is a micrograph.

17. Dark-Field Microscopes Pale objects are best observed with dark-field microscopes, which utilize a dark-field stop in the condenser that prevents light from directly entering the objective lens. Instead, light passes into the slide at an oblique angle. Only light rays scattered by the specimen enter the objective lens and are seen, so the specimen appears light against a dark background.

18. Phase Microscopes Phase microscopes use a phase plate to retard light rays passing through the specimen so that they are 1⁄2 wavelength out of phase with neighboring light waves, thereby producing contrast. Phase-contrast microscopes produce sharply defined images in which fine structures can be seen. Differential interference contrast microscopes create phase interference patterns and use prisms to split light beams into their component colors, giving images a dramatic three- dimensional or shadowed appearance.

20. Fluorescent Microscopes Fluorescent microscopes use an ultraviolet (UV) light source to fluoresce objects. Since UV light has a shorter wavelength than visible light, resolution is increased. Contrast is improved because fluorescing structures are visible against a black background.

21. Confocal Microscopes Confocal microscopes use fluorescent dyes in conjunction with UV lasers to illuminate the fluorescent chemicals in only one thin plane of a specimen at a time. Several images are taken and digitized, and then computers construct three-dimensional images of the entire specimen.

22. Electron Microscopy Because the shortest wavelength of visible light is about 400 nm, structures closer together than about 200 nm cannot be distinguished using light microscopy. By contrast, electrons traveling as waves have wavelengths between 0.01 nm and 0.001 nm; thus, their resolving power is much greater, and they typically magnify objects 10,000× to 100,000×.

23. There are two general types. Transmission Electron Microscopes Scanning Electron Microscopes

24. Transmission Electron Microscopes (TEM) A TEM generates a beam of electrons that passes through a thinly sliced, dehydrated specimen, through magnetic fields that manipulate and focus the beam, and then onto a fluorescent screen that changes the electrons’ energy into visible light.

25. Scanning Electron Microscopes (SEM) In SEM, the surface of the specimen is first coated with a metal such as platinum or gold. The SEM then focuses the beam of electrons back and forth across the surface of the coated specimen, scanning it rather than penetrating it. Electrons scattered off the surface of the specimen pass through a detector and a photomultiplier, producing a signal that is displayed on a monitor.

26. TEM? Or SEM?

28. Probe Microscopy Probe microscopes use miniscule electronic probes to magnify specimens more than 100,000,000×. There are two types. Scanning tunneling microscopes – pass a pointed metallic probe across and above the surface of a specimen and measure the amount of electron flow. – They can reveal details on a specimen surface at theatomic level. Atomic force microscopes – traverse the tip of the probe lightly on the surface of the specimen. – Deflection of a laser beam aimed at the probe’s tip measures vertical movements that are translated by computer to reveal the specimen’s atomic topography.

32. Staining Both light and electron microscopy use staining—the coloring of specimens with dyes—to increase contrast.

33. Preparing Specimens for Staining Preparing specimens for staining involves making a thin film of organisms—or smear— of the specimen on a slide, and then either passing the slide through a flame (heat fixation) or applying a chemical (chemical fixation) to attach the specimen firmly to the slide.

34. (animation)

35. Q1 In detail, describe the procedure in preparing a specimen for staining. Why must a smear be fixed to the slaid?

36. Principles of Staining The colored portion of a dye, known as the chromophore, typically binds to chemicals via covalent, ionic, or hydrogen bonds. Anionic chromophores called acidic dyes cationic chromophores known as basic dyes used to stain different portions of an organism to aid viewing and identification.

37. Simple Stains Simple stains are composed of a single basic dye such as crystal violet and involve no more than soaking the smear in the dye and rinsing.

38. Differential Stains Differential stains use more than one dye so that different cells, chemicals, or structures can be distinguished. The Gram stain differentiates between purple-staining Gram- positive cells and pink-staining Gram-negative cells. The procedure has four steps: 1. Flood the smear with the primary stain, crystal violet, and rinse. 2. Flood the smear with the mordant, iodine, and rinse. 3. Flood the smear with the decolorizing agent, a solution of ethanol and acetone, and rinse. 4. Flood the smear with the counterstain, safranin, and rinse.

40. Q2 In a Gram stain, one step could be omitted and still allow differentiation between gram- positive and gram-negative cells. What is that one step?

41. The acid-fast stain is used to differentiate cells with waxy cell walls, such as cells of Mycobacterium and Nocardia.

42. 1)Cover the smear with a small piece of tissue paper to retain the dye during the procedure. 2)Flood the slide with the red primary stain, carbol­fuchsin, for several minutes while warming it over steaming water. In this procedure, heat is used to drive the stain through the waxy wall and into the cell, where it remains trapped. 3)Remove the tissue paper, cool the slide, and then decolorize the smear by rinsing it with a solution of hydrochloric acid (pH < 1.0) and alcohol. The bleaching action of acid-alcohol removes color from both non­acid-fast cells and the background. Acid-fast cells retain their red color because the acid cannot penetrate the waxy wall. The name of the procedure is derived from this step; that is, the cells are colorfast in acid. 4)Counterstain with methylene blue, which stains only bleached, non-acid-fast cells.

43. Endospores cannot be stained by normal techniques because their walls are practically impermeable to all chemicals.

44. The Schaeffer-Fulton endospore stain uses heat to drive the primary stain, malachite green, into the endospore.

45. Special Stains Acidic dyes are repulsed by the negative charges on the surface of cells and therefore do not stain them. Flagellar stains bind to flagella, increase their diameter, and change their color, all of which increases contrast and makes them visible.

47. Such dyes that stain the background and leave the cells colorless are called negative (or capsule) stains.

48. Stains for Electron Microscopy Stains used for TEM are chemicals containing atoms of heavy metals such as lead which absorb electrons.

49. Q 2 Explain how stains used for electron microscopy differ from those used for light microscopy.

50. Classification and Identification of Microorganisms Scientists sort organisms on the basis of mutual similarities into non overlapping groups called taxa. Taxonomy is the science of classification.

51. Linnaeus, Whittaker, and Taxonomic Categories Carolus Linnaeus invented a system of taxonomy, grouping similar interbreeding organisms into species, species into genera, genera into families, families into orders, orders into classes, classes into phyla, and phyla into kingdoms. Domain (newly proposed)

52. He gave each species a descriptive name consisting of a genus name and specific epithet. This practice of naming organisms with two names is called binomial nomenclature. Today, taxonomists place less emphasis on comparisons of physical and chemical traits, and greater emphasis on comparisons of their genetic materials.

53. Scientist in taxonomy 1.Carolus Linnaeus (1758) 2.Robert Whittaker (1920-1980) - Proposed the 5 kingdoms [Animalia, Plantae, Fungi, Protista, Prokaryotae (Monera)] 3. Carl Woese (1928) - Proposed domain.

54. Domains Carl Woese proposed the existence of three taxonomic domains based on three cell types revealed by rRNA sequencing: Eukarya, Bacteria, and Archaea. Cells of the three domains differ in many other characteristics, including their cell membrane lipids, transfer RNA (tRNA) molecules, and sensitivity to antibiotics.

55. Taxonomic and Identifying Characteristics Taxonomists use one or more of five procedures to identify and classify microorganisms: 1.Many physical characteristics are used to identify microorganisms. -For example, scientists can usually identify protozoa, fungi, algae, and parasitic worms based solely on their morphology. -The appearance of bacterial colonies also gives clues to help identify microorganisms. 2. Microbiologists also use biochemical tests, noting a particular microbe’s ability to utilize or produce certain chemicals.

56. 3. Serological tests using antiserum (serum containing antibodies) can determine whether a microorganism produces an antigen-antibody reaction in the laboratory. – In an agglutination test, antiserum is mixed with a sample that may be antigenic: clumping of antigen with antibodies (agglutination) indicates the presence of the target cells. 4. Bacteriophages (or simply phages) are viruses that infect and usually destroy bacterial cells. – Whenever a specific phage is able to infect and kill bacteria, the resulting lack of bacterial growth produces within the bacterial lawn a clear area called a plaque. – Phage typing may thus reveal that one bacterial strain is susceptible to a particular phage, whereas another is not, and allow scientists to distinguish between them.

57. 5. Scientists also analyze a specimen’s nucleic acids. Taxonomic Keys Microbiologists use dichotomous keys, which involve stepwise choices between paired characteristics, to assist in identifying microorganisms. The information are contain in Bergey’s Manual of Systematic Bacteriology. (animation)

59. Isolation of Microorganisms Objectives -To separate the wanted microorganism in a specimen from the normal microbiota. -To separate microorganism in pure cultures.

60. Streak Plates -The use of an inoculating loop to spread an inoculum across the surface of a solid medium in Petri dishes. -Streak in a pattern that gradually dilutes the sample that CFUs are isolated from one another. -Various types of organisms present are distinguished from one another by differences in colonial characteristics. Pour plates -The CFUs are separated from one another using series of dilution.