Today

1
Today

• Assignments
• Collect MWA 1, Pre-lab 1
• Exercise 1
• Microscopy
• Care and Maintenance of a Microscope
• Environmental Isolate
• Choose Isolated Colony

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McMillan

• Preface
• Biologists need to think clearly about science
  and creatively about writing
• The point of this book?
• To teach students how to write effectively in the
  sciences

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McMillan

• Introduction
• Misconception 1 Biologists, and other
  scientists, dont write much, and so do not need
  to worry about it.
• Misconception 2 Scientific writing is dry,
  boring, impenetrable.etc.

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McMillan

• The primary aim of scientific writing is to
  communicate as clearly, succinctly, and
  accurately as possible.
• Scientist normally contribute two types of papers
  to scientific journals
• Research paper
• Review Paper

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McMillan

• Research Paper
• Assumptions should be clear
• Methods repeatable
• Interpretations separate from the data/results
• The purpose of a research paper is to present
  findings/conclusions and argue for or against
  other hypotheses.
• These papers are evaluated by peers in the field
  and corrections are suggested.
• It often takes several months for a manuscript to
  be published.

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McMillan

• Review Paper
• Brings together the research of many different
  people on one subject
• No new research is presented
• Summarizes information, provides analysis, often
  includes historical perspective
• Still must be reviewed and conform to journal
  specifications

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McMillan

• Other forms of writing
• Conference presentation presented orally, or in
  poster format at an official meeting of
  scientists. Present unpublished material
  currently in progress.
• Research (Grant) proposal an organized plan for
  future research that is submitted to a committee
  to obtain funds for the research. Include a
  review of the current research in the area, and a
  lengthy description of the methods to be used.

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McMillan

• Relaxed writing
• Not all the writing scientists do is for
  journals.
• Some scientists write article for magazines and
  newspapers that are for a non-scientific audience
• Any biologist that teaches must also write
  lecture notes, presentations, assignments etc.

9
Isolating a Colony

• Choose a partner. You will be working together
  the rest of the semester.
• Inspect plates for growth.
• Record the number and types of colonies.
• Select two colonies, per person, as a team.
• Do NOT open plates until inspected by the TA.

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Isolating a Colony

• Choose a colony that is isolated
• Good Colony
• Bad colony

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Isolating a Colony

• Of the two chosen colonies, notice size, color
  and morphology (Chart in Exercise 2)

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Isolating a Colony

• Get a new agar plate for each colony (4 plates)
• Label plates with
• Name
• Date
• Lab Section
• Exercise (ex. Env. Iso. A1, Env. Iso. B1)
• Draw sections and streak.

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Isolating a Colony
ISOLATION STREAK PATTERN
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Isolating a Colony

• Incubate plates upside down, at room temperature.
  (aka on the shelves )
• Check every 24 hours until growth appears.
• Record number of hours
• Ideally you want 24-48 hours for growth

15
The Microscope
Parts and Maintenance
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Microscope Care and Maintenance

• At the beginning of lab, check that the
  microscope was cleaned and put away properly
• Eyepieces cleaned and pushed together
• Objectives cleaned (particularly 100x) and in
  proper position
• Stage and condenser cleaned and lowered
• Power cord wrapped around hanger
• Dust cover on
• Microscope in proper shelf

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Microscope Care and Maintenance
18
Microscope Care and Maintenance
19
Microscope Care and Maintenance

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Microscope Care and Maintenance
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Microscope Care and Maintenance
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Microscope Care and Maintenance
23
Microscope Care and Maintenance
24
The Microscope

• Before you out you scope away
• Clean stage, body and lens
• Condenser all the way down
• Stage all the way down
• Phase ring set to 0
• Oculars closed
• Stage centered
• Light source to lowest setting
• Power off
• Cord wrapped
• Cover on
• The TA must check your microscope before you can
  leave the lab!

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Microscopy

• The three factors in obtaining an image
• Magnification
• Resolution
• Contrast

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Microscopy

• Magnification The extent to which the image of
  an object is larger than the object itself.
• The total magnification is the product of the
  magnification of the powers of the two lenses.
  The magnification of the objective lens (10x,
  40x, 100x) multiplied by the magnification of the
  eyepiece lens (10x). The total magnification
  depends upon the focal lengths of these lenses
  (100x, 400x, 1000x respectively).

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Microscopy

• 2. Resolution The ability of a microscope to
  reveal fine detail in a specimen.
• Resolving Power depends upon the wavelength of
  light and the property of an objective lens
  called the numerical aperture (NA). The higher
  the numerical aperture of an objective the better
  the resolving power (Pg 1-3 in lab manual)

• Refraction When light passes through a
  transparent material of one density into one of
  another density, the light is bent. The
  refractive index of glass is 1.5 and of air in
  1.0 by definition. Less light is lost if
  something is placed between the lens and the
  glass slide such as water or oil (which has a
  refractive index of 1.0) by this process less
  light is lost and magnification is increased.

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Microscopy

• 3. Contrast The use of elements, such as colors,
  light, forms, or lines, in proximity to produce
  an intensified effect.
• The most important aspect of successful
  microscopy is contrast. No matter how good
  magnification or resolution contrast is the key
  to successful microscopy. To enhance contrast
  you alter the optics of the scope by adjustment
  of the condenser, rheostat, and/or the iris
  diaphragm.

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Microscopy

• To Enhance Contrast Alter Optics by Adjustment
  of
• Condenser . . . knob on the left side of the
  scope underneath the stage
• Rheostat . . . the light adjustment located on
  the right hand side of the body of the scope
• Iris diaphragm . . . lever in front of the
  condenser (alters light intensity when using
  bright-field)
• Phase Contrast Condenser . . . dial with numbers
  on it underneath the stage.

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Microscopy

• Dark-field Used for viewing live, unstained
  material. The specimen appears bright on a dark
  background. For low- or medium-power work.

Diatom
Rotifer
Cyanobacteria Nostoc
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Microscopy

• Phase contrast Microscopy used when a colorless
  specimen, which absorbs little light, (e.g. a
  non-pigmented living cell) is not clearly visible
  by bright-field microscopy

Bacteria
Amoeba
Rotifer
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Microscopy

• Bright-field
• The most common form of light microscopy.
  Extensively used for the visualization of
  microorganisms usually necessary to stain
  specimens for viewing.

Enterococcus
Anthrax spore stain
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Microscopy

• Fluorescence microscopy
• Fluorochrome treated specimens (fluorescent
  stained) are irradiated with ultra-violet
  radiation and the light emitted forms the image
  of the specimen in a manner similar in principal
  to that in bright-field microscopy. The
  fluorescent scope is designed so that the
  specimen can be illuminated at one wavelength of
  light and observed by light emitted at a
  different wavelength.

Yersinnia pestis
Rhizopus rot-Black bread mold
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Microscopy

• Electron microscopy microscopy in which an
  electron beam interacts with a specimen and
  contributes to an image of the object. Electron
  microscopy is used for examining viruses,
  macromolecules, and the ultra structure of cells.
  (electronically colored)

 Vibrio parahaemolyticus
Mixed Bacteria
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Microscopy

• Nomarski differential interference contrast
  microscopy a combination of light waves that are
  out of phase with each other and produces
  interference that alters the amplitude of the
  light waves. It produces high contrast images of
  unstained, transparent specimens in what appear
  to be three dimensions.

Heliozoan Actinomycies
Amoeba Nucleus and Vacuole
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Microscopy Todays Experiment

• We will be using Phase Contrast Microscopy
• You will be viewing a Hay infusion.
• Hay infusion is made from hay that has been
  aerated in pond water for 5 days.
• After viewing the pond water, you will view
  bacteria (Bacillus).
• Remember, you are looking at live organisms!

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Preparing a Slide

• Clean a slide with 70 ethanol.
• Add a small amount of sample. (1-2 drops)
• Place a coverslip at an angle on the slide.
• Gently lower onto sample.

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Viewing a slide

• You are viewing your slides under phase contrast.
• You must change the condenser to phase contrast.
• There is a different setting for each
  magnification!
• Begin with 10x, then 40x, then 100x with NO oil.
• Have the TA check you off before you add oil.
• View under 100x with oil. Have the TA check you
  off again.

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Important Info

• Do not add oil when viewing your slides under 10x
  or 40x.
• You only need a small drop of oil when viewing
  under 100x.
• Only use the fine adjustment knob when viewing
  under 40x and 100x.
• Where do you dispose of slides?

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Next Week

• Assignments
• MWA 2 making graphs
• Pre-lab 2 due
• Exercise 2
• stains
• Environmental Isolate
• Purification continued