Update for 11:30 AM, Dec. 20, 2005
The final exams are graded and the average was 86.6 (out of 100) – quite better than the "average" average! As for other averages this semester: Quiz 1 - 33.3/40; Quiz 2 - 32.8/40; the take-home (i.e., Quiz 3 & Prob. Set 2) - 45.3/50; and Prob. Set 1 - 9.4/10. Both sections were remarkably 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 Department Office – Room 120 Old Biochemistry. You should be able to access your final letter grade soon. I will be gone for probably a week or so starting mid-day today.
The teaching staff thanks you for a great semester! Have a totally cool and glorious holiday break! Click here.
Update for 11:30 AM, Dec. 16, 2005
Regarding the infamous Question 5 on page 4 of the take-home: If you would have added galactose and ornithine to the KIA (instead of fructose and ornithine), the organisms would not be clearly differentiated from each other as required in Part a of the question; Splammobacter and Sorgobacter would wind up looking like some of the "all other genera" in the medium (i.e., your modified KIA).
Why is this?
Note that those in the "all other genera" category all ferment galactose; the large amount of acid (coming from the fermentation of the large amount of galactose) would permeate throughout the medium including the slant. (Just like we have seen in regular KIA if lactose is fermented – we at least see that acidic reaction up through the slant region.) Splammobacter and Sorgobacter also ferment galactose. Those of the "all other genera" that decarboxylate ornithine are like Splammobacter in that respect, and those of the "all other genera" that do not decarboxylate ornithine are likewise like Sorgobacter.
So the only way to really differentiate between the organisms is to add fructose and ornithine as per the attached sheet to the take-home quiz/problem set which also attempts to explain what would be necessary for a 100% (i.e., maximum) recombination frequency to occur in a problem such as no. 2. (Can we really determine conjugation frequency? No, but the number of pairs that conjugated was added as some extraneous information to Problem 2.)
Update for 12:45 PM, Dec. 15, 2005
Sorry for the delays in getting back your Reports and Exp. 17 Unknowns, but I can now (finally!) start finishing them up and they will be ready to hand back at the final. Remember that the best review materials for what is covered in the Reports are (1) the introductory material in Exps. 10 and 11 and also (2) the Appendix X review questions in the manual.
For the alternate final exam times, come to the lab. Otherwise, the scheduled final will be in 125 Biochemistry on Sunday morning at 7:45 AM. (Not my choice of times by any means.)
Update for 9:00 AM, Dec. 12, 2005
The room for the scheduled final will be 125 Biochemistry. If you need to re-schedule (due to conflicts, too many tests, etc.) we can arrange a time this week.
Here are some items to consider in reviewing for the final exam. When we have a review in lab (Wednesday or Thursday this week), be sure to bring some good questions!
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 grading "traditionally" 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.
One of the most overly-used (and often overly-misused) terms among bacteriologists is strain which is not synonymous with species or culture. Our attempt to define this term is here. Strain is also synonymous with the term clonal group. Is species the plural of specie? Not in biology. The term specie refers to coins and legal matters; see its definition here.
Interested in emerging infectious diseases? Click here.
Update for 1:15 PM, Nov. 28, 2005
A change in the schedule: The 3rd Quiz (which is the take-home quiz) will be passed out Monday and Tuesday next week. It is to be worked on individually and outside of lab, and it will be due the following Monday or Tuesday before the opening lab lecture. We will endeavor to have them graded within two days, as the end of the semester is coming up fast!
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 Exp. 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 for identifying each unknown to genus.
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:
Need a review about general catabolism? Click here and note the links to our main catabolism page and the page on oxygen relationships. This is always good stuff to know, and we basically covered it in the first several weeks of the semester. On Quiz 3 or the Final in previous semesters, we have included a question much like (if not identical to) Question 3 here.
Update for 6:00 PM, Nov. 22, 2005
In case you missed the announcements, the lab reports can be turned in to the locked box outside Room 70 which is the large teaching lab down the long hallway on the same floor as our lab. It's a wooden box with a combination lock, and it has a sign on it for Bact. 102 reports. Be sure to label your report prominently with Bacteriology 102 on the front cover. I suppose the main office would accept the reports as well, but it's best to put them in the locked box which will remain available until the building is locked up Wednesday evening (probably around 5:00-5:30 or so).
Have a great break!
Update for noon, Nov. 17, 2005
Here are some "trouble spots" that have been noted during the grading of lab reports in recent semesters:A Bacillus isolate does not have to break down starch in order to be identified as Bacillus. Likewise not all Streptomyces isolates will produce antibiotics!
There is generally too much about Streptomyces "thriving" on Actinomycete Isolation Agar without giving the real reason why (restrictive nutrients, extracellular enzymes, and the connection between these two ideas). Also, not everything on that medium was Streptomyces!! Remember how we had to pick & choose likely colonies and maintain them through the following periods – not choosing (instead) those bushy mold colonies or the relatively smooth and shiny colonies which could not be Streptomyces. Penassay Agar is simply a medium that has become standard (for better reproducibility) in many antibiotic studies. It is not selective for antibiotic-producing bacteria.
Remember that we pointed out in lab the real importance of using a good all-purpose medium in Period 2 of Exp. 10.2: We wanted to have the contaminants "thrive" (there's that cute word again) and be better recognized as contaminants so we could avoid them better and only continue with those colonies that looked like Streptomyces (small, round, hard, etc.). Anything smooth and shiny should not have been carried through the testing for antibiotic production – just like we tried to stay away from them when we picked our initial isolates in the second period.
We did not have to identify the nitrogen-fixers, but the manual tells how Azotobacter is recognizable, and we added (in lab) how Bacillus is as well. We would not identify any of our isolates as Klebsiella; there are too many tests to run which we did not do. Keep in mind the importance of that last test we did for our isolates in Exp. 11.3!
Likewise keep in mind the importance of that last test we did for our isolates in Exp. 11.1 and why we would not call a purple non-sulfur photosynthetic isolate a facultative anaerobe if it grew aerobically and anaerobically in this test. Also, if we could not tell if an isolate was Rhodobacter or Rhodopseudomonas, that possibility was anticipated in the manual.
Traditionally, the guidelines involving page 149 in the manual get ignored. It appears that the deal about genus and species does not get taught in (or retained from) introductory biology courses – college-level or otherwise. (I had to learn that stuff in fifth grade.)
A suggestion about writing the report which may be useful: Start with a general outline (including the four major parts) and then fill in the details – not necessarily in order from beginning to end. We do highly recommend double-spacing the report, although it is not required.
In addition to our material on the web (some of which is indexed here), 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! Also, if you are writing about nitrogen-fixers, please do not say that they "pull nitrogen out of the atmosphere"! That's some unfortunate and regrettable phraseology that appears in the Bact. 102 manual and hopefully nowhere else.
Here are a couple sites where you can search the university resources for various topics: MadCat and PubMed.
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.
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 summarized on Table I on page 82 in the manual – which is expanded in the handout that you are getting for Exp. 14 this week. (The concept of pH-based differential media is expanded even further on the web here.) Understand the basics and don't memorize all the intricate details. Once the basics are understood, you can understand these media better and also have fun with items like the "thought questions" on the same handout.
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 8:00 PM, Nov. 7, 2005
For Wednesday and Thursday this week, be sure to have read over Experiment 15 (especially the introduction) which is on water analysis. 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 that will be passed out is based on the web page here. In this experiment, we will also learn about coliforms and their use as "indicator organisms."
Read over again the introduction to Experiment 11 and also the introductions to the three parts: 11.1, 11.2, and 11.3. You may have seen the following links elsewhere and checked on them: We do have some material on the web about purple non-sulfur photosynthetic bacteria and Bacillus, and there are some miscellaneous observations of Streptomyces and the nitrogen-fixers here.
Exactly one year ago tonight we had a big-time aurora event all over the country. Click here.
Update for 7:30 PM, Nov. 2, 2005
For the formal report which we will talk about next week, we will not be using the guidelines that are in the manual at the end of Experiment 11. Rather, we will pass out a handout that is much clarified over what is in the manual; this handout is already on the web 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 will not be doing posters at all this semester.
Update for 4:15 PM, Nov. 1, 2005
For that old photo of the "white board" (discussed in lab Monday & Tuesday this week) which shows an attempt to summarize the various aspects of a bacterial vegetative cell, click here. It now goes along with the slightly revised course introduction found on the home page of this Bact. 102 website; this "introductory essay" might make a bit more sense now than it did at the very beginning of the semester.
Update for noon, Oct. 28, 2005
(Updated further at 11:30 AM, Oct. 29)
If you missed any of the summary of how to analyze the Exp. 8.2 results (and cannot wait till the review in lab on Monday or Tuesday), the "white board" diagram 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 we showed in lab 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 8:45 AM, Oct. 25, 2005
MAJOR CORRECTION REGARDING QUIZ DATES INSERTED SUBSEQUENTLY
The second quiz will be on November 2 and 3 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 touched on genotypic identification and dichotomous keys very briefly in connection with Experiment 7, and we will not ask questions of any detail about these on the quiz. Both concepts will be seriously gone over with Experiments 14 and 17.
Looking ahead to Experiment 17 (coming after Thanksgiving Break): It will be a lot like your unknown isolation and identification in Exp. 7.2, and you will be pretty much on your own, already having experience with the various techniques and tests throughout the semester. For an identification key you will use a dichotomous key of your own construction to differentiate the 12 genera. The instructors will be available if you really need us (malfunctioning microscopes, etc.).
Update for 8:45 AM, Oct. 24, 2005
Some reminders of things we will mention in lab today and tomorrow: (1) Be sure to read over the handout for Exp. 8. This gives a lot of explanatory information that we do not have in the lab manual. (2) For Wednesday & Thursday this week, read over the introduction to Experiment 11. (3) Also, as mentioned below: Between you and your partner, try to bring in a water sample and a soil sample (outdoor samples only!).
Update for 9:15 AM, Oct. 18, 2005
(Updated further at 8:15 AM, Oct. 19)
Finally, the first take-home problem set is being passed out Wednesday and Thursday this week! It is due in one week at the beginning of lab (before the lab lecture starts). This has to be worked on outside of lab and on your own! We can go over any specific questions about the problems next Monday & Tuesday. It's all the kind of thing you will have considered through this week, including a phage quantitation problem.
The "official" key to the twelve Experiment 7.1 species is posted here.
The handout that is being passed out Wednesday and Thursday this week (to go along with Experiments 8.1 and 8.2) is also on the web here.
Looking ahead to next week, specifically Wednesday & Thursday, Oct. 26 & 27: We are getting into the enrichment & isolation experiments which are 10.2, 11.1, 11.2, and 11.3. (We will not do 9.3.) Between you and your lab partner, please try to bring in a soil sample and a water sample. Both must be from outdoors – no drinking or aquarium water or potting soil! The instructors have always brought in samples in the past (and will still do so), but use of only these samples has not resulted in much "diversity" among the organisms isolated.
Information which supplements the introduction to Exp. 11 in the manual can be found on the web here. Our initial lab lecture (coming next week) 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.
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 (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. The whole process 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.
Update for 1:45 PM, Oct. 10, 2005
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.
Here are a couple things that have come up over the years regarding understanding some of the material taught in Bacteriology 102:
Update for 5:45 PM, Oct. 4, 2005
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 Exp. 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 (which in this case just happens to be fluorescent – i.e., able to glow under a U.V. light) is produced by the organism on medium than on the other. We unfortunately "give it away" in the lab manual when it comes to the reasoning behind this demonstration. An illuminating photo is shown 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 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 12:45 PM, Sept. 28, 2005
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 can be helpful:
Update for 8:45 PM, Sept. 20, 2005
This question always comes up about heat-fixing: What really makes the cells stick to the slides? Click here for the fried-egg analogy.
Going along with Experiment 4 (Wed. or Thu., Sept. 21 or 22) is Appendix C (Dilution Theory) and also page 118 which has the directions you can always refer to for the pipettors. Some feel that our "second dilution-plating web page" (along with the first) tends to explain "dilution theory" more clearly than Appendix C.
A few semesters 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.
As will be mentioned in lab this week (Wed. & Thu.), 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. 26 or 27. Our first set of practice dilution problems should be worked on for the next lab; these problems are on pages 122 (example no. 2) and 168-169 (nos. 1-8) plus one more that will be given in lab this week.
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.
Update for 7:45 PM, Sept. 13, 2005
For Lab 4 (Mon. or Tues., Sept. 19 or 20), 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 the "dilution theory" recently covered in Exp. 1, a fairly simple explanation is found in our "first dilution-plating page" on the web; click here.
Update for 8:45 AM, Sept. 8, 2005
For Lab 2 (Mon. or Tues., Sept. 12 or 13) be sure to look over Experiments 1 and 2 in the Lab Manual, and also read Appendices A and G.2. Relating this to the lab schedule, note that we are doing Period 1 of both Experiments 1 and 2 at the first lab session this week.
Update for 11:00 AM, Aug. 4, 2005
Your first lab session for the fall semester will meet on Wednesday, Sept. 7 or Thursday, Sept. 8 – 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 office hours (in 20A Old Biochem. – the very small room adjacent to the lab) will be Monday and Wednesday afternoons 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 firstname.lastname@example.org.
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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