BIO112 Principles of Biology II

Spring 2017

Laboratory Guide





Week  Date Laboratory Exercise/Exam
1 Jan. 9, 10 No Labs

Jan. 17, 18

Lab I: Taxonomy and Systematics
3 Jan. 24, 25 Lab 2: Simulations in Evolution & Population Genetics

Jan. 31, Feb. 1

Lab 3: Diversity of the Bacteria and Protists

Feb 7, 8

Lab 4: Diversity of the Fungi


Feb. 14, 15



Feb. 21, 22

Lab 5: Diversity of the Invertebrates I

Feb. 28, March 1

Lab 6: Diversity of the Invertebrates II


March 7, 8

No Labs - Spring Break

March 14, 15

Lab 7: Diversity of the Vertebrates I

March 21, 22

Lab 8: Diversity of the Vertebrates II

March 28, 29


April 4, 5

Lab 9: Diversity of the Plants I

April 11, 12

No Labs - Student Scholarship Day and Holiday
14 April 18, 19 Lab10: Diversity of the Plants II

April 25, 26

Lab11: Ecology
16 May 2, 3 No Labs

Final Exam Week



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Laboratory study and investigation can be both fun and rewarding; however, it can involve a certain amount of risk due to the nature of the equipment (e.g., glassware, hot plates), specimens (e.g., Ascaris, bacteria) and/or chemicals (e.g., formalin, hydrochloric acid, sodium hydroxide) used. In order to minimize the chances of accidents and injury, the following precautions must be followed in all scientific laboratories:

1. NO SMOKING, EATING, or DRINKING at any time.

2. Shoes must be worn at all times (sandals are not shoes).

3. Safety glasses and/or aprons (supplied by the department) will be required for the duration of some labs. You will be notified by the instructor when these must be worn.

4. Know the locations of fire extinguishers, eye-wash stations, fire blankets, safety showers, first aid stations, and containers for broken glass.

5. In case of defective or broken equipment:
-- Do not attempt to unplug frayed electric cords yourself;
-- Do not attempt to clean up any broken glassware yourself;
-- Report all defective equipment to the instructor.

6. Be sure electrical cords (e.g., of microscopes and hot plates) are out of the way of traffic. Tuck them under the desk.

7. Use hot plates with care:
-- Remove beakers from hot plates using a suitable protective device (e.g.,
asbestos glove or tongs);
-- Do not let solutions on hot plates boil dry;
-- Turn off and unplug hot plates after use.

8. Use all chemicals with care:
-- Read labels carefully before you open a bottle;
-- Do not return unused reagents to the bottle;
-- Dispose of waste in proper container;
-- Dispose of biohazardous materials in autoclavable BIOHAZARD BAG;
-- If chemicals get into your eyes or on your skin, FLUSH THE AFFECTED

9. Report major chemical spills to the instructor immediately.
-- Do not attempt to clean up such spills yourself (NOTE: this includes broken
thermometers, which contain toxic mercury).

10. Report IMMEDIATELY all personal injuries to the instructor.

11. Be sure to sign the lab safety sheet and return a signed copy to the lab instructor.

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The microscopes that you will be using for this course are binocular compound scopes.  You may use these at any time, as long as you do not disrupt or interfere with other ongoing laboratory or class sessions.  Demonstration slides will be set up on some of these scopes and should remain on the work tables in the back o f the room.  You should familiarize yourself as soon as possible with how the microscopes work.  Here are a few rules for use and care to keep in mind while you use the scopes:


-     If you have never used a compound binocular microscope before, ask the instructor to demonstrate it before you use it.  Microscope use will be demonstrated at the start of the course, so pay close attention during this demonstration.


-     Always carry the microscope with one hand grasping the neck and the other supporting the base.  Make sure that the cord is securely wrapped around the base.  Never try to support a microscope by the oculars (eyepieces) or the stage.  Never carry a microscope with a slide on the stage.


-     When you are finished with the microscope, put it away where you found it.  Remove the slide, turn off the light, unplug it, wrap the cord around the base, put the cover on, place it gently in its cabinet, and close the door.


-     The microscope has four objectives.  The highest power objective is an oil immersion lens.  This means that it will only be in focus and provide a clear image when there is a droplet of oil between it and the slide.  In general, the only time you will need to use oil immersion will be on some demonstration slides which will be set up for you.  If you feel that you need to use oil immersion on your own with the loan slide collections, consult with the instructor first.  With oil immersion the objective is very close to the slide, so use extreme caution (see next point).


-     When viewing a slide always start at low power.  Start with the microscope focused down as far as possible, insert the slide, and bring the slide into focus by focusing up.  Use the coarse focus knob first, then the fine focus. Never focus down on the coarse focus while looking through the microscope.   The microscope is parfocal (more or less), which means that if the slide is in focus at low power, it will remain approximately in focus as you switch to higher powers.  Use only the fine focus at higher powers.  Use the coarse focus only with the lowest power objective.  The reason for all of these rules will be obvious when you view your first slide.  It is quite possible to run the higher power objectives into the slide, thereby breaking the slide (bad) or scratching the objective (very bad).


-     Lens papers, lens cleaning solution, and KimWipes will be provided at the front desk. Never use any other materials or solutions to clean microscope lenses or slides.


-     Use the stage control knobs for moving the slide.  Don't push directly on the slide or the stage.


-     If you are using a microscope that doesn't seem to work properly, tell the instructor or leave a note on the microscope so that it can be repaired as soon as possible.


-     Handle the loan collection slides with care.  Keep them in their box slots when not in use, not piled on the table, or on your books, or in your pockets.  Handle slides only over the tables, not over the floor.  Make sure that the slide box is latched before you carry it anywhere.  Make sure that the box is right side up before you open it.  If you do break a slide, tell the instructor so that it can be replaced as soon as possible.


The binocular microscope is designed to be looked through binocularly, that is with both eyes.  If the two images don't seem to line up, try adjusting the interocular distance by sliding the two oculars at their base.  The light intensity may be adjusted by turning the rheostat knob.  In general you will want it near the maximal value.  The condenser should be adjusted (by moving it up or down) to maximize the apparent brightness and provide uniform illumination to the field.


The adjustment of the diaphragm will depend on the lighting effect that you want.  A good general purpose setting will be to close the diaphragm just enough to get some dimming at the rim of the field.   If you want greater contrast (at the expense of some resolution), close the diaphragm more.  This will be especially useful when viewing thin, transparent specimens such as blood smears, areolar C.T., etc. or specimens of varying optical density such as bone. If you need maximal resolution and illumination, open the diaphragm fully.  This will be useful for thick, optically uniform specimens.


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Living bones are remarkably sturdy structures.  Dead bones may be surprisingly fragile.  The skeletons we will be using for this class do not have movable joints, so do not try to bend them Bend the joints on the skeleton and disarticulated limbs carefully or not at all.  For obvious reasons, never use pencils, pens, or markers as pointers.  A good rule of thumb for handling the skeletons and disarticulated bones, especially the skull, feet, and hands, is to treat them as if they were irreplaceable.  They are. 


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In this course you may have the opportunity to dissect and handle preserved animals and animal organs.  These guidelines also apply to preserved specimens.


-     Always wear gloves when handling animal tissue.  Avoid touching your face with the gloves.  Always remove and dispose of the gloves, then wash your hands when you are done.


-     If you feel faint, first tell someone, then find a quiet place and sit down.  If you still feel faint, get someone to help you lie down on one of the tables or help you leave the room to get some fresh air.  Don't be shy or embarrassed about admitting that you feel badly and asking for help.  In a similar vein, keep an eye on those around you, and be ready to help them if they appear to need it. 


-     Preserved specimens must not be allowed to dry out.  A single two-hour exposure will ruin most organ preps.  Whenever you are finished examining a specimen, immediately return it to its fluid-filled container, and seal the container.


-     Handle the specimens with extreme care.  Do not pull on structures to see behind them.  Do not directly handle blood vessels or nerves; use the probes to gently lift them or displace them to one side.  Remember that you or someone else put quite a bit of time into dissecting the specimen, that once you damage something it will stay damaged, and that material will be used on the exams whether it is damaged or not..


-     Use only probes or your fingers as pointers.  Point, don't poke.  Never use pens or pencils as pointers.


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