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E-mail: lindquis@bact.wisc.edu. Return to the home page of the Page last modified on 12/23/06 at 9:45 PM, CST. |
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Bacteriology 102:
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Update for 9:45 PM, December 23, 2006
The average on the final exam was 82.6 (out of 100) – a couple points lower than the "average" average! What helps with the overall average and the grade distribution is the 5 bonus points spontaneously given everybody for perfect attendance on the last Monday and Tuesday. (Should be no surprise as it was announced in both sections.) Bact. 102 is still a 360-point course.
Those who heeded the chronic directive to think about and understand concepts & patterns (found in: dilution theory, enrichment/isolation, reasons for pH shifts in differential media, the 5 general catabolic processes, what is the basis for the oxygen relationship test, conjugation & recombination, bacteriophages, cell division & specialization, and other such things worth taking good notes on) had an easier time getting along with all the "minutiae" which may seem somewhat boring and trivial unless one sees how they fit into the bigger scheme of things.
A review of other averages this semester: Quiz 1 – 34.9(/40); Quiz 2 – 34.6(/40); Quiz 3 + Prob. Set 1 – 42.8(/50); Lab Report – 48.1(/50); and Prob. Set 2 – 8.9(/10). All sections were quite close to each other on each.
You can pick up your exam and any other things not picked up yet (which are all stapled to the exam) in the main office (Room 120, Old Biochem). You will be able to access your letter grade for the course on-line Tuesday if not a day or two earlier.
The teaching staff thanks you for a great semester! Have a totally cool and glorious break! Click here.
Don't forget to submit an evaluation! See the later Dec. 13 update below.
Update for 7:45 AM, December 18, 2006
Good news about the reports! They will be ready to hand back Tuesday at 9 AM in the lab.
Also, as you read over the Experiment 11.2 introduction, don't forget those questions in that little box at the end. Note why we had to incubate our isolation plates aerobically.
Update for 7:30 PM, December 13, 2006
Second update for today!
Here's a new, additional time for the early final to add to those that were posted in the lab: Thursday (exam day) at 12:25 PM in the lab.
An Evaluation of Bacteriology 102 can be made on-line! Please do so at your earliest convenience. Go to the Microtextbook home page and click on Submit an Evaluation. You will need to give your name and student ID number to get in. Also, the password for this evaluation is bact102.
Update for 1:30 PM, December 13, 2006
The key to the 2nd take-home problem set will be found here after the deadline for handing them in has passed. Check it out after 3:00 PM Thursday, Dec. 14.
A few more sets of items presented in lab recently:
Update for 6:45 PM, December 12, 2006
The room for the scheduled final will be 125 Biochemistry. If you need to re-schedule (due to conflicts, too many tests, etc.) possible times to take the exam early are indicated on the blackboard.
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 the Appendices – especially B, C and D) and supplemented by the handouts and your notes from the lab lectures. Helpful links to supplementary information on the web are given in the menu on the home page including terms and concepts needing further explanation (i.e., items not explained too well in the manual).
Considering the various organisms we worked with, do not memorize tables of individual species 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" (e.g., Bacillus, Mycobacterium, Streptomyces). In general, consider how organisms can be classified according to carbon and energy sources and (to a more limited extent) 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.
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 and the one given in the 4th edition of the manual is different than the one in earlier editions. As noted in the previous update, you can download a copy of the old final that is in the new (4th) edition of the manual here; a pdf file of it can be obtained here. Our on-line keys for the review questions and problems in the manual (Appendices X, Y and Z) are indexed here.
Hailstones and their relationship to purple non-sulfur bacteria? Click here.
Update for 6:00 PM, Dec. 11, 2006
Expanded 7:30 PM, Dec. 11
Unfortunately the report grading is proceeding very slowly, so they won't be ready to hand back any time soon. Hopefully Monday and Tuesday next week.
We plan on a review for the final in the Wednesday and Thursday labs this week. A brief discussion of some things to keep in mind is being made in the Monday and Tuesday labs:
If (for whatever reason) you are using the 3rd (older) edition of the manual instead of the current 4th edition, you need to see the old exam that is in Appendix Z of the 4th edition. Click here or download a pdf file of it here.
Update for 3:30 PM, Nov. 30, 2006
Slightly revised 7:15 PM, Dec. 5
A note about the take-home Quiz/Problem Set for Section 001: Disregard "indicate the letter" in Question 4 on Page 4. Also note that the second "page 2" is really "page 3."
Update for 2:15 PM, Nov. 29, 2006
It appears that the API-20E demonstration for Exp. 14.1 (Period 4) may not be happening in the lab anytime soon, but there is a "virtual demonstration" on the web here.
As you proceed with Exp. 17 and recall the basic procedures of the various tests we ran over the semester, remember how we made a big deal over certain things that could happen if we made too-thick smears, let cultures go too long, had dirty slides and lenses, etc. You should readily recall the answers to these questions from your experience:
Update for 5:30 PM, Nov. 27, 2006
Remember that the report is due Wednesday or Thursday this week, depending on your lab section.
Also, the 3rd Quiz (which is the take-home quiz) will be passed out Wednesday and Thursday this week. It will actually be a combination Quiz #3 and Take-Home Problem Set #1. It is to be worked on individually and outside of lab, and it will be due the following Wednesday or Thursday (Dec. 6 or 7) at the start of lab – i.e., before the opening lab lecture. We will endeavor to have them graded as soon as possible!
Be sure to have read over Experiment 17 ("The Final Great Unknown") for the Wednesday or Thursday lab this week. For this exercise, you will follow the same general plan as in Experiment 7 – starting with the mixture of unknowns, streaking plates for well-isolated colonies, making slant cultures of your three isolated unknowns, and then running the relevant tests based on what the isolates might be. Your dichotomous key – which does not have to be used as a "flow chart" – will help in choosing the relevant tests to identify each unknown to genus. As per the "fine print" in Experiment 17, the key should be turned in Monday or Tuesday next week (i.e., Dec. 4 or 5), but in any event it needs to be checked over for accuracy before you hand in the identifications of the unknowns. (We want to make sure everyone gets the full 10 points for this key.)
Update for 5:30 PM, Nov. 19, 2006
Our Differential Media Site includes 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 that is summarized on Table I on page 82 in the manual. This table is expanded in the handout that you got for Exp. 14, and – for those interested – the concept of pH-based differential media is expanded even further on the web here.
Remember our discussion from earlier in the semester that when we are determining whether an organism can break down a sugar such that acid is ultimately produced, we must also realize that there is usually an alkaline reaction happening due to aerobic deamination of amino acids – the amino acids being in medium ingredients such as peptone and yeast extract. In Experiment 14.1, we set these processes in direct opposition (that is, we let them compete for dominance) in Kligler Iron Agar which we will have fun with this week. Also in Exp. 14.1, we introduce the process of amino acid decarboxylation and how this anaerobic alkaline reaction can be detected.
The API-20E demonstration (which will be shown in Period 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.
Update for 3:00 PM, Nov. 15, 2006
Another change in the office hours: As the Lab Report deadline has been extended to Wednesday and Thursday, November 29 and 30 (I can still hear the cheers), there is probably little need to come in and discuss reports on Friday this week. So, the additional open office hours announced previously for Friday, Nov. 17 will not be happening. Starting next week I will maintain the usual schedule through the rest of the semester.
Here is the list of samples we provided that have been on the green board for some time – plus the one we used in Exp. 15:
Update for 1:30 PM, Nov. 13, 2006
with a 7:45 PM modification about open office hours
A clarification of the test we did in Experiment 11.1 to verify we had anoxygenic phototrophs (and to distinguish between facultative phototrophs and strict phototrophs which would not show respiration) is explained here. This test works really well if we have plenty of inoculum which was hard to obtain with some of our small colonies.
An example of a lab report submitted in a previous semester (when our guidelines were not so detailed and we were not doing that special test in Exp. 11.1) can be found here.
Open office hours on Wednesday this week will only go until 3:30 (and I will announce that in lab Tuesday and Wednesday). However, open office hours are still on this week for Friday morning from 9 to noon. So, if you have questions about the lab report, you can ask in lab or during office hours, and of course I'm always e-mailable.
Update for 11:15 AM, Nov. 7, 2006
Never fear! The first 10-point take-home problem set should be coming soon. Sorry it's been late in coming.
For Wednesday and Thursday this week, hopefully you have been heeding the schedule and are reading over Experiment 15 in the manual. The introduction is especially important. This experiment is on water analysis and includes the very important concept of indicator organisms and how coliforms can be used as such. A new method to estimate the concentration of organisms in a sample will be introduced which is the Most Probable Number (MPN) Method. The handout on the MPN method that will be passed out this week is based on the web page here.
Read over again the introduction to Experiment 11 and also the introductions to the three "sub-experiments" (11.1, 11.2, and 11.3) and also 10.2. We do have some material on the 102 website about purple non-sulfur photosynthetic bacteria and Bacillus, and there are some miscellaneous observations of Streptomyces and the nitrogen-fixers here.
For the formal report which we will be talking about soon, the guidelines to follow are in the present (4th) edition of the manual at the end of Experiment 11. The handout we used to pass out to update previous editions of the manual is still here. The individual report can be on any one of the four "enrichment/isolation experiments" (10.2, 11.1, 11.2, 11.3), and we have ceased doing posters some time ago.
Here is a suggestion about writing the report which may be useful: Start with a general outline and then fill in the details – not necessarily in order from beginning to end. The report should be double-spaced but not double-sided! That is, stay on one side of the sheets.
In addition to our material on the web, you can find lots of information on various kinds of bacteria such as what you may be writing a report on. A good textbook (such as Brock's) can be consulted, and in the Steenbock Library reserve room you can find excellent isolation information in The Prokaryotes and Bergey's Manual of Systematic Bacteriology. You can also go to the on-line edition of The Prokaryotes and type the organism's name in the search box (without quotes), and you will find a variety of items at various levels of detail. Also see Dr. Ken Todar's overview of the major groups of procaryotes here and other resources listed here. At any rate, please do not use just the lab manual (by what's-his-name) as your only reference!
Some things we have found troublesome while grading lab reports do tend to recur every semester. Take a look at the suggestions listed in the "green box" under the November 17, 2005 update here. If you are writing about nitrogen-fixing bacteria, please do not say that they "pull nitrogen out of the atmosphere"! That's some unfortunate and regrettable phraseology that appeared in the third edition of the manual that will pull your grade down for sure.
Here are a couple sites where you can search the university resources for various topics: MadCat and PubMed.
Update for 12:15 PM, Oct. 25, 2006
A "white board" diagram summarizing the results for Exp. 8.2 can be seen here. (For convenience, we can treat cells and CFUs as equivalent in this experiment.) Realize that the actual concentration of cells (no. per ml) cannot change when you mix together two cultures having equal cell densities. Also remember our definition of recombination frequency: It is the number of recombinant CFUs per ml of the mixture (determined from your plate count of the mixture) divided by the total number of cells in the mixture that could conceivably undergo recombination (which would only be half of the population – i.e., the F-minus cells which are at 5 X 107/ml). You can leave the recombination frequency as a fraction or convert it to a decimal or percentage.
For Exp. 8.1, here is the photo of plates that were inoculated with approx. 1 X 109 CFUs of Staphylococcus epidermidis in the first period; the plate on the left contains a relatively low amount of streptomycin and the other contains a relatively high amount. (1) Mutants with altered permeability of the cell membrane (represented by the numerous small colonies) can stand a low concentration of streptomycin but are "overwhelmed" on the plate containing the high concentration. (2) Mutants with altered ribosome – now resistant to streptomycin – will carry on as they would normally, not affected by any concentration of streptomycin that we give them. Protein synthesis is not hindered, and the cells give rise to normal-sized colonies (the relatively larger ones on these plates).
Don't forget to review the Exp. 8 Handout which explains the basic material much better than what is in the manual. The handout is also found here, and mutation and recombination frequency are explained here.
Update for 6:15 PM, Oct. 23, 2006
We are getting into the concept of enrichment & isolation which involves Experiments 10.2, 11.1, 11.2, and 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 on the isolation of organisms from natural sources will basically cover Parts I and II of this web page. The "worksheet" found here will be 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. These are handy things to consider in your report, more of which will be discussed later.
The second quiz will be on November 1 and 2 and will cover Experiments 5.4 through 9.2. Especially helpful in studying for this quiz are the old quiz questions in Appendix X in the manual. Going along with Experiments 8.2 and 9.1 is the "second set of practice problems" – i.e., nos. 9, 10 and 11 on pages 170-171 in the manual, but any relevant problems on the quiz will be more simple and straightforward, as we intend to hit the "basics" and that should not involve an excess of calculations. Remember that solutions to the practice problems and answers to the old quiz questions are on this website; for the "index" to the keys, click here.
We barely mentioned genotypic identification and dichotomous keys at all in connection with Experiment 7, and we will not ask questions about them on the quiz. Both concepts will be seriously gone over with Experiments 14 and 17.
Update for 8:30 PM, Oct. 16, 2006
Remember that the growth curves and calculations (i.e., the things mentioned in "For Your Report" on page 24 in the manual) will be due Wednesday and Thursday this week. The first take-home problem set is still coming.
The handout that will be passed out Wednesday and Thursday this week (to go along with Experiments 8.1 and 8.2) is also on the web here.
Some words to live by: 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. The drying stops 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 (don't forget to do!), stain and observe it at your convenience at some other time if more pressing things need to be done first, such as inoculating media. Two or three smears can fit comfortably on the same slide, as we saw back in Experiment 2. The whole process of making, staining, and observing smears can be interrupted at any point (even in the middle of the gram-stain procedure) and picked up later. If you need to remove oil from a slide, see the footnote on page 4 of the Manual.
The "official" key to the twelve Experiment 7.1 species is posted here.
Update for 6:00 PM, Oct. 11, 2006
Our severe-weather policy: If you miss lab due to inclement weather, do not worry about missing essential material in the lab, not taking a quiz that is given that day, or not starting an unknown that is passed out that day. Unless the University publicizes the fact that it is closing down due to bad weather conditions, our course is still on, and you should use your best judgement about coming in or not. The lab material for the day can be easily made up later.
Things related to phenotypic characterization of bacteria such as what we are considering in Experiment 7 are discussed on our first bacterial identification page. When we will be mentioning dichotomous keys to help in the testing and identification of our Exp. 7.2 unknowns, a relevant web page on the subject is here. Toward the end of the semester, you will be constructing your own dichotomous key to help with unknown identification in Exp. 17.
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).
The three catabolic reasons why an organism may grow anaerobically are summarized here. We already considered fermentation and its relevance in the test for oxygen relationships in Exp. 5.1. In Exp. 7, we are getting into anaerobic respiration. Later on, in Exp. 11.1, we will consider anoxygenic phototrophy with photosynthetic bacteria.
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. Go ahead and interact with a segment of the 16S rRNA gene here. A self-explanatory, simplified guide to how a phylogenetic tree can be constructed (taken from an old handout) is here.
In case you are wondering about our use of the term "strain," our official definition is given here. We used an unusual orange-pigmented strain of E. coli in Experiment 5.4 – a photo of which is here. Otherwise, the cultures we use in our various experiments (including those where we identify unknowns) tend to be typical strains of their species.
Update for 9:30 AM, Oct. 4, 2006
How Experiment 5.2 turned out for us is shown here. This experiment is merely a demonstration about how an organism which needs a growth factor (in this case, Arthrobacter flavescens) can grow when the growth factor (in this case, a suitable siderophore) is provided in the medium. Note the absence of growth on the "control" plate which contains no siderophore added in any form.
In Experiment 5.3, we are demonstrating two media that differ in the relative amount of iron, and we can see the difference in cultures of Pseudomonas fluorescens growing on these media in that more siderophore is produced by the organism on one medium than on the other. An illuminating photo of our results is shown here. The siderophore produced by P. fluorescens is called "fluorescein" as it happens to be fluorescent – i.e., able to glow under a U.V. light. In normal light you see a yellowish green pigment diffusing into the medium.
Here is a word to the wise about dealing with apparent "conflicts" regarding bacteriological terms you may hear or read about in different courses, textbooks, reference works, etc.: Be able to discern the difference between a definition and a description. In Bact. 102, we have given the original, strict definitions of chemotroph, phototroph, organotroph, lithotroph, heterotroph and autotroph in Appendix D of the lab manual (which, by the way, is also found on the web here), and each of these terms deals with a certain aspect of metabolism or nutrition. Now, if you were to see a description of a certain kind of organism – say, for example, a typical chemolithotrophic organism – one may see in the list of this organism's characteristics that it uses carbon dioxide as its source of carbon. But this use of CO2 is not part of the definition of the term chemolithotroph! It just happens that this particular chemolithotroph is also an autotroph, as most of them are.
Also, be careful how you combine terms. "Photochemotroph" incorporates two terms that are in opposition according to their strict definitions, and such a combination into one word would make no sense.
Update for 4:15 PM, Oct. 2, 2006
With the Bacteriology 101 exam also happening on Wednesday, Oct. 4, the first quiz in Bact. 102 has been moved to Monday, Oct. 8 for the first section by a near-unanimous vote this morning, and I would expect a similar vote in the second section for the postponement of the quiz until the following Tuesday. For a short review session in each section, bring some good questions on Wednesday and Thursday this week!
We will be touching on dilution theory and differential media throughout the semester, and we have noted some basic patterns that apply to virtually all dilution plating problems and differential media that contain pH indicators as shown here and here.
If you are willing to spend a little extra time learning the basics, you will not have to spend a lot of time memorizing details. After awhile you will be able to look at the formulation for just about any differential medium and tell what can happen in it without having to learn each different medium "from scratch." There are few if any "exceptions to the rules."
Note that Bact. 102 uses Glucose O/F Medium as it was originally intended for bacterial identification back in the 1950s (which I remember well): To be able to differentiate between gram-negative bacteria (1) that can ferment, (2) that only catabolize glucose by respiration and (3) that do not catabolize glucose at all. Knowing this sort of thing does not happen to be important to the identification of gram-positive bacteria, and it so happens that gram-positive bacteria don't grow in this medium too well anyway – probably because of some sensitivity to the pH indicator. So that is why we only tested the gram-negative bacteria in Glucose O/F Medium in Exp. 5.1 and didn't wa$te an equal number of tubes on the gram-positive cultures.
Update for 5:45 PM, Sept. 27, 2006
A reminder that the first quiz is coming up Wednesday or Thursday, October 4 or 5. It's an in-lab quiz, and the format is like the sample final in the manual (Appendix Z), although it will be worth only 40 points and will cover Experiments 1 through 5.3. Note also the relevant material in the appendices, especially Appendices B, C and D. (Also see the previous update, below.)
A couple of the "whiteboards" shown in lab are reproduced on the web:
Update for 6:30 PM, Sept. 26, 2006
With the first quiz and take-home problem set coming up – and the fact that we will soon be getting into the growth curve experiment and are presently dealing with nutrition and catabolism – the following links to relevant material on the web might be helpful:
A few years ago for Exp. 4, we tested hamburger samples from Mason City (Iowa) and Madison, and the results of this classic experiment can be found here.
Update for 7:15 PM, Sept. 18, 2006
Going along with Experiment 4 (Wed. or Thu., Sept. 20 or 21) is Appendix C (Dilution Theory) and also page 118 which has the directions you can always refer to for the pipettors. Our second dilution-plating web page (along with the first) may explain these aspects of "dilution theory" more clearly than Appendix C. The term colony-forming unit (CFU) is defined and discussed here. Also, if understanding scientific notation is still a problem, perhaps this page will help.
As will be mentioned in lab this week, it is important to have read Appendix D (Nutrition & Cultivation of Bacteria) and also the introduction to Exp. 5.1 for Mon. or Tues., Sept. 25 or 26.
You can start working on the first set of practice dilution problems; these problems are on pages 122 (example no. 2) and 168-169 (nos. 1-8) and also the one we added in lab Monday or Tuesday this week. They are not to be handed in. You will be getting a 10-point take-home dilution problem set soon. If you would like to check your solutions to the practice problems with the key, click here. (Don't check the key without having first done the problems!)
Update for 7:45 PM, Sept. 11, 2006
If you are having problems obtaining the lab manual, the procedures for Period 3 are posted here, and Period 4 is here.
For Period 4 (Monday or Tuesday next week), read through Appendix B in the lab manual and also the material on the capsule stain and acid-fast stain in Appendix G.
To help understand "dilution theory" as it is being covered in Exp. 1, a relevant and fairly simple explanation is found in our "first dilution-plating page" on the web; click here.
Update for 4:30 PM, Sept. 6, 2006
For the second lab session (Mon. or Tues., Sept. 11 or 12) be sure to look over Experiments 1 and 2 in the Lab Manual, and also read Appendices A and G.2. According to the schedule we will be doing Period 2 of both Experiments 1 and 2 on this day.
Update for 5:00 PM, Aug. 15, 2006
(Modified 6:45 PM, Aug. 29)
Your first lab session for the fall semester will meet on Wednesday, Sept. 6 or Thursday, Sept. 7 – depending on your lab section.
You will need to get the following before the second session meets:
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. 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. (Etc.)
My open office hours (in 20A Old Biochem. – the very small room adjacent to the lab) will be on Monday and Wednesday between 12:30 and 4:00 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 always 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.
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E-mail: lindquis@bact.wisc.edu. Return to the home page of the Page last modified on 12/23/06 at 9:45 PM, CST. |
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