Update for 3:00 PM, May 14, 2006
The average on the final exam was 84.7 (out of 100) – pretty close to the the "average" average! A review of other averages this semester: Quiz 1 – 34.1(/40); Quiz 2 – 35.1(/40); Quiz 3 – 36.8(/40); Lab Report – 47.1(/50); Prob. Set 1 – 9.2(/10); and Prob. Set 2 – 8.6(/10). All sections were remarkably close to each other on each.
You can still pick up your exam and any other things not picked up yet (which are all stapled to the exam) in the lab from 9 AM to at least 1PM each day this week except Friday. You are probably able to access your letter grade for the course on-line now.
The teaching staff thanks you for a great semester! Have a totally cool and glorious summer! Click here.
Update for 7:45 PM, May 9, 2006
You should be able to access your grade for the course by the end of this week. Exams and any other graded items will be ready to pick up in the lab (not the main office) at the times listed here. (Other times for pickup? Just e-mail me.) A key for the final will be posted 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.
Note that there is an evaluation sheet attached to your lab report which is based on the lab report guidelines handout. A lot of people missed the requirement in the guidelines to follow page 149; I didn't get picky and take off about those things, although you should have learned the meanings of genus and species from previous biology courses. I had to learn all that taxonomy stuff back in 5th grade – i.e., 1956! (To see what I was into in 2nd grade, click here.) Also, take another look at the third page of the guidelines handout which lists a lot of things we have seen too much in reports in previous semesters; I am going to have to expunge the word "thrive" from the manual in the next revision.
Info about the average score for the exam will be in our final posting later on in the week.
Update for 3:00 PM, May 4, 2006
Reminder: The scheduled final will be given in 125 Biochemistry at 5:05 PM, Monday, May 8. The lab reports will have been graded and will be ready to pick up by exam time.
Seeing how the 2nd problem set should have been turned in by now – and you may not get it back in time for the exam – you can view the solutions on our website here.
Plan on coming on time for any alternate exam time or review session – especially if it is given on Sunday. The Biochemistry building will be locked all day Sunday, so we will have to be at the door to let you in. Use the door nearest University Avenue on the side of the building by the big oak tree.
For the alternate exam times that we have set up, the exam will take place in the lab.
Here are the times and places for the review sessions conducted outside of lab-time:
John L. will not be around much on Friday or the weekend but will be emailable for sure by late Sunday afternoon.
Update for 3:00 PM, April 26, 2006
If you missed getting a copy of the 2nd take-home problem set (which by the way erroneously indicates it is "problem set #1"), a PDF file is available here for downloading. Remember that the final answers are your own, and the problem set is due next week on Wednesday or Thursday (depending on your lab section).
Here is something to ponder and reflect upon:
Update for 9:15 AM, April 25, 2006
Hailstone photos? Click here.
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 before then. Possible times are indicated on the blackboard.
Here are some items to consider in reviewing for the final exam. When we have a review in lab (Wednesday or Thursday in lab next week, and perhaps another evening session), 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 (i.e., those 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 9:30 AM, April 13, 2006
(with some links added 8:45 PM, April 16)
To reiterate the announcement in lab, you can hand in your report next week – either Wednesday or Thursday, depending on your lab section. Our offer to look over the report ahead of time (as per the syllabus) still stands. My extended open office hours Friday the 14th (9-noon) are also still in effect.
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 as soon as possible!
Be sure to have read over Experiment 17 ("The Final Great Unknown") for the Wednesday or Thursday lab next 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.
Thank you for finding my web efforts useful this semester – i.e., the Bact. 102 site (where you are now) and the related general "microsites" such as dilution theory, bacterial identification, and differential media. These items on the web apparently have been my best-kept secret around here over the past seven years. Also be sure to check out the material prepared this semester by Tim Paustian here (on the department website).
Update for 3:15 PM, April 5, 2006
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. We will be working with the following media next week:
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 are getting for Exp. 14 this week, and 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 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 next 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 8:30 PM, March 28, 2006
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, 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 have ceased doing posters altogether in this course.
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! 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 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 9:15 AM, March 21, 2006
A review sheet to help study for the second quiz is now here. This goes along with the review session scheduled for this evening (see March 10 update, below).
Update for 1:15 PM, March 10, 2006
We have tentatively scheduled a review session for the second quiz from 6:00 to 7:00 PM on Tuesday, March 21 in Room 132 Biochemistry. It will again be run by Loretta Pfannes who teaches in Section 003. Look over the material and bring some good questions! Also, you can email in some suggested topics, concepts, problems, etc. ahead of time! What a deal!
Update for noon, March 8, 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 3:45 PM, March 5, 2006
Looking ahead to the week after Spring Break:
Update for 2:15 PM, March 3, 2006
The first take-home problem set is due at the beginning of lab (before the lab lecture starts) Wednesday or Thursday, March 8 or 9 (depending on your lab section). This has to be worked on outside of lab and on your own! We can go over any specific questions about the problems this coming Monday & Tuesday.
The handout that was 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 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 1:00 PM, Feb. 27, 2006
The "official" key to the twelve Experiment 7.1 species is posted here.
Update for noon, Feb. 16, 2006
Further expanded at 7:15 PM
A years-overdue 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. With blizzard conditions such as what we are experiencing today, I would stay home if I were a student not residing on an operating bus line. Today's material 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.
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 11:45 AM, Feb. 14, 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. We unfortunately "give it away" in the lab manual when it comes to the reasoning behind this demonstration. An illuminating photo 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 7:15 PM, Feb. 13, 2006
A review sheet to help study for the first quiz is now here.
Update for 3:00 PM, Feb. 9, 2006
The first quiz will cover Experiments 1 through 5.3 and also the associated material in the Appendix (especially Appendices B, C and D). Don't forget about the terms, questions and problems in Appendices W, X and Y. (See Feb. 8 update.)
We will have a review session for the quiz at 6:30 PM on Monday, Feb. 13 in Room 132 Biochemistry. It will be run by Loretta Pfannes, a teaching assistant in one of our Tuesday/Thursday sections. Look over the material and bring some good questions!
Update for 8:45 AM, Feb. 8, 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 can 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 8:15 PM, Jan. 30, 2006
(Further updated at 9:00 PM)
This question always comes up about heat-fixing: What really makes the cells stick to the slides? Click here for the fried-egg analogy on an outside website.
Going along with Experiment 4 (Tues. or Wed., Jan. 31 or Feb. 1) 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) tends to explain "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., Feb. 6 or 7.
Also, if you haven't already done so, 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). If you already noticed these listed in the footnote on the schedule and would like to see if you got the solutions correct, click here for the key. (Don't check the key without having done them!) There is also one more we would like to throw out for you to play with that will be given in lab Tuesday and Wednesday this week.
Update for 7:15 PM, Jan. 24, 2006
Tim Paustian – who teaches in the Tuesday-Thursday afternoon section – is putting together a virtual laboratory course based on the current Bacteriology 102. As the semester continues, you will see an increasing number of photos, movies and other things presented on the Bacteriology Department web domain which will make for some great review material. Click here.
Update for 3:45 PM, Jan. 23, 2006
If you are having problems obtaining the lab manual, the procedures for Period 3 are posted here.
For Period 4 (Thu. or Mon., Jan. 26 or 30), 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 recently 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 7:15 PM, Jan. 17, 2006
For the second lab session (Thu. or Mon., Jan. 19 or 23) 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 would be doing Period 2 of both Experiments 1 and 2 on this day.
Update for 3:45 PM, Jan. 10, 2006
Your first lab session for the spring semester will meet on Tuesday, Jan. 17 or Wednesday, Jan. 18 – 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 Monday and Wednesday afternoons between 12:30 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 email@example.com.
Please note that the lab is always closed Fridays through the weekends.
Be sure to look over the rest of the Bacteriology 102 website and the various links, as we will touch on most of these things 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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