Update for 12:45 PM, May 20, 2003

Posters can be picked up in the lab; they are presently on the stage. Everything else (finals with attached key, poster evaluations, leftover graded items – all stapled together) is available in the main office, Room 114 Fred Hall. Average grade on the final was 82.3 out of 100.

My new office is 20A Biochemistry! Same phone no. and email address.

It has been a pretty good semester! Click here.

Update for 9:45 AM, May 16, 2003

Everything except posters (and finals taken so far) has been graded and will be available to pick up at the final this evening. Sorry for the delay in grading things. Remember the final is at 5:05 PM in 125 Biochemistry.

Posters (with evaluation sheet) and finals will be available Monday morning after 9 in the lab; if a different location, there will be a sign on the door.

During the big move (which is still ongoing) I am hard to reach by phone, but I'm always e-mailable!

Update for 8:45 AM, May 13, 2003

Today is my Mom's 91st birthday.

Following is a schedule of what's happening this week. What is not happening soon enough is the grading of reports and posters which I'm hoping (after a few late-nighters) to be done after noon on Friday. On with the schedule of what's definitely going on:

• Tuesday, May 13:
  
  • Early Final at 12:25 in 22 Fred.
    
  • Jessica's Review at 4PM in 22 Fred. (As I live in 22A Fred, I'll be there too.)
    
• Wednesday, May 14:
  
  • In the morning, Room 22 will be avoidable as we make the first of 2 or 3 big moves out of here and into Old Biochemistry.
    
  • Early Final at 12:25 in 104 Russell – just across the street: the building between Steenbock & Linden Drive.
    
• Thursday, May 15:
  
  • Early Final at 10:05 in 22 Fred.
    
  • Early Final at 12:25 in 22 Fred.
    
  • Lisa and Corinnes's Review at 5PM in 104 Fred (on first floor).
    
• Friday, May 16:
  
  • Regular Final at 5:05 PM in 125 Biochemistry.
    

Update for 3:30 PM, May 8, 2003

SPECIAL REVIEW SESSIONS: See above update for special reviews and early exam times.

The key to the second take-home problem set is posted here. Note my mistake in numbering the problems and also indicating point values on the problem set sheet. The actual point values (shown in red on the key) are fairly proportional to what is on the problem set: "3 points" become 2 and "2 points" become one; then it adds up to 10 points total. Hopefully everyone got everything OK anyway.

You can come to any of the early final times even without signing up! The early finals will be given in Fred Hall; the actual place will be indicated on a sign on the door to the lab. Wednesday, May 14 is the big move when the lab (and much of my office) gets moved to Biochemistry. Actual demolition day for Fred Hall comes later this year.

I am hoping to have the reports & posters graded by final exam time. Being so slow in getting this done has become a tradition.

Update for 7:30 PM, April 28, 2003
(April 28 is Ann-Margret Day.)

The correct date and time for the final is Friday, May 16 at 5:05 PM. The place will be 125 Biochemistry. If you need to re-schedule (due to conflicts, too many tests, etc.) we can arrange that individually.

Here are some items to consider in reviewing for the final exam. When we have a review (most likely the last period next week), be sure to bring some good questions!

• As you go through the procedures in the manual experiments, ask yourself "what did I do and why?"
  
  
• Consider the basic concepts explained in the manual (the experiments and Appendices B, C and D) and supplemented by the handouts and your notes from the lab lectures. As an additional supplement: Many of these concepts are summarized here on the web, sometimes in a way that is easier to understand than how they are presented in the manual; note the various items in the menu on the home page including terms and concepts needing further explanation (i.e., items not explained too well in the manual)!
  
  
  • You should have a good understanding of dilution theory (plating and MPN), principles of enrichment and isolation, aseptic technique, and microscopy.
    
    
  • You should have a pretty good understanding of the organisms and media, but do not memorize detail! See expanded comments below.
    
    
  • We also covered other things including staining, CFUs, growth curves, bacteriophages, antibiotics, mutation and recombination.
    
  
  
• As you may look at the various organisms we worked with, do not memorize tables of individual organisms such as what we have used as keys in Experiments 7 and 14. It would be better to have a good understanding of the characteristics of certain groups ("enterics" in general and coliforms more specifically, "lactics", and the "purple non-sulfurs") and recognize that some genera and species had "special features" (Bacillus, Staphylococcus aureus, Mycobacterium, Neisseria, Streptomyces). In general, consider how organisms can be classified according to carbon and energy sources and oxygen relationships (as explained in Appendix D and the introduction to Experiment 5.1).
  
  
• Also, in considering the media we used, do not memorize the specific ingredients of the various media. These recipes are given in Appendix E, but the additional comments made about the media may be more useful. Appendix D includes a general classification of media based on their use, and it is important to know about the use of "selective" and "differential" media. We specified some of these media on occasion and spent a little extra time on differential media formulation, basing some hypothetical media on MacConkey Agar and KIA in some "thought exercises" associated with Experiment 14. Also note that many media we used are simply "all-purpose," not especially formulated to inhibit anything in particular.
  

You are already aware of the "review material" in Appendices W, X and Y. Also, Appendix Z is an old final you can test yourself with. Remember that our on-line keys for the review questions and problems in the manual (Appendices X, Y and Z) are indexed here.

Report and Poster grading sometimes gets delayed. For the exam, the best review questions concerning the enrichment and isolation experiments are those in Appendix X that are indicated for Exps. 10.2 and 11.

Update for 7:30 PM, April 16, 2003

Our Differential Media Site shows some things mentioned as demonstrations in some of the experiments we are doing these days. Note how the differential media in Experiments 14.1 and 15 follow the "general plan" for pH-based differential media summarized on Table I on page 82 in the manual. (The concept is expanded on the web here.) This is the main point: Understand the basics and don't memorize all the intricate details. Once the basics are understood, you can go ahead and have fun with items like Question 14I on page 166.

• EMB Agar (Exp. 15, Period 4): Click here.
  
  
• Pathogenic streptococci on Blood Agar (Exp. 13.1, Period 2): Click here.
  
  
• The appearance of Streptococcus salivarius on Heart Infusion Agar + Sucrose (Exp. 13.1, Period 2): Click here. Note: If another sugar were to be present in place of sucrose, these colonies would look like those typical of lactic acid bacteria – i.e., among the smallest we have seen for bacterial colonies this semester. (What is the probable reason? Also, why must we have a sugar in the medium for lactic acid bacteria anyway? These questions were considered during and prior to Exp. 7.)
  
  
• Enteric plating media (Exp. 14.1, Period 2): Click here. Modified MacConkey Agar is the main one to consider.
  
  
• Kligler Iron Agar (Exp. 14.1, Period 3): Click here. As for the other media on the same web page, don't worry about TSI and LIA (not used in this course), but the MIO reactions will be observed in Period 4.
  

The API-20E demonstration (which will be shown in Periods 3 and/or 4 of Exp. 14.1) is expanded considerably here.

You may find our Salmonella page interesting. It includes a discussion of serotyping, expanding on the information given in Experiment 14.2.

Our official definition of "strain" is given here.

Update for 10:00 PM, April 8, 2003

The table which explains what can grow in the various selective-enrichment media in Experiment 15 (i.e., LLTB, BGLB and EC Broth) which was on the board today is now here (scroll down a little).

A photo of "Orange Moose Pond No. 1" from which we got the samples for Experiment 15 is here in the upper left corner of the page. Click on the photo for a larger view.

Update for 8:00 PM, April 7, 2003

Going along with the new report & poster guidelines handout (which is also on the web here), a sample lab report from around 1995 can be found here.

Here are a couple sites where you can search the university resources for various topics: MadCat and PubMed.

If you would like another perspective on the most-probable number (MPN) method which we are using in the water analysis experiment (Exp. 15), click here.

We are getting into some experiments involving some groups of bacteria, and the Experiments 12, 13 and 14 page may help tie some things together. Note the reference to dichotomous keys which will be discussed more in lab. You will be making your own dichotomous key to help identify the three unknowns later on in Experiment 17.

The definitions and descriptions of various types of antimicrobial agents given in the introduction to Experiment 10 need some improvement. (Looks like a little mixing of apples and oranges.) Click here for the meanings of the following terms:  antiseptic, disinfectant, preservative, antibiotic and chemotherapeutic agent.

Interested in emerging infectious diseases? Click here.

Update for 7:00 PM, March 30, 2003

First of all, a very belated update about a problem on the MW morning take-home quiz. A reasonable answer based on the results indicated in the problem will be credited, but we should clarify our intentions about the problem as follows: "Concerning Problem #2 section IV, assume the colony count for the MM no methionine is 124 for the 10^–6 dilution. HINT: You're trying to find genes responsible for methionine biosynthesis. In order to identify mutants, you need to find guys who cannot make their own methionine, and therefore will not show up on the no methionine MM plate."

The two problem sets which are 10 points each are take-home items which are still yet to come. I should have issued the first one several weeks ago. Remember that the practice problems in Appendix Y are just for practice, not points, and the solutions which are on the web are linked from here.

Still wondering about how anaerobic growth relates to catabolism (and vice-versa) and also about our definitions of the oxygen relationship categories? Remember that the lab manual as well as our web material defines the oxygen relationship categories based on the Bergey's Manual definitions and the test with Thioglycollate Medium. This medium supports the growth of a wide variety of chemoheterotrophic organisms (but not much else) and we can see whether or not an organism can respire (aerobically – i.e., with oxygen) and also whether or not an organism can ferment. This is explained best on our oxygen relationship page. Also note on this page the "popular" definitions of "strict aerobe," "facultative anaerobe" and "strict anaerobe" – which are OK if you really intend to use these terms in "the most general sense."

Reasons why an organism can grow anaerobically are illustrated here.

First Update for 5:15 PM, March 23, 2003

As we are getting into the enrichment & isolation experiments (10.2, 11.1, 11.2, 11.3 – we will not do 9.3), information which supplements the introduction to Exp. 11 in the manual can be found on the web here. Our initial lab lecture this week on the isolation of organisms from natural sources will basically cover Parts I and II of this web page. The table found here is on the handout provided with this lecture and is intended to be filled in during the course of these experiments in order to serve as a summary of important items to consider in the isolation of these types of organisms.

Various relevant and interesting items about these organisms can be pursued in a good textbook (such as Brock's) and also in the Steenbock Library where you can find excellent isolation information in The Prokaryotes and Bergey's Manual of Systematic Bacteriology (in the reserve room). We have items on the web about the enrichment and isolation experiments including photos of various types of colonies; click here for an index. In these web pages, each of the bacterial groups is discussed to a greater or lesser degree. The purple non-sulfur photosynthetic bacteria (Exp. 11.1) and Bacillus (Exp. 11.2) are discussed most extensively.

Later on, we will talk about the reports and posters – information about which is given here. This web page totally replaces the Appendix to Exp. 11 and will be given out as a handout.

Second Update for 5:15 PM, March 23, 2003

Here, finally, are the results of Experiment 4 in which we tested two packages of hamburger. Recall that one ("B") was from Mason City, Iowa; it was purchased the morning of Sunday, February 2 and then kept sealed and packed in ice (but not frozen) until the morning of Wednesday, Feb. 5 at which time a portion of it was used for Section 001 (diluted 1/10 and tubed up in 1 ml amounts). The other package ("A") was purchased in Madison on the evening of Monday, Feb. 3 and likewise kept "on ice" until used for Section 001.

Both packages were then placed under normal refrigeration (about 4-6°C) until the morning of Thursday, Feb. 6 at which time another portion of each was diluted and tubed up for the remaining two sections of Bact. 102; tubes for the afternoon section were refrigerated until lab time. Microbial growth in the hamburger was kept at a minimum while on ice, but some growth could be expected in the refrigerator. The results were as expected (i.e., relatively high contamination for "A" and low for "B"), having been the usual outcome of our "February Iowa vs. Wisconsin hamburger freshness tournament" for the previous several years. All counts in this table are CFU/gram.

PCA = "Plate Count Agar" – the "all-purpose" medium.
MAC = "MacConkey Agar" – the "selective" medium, allowing only growth into colonies of gram-negative CFUs. (The "differential" aspect was ignored in this table.)
* = Too few colonies (< 30) showing up on any plate to give good results. (Few plates had any colonies for Sample B in Section 001.) With the "30-300" rule, less than 30 colonies on a plate with a 10^–3 "plated dilution" (our lowest) should yield a result of "< 3.0 X 10⁴" CFU/gram. Had we used plates representing 10^–1 or 10^–2 plated dilutions, we would have gotten more definitive counts for the Iowa sample (certainly not zero!).

Update for 10:15 AM, March 3, 2003

Today is 03/03/03!

The "official" key to the Experiment 7.1 cultures is posted here.

In case you are wondering about our use of the term "strain," our official definition is given here. We used an orange-pigmented strain of E. coli in Experiment 5.4 – a photo of which is linked from the strain discussion. Otherwise, the cultures we use in our various experiments are usually of typical strains of their species.

Update for 9:15 AM, Feb. 26, 2003

A reminder about my open office hours: I am available Monday and Wednesday afternoons between 1:00 and 3:30 PM. If these times are not OK, then we can arrange some other time. I am most avoidable during lab preparation as I have seven two-hour labs to get various things ready for in any given week (six after spring break), and my Tuesday "noon hour" is non-existant.

Looking ahead at what is coming up in a certain lab period (as per the schedule) is always encouraged. Remember that smears (such as for gram and other staining procedures) will last indefinitely once they are dried (which stops any degredative enzymatic activity). If you receive a "young" culture that needs to be gram-stained, at least make the smear on that day; you can heat-fix, stain and observe it at your convenience at some other time if more pressing things need to be done first, such as inoculating media. The whole process can be interrupted at any point and picked up later. If you need to remove oil from a slide, see the footnote on page 4 of the Manual. (And don't forget to heat-fix the slide after you make the smears!)

The handout that will be passed out along with Experiments 8.1 and 8.2 is on the web here.

The Differential Media site explains (with color photos) some of the media we use in Experiments 6 and 7 – most notably Motility Medium, Starch Agar, and Glucose Fermentation Broth. With Starch Agar and the amylase test, we are introduced to the topic of extracellular enzymes – one of the terms not explained too well in the manual (click here). Reasons why an organism may grow anaerobically are summarized here, and we are also getting into anaerobic respiration in Experiment 7 for the first time.

Things related to phenotypic characterization of bacteria such as what we are considering in Experiment 7 are discussed on our first bacteriological identification page. Our mention in lab of dichotomous keys to help in the testing and identification of our Exp. 7.2 unknowns is included here. Toward the end of the semester, you will be constructing your own dichotomous key to help with unknown identification in Exp. 17.

If you are interested in genotypic characterization of bacteria, go to this page which focuses on 16S rRNA gene analysis, one of the more important methods by which bacteria are identified genotypically and a major consideration when it comes to defining bacterial species. Going along with this is the construction of phylogenetic trees. You can interact with a segment of the 16S rRNA gene here.

Our site outline may indicate some additional items of interest.

Update for 3:15 PM, Feb. 18, 2003

A word to the wise about dealing with apparent "conflicts" regarding the terms you may see in Bacteriology 102 vs. other courses, textbooks, reference works, etc.:

Be able to discern the difference between a definition and a description. In our course, we have given the original, strict definitions of chemotroph, phototroph, organotroph, lithotroph, heterotroph and autotroph in Appendix D of the lab manual (which is also found on the web), and each of these terms deals with a certain aspect of metabolism or nutrition. Now, included in the description of a certain kind of organism – say, for example, typical chemolithotrophic organisms – one may see the fact that these organisms tend to utilize carbon dioxide as their source of carbon. But such use of CO₂ is not part of the definition of the term chemolithotroph! One can say that chemolithotrophs are usually also autotrophs (due to their use of CO₂ as carbon source).

Update for noon, Feb. 12, 2003
(Revised and expanded at noon, Feb. 18)

How Experiment 5.2 should have turned out for us is shown here. This experiment is merely a demonstration about how an organism which needs a growth factor can grow when the growth factor (in this case, a suitable siderophore) is provided in the medium.

The diagram giving an overview of catabolism which is now being shown in lab is here. Hopefully this will help to show where some of the terms we have covered fit into the larger scheme of things – i.e., chemotroph & phototroph, organotroph & lithotroph, and also respiration, fermentation & phototrophy. Basically, this diagram is an ultra-simplified representation of what happens where there is an oxidation of some compound (the "electron donor") that leads to the generation of ATP (phosphorylation); this occurs at various places in a catabolic pathway (a sequential conversion of one compound into another, and then into another, etc.) – the likes of which you will learn in greater detail in the lecture course. We will touch on fermentation pathways in Experiments 12 (the lactic acid bacteria) and 14 (the enteric bacteria).

Update for 12:30 PM, Feb. 5, 2003

Our first and second dilution plating pages cover basic Dilution Theory, going along with what we have done in Experiments 1 (lake & soil samples) and 4 (hamburger samples). Keep in mind we are testing two hamburger samples in Exp. 4 – one purchased in Mason City, Iowa and the other in Madison. From the results turned in next week, we will post the results here.

With the first quiz and take-home problem set coming up – and the fact that we are getting into the growth curve experiment and items related to oxygen relationships – the following links to relevant material on our website can be helpful:

• Here are solutions to the first set of practice dilution problems: example #2 on page 122 and problems #1-8 on pages 168-169. The solutions should be looked at only after you try them yourself!
  
  
• Here are answers to the sample quiz questions in Appendix X. There are no definitions posted for the terms in Appendix W. However, you can click here for items not explained too well in the manual. Make sure you are taking good notes of the lectures (and occasional demonstrations) and also your observations in the lab!
  
  
• The catabolism & oxygen relationships handout that will be passed out next week is also found here on our website (slightly expanded). The growth curve handout which will be passed out soon is based on this page.
  
  
• The Differential Media Site has links to some of the media we are using in the lab such as Glucose Fermentation Broth and Glucose O/F Medium which can be found here in blazing color!
  

Update for 2:30 PM, Jan. 22, 2003

A correction about the time and day of the final exam: 5:05 PM Friday, May 16. Place to be announced later.

A reminder about next week: There will be no lab on Thursday, Jan. 30. (The Tuesday-Thursday sections actually started a day early as per the Timetable, so this will make up for it.) No one will be in residence from noon Wednesday, Jan. 29 through the weekend. To reach John L. by e-mail during this "off period", use the new, handy alternate e-mail address: jlindquist@elvis.com.

If you have problems obtaining the lab manual, the procedures for the next period (Period 2) are posted here. Period 3's procedures are posted here. That takes us up through next week.

Update for 6:00 PM, Jan. 1, 2003

Your first lab session for the spring semester will meet on Tuesday, January 21 or Wednesday, Jan. 22 – depending on your lab section. As per the schedule, there is no lab on Monday, Jan. 20 or Thursday, Jan. 30.

You will need to get the following before we meet at our second session:

• Lab Manual:  General Microbiology: A Laboratory Manual, 3rd edition, by J. A. Lindquist – published by McGraw-Hill/Primis Custom Publishing (ISBN 0-07-235906-4). It is available only at University Book Store on State Street.
  
  
• A box each of microscope slides and cover slips. These are also available at the book store.
  

As most will be without the lab manual on the first day of lab, we will be providing the lab procedures on a special handout which is reproduced here for your convenience.

My office hours (in 22A Fred Hall) will be Monday and Wednesday afternoons between 1:00 and 3:30 PM. If these times are not satisfactory, we can arrange an alternate time individually. Unless announced otherwise, I am gone and not available on Fridays. I am available the 60 minutes before any lab period only by appointment. I check my e-mail quite often; the address is lindquis@bact.wisc.edu.

Please note that the lab is closed Fridays through the weekends.

Be sure to check out the rest of the Bacteriology 102 website and the various links, as we touch on everything sooner or later. Some items you will be receiving on handouts on the first day of lab are also posted on the web:

• The introduction to Bacteriology 102.
  
  
• The schedule of experiments which is useful for planning your upcoming lab activities. (Eventually you may wish to prepare flow charts for the various experiments or laboratory periods.)
  
  
• The grading scheme. We don't assign letter grades until all the points are in. If we assigned letter grades to the individual quizzes, then we would have to do the same for the unknowns (where almost everyone gets an "A") and other items.
  
  
• The "lab manual index" – this can be quite useful, although an expanded table of lab manual topics and relevant web links can be found here.
  
  
• Handouts for our regular microscope and the phase-contrast microscope.