BIOL 4724/4720L - Protistology, Fall, 1999, TR 12-3:20

• Office: SCEN 528/529
• Phone: (501) 575-6343 (Please, no phone calls at home except in a mjor emergency
• Fax: (501) 575-4010
• email: fspiegel@comp.uark.edu
• Web: http://comp.uark.edu/~fspiegel/
• Office Hours: TR 8:00-9:30 and by appointment. Don't look for me on MWF mornings.

• Sign in with your name, date, and time started
• Turn on light at power source all the way up (at least for photos)
• Place slide on stage
• Adjust oculars to your interpupilary distance
• Set objectives to 10x or 4x and scan for specimen (joy stick hangs down from the stage on the right)
• When specimen is found, focus on it with focus controls
• When specimen is in focus, close field aperature (lever "F" at light source)
• Focus aperature blades by moving condensor up and down (knobs on either side of condensor). This will give you Koehler Illumination which you need for good viewing. Do this with every objective for best viewing
• For bright field microscopy, set the condensor to "O" for every objective. You can control contrast by opening and closing the condensor aperture (lever on the left side of the condensor)
• For Differential Interference Contrast microscopy (aka DIC or Nomarski) use the 10x, 20x, or 40xDIC objectives. Open the condensor aperture all the way. Make sure you are at Koehler Illumination. Push in polarizer (little bar below objectives), and turn prism wheel above it from "OUT" to "IN". Rotate condensor to "10", "20", or "40" to match the power of the objective you are using. You may then adjust the shadowing effect by turning the little knob in the middle of the prism wheel back and forth. If you want color in the background, move the lambda plate from "OUT" to "IN". (lever on right side of condensor) The yellow to magenta background photographs best on this system.
• For Phase Contrast microscopy, use the 40x PH objective. Make sure the condensor aperture is all the way open, the lambda plate is "OUT", the prism wheel is "OUT", and the polarizer is pulled out. Turn the condensor to PH2 and you should have phase contrast. If not, contact me (not at home; it can wait).
• To take a photograph (this can be done in any mode):
  • Pull the wind lever of the camera out til it clicks (ca. 5mm).
  • Pull out the "BI/Photo" bar on the right side of the scope. (Leave the CINE bar pushed in!) Your specimen will look darker because 90% of the light is going to the camera.
  • Focus each ocular so that the circle in the middle of the photo reticule is clearly visible as two fine concentric lines. This means you are focused on the focal plane the camera "sees". (If you see no photo reticule, carefully pull the bar just above the right hand focus knobs all the way out.)
  • Focus and frame your specimen within the corners marked at the outside edge of the photo reticule.
  • Make sure the camera is wound, then release the shutter with the shutter cord attached to the camera. Make sure your specimen is still and you don't touch the scope or desk during the exposure.
  • Make sure you are looking through the oculars during the photo.
  • Make sure the film canister cap is covering the eyepiece of the camera.
  • After the exposure record you picture on your film log.
  • When you are done taking photos, turn off the camera by pushing the wind lever flush with the back of the camera. (If you leave the camera on you must buy 2 new MS76 batteries to replace the ones you wore out.) Push in the BI/Photo bar as well.
  • If the shutter does not work right:
    • check to see that the BI/Photo bar is pulled out. If not, pull it out and the shutter will fire on a shot that will be a dud.
    • check to see that the battery is live. Push down the little lever on the back of the camera to the left of the eyepiece. If the red light does not come on the battery is dead. Find me to replace it.
    • check to see the shutter speed dial is on "AUTO". If not twist it to line up the AUTO setting with the index mark to the left of the dial
    • If nothing works, stop and get me to check it out.
  • To load and unload film (use only 36 exposure rolls of ASA/ISO 100 film):
    • Make sure the last shot has been taken. Counter on upper right of camera should be on 36
    • Push in the rewind button on the bottom left of the camera, and rewind the film by unfolding the rewind knob on the top left of the camera clockwise until 4 turns after you feel no resistance
    • open the camera (takes 2 hands) by pulling the lever at 10 o'clock on the rewind knob toward you, and simultaneously pulling the rewind knob straight up. The back of the camera will pop open.
    • Remove old roll of film and put in new one, raised end down. Push the rewind knob all the way down. Pull the film leader across and insert into slot on take-up spool. Wind camera and fire shutter once or twice to make sure the film is being advanced.
    • Close camera back and advance film to "1" on the counter. Watch to see that rewind knob turns when you advance the film. Remember, you have to fire the shutter to advance the film, so make sure light is getting to the camera from the specimen.
• When you are done:
  • Turn off the light at the power source
  • Make sure the wind lever on the camera is pushed in (or you buy batteries)
  • Make sure the BI/Photo bar is in
  • Make sure the scope is set up for bright field (condensor at "O", prism wheel turned to "OUT", polarizer pulled out)
  • Remove your slide(s) and clean up the area

Grading: I expect you to work hard and learn a lot of material on protists. If you show me you have learned a lot, you should earn an A. I will have you do a number of presentations on various topics throughout the semester. You will have to write a term paper, and you will have to keep a laboratory notebook. There will be no exams. You will contract with me to determine what percentage of your grade will be determined by which exercises. No exercise may be worth less than 10% of your grade. Default values are: presentations 1/3, paper 1/3, notebook 1/3.

Tentative Topic Outline:

WEEK OF	TOPIC
1 (8/24)	Introduction to Eukaryote Diversity and Structure
2 (8/31)	History of Thought on Eukaryote Classification
3 (9/7)	Tree of Life Approach to Eukaryotes
4 (9/14)	First Talks - Origins of Mitochondria and Plastids
5 (9/21)	The Amitochondriate, Basal Eukaryotes
6 (9/28)	The Euglenoids, s.l, and the Heterolobosea
7 (10/5)	The Crown Eukaryotes, Stramenopiles (Paper topic - 10/7)
8 (10/12)	Stramenopiles
9 (10/19)	Spiegel out of town
10 (10/26)	Alveolates (Paper outline and list of references - 10/28)
11 (11/2)	Second Talks - The Biota of...
12 (11/9)	Alveolates
13 (11/16)	Eumycetozoans (First draft of paper - 11/18)
14 (11/23)	Cryptomonads and Choanoflagellates
15 (11/30)	Red Algae
16 (12/7)	Green Algae (Final draft of paper and lab notebook - 12/7)
FINAL TALKS	The Amoeboid Protists, Their Phylogenetic Positions Saturday, 11 December, 10:00-12:00 and 3:00-5:00

• A. The lab room (SCEN 503) is very cramped, therefore, please:
  • 1. Do not bring lots of extra stuff and pile it on the tables.
  • 2. Hang up your coats and backpacks.
  • 3. Carefully bring out your microscopes at the beginning of the lab period.
• B. You may bring food and drinks to lab if you do not create a mess.
• C. Microscopes are important tools in lab; please:
  • 1. Use the same scope each lab period. Take it from and return it to the same slot every lab. Sign up for your scope.
  • 2. You should put your scope away on low power (4x), with the light rheostat turned all the way down, with the cord wrapped around the base, with the head locked, and with the arm facing out. There should be no slides left on the stage. The scope should be in that configuration when you take it out. If not, report this.
  • 3. Clean lenses only with lens paper, NEVER with paper towels or Kimwipes.
  • 4. Clean and COMPLETELY dry your slides and coverslips. Do not use lens paper on slides and cover slips.
  • 5. Avoid getting liquids on the stage or lenses of the microscope. If you do, clean them up immediately. Do not use a slide with liquids on top of the cover slip.
  • 6. When observing material on open petri dishes, remove the stage clip.
  • 7. When observing material without coverslips, take care not to touch the objective to the specimen.
  • 8. If you make a mess with your scope, report it to one of us immediately so we can fix it. There will be no penalty if you report a mess quickly. If you make a mess, and hide it, it will cost you two letter grades on you lab grade.
  • 9. Put prepared slides back where you got them in good condition. Immediately report any damage to a prepared slide.
• D. Sometimes you will have the perfect example of some specimen. Be prepared to share it with the whole class. Help each other out in lab, but:
  • 1. Do not allow a classmate to copy your work into her/his notebook unless s/he cites you.
  • 2. Do not copy someone else's work into your notebook without citing it. This includes drawings put on the board.
  • 3. Anyone who turns in a notebook for grade at the end of the semester with uncited copies will fail the course.
• E. The lab will be available all day all week since we are the only class in here. Feel free to come in to work during those times. We can also work out ways for you to stay after lab if you wish. There will be a slide projector to review slides of the organisms we have covered. If you wish to review projected slides:
  • 1. Arrange to be shown how to use the projector.
  • 2. Do not project any slide for more than 2 minutes at a time,
  • 3. NEVER remove a slide from a carousel.
• F. If you miss a lab that uses live material, arrange to make it up as soon as possible. We may not be able to find good live material after too long a delay.
• G. Your lab notebooks should include the directions for each period's labs and those exercises. Do not mix material up. Do not include class notes in lab notebooks.

Drawings.

• Your lab notebook will consist primarily of drawings of the organisms we encounter throughout the semester. Drawings must be in pencil (3H or colored pencil) or ink on Botany Paper, a 3 hole-punched, heavy, high quality drawing paper. The drawings of organisms must be arranged by major group (I will discuss these with you.). Because we will be looking at most samples by habitat, you must limit your drawings to one organism (genus) per page. You may add to this as you encounter the organism repeatedly. Each page must identify the organism to genus (when possible) and have labels for all the important structures. Each page should include as many habit and detail drawings as is appropriate (see below). The location and habitat from which the organism was collected should be included whenever possible. The drawings of each organism should include at least two references to journal articles that cover that organism or other members of its group (if possible, one of these references should cover the ultrastructure of the organism).
• The Habit Drawing. A habit drawing is a drawing of the whole organism, or a very large portion of the organism. The purpose of such a drawing is to give an idea of what the whole organism looks like and to arrange the drawing in such a manner as to show the important characteristics of the organism. In the habit drawing, you must learn to exercise some editorial control over yourself by learning to recognize that it is not necessary to draw lots of examples of repeated parts. The goal of the habit drawing is to make an accurate representation of the important aspects of the whole organism. Remember, pretty is not as important as accurate.
• The Detail Drawing. Detail drawings, as should seem obvious, are drawings of parts of an organism that are important and need to be highlighted.

Photomicrographs.

• Drawings are probably the best way for you to interpret each of the organisms you will be observing. However, photomicrographs are often quite useful in helping you to see what an organism "really looks like." Photomicrography is a very useful skill for one who is interested in studying small organisms. Therefore, you will turn in 10, 35mm color slides with your lab notebook. The subjects of the slides will be determined in discussion with me. At least one slide will use DIC optics and one will use phase contrast optics. You should plan not to begin your photomicrography before October. You will be given one roll of film. If you need additional rolls, you must purchase them yourself. You will not be cleared for photomicroscopy until you have gone through a training program with me. (If you wish to learn how to shoot and print black and white photomicrographs, discuss this with me.)

Anaerobic flagellates

__s__ One trichomonad - Some people saw a few trichomonads from termites

__x__ One oxymonad - Pyrsonympha and others from termites

__x__ One hypermastigid - Trichonympha and others from termites

Pelobionts

____ One pelobiont

Heterolobosea

__x__ One heterolobosean - Acrasis rosea, amoebae and fruiting body, Vahlkampfia sp. by some

Euglenoids/Kinetoplastids

__x__ One photosynthetic euglenoid - Euglena spp., Phacus spp., Trachelomonas spp.

__x__ One nonphotosynthetic euglenoid - Peranema sp., Entosiphon sp., Anisonema sp., Petalomonas sp., Notosolenus sp.

__x__ One bodonid - Bodo spp., Cephalothamnion sp.

____ One trypanosome (prepared slide if we can find one that's informative)

Eumycetozoans*

__x__ One protostelid including fruiting body

__x__ One dictyostelid including amoeba, aggregation and fruiting

__x__ One myxomycete including plasmodium and fruiting

Alveolates

__x__ One dinoflagellate - Peridinium spp.

____ One sporozoan (prepared slide if we can find one that is informative enough to look at)

Ciliates

__x__ One colpodid

__x__ One hymenostome

__x__ One peritrich

____ One peniculine

__x__ One hypotrich

____ One suctorian

Stramenopiles*

__x__ One unicellular chrysophyte Ochromonas

__x__ One colonial chrysophyte Synura

__x__ One xanthophyte Vaucheria

__x__ One filamentous brown alga Ectocarpus

__x__ One brown seaweed Laminaria, Fucus, Sargassum

__x__ One diatom - Lots, including Navicula spp., Cymbella sp., Surirella sp., etc.

____ One pedinellid

__x__ One oomycete including mycelium, zoosporangia and sex

__s__ One labyrinthulid (maybe)

Prymnesiophytes

____ One prymnesiophyte (maybe)

Cryptomonads

__x__ One colorless cryptomonad

__x__ One photosynthetic cryptomonad

Red algae*

__x__ One floridean red alga several

____ One nonfloridean red alga

Choanoflagellates

__x__ One unicellular choanoflagellate

__s__ One colonial choanoflagellate

Green algae*

__s__ One flagellated unicellular green

__x__ One flagellated colonial green - Eudorina sp., Pandorina sp.

__x__ One nonmotile unicellular green - Desmids, e.g., Closterium sp., Cosmarium sp., Micrasterias sp., Staurastrum sp.

__s__ One nonmotile colonial green - Pediastrum spp.

__x__ One unbranched filamentous chlorophyte - Oedogonium spp.

__s__ One branched filamentous chlorophyte

__s__ One unbranched filamentous charophyte

__x__ One branched filamentous charophyte - Chara sp.

__x__ One ulvophyte Acetabularia

Amoebae, incertae sedis

__x__ One actinophryid

__s__ One centrohelid

__s__ One Acanthamoeba

____ One Amoeba

__x__ One Mayorella

__x__ One testate amoeba

__s__ One foraminiferan (maybe)

__s__ One radiolarian (maybe)

* Groups in which several stages of the life cycle need to be illustrated.

• The phylogeny of some group of protists
• The biogeography of some group of protists
• The developmental biology of some protist or group of protists
• The ecology of some protist or group of protists
• The molecular biology of some protist or group of protists
• The genetics of some protist or group of protists
• The economic impact of some protist or group of protists
• Some aspect of the metabolism of a protist or group of protists
• Origin and distribution of selected organelles
• Origins of multicellularity
• Origin of sex and its distribution among protists
• History of thought on protists
• Protists (the first of all) vs. Protoctists (the first settlers)
• Cladistic treatments of protists or groups of protists
• What is primitive among protists?
• Model protists
• The history of the use of protists as model organisms
• Stengths and weaknesses of the endosymbiotic origin of flagella, plastids, mitochondria, other
• Disease(s) caused by a protist or group of protists
• Protists in human modified environments
• What was the first eukaryote (Eukarya) like?

I. Find the call numbers of the following journals:

• Journal of Eukaryotic Microbiology
• European Journal of Protistolology
• Archiv fur Protistenkunde
• Mycologia
• Mycological Research
• Experimental Mycology
• Journal of Phycology
• Phycologia
• Canadian Journal of Botany
• Canadian Journal of Microbiology
• Canadian Journal of Zoology
• Transactions of the American Microscopical Society
• Protoplasma
• Cell
• Plant Cell
• Journal of Cell Biology
• Developmental Biology
• Journal of Bacteriology
• BioSystems
• Systematic Biology
• Ecology
• Oecologia
• Evolution
• Genetics

  Find at least five other journals that carry papers on protists.

II. Find the range of call numbers for each of the following disciplines (some categories may be spread among several disciplines):

• Protozoology
• Phycology (Algae)
• Mycology (Fungi)
• Microbiology
• Plant Physiology
• Animal Physiology
• Microbial Ecology
• Evolutionary Biology
• Taxonomy/Systematics
• Developmental Biology
• Genetics