Bacteriology 102:
Instructions for Teaching Personnel

These expectations and helpful hints have been written to assist you in your instruction
of the laboratory and to prevent some problems which may arise in the lab.

FOR THE PRIMARY LAB INSTRUCTOR OF THE SECTION:

Lectures: You will be giving the bulk of the lab lectures for your section. The 102 coordinator (who is sometimes the primary lab instructor of one or more sections – such as when a graduate student is not available) will probably "butt in" from time to time to do a lecture on his specific areas of expertise (especially for Exps. 7, 11.1 and 14) and may also do the first several lab lectures in the semester. Although the "poop sheets" provided by the 102 coordinator outline the minimal material to cover, you are free to rearrange and add to the material as you see fit, within the confines of a lab lecture of reasonable length. Here are some things to consider in your lab lectures:

• Be sure to have read the manual ahead of time! Know what is in it. (Perhaps this page can help.) If there is any confusion over the material, or if a better way of doing things can be done (aseptic technique, streak plating, microscope technique, etc.), please do not hesitate to check it out with the lab coordinator.
  
  
• Feel free to use the blackboard. The 102 coordinator will usually fill the far left 15-20% of the board with the list of media and cultures (with their color codes) for the various experiments being done (usually indicated with their period and page numbers). To eliminate possible confusion by the students, please do not replicate any of that material. Nor should any steps already given in the manual be repeated on the board or unnecessarily on handouts. If an outline of "things to do" can be inferred from what the coordinator has written, then duplicating it would be unnecessary.
  
  
• Refrain from a line-by-line explanation of the protocol. A good overview of theory and techniques is much better. Blackboard material and/or supplementary handouts which clearly outline the concepts are a good idea. If you come up with a good handout, why not make it available to all sections. Any good display material which is relevant to the lab material is always welcomed and should be made available for all sections to observe.
  
  
• If the students are setting up an experiment to learn something directly from its outcome, do not give away the expected result! This spoils the fun and reduces the experiment to a mere demonstration.
  
  
• If you speak softly, you may need to use the microphone. Practice with it before you use it, so that you can eliminate any problems which may arise. For example, if worn the wrong way, there will be occasional "feedback" from the speakers. For optimum performance, the microphone should be kept vertical (not tilted at all) and positioned directly underneath the chin.
  

Quizzes: You will also be preparing the quizzes for your section, although the lab coordinator will probably take the lead on at least the first one. Make them as organized and reader-friendly as possible. No trivia! The coordinator has sample quizzes from previous semesters. Urge the students to go over the study material in the back of the manual, including the terms and old quiz questions in Appendices W and X which are arranged according to experiment. Answers to the questions in Appendix X are posted here.

Final Exam: The final exam is the responsibility of the 102 coordinator who appreciates any and all input! We recommend that students include the old exam given in Appendix Z in their review of material; answers for this exam are posted here.

FOR THE ASSISTANTS:

Your major duties are to assist in teaching the students during the laboratory period. This includes helping the students to become adept at using the microscope, to acquire the proper aseptic techniques, to become comfortable with "dilution theory" and to understand other basic concepts as they come up. Please note that you are to assist in the learning process, not to do the work for the student. In order to accomplish these things most effectively, it is important that you be available for questions and, on occasion, initiate the exchange yourself – e.g.: "What are you seeing?" "What does this mean?"

You are encouraged (but not required nor expected) to prepare and deliver an introductory lab lecture on an occasional basis. For assistance, see the laboratory instructor and/or 102 coordinator.

You are expected to help in the grading of quizzes and the final examination. Other grading opportunities may come up on occasion. Also, please be available to help proctor quizzes and the final exam. If you are not familiar with the material in the lab, it is highly recommended that you ask questions of the lab instructor or 102 coordinator ahead of time.

Any substantial commitment to assisting students outside of the lab is probably tutoring. If you wish to tutor a student for free, that is up to you, but it is certainly not expected. Paid tutors may earn a fair amount per hour, depending on the expertise of the tutor. You are free to make arrangements with individual students who request such a service from you.

A few assistants in the past got into the practice of sitting on the stage during the lab lecture. Please do not do this, as it is distracting and not at all helpful to the instructor or students. (Besides, you'll accumulate a lot of chalk dust!)

FOR ALL LAB TEACHING PERSONNEL – HOW WE APPROACH CERTAIN SUBJECTS:

1. DILUTION THEORY: Here is where we sometimes have major difficulty with what is really supposed to be a simple concept.
   
   
   • We will have a very brief introduction to dilution theory along with the third period of Exp. 1. No formulas will be given, as the student should be expected to understand analogies like this:
     

     "If 200 colonies were counted on a plate which had been inoculated with 1 ml of a 1/100 dilution of lake water, then there would have been 20,000 (from 200X100) colony-forming units per ml of the undiluted sample of water."

     By now the concept of the colony-forming unit (the cell or cells that are inoculated onto the plate which eventually – during incubation – result in a colony of millions of cells, visible to the naked eye) should be fairly clear. The terms colony-forming unit and colony are never to be used interchangeably. This is explained in the introduction to Exp. 1 and also here. Going along with this is the first dilution theory page on the web. When you get to the result, do not say this is the number of anything without saying per ml or per gram! We're most interested in the concentration of organisms in the sample (number per unit volume), rarely the total number.

   • We will go over dilution theory in more detail – with Appendix C – at the time of Experiment 4. At this time we will indicate some practice problems: Example 2 on page 122 and problems 1-8 in Appendix Y on pages 168-169. (Other problems in Appendix Y are associated with later experiments.) The formulas in Appendix C are meant to work successfully with all dilution-plating situations. Clarification is given on the second dilution theory page. Solutions to all problems in Appendix Y are given here.
     

     If you have a different way of approaching dilution theory which you feel is more clear and efficient, see the coordinator about its use as an alternative method. However, keep in mind that the "Appendix C method" permeates the entire manual and the posted answer keys. We have had unfortunate logical disasters with some alternate methods, and it is unfair to the students should they encounter inconsistencies and when we have to re-explain ourselves!

     
     
   • We will introduce the most-probable number (MPN) method of estimating microbial numbers along with Experiment 15. The third dilution theory page does a better job explaining it than what is in the manual!
     
     
   • As for preparing the two sets of take-home dilution problems (the first given about 1/3 the way through the semester, the other given about the time we do Exp. 15), these are the primary responsibility of the 102 coordinator, but input is greatly appreciated!
     
     
2. OXYGEN RELATIONSHIPS AND CATABOLIC PROCESSES: Here is another concept that can get confusing if not approached properly. Oxygen relationships – usually associated with labels such as strict aerobe, facultative anaerobe, etc. – are actually made too much of a big deal in many courses and references. It is more important to realize how organisms can be characterized by their catabolic capabilities – such as whether an organism can obtain energy by one or more of these ways:
   
   
   • aerobic respiration
     
   • anaerobic respiration
     
   • fermentation
     
   • anoxygenic phototrophy
     
   • oxygenic phototrophy
     

   Note how we reduce catabolism to its basic essentials here, and what the concept of "oxygen relationships" is all about here. On our page of so-called thought questions, we have a matching set which students should do well on once we consider the anoxygenic phototrophs (Exp. 11.1). Overall, we follow this general sequence:

   • In Exp. 5.1, we test O₂ relationships with Thioglycollate Medium where anaerobic growth, if it occurs, is only due to fermentation – not to anaerobic respiration or any form of phototrophy. The main value of O₂ relationships in Exp. 5.1 is to show how the labels (strict aerobe, etc.) can be handy when discussing and comparing the common chemoheterotrophs and how we can tell from the labels (and associated reactions like the catalase test) whether an organism has the ability to respire (aerobically) or ferment or do both. We base our definitions of O₂ relationships on those of Bergey's Manual which, by the way, only apply to chemotrophs as explained here. (Note Bergey's definition of "strict anaerobe.") Do not introduce spurious terms like "facultative aerobe" or use the term "facultative" by itself, as it has to describe something and never automatically means "facultative anaerobe"!
     
     
   • In Exp. 7.1 we introduce the concept of anaerobic respiration and how organisms defined as "strict aerobes" can grow anaerobically if they are able to use an "oxygen substitute" (like nitrate) as a terminal electron acceptor.
     
     
   • In Exp. 11.1 we introduce the concept of phototrophy and how the anaerogenic (non-oxygen-producing) photosynthetic bacteria have the ability to grow anaerobically if light is present. With a suitable medium, we will be able to tell if any of our isolates are "facultative phototrophs" or "strict phototrophs."
     
     
3. DIFFERENTIAL MEDIA: Perhaps more than any other of our lab courses we get into the workings of differential media – especially those media that have a variety of substrates from which acidic and alkaline reactions can be generated. The net pH that results can help in identifying organisms, and we find that the enteric bacteria (Exp. 14) make good models for a wide variety of reactions. Of course there are differential media that do not depend on pH reactions, such as Thioglycollate Medium and Motility Medium. See our differential media site. General concepts of bacterial nutrition are covered in Appendix D of the manual which is reproduced and expanded here. In keeping with new methods to identify bacteria, we will touch on 16S ribosomal gene analysis and the construction of phylogenetic trees. A web page which goes along with this discussion is here.
   
   
4. ENRICHMENT AND ISOLATION OF BACTERIA: How we approach this is explained in the opening paragraphs of Experiment 11, and another essay on the subject is given here. When we are trying to isolate a certain type of organism from a natural sample, we learn why we do not want to reproduce the habitat of that organism in the laboratory and also how we can utilize the appropriate selective media and conditions to reduce interference from other organisms.
   

OTHER ITEMS FOR ALL LAB TEACHING PERSONNEL:

If you took Bact. 102 any time through the mid-90's, be advised that the course may be similar to "way back then," but organization and content have been greatly improved in recent years by the coordinated efforts of the lab teaching personnel. Also be advised that no lab course can be judged by looking only at the lab manual. Although the department instituted a separate beginning lab course for majors (Bact. 304) with a number of relatively advanced topics being included, we can keep improving Bact. 102 in providing the students not only with a substantial, valuable UW-quality course but an interesting one as well. It is very highly thought of by bacteriology instructors elsewhere (we get e-mail from around the world concerning the 102 website), and we have good communication with a number of area high schools.

If you taught and/or took a different introductory lab course than Bact. 102, do not expect that the same way of doing things will be appropriate. Also, know what is available on our website! Always encourage the students to make full use of the resources available. Many times things are explained better on one of 102's web pages than in the manual!

You are expected to remind the students of any safety hazards and to teach them proper microbiological technique. If you are working with a potential pathogen, be sure the students are informed and have been instructed in the proper handling of the organism. Please note the procedures as they are explained in Appendix B of the manual. As we work in a lab (and building) which is far from clean (using strict microbiological standards), don't encourage the use of methods that cause plates to be openly exposed for extended periods. So, when it comes to streaking a plate, the plate should be on the table with its lid opened just enough to allow entry of the loop.

We have a number of efficient methods for the use of the regular microscopes (for which the coarse adjustment is not used for routine focusing), phase-contrast microscopes (which are usually "ready-to-use" with no need to make adjustments), reading motility medium (always held against a distant, dark background), observing colonies on petri dishes (always from the top, rather than through the bottom of the plate), and a number of other things. (For the phase scopes, please don't change lenses or pull out the "phasing unit" unless you're right there to change it back afterwards.) Let's strive to be consistent among ourselves and (hopefully) with the manual.

Always strive for credibility. Be careful with your spelling and pronunciation. It is often more difficult to un-teach the wrong way than to teach the right way from the get-go. Always use the proper terminology, even in informal conversation! There is a good discussion of singular vs. plural forms of terms on page 150 in the manual (reproduced here) which we will point out to the students at the appropriate time. Use of media and bacteria as singular words is unacceptable in the outside world of microbiology and should be here as well, as such usage may show that the speaker is not really comfortable with his/her subject matter! Don't get stung by students who ask why the instructor thinks it is OK to say "media is" when the manual sternly prohibits such mis-usage. The students will not be asking where we might "draw the line" when we are consistent in correct usage of terms.

If you do not know the answer to a question, be honest about your lack of knowledge and either ask someone more knowledgeable or look up the answer in a text or other reference material. It is far more damaging to give a wrong answer than no answer at all. However, do not let this prevent you from speculating on those questions for which an answer is not yet known. (Be sure the student knows that you are speculating!)

Please do not encourage students to come in early (before the "lab open" times or during off-hours, unless you (yourself) are in the lab to supervise and take care of all questions or problems during those times! Before labs, the 102 coordinator is generally busy getting the lab set up (cultures dispensed, etc.) and often wishes he had gotten out of bed for this and other required job activities a couple hours earlier.

It should be noted that whenever we post answers and solutions to practice questions and problems, we expect that the students would have worked them out for themselves on their own. The only purpose in posting answers is for the students to check themselves.

Condescension and derision inhibit the learning process. Do not make the student feel stupid for asking a question. If the answer is readily given in the lab manual, handout or blackboard material, point that out to the student so they will look before asking next time. Be careful of inadvertent wording which could alienate. Harassing language (sexual, racial, ethnic, political, etc.) does not belong in any academic situation, nor does foul language or chronic negativity.

Be sensitive to the pressures students are under. If a student appears distressed, drop what you are otherwise doing at the time and suggest help. If the difficulty is with study skills or exam-taking, the office of the Dean of Students should be consulted by the student. Information is available from this office on free short courses which assist with various problems. If the difficulty is severe, advise the student of the assistance available on campus to help with problems (see following pages). If the student is in crisis, the Dean of Students office is available immediately any time during the day, or call the Crisis Intervention Line (251-2345), the University police (262-2957), or the Madison police (257-4888). You will find trained professionals at each of these places.

Grading quizzes and exams: Grade consistently, accurately and informatively. One of the most-often complaints from students is not mistakes in grading but inconsistency from one student's paper to the next. They DO compare! If you do not know if the answer is correct, look it up. Be aware that students have taken many other courses and have many different experiences. It is possible they will give a reasonable answer to a question, even if it is not the answer you taught them in class. Make the quiz or exam a learning experience for the student. This definitely takes more time, but it is better for the student. Also, correct misconceptions! For example, if the student puts down that Azotobacter can grow in a nitrogen-free medium because it doesn't require nitrogen, remind the student that all cells require nitrogen, but Azotobacter cells can obtain theirs from the fixation of N₂ from the air if nitrogen is not part of the medium formulation.

Grades: The 1974 Student Privacy Law prohibits access to student records without the express consent of the individual student. To comply with this, it is important to return quizzes, exams, etc. in such a manner as to prevent students from seeing the grades of any other student. Also, grades can be posted only if the identity of the student is disguised, such as by student ID number. We have stopped the practice of posting final grades, as the student can access his/her grade with a Touch-Tone telephone.

Academic dishonesty: The University has set policy for the handling of academic misconduct. This policy insures rights to the students and legal protection to the instructors. Many measures can be taken to discourage dishonesty, such as proper proctoring (wandering eyes are extremely easy to spot), protective grading (e.g., marking where answers are not given, so correct answers cannot be written in after the exams are returned), peer pressure, etc. Unfortunately, this is sometimes not enough. If you suspect academic dishonesty, seek assistance from the lab instructor who has a file of proper procedures to follow.

Accidents: Any accidents in the laboratory should be reported to the department office. You should make the students aware, however, that the University does not have a blanket insurance policy for accidents. It is assumed that each student has the means or insurance to pay for any medical care arising from injury in the laboratory. The only recourse they have for University payment (or payment from you, personally) is by civil suit in which they must show negligence by the employee in charge. This underscores the need for good safety training and safety procedures in the lab. The lab instructor will always endeavor the point out possible hazards and the best ways to proceed safely.