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E. B. Fred
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E. B. Fred Hall
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The Archived
BACTERIOLOGY
3 0 4
WEB SITE
for
FALL SEMESTER, 2003
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Links to images open them up in separate window.
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From the C. B. E. Course Description: Bacteriology 304 introduces students to the microbial world by doing investigative experiments often on samples that the students bring in. The course has three goals. First, to introduce students to the basic techniques used by scientists to investigate the fascinating world of microorganisms. The experiments in the course will instruct students in microscopy, aseptic technique, the biochemistry, physiology, genetics and molecular biology of microorganisms. A second goal is to introduce students to the major representative groups of microorganisms. Students will examine microorganisms that are important in antibiotic production, in sewage treatment, in disease, in food manufacture, and in ecology, to name a few. The third and most important goal is to teach the scientific process. Learning how to be a good scientist involves developing hypotheses, designing experiments, performing experiments, collecting data, analyzing it critically, and reporting it to others.
One of the innovations in this course has been the development and use of discussion groups. Click here.
Laboratory Teaching Personnel for This Semester
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Graduate Students |
Undergraduate Students |
Coordinator and Additional Instructor |
Section 001
(MW afternoon) |
Ryan Newton
Greg Richards |
Anders Christopher Boyd
Adam Brinkman |
John Lindquist
(Office hours: MW 10:30-noon plus other times as arranged. Not available during lab preparations or TR noon hour.) |
Section 002
(TR morning) |
Yolande Chan |
(We just could not fill this spot!) |
Section 003
(TR afternoon) |
Mary Pat Craver
Carolyn Lipke |
Cristin Heyroth |
12/19/03:
- By now all the graded items are available in the main office (Room 120) and organized according to section, and pretty soon the letter grades should be accessible at My UW-Madison.
- Great semester! Let's do it again sometime. :-) Click here.
12/10/03: (Additional comments inserted 12/30/03.)
11/26/03:
- Back to stuff we've had on the board: Here is the outline regarding your Experiment 9 Report which can supplement the general guidelines given in the manual. If you need to review the usage of microbiologically-related terms, click here; the definition of "strain" comes along as a bonus. It appears that general biology courses do not cover these things to any substantial degree.
- You may need to review the theory behind the differential media used in Experiment 9. Kligler Iron Agar (KIA) is an excellent medium with which to get a feeling for the competing acidic and alkaline reactions in many of our pH-based differential media. Remember that amino acid deamination is always going on for any enteric inoculated into KIA; it may be overneutralized by excess acid production from fermentation, but it is happening nonetheless and is not a reaction that we record for any organism anyway (as it's always expected to be "+"). A red slant is not caused by slight fermentation of glucose (something we have noted often in the answers to the last quiz). It's simply this: (1) If an organism just ferments the small amount of glucose in KIA, the small amount of acid produced is not enough to overneutralize the alkaline reaction of amino acid deamination which is responsible for the red (=alkaline!) slant. (2) And then for an organism that ferments lactose (in addition to glucose), the large amount of acid will diffuse throughout the medium and cause a net acidic reaction (yellow slant and butt). Click here for the KIA summary.
- Fast becoming my favorite aspect of environmental microbiology is epidemiology. This is a good, useful, practical branch of microbiology to check out – and so is food microbiology, by the way. Click here for some interesting links concerning bioterrorism.
- By the way, my paper (with co-authors from the CDC) on the new genus and species first found near Hayward (by accident – while I was trying to do an epidemiologically-related thing concerning the pathogen Edwardsiella tarda) will be coming out in 2004. I will get into details about it on the web once it is finally published, but – in the meantime – its 16S rRNA gene sequence already got leaked and onto the web; go here and search Nucleotide for AF015258. And here they all thought that those hundreds of water samples I was bringing in had something to do with microbial diversity. :-)
- Have a Happy Thanksgiving Break!
11/17/03:
- The answers to the added review questions for the enteric experiment are illustrated here. Note that some of the differential media we use in lab (including MacConkey Agar and KIA) are explained on the Differential Media Site.
- Also, the latest list of items we had on the board concerning lab notebooks is here.
11/4/03:
- We have better data now for the mutant strain grown in glucose for the beta-gal experiment. Click here.
11/3/03:
- The betagalactosidase data here are apparently faulty for the mutant grown in MM+glucose. We are still looking for a good representation of what we generally saw in the experiment.
- The Differential Media Site has some explanatory material on several of the media we are using these days: KIA and MIO, MacConkey Agar, and EMB Agar.
- The MPN handout is based on this page.
10/30/03:
- Some pretty good lab data that you can use to graph the beta-galactosidase experiment is here.
- An adjustment to the point system has been found necessary: Seeing how you are doing so much work in getting your lab notebooks in shape (but don't rewrite your in-lab data/observations!), each set of lab notebooks that you will be handing in will be worth 40 points.
- QUIZ 2 will be passed out Wednesday and Thursday, November 19 & 20 and will be due the following lab period, Monday and Tuesday, November 24 & 25.
10/28/03:
- An eleventh-hour alert about a significant discrepency in the lab manual. Apparently the manual got published before the problems got fixed, but we can overcome this as follows:
- The real period 3 of experiment 9 (i.e., 9.3) in the manual is found on page 89: The top three steps should have "Water Analysis" as their heading, and the two steps under "General Enteric Isolation" on page 89 also apply to period 3. (You will get a revised protocol for period 3 in lab.)
- The real period 4 starts on page 90, and the real period 5 (which is correctly labeled as such) starts on page 92.
- Also, the quote on page 81 is probably a version of Ambrose Redmoon's famous saying: "Courage is not the absence of fear, but rather the judgement that something else is more important than one's fear."
- For those in need of such a thing, we're getting a summary of data from the beta-gal experiment (period 2) that one can utilize to make graphs for proper interpretation of what went on for both strains under both growth conditions.
10/14/03:
- "The Plan" for period 2 of exp. 6 (i.e., 6.2) is shown here. This sort of thing can serve as a "general outline" when it comes to broadly summarizing the procedure in a lab notebook.
- For the practice growth curve problem that was intended to be worked on for the Monday or Tuesday labs this week, here is what the points would look like when plotted on semilog paper. In actual practice, we would not want to connect the dots as shown here but rather isolate the growth phases and draw the "best straight line" among the appropriate points, such as what is done here for the exponential phase. Using the terminology and formulas in the manual, here is how one would work out the solutions to finding the growth rate and generation time. Note the "easy" points that were chosen – i.e., those for which the logarithm can be seen immediately.
9/30/03:
- The different growth conditions for Exp. 4.1 will be as follows. (This is an update of the handout passed out Monday, Sept. 29.)
- Flasks of Nutrient Broth on a shaker
- Flasks of Nutrient Broth plus 0.2% Potassium Nitrate - non-shaken
- Flasks of Nutrient Broth plus 0.2% Glucose on a shaker
- Flasks of Nutrient Broth plus 0.2% Glucose and 0.2% Potassium Nitrate - non-shaken
- Flasks of Nutrient Broth plus 0.2% Glucose - non-shaken
9/28/03:
- Contrary to the new schedule handout (on the back side) the first notebook check will be on October 6 or 7, depending on your section.
- You will get a new protocol for 4.1 on September 29 or 30 which will allow us to do a growth curve experiment in class on October 1 or 2, rather than coming in at special times on Thursday or Friday (Oct. 2 or 3) as in the old schedule. Each pair will sample two time points during the growth of an assigned culture (one near the start of lab and one near the end), each time making a number of dilutions and inoculating 8 plates to determine CFUs/ml at that particular time point. Between the morning and afternoon sections' sampling of the various cultures (which are to be set up at different times), we should be able to generate a growth curve for each culture from the overall class data such that we can determine relative growth rates for an E. coli culture growing under various conditions. Be sure to read Exp. 4 (intro., etc.) in the manual ahead of time! Note the links below (next section) regarding aseptic technique and growth curves.
Links to Supplementary Information
The following are links to web pages (on this 304 site and elsewhere – in addition to those indicated in the links above) that can help in your understanding of some of the important concepts covered so far. Some have been referred to in the lab lectures already and/or have had sections included in handouts and other material. Items 6-9 can help to supplement the nutrition lecture(s). Please inform us of other pages you find more helpful, and we will include them here.
- Aseptic Technique Procedures including how to hold the tubes and loops and how to use the pipettor properly.
- Review of the Light Microscope which we use to observe stained smears.
- Review of the Phase-Contrast Microscope.
- Dilution Plating: All you need to know, covered in two pages.
- Dr. Scott Cayley's explanation of the selectivity of MacConkey Agar is here.
- Bacterial Nutrition.
- Review of Catabolism.
- Thioglycollate Medium and the Concept of Oxygen Relationships.
- Glucose O/F Medium. The white-board diagram shown in lab is reproduced here.
- More differential media we use in lab can be found on the Differential Media Site – including Glucose Fermentation Broth, MacConkey Agar, Motility Medium and Starch Agar.
A good thing to keep in mind: When we are determining whether an organism can ferment a certain sugar by looking for an acidic reaction, realize that there is (usually) also an alkaline reaction happening due to deamination of the amino acids in medium ingredients such as peptone and yeast extract; one normally does not learn about this alkaline reaction and comes away from a bacteriology lab course believing a negative reaction has to be neutral. We expect that any acid produced from fermentation (if it occurs) will overneutralize the alkaline reaction. Features found in many of our differential media are tabulated here. With a pattern in mind, none of these media have to be learned (or taught) "from scratch" as a special case, and one can use these principles to formulate new selective-differential media to help us isolate certain types of organisms.
- Bacteriology 102's Growth Curve Page can help with some of the theory in Experiment 4.
- Bacterial Identification. This page has a useful table to help you sort out your nature isolates and was, in fact, made years ago with Bact. 304 in mind.
- Bact. 102's pages on the enrichment & isolation concepts may have some useful information. Click here.
- The three quizzes given this semester are archived on this site: Quiz 1, Quiz 2, Quiz 3.
