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MICROSCOPY
 THE ACUITY OR SHARPNESS OF THE EYE IS AT A MAXIMUM OF 4 MICR
OMETERS AND IT CANNOT SEE OBJECTS SMALLER THAN THESE.
 TYPICAL SIZE OF A COMMON BACTERIUM IS ABOUT 2 MICROMETERS.
 TO ALLOW ONE TO MAKE VISUAL OBSERVATIONS OF MICROORGANIS
MS, AN INSTRUMENT IS REQUIRED.
 MICROSCOPE
 SIMPLEST MICROSCOPE IS A SINGLE CONVEX LENS – M. G.
 MAGNIFICATION
 RESOLUTION
 RESOLVING POWER
 NUMERICAL APERTURE
 REFRACTIVE INDEX
 OIL IMMERSION LENS
 CONTRAST
Types of microscopes
 Light Microscopy
 The light microscope uses visible light to detect s
mall objects
 The following challenges are often encountered
when using a light microscope
 obtaining sufficient contrast
 finding the focal plane
 obtaining good resolution
 recognizing the specimen when one sees it
 Bright Field Microscopy
 Light from an incandescent source is aimed toward a lens b
eneath the stage called the condenser
 This passes through the specimen, through an objective len
s, and to the eye through a second magnifying lens, the ocu
lar or eyepiece
 Objects are seen in the light path because natural pigmenta
tion or stains absorb light differentially, or because they are
thick enough to absorb a significant amount of light despite
being colorless
 A Paramecium should show up fairly well in a bright field micros
cope
 However, it will not be easy to see cilia or most organelles
 The condenser is used to focus light on the specimen th
rough an opening in the stage
 After passing through the specimen, the light is display
ed to the eye with an apparent field that is much larger
than the area illuminated
 The magnification of the image is simply the objective l
ens magnification times the ocular magnification
 Some condensers are fixed in position, others are focusable, so
that the quality of light can be adjusted
 Usually the best position for a focusable condenser is as close t
o the stage as possible
 The bright field condenser usually contains an aperture diaphra
gm
 This is a device that controls the diameter of the light beam co
ming up through the condenser
 When the diaphragm is stopped down (nearly closed) the light
comes straight up through the center of the condenser lens an
d contrast is high
 When the diaphragm is wide open the im
age is brighter and contrast is low
 A disadvantage of having to rely solely o
n an aperture diaphragm for contrast is t
hat beyond an optimum point the more c
ontrast you produce the more you distort
the image
 With a small, unstained, unpigmented sp
 Brightfield Microscope
Study size, shape & arrangement of microbia
l cells, little information about internal
cell structure.
Tips:
 Molds & large protozoa-10x, 40x
 Bacteria,yeasts,small protozoa-100x oil
immersion objective
 Increase amount of light when using th
e 100x oil immersion objective lens
BRIGHTFIELD MICROSCOPE
 Allows light rays to pass directl
y through the eye without bein
g deflected by intervening opa
que plate in the condenser.
Dark Field Viewing
 Dark-field Microscope (=Ultra-microscope)
 It was invented by Zsigmondy (1905)
 A special condenser lens is used with an opaque disc at the
centre, so that direct rays don’t enter the objective lens
 Only light scattered by the specimen enter the objective len
s to form a bright image against dark background
 Dark field microscope does not have a good resolution
 It is commonly used in microbiology
Darkfield Microscope
 Designed to eliminate the need
for staining to achieve contrast
between the specimen and the
background.
 Condenser lens- focuses light o
n the specimen at an oblique a
ngle.
 Microorganisms appear very br
ight on a dark background
Fluorescence Microscopy
 Allows the detection of molecules and ions within cells
 Fluorescent dyes absorb short wavelengths of light and emit longe
r wavelengths
 Barrier filters and a dichroic prism select the excitation wavelengt
h that strikes the specimen and exclude the excitation wavelength
from the detector
 This allows only emitted light to reach the detector (oculars)
 uses uv light source = mercury or xenon arc lamp.
 - high contrast, high resolution image
 special fluorescent dyes used to locate “mole
cules” in a specimen
 - black background, bright-stained specimen
 - no condenser required, light comes from ab
ove (“epi”) specimen
 - multiple fluorescent probes available
 - detects small quantities, molecules; can use
antibody staining techniques
Fluorescence microscope
 Specimen is illuminated at one wa
velength of light and observed by a
light emittted at a different wavele
ngth
 Fluorexcein isothiocyanate
 Excitation wavelength and emissio
n wavelength
 Excitation filter and barrier filter
Fixed (Preserved) Specimens for Hist
ology--the Study of Tissue
 1) Specimens may be preserved using chemicals suc
h as formalin, acetic acid, ethanol, and methanol
 Fixation immobilizes molecules such as proteins and
lipids
 2) Fixed specimens are dehydrated by serial transfer
through an ascending alcohol series, to 100% alcoho
l
 3) Specimens are infiltrated with melted paraffin, pa
raffin substitute, or plastic and placed in a mold to h
arden
 4) Specimens are cut into 5-10 um thick sect
ions using a steel knife or razor on an instru
ment called a microtome
 5) Sections are then mounted on slides,
 6) Stained to achieve contrast or identify cell
structures or components, and
 7) Viewed microscopically
 Many variations in technique are used to pre
pare specimens for light microscopy
 Some omit the dehydration, infiltration, emb
edding and sectioning steps and use aqueous
staining systems for viewing whole mounts (
unsectioned tissues or cells)
 Freezing may be used instead of chemicals to
fix tissues that need to be examined quickly
or that have components damaged by the ch
emicals
 Examples are frozen biopsies and tissues in
which heat-labile structures are to be stained
 Frozen specimens are sectioned using a cryot
ome, a microtome encased in a freezing cha
mber
 Permanent slides may be made from paraffin
sections but not from frozen sections
Transmission
Electron Microscopes
 TEM makes high-resolution (
± 1 nm) views of the inner si
de of objects. Mostly TEM is
applied on material (e.g. cell
s) that has been previously '
stained' and cut into ultrathi
n sections, but sometimes al
so intact objects < 1 µm, like
viruses and aggregates of m
acromolecules, are visualize
d.
Principle
 Fixed, dehydrated specimens are embedded in a resin, hardened,
sectioned, stained with heavy metals such as uranium and lead, a
nd inserted into the electron column in the microscope
 The electron beam is absorbed or deflected by the heavy metal st
ains and shadows are cast onto film or a phosphorescent plate at
the bottom of the column
 - 2-D image
 - reveals internal cell structure
 - high resolution, high magnification
 - electron beam is focused by magnetic field
TEM images
Scanning Electron Microscope
 In SEM the image primary el
ectrons from the source bo
mbard the sample according
to a scanning pattern and ca
use emission of secondary e
lectrons. In SEM an image of
the surface of the object is
made.
Principle
Fixed, dehydrated specimens are mounted on stubs and surface-coated with
gold, palladium or rhodium
The specimen is placed in a vacuum and an electron beam scans back and fo
rth over it
Electrons that bounce off the metal-coated specimen surface are collected, c
onverted to a digital image and displayed on a TV-like monitor
- Electron beam is focused using a magnetic field - SEM provides a 3-D ima
ge
-Gives information about external topography of specimen
-Much higher resolution and magnification than possible in light microscope
Micrograph
 A. Example of application of Transmission Electron Microscopy (TEM)
Organelles in a pollen grain of tobacco (Nicotiana tabacum; AF = Actin filaments; G
= Golgi apparatus; Mi = Mitochondrion; Mt = Microtubule).
 B. Example of application of Scanning Electron Microscopy (SEM)
Overview of gills of a fish, the mudskipper (Periophthalmus argentilineatus).
Specimen Preparation
Light Microscopy
Live Mounts
To view organisms, tissues, or cells in as close to the natural st
ate as possible, unstained live Viewing time of live mounts is limi
ted
Unstained specimens have low contrast
Supravital stains may be applied to provide more contrast or id
entify certain components--these are stains that are not harmful to
living cells
mounts are used
Fixed (Preserved) Specimens for Hist
ology--the Study of Tissue
 1) Specimens may be preserved using chemicals such as f
ormalin, acetic acid, ethanol, and methanol
 Fixation immobilizes molecules such as proteins and lipid
s
 2) Fixed specimens are dehydrated by serial transfer throu
gh an ascending alcohol series, to 100% alcohol
 3) Specimens are infiltrated with melted paraffin, paraffin
substitute, or plastic and placed in a mold to harden
 4) Specimens are cut into 5-10 um thick sections usi
ng a steel knife or razor on an instrument called a mi
crotome
 5) Sections are then mounted on slides,
 6) Stained to achieve contrast or identify cell structur
es or components, and
 7) Viewed microscopically
Preparing Specimens for Scanning Electron
Microscopy (SEM)
 1) Fixation--fixatives used are glutaraldehyde, paraformaldehy
de, osmium tetroxide
 2) Dehydration is accomplished by carrying the specimens thro
ugh an ascending alcohol series, to 100% alcohol (i.e., no water
), then to an organic solvent such as acetone or propylene oxide
 Specimens for SEM may also be processed in a critical point dr
ying apparatus
 3) Specimens are mounted on aluminum stubs using sticky tape
 4) A sputter coater coats the specimen with gold, pal
ladium or rhodium in a special chamber to cover the sp
ecimen with a 10-20 nm thick metal layer
 5) The stub is inserted into the SEM, scanned and obser
ved on a video display
Preparing Specimens for Transmission El
ectron Microscopy (TEM)
 1) Fixation--specimens are fixed in glutaraldehyde, o
r paraformaldehyde-glutaraldehyde mixtures, followe
d by osmium tetroxide
 2) Dehydration is accomplished by carrying the speci
mens through an ascending alcohol series, to 100%
alcohol (i.e., no water), then to an organic solvent su
ch as acetone or propylene oxide
 3) Specimens are then infiltrated with an epoxy or pl
astic resin and placed in plastic molds to harden
 4) An instrument called an ultramicrotome is used to section the
specimen
 Glass or diamond knives are used to cut the ultrathi
n sections
5) Sections are transferred to tiny metal grids for support (the equivalent of th
e function of the glass slide in LM)
 6) Heavy metal stains such as uranyl acetate and lead citra
te are applied to make certain structures electron dense
 7) Grids are then inserted into the transmission electron m
icroscope and observed

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Lecture 2 MICROSCOPY.pptx

  • 1. MICROSCOPY  THE ACUITY OR SHARPNESS OF THE EYE IS AT A MAXIMUM OF 4 MICR OMETERS AND IT CANNOT SEE OBJECTS SMALLER THAN THESE.  TYPICAL SIZE OF A COMMON BACTERIUM IS ABOUT 2 MICROMETERS.  TO ALLOW ONE TO MAKE VISUAL OBSERVATIONS OF MICROORGANIS MS, AN INSTRUMENT IS REQUIRED.  MICROSCOPE  SIMPLEST MICROSCOPE IS A SINGLE CONVEX LENS – M. G.  MAGNIFICATION  RESOLUTION  RESOLVING POWER  NUMERICAL APERTURE  REFRACTIVE INDEX  OIL IMMERSION LENS  CONTRAST
  • 2. Types of microscopes  Light Microscopy  The light microscope uses visible light to detect s mall objects  The following challenges are often encountered when using a light microscope  obtaining sufficient contrast  finding the focal plane  obtaining good resolution  recognizing the specimen when one sees it
  • 3.  Bright Field Microscopy  Light from an incandescent source is aimed toward a lens b eneath the stage called the condenser  This passes through the specimen, through an objective len s, and to the eye through a second magnifying lens, the ocu lar or eyepiece  Objects are seen in the light path because natural pigmenta tion or stains absorb light differentially, or because they are thick enough to absorb a significant amount of light despite being colorless
  • 4.  A Paramecium should show up fairly well in a bright field micros cope  However, it will not be easy to see cilia or most organelles  The condenser is used to focus light on the specimen th rough an opening in the stage  After passing through the specimen, the light is display ed to the eye with an apparent field that is much larger than the area illuminated  The magnification of the image is simply the objective l ens magnification times the ocular magnification
  • 5.  Some condensers are fixed in position, others are focusable, so that the quality of light can be adjusted  Usually the best position for a focusable condenser is as close t o the stage as possible  The bright field condenser usually contains an aperture diaphra gm  This is a device that controls the diameter of the light beam co ming up through the condenser  When the diaphragm is stopped down (nearly closed) the light comes straight up through the center of the condenser lens an d contrast is high
  • 6.  When the diaphragm is wide open the im age is brighter and contrast is low  A disadvantage of having to rely solely o n an aperture diaphragm for contrast is t hat beyond an optimum point the more c ontrast you produce the more you distort the image  With a small, unstained, unpigmented sp
  • 7.  Brightfield Microscope Study size, shape & arrangement of microbia l cells, little information about internal cell structure. Tips:  Molds & large protozoa-10x, 40x  Bacteria,yeasts,small protozoa-100x oil immersion objective  Increase amount of light when using th e 100x oil immersion objective lens
  • 8. BRIGHTFIELD MICROSCOPE  Allows light rays to pass directl y through the eye without bein g deflected by intervening opa que plate in the condenser.
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  • 10. Dark Field Viewing  Dark-field Microscope (=Ultra-microscope)  It was invented by Zsigmondy (1905)  A special condenser lens is used with an opaque disc at the centre, so that direct rays don’t enter the objective lens  Only light scattered by the specimen enter the objective len s to form a bright image against dark background  Dark field microscope does not have a good resolution  It is commonly used in microbiology
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  • 12. Darkfield Microscope  Designed to eliminate the need for staining to achieve contrast between the specimen and the background.  Condenser lens- focuses light o n the specimen at an oblique a ngle.  Microorganisms appear very br ight on a dark background
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  • 14. Fluorescence Microscopy  Allows the detection of molecules and ions within cells  Fluorescent dyes absorb short wavelengths of light and emit longe r wavelengths  Barrier filters and a dichroic prism select the excitation wavelengt h that strikes the specimen and exclude the excitation wavelength from the detector  This allows only emitted light to reach the detector (oculars)  uses uv light source = mercury or xenon arc lamp.  - high contrast, high resolution image
  • 15.  special fluorescent dyes used to locate “mole cules” in a specimen  - black background, bright-stained specimen  - no condenser required, light comes from ab ove (“epi”) specimen  - multiple fluorescent probes available  - detects small quantities, molecules; can use antibody staining techniques
  • 16. Fluorescence microscope  Specimen is illuminated at one wa velength of light and observed by a light emittted at a different wavele ngth  Fluorexcein isothiocyanate  Excitation wavelength and emissio n wavelength  Excitation filter and barrier filter
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  • 20. Fixed (Preserved) Specimens for Hist ology--the Study of Tissue  1) Specimens may be preserved using chemicals suc h as formalin, acetic acid, ethanol, and methanol  Fixation immobilizes molecules such as proteins and lipids  2) Fixed specimens are dehydrated by serial transfer through an ascending alcohol series, to 100% alcoho l  3) Specimens are infiltrated with melted paraffin, pa raffin substitute, or plastic and placed in a mold to h arden
  • 21.  4) Specimens are cut into 5-10 um thick sect ions using a steel knife or razor on an instru ment called a microtome  5) Sections are then mounted on slides,  6) Stained to achieve contrast or identify cell structures or components, and  7) Viewed microscopically
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  • 23.  Many variations in technique are used to pre pare specimens for light microscopy  Some omit the dehydration, infiltration, emb edding and sectioning steps and use aqueous staining systems for viewing whole mounts ( unsectioned tissues or cells)  Freezing may be used instead of chemicals to fix tissues that need to be examined quickly or that have components damaged by the ch emicals  Examples are frozen biopsies and tissues in which heat-labile structures are to be stained
  • 24.  Frozen specimens are sectioned using a cryot ome, a microtome encased in a freezing cha mber  Permanent slides may be made from paraffin sections but not from frozen sections
  • 25. Transmission Electron Microscopes  TEM makes high-resolution ( ± 1 nm) views of the inner si de of objects. Mostly TEM is applied on material (e.g. cell s) that has been previously ' stained' and cut into ultrathi n sections, but sometimes al so intact objects < 1 µm, like viruses and aggregates of m acromolecules, are visualize d.
  • 26. Principle  Fixed, dehydrated specimens are embedded in a resin, hardened, sectioned, stained with heavy metals such as uranium and lead, a nd inserted into the electron column in the microscope  The electron beam is absorbed or deflected by the heavy metal st ains and shadows are cast onto film or a phosphorescent plate at the bottom of the column  - 2-D image  - reveals internal cell structure  - high resolution, high magnification  - electron beam is focused by magnetic field
  • 28. Scanning Electron Microscope  In SEM the image primary el ectrons from the source bo mbard the sample according to a scanning pattern and ca use emission of secondary e lectrons. In SEM an image of the surface of the object is made.
  • 29. Principle Fixed, dehydrated specimens are mounted on stubs and surface-coated with gold, palladium or rhodium The specimen is placed in a vacuum and an electron beam scans back and fo rth over it Electrons that bounce off the metal-coated specimen surface are collected, c onverted to a digital image and displayed on a TV-like monitor - Electron beam is focused using a magnetic field - SEM provides a 3-D ima ge -Gives information about external topography of specimen -Much higher resolution and magnification than possible in light microscope
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  • 31. Micrograph  A. Example of application of Transmission Electron Microscopy (TEM) Organelles in a pollen grain of tobacco (Nicotiana tabacum; AF = Actin filaments; G = Golgi apparatus; Mi = Mitochondrion; Mt = Microtubule).  B. Example of application of Scanning Electron Microscopy (SEM) Overview of gills of a fish, the mudskipper (Periophthalmus argentilineatus).
  • 32. Specimen Preparation Light Microscopy Live Mounts To view organisms, tissues, or cells in as close to the natural st ate as possible, unstained live Viewing time of live mounts is limi ted Unstained specimens have low contrast Supravital stains may be applied to provide more contrast or id entify certain components--these are stains that are not harmful to living cells mounts are used
  • 33. Fixed (Preserved) Specimens for Hist ology--the Study of Tissue  1) Specimens may be preserved using chemicals such as f ormalin, acetic acid, ethanol, and methanol  Fixation immobilizes molecules such as proteins and lipid s  2) Fixed specimens are dehydrated by serial transfer throu gh an ascending alcohol series, to 100% alcohol  3) Specimens are infiltrated with melted paraffin, paraffin substitute, or plastic and placed in a mold to harden
  • 34.  4) Specimens are cut into 5-10 um thick sections usi ng a steel knife or razor on an instrument called a mi crotome  5) Sections are then mounted on slides,  6) Stained to achieve contrast or identify cell structur es or components, and  7) Viewed microscopically
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  • 36. Preparing Specimens for Scanning Electron Microscopy (SEM)  1) Fixation--fixatives used are glutaraldehyde, paraformaldehy de, osmium tetroxide  2) Dehydration is accomplished by carrying the specimens thro ugh an ascending alcohol series, to 100% alcohol (i.e., no water ), then to an organic solvent such as acetone or propylene oxide  Specimens for SEM may also be processed in a critical point dr ying apparatus  3) Specimens are mounted on aluminum stubs using sticky tape
  • 37.  4) A sputter coater coats the specimen with gold, pal ladium or rhodium in a special chamber to cover the sp ecimen with a 10-20 nm thick metal layer
  • 38.  5) The stub is inserted into the SEM, scanned and obser ved on a video display
  • 39. Preparing Specimens for Transmission El ectron Microscopy (TEM)  1) Fixation--specimens are fixed in glutaraldehyde, o r paraformaldehyde-glutaraldehyde mixtures, followe d by osmium tetroxide  2) Dehydration is accomplished by carrying the speci mens through an ascending alcohol series, to 100% alcohol (i.e., no water), then to an organic solvent su ch as acetone or propylene oxide  3) Specimens are then infiltrated with an epoxy or pl astic resin and placed in plastic molds to harden
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  • 41.  4) An instrument called an ultramicrotome is used to section the specimen
  • 42.  Glass or diamond knives are used to cut the ultrathi n sections
  • 43. 5) Sections are transferred to tiny metal grids for support (the equivalent of th e function of the glass slide in LM)  6) Heavy metal stains such as uranyl acetate and lead citra te are applied to make certain structures electron dense
  • 44.  7) Grids are then inserted into the transmission electron m icroscope and observed