More course-related links are added during the
semester, and we will eventually get to each one.
UW-Madison Academic Calendar
UW-Madison Schedule of Classes
GENERAL COURSE-RELATED ITEMS:
The Syllabus and Schedule for this semester.
Some frequently-asked-about policies:
·Getting your two credits-worth
·Bad weather policy (Also see the weather
link at the bottom of the page.)
Take-Home Problem Set No. 1
Take-Home Problem Set No. 2
Old Quiz Questions (Exps. 1-7)
Old Quiz Questions (Exps. 8-17)
Sample Final Exam Questions
SOME IMPORTANT HANDOUTS:
Our Microscope Handout is now part of the lab
manual as Pages 90A and 90B.
Lab Manual Pages for Weeks 1 and 3 – in case
you are without the manual on those days.
Catabolism: introductory and more detailed.
LAB LECTURE NOTES:
[If marked *, it is a "rough draft."]
Week 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13+14.
THE COMPLETE VIRTUAL LABS:
[Complete list for the Semester. See the
instructor for updated links if necessary.]
Introduction to the Virtual Lab Experience
Virtual Experiment 3B (Scroll to "Period 4.")
Virtual Experiment 4B
Virtual Experiment 5A
Virtual Experiment 5B:
·Growth Factor Requirement (siderophores)
·Supplementary siderophore diagram
Virtual Experiment 6. This is supplemented
with virtual demonstrations showing flagellar
and gliding motility. (The latter shows a
gliding mass of cells.)
Virtual Experiment 8B:
·Solutions to the problems are posted here.
Virtual Experiment 9B
Virtual Experiment 10 (A handout will be pro-
vided in lab to replace the on-line images,
and a helpful diagram can be found here.)
Virtual Experiment 11D
Virtual Experiment 12
Virtual Experiment 13
Virtual Experiment 14B
Virtual Experiment 15B which deals with the
MPN Method of enumerating bacteria. The
solutions are posted here.
Virtual Experiment 16 which deals with Koch's
Postulates (p. 81).
BASIC METABOLISM & MEDIA LINKS:
Catabolism & Oxygen Relationships:
·Chemotrophy vs. Phototrophy
·Oxygen Relationships Summary
Differential Test Media (mainly pH-based):
·Whiteboard overview (with "O2 relationships")
·Our DIFFERENTIAL MEDIA WEBSITE
has a General Overview and includes basic
media such as Motility Medium, Starch Agar
and Glucose Fermentation Broth.
·Glucose O/F Medium – comparison with
Glucose Fermentation Broth. (Another
summary is here.)
·More about Glucose O/F Medium (for those
who are interested): official web page and
a virtual demonstration.
·Reactions in Modified MacConkey Agar
·Reactions in KIA (plus a new summary
and errors in inoculation & incubation).
·Decarboxylation Test Media plus an
alternate view showing motility in MIO.
·Enteric Test Reactions (other than KIA)
[Complete list for the Semester.]
·General list of procedures
·Tube-to-tube transfers with video
·Three-phase plate-streaking with video
CFU, Colony, Isolate and Strain:
·Definition of colony-forming unit (CFU)
·From CFU to colony
·Definitions of isolate and strain
The Growth Curve (Exp. 5C):
·If not given out as a handout, a revised intro-
duction is here. Be sure to note the third
paragraph which can be clarified in lab.
Mutation and Recombination (Exp. 8):
·Our old handout – HTML and PDF
·Dilution Plating: Pages 1, 2
·Most Probable Number (MPN) Method
Enrichment & Isolation of Bacteria (Exp.11):
·Our old Exp. 11 supplementary worksheet
·Diagram of endospore cycle with how an
endospore can be a CFU.
·Exploitable characteristics of certain bacteria
·Definition, isolation and identification
·Flow chart summary of procedure
·A Coliform Review
·An Official Boil Water Notice
·Basic facts and isolation
·Flow Charts, Tables and Dichotomous Keys
·Handout with an example
(newest updates first)
Monday, May 19, 2014
I'm almost finished grading the exams and will post the scores on Learn@UW as soon as I can. Final letter grades will be sent to the Registrar Tuesday PM or Wednesday AM. I was happy to see that autotroph, organotroph and chemotroph were defined correctly (according to Appendix D) for the most part – as they were relevant to carbon source, electron donor and general energy source, respectively.
Those who defined autotroph the way I mentioned not to in the introduction to that section unfortunately got no credit if that showed up anywhere in the answer; there can be no such thing as "an organism that makes its own food" or energy either. An autotroph would use carbon dioxide in its "food" in order to make organic compounds. A bacteriologist would never refer to an organism's nutrients as "food." We went over these things many times since early in the semester.
Thursday, May 15, 2014
Report Scores Posted
In grading the reports which took awhile and was somewhat subjective, I assigned a letter grade along with some comments on each report. The Bacillus reports appear to have gotten the most comments. I eased up on the usual grading scale (for the reports) and gave points as follows: A=60, AB=58, B=56, BC=54, C=52.
I will still accept late things and grade corrections through Friday afternoon.
Wednesday, May 14, 2014
The reports are pretty slow-going, but I hope to be done such that I can have the grades posted at Learn@UW by Friday noon. I may even have the reports ready to hand back at the scheduled exam Friday.
I noticed that a number of the references have the "old school" way of expressing oxygen relationships and coliform definitions. In the manual we try to give current bacteriological definitions that are (by the way) ultimately based on recent editions of Bergey's Manual which we should be incorporating in 102; perhaps you heard about it in 101. I don't take off if what you cite or quote are directly from reference material.
One certainly should use encylopedias and Wikipedia with extreme caution, but the references they use are among the best.
I often see in references (some of which should know better about various aspects of bacteriology) that Bacillus is characterized as "aerobic or facultatively anaerobic" (the latter sometimes "facultatively aerobic" or just "facultative"). As we now look at things, a given Bacillus culture, strain or species certainly could not be both. We indeed made a point that some species are strictly aerobic and others are facultatively anaerobic; see the bottom paragraph on page 54. Exp. 5A was meant to get us to use bacteriological definitions based on catabolic reactions. See the table on page 22 which takes into account more than just the ability to tolerate oxygen (which is definitely "old school" as we pointed out in February).
Another case in point: Coliforms are often described in the literature as "aerobic or facultatively anaerobic." Like for many species of Bacillus, coliforms are all facultatively anaerobic, as they can ferment and – under aerobic conditions – do aerobic repiration. And coliforms have additional requirements, being gram-negative and lactose-fermenting (with gas along with the acid). It's nice to see the definition extended to indicate the enrichment and detection media that they do this in.
Tuesday, May 13, 2014
SECOND UPDATE for today
The question came up about asking questions regarding virtual experiments, especially those which were not discussed in lab. Like the sample final, there will be a set of questions from those virtual experiments from which you can choose which ones to answer – probably two or three. An MPN-related question (Exp. 15B, which is self-explanatory) may be included as one of the choices, and I will not include an MPN problem anywhere else in the exam.
Tuesday, May 13, 2014
This was mentioned in all of the lab sections but not perfectly clearly in the updates below: The early exams are given in our lab and not at the official place which is in Biochemistry.
Also, don't worry if you didn't sign up. Just come!
Monday, May 12, 2014
Hopefully I'll have these reports graded by the time of the final scheduled for Friday. I'm presently on the Bacillus reports. Some items of concern:
- Vegetative cells of Bacillus can be gram-negative. We were hoping to see this in Experiment 3A with the old culture, as they would be expected to show up sooner or later as a culture of a gram-positive bacterium (such as Bacillus) gets older; note the top paragraph on page 117. Also, we would expect endospore development in older cultures of Bacillus. Therefore endospores would be seen in the center (oldest part) of a colony more than toward the edge (newest/youngest part). Note the steps in colony development which we discussed on the whiteboard as shown here.
- Anything on plates inoculated from a heat shocked soil sample and incubated under aerobic conditions would be expected to be Bacillus. Colony characteristics can vary greatly as we saw in Exp. 7A and also in considering B. mycoides.
- We made a point of saying that any given species (or isolate) of Bacillus can be either a facultative anaerobe or a strict aerobe. See the last paragraph on page 54 and the Lab Lecture Notes for Week 10. We shouldn't imply that both conditions are possible for an organism in the genus Bacillus.
- Also, we don't use common dictionary definitions for aerobe and facultative anaerobe based on whether they "like" or "tolerate" aerobic vs. anaerobic conditions or can grow in either. We got over that in Virtual Exp. 5A in favor of bacteriological definitions (see table on p. 22) and made a good review of it in the last period this semester.
- Amylase production (starch breakdown) is not a feature required to define Bacillus and it certainly has nothing to do with "oxygen relationship." We had positive and negative reactions show up for our Bacillus unknown and known cultures in Exp. 7A.
- Soil, bacterial cells and other insoluble particles do not make solutions; they make suspensions!
Other than these problems which were seen on occasion, the Bacillus reports generally look pretty good.
Saturday, May 10, 2014
Later on this afternoon, I'll put up the scores for the Experiment 17 checklist and catch up on some older things I recently got scores for. And then most of my time in the next few days will be taken up with the lab reports. Glad to see so many italicized the scientific names and didn't say "media is" or "bacteria is" all that much.
Monday, May 5, 2014
This evening I have formatted the grades section at Learn@UW, and you probably see a lot of zeroes. I plan on filling in the grades Tuesday (tomorrow) late afternoon and evening, and you can check to see if I've recorded them correctly on Wednesday. Sorry for the delay!
Bring some good questions this week for a review for the final exam.
Soon you will have the opportunity to evaluate the course for some bonus points to add to your overall score! Stay tuned for an email from the Department which should come in a few days.
Monday, May 5, 2014
A few odds and ends, edited Monday evening.
Why are the organisms in 11B called "non-sulfur" photosynthetic bacteria?
- "Non-sulfur" is only relevant to when they are growing as lithotrophs and one is considering what electron donors they can use. It was long thought that they could not use hydrogen sulfide as an electron donor. However, hydrogen sulfide can be used if it is not in a toxic amount. This is basically what the manual says in the introduction to Exp. 11B. As all organisms need sulfur for varioius reasons (structural and physiological), no organism can do without it as a nutrient, so "non-sulfur" certainly does not mean these organisms can do without it altogether.
- When they are growing as organotrophs, they can use a variety of organic compounds as electron donors. In their medium, we provided sodium succinate as electron donor (and also carbon source) which most other organisms cannot utilize as such.
Still confused about these terms? If you don't have the catabolism handout which was passed out and discussed earlier in the semester, it is on-line here and here. As mentioned before, I would never recommend that anyone go beyond this and memorize any specific pathway or cycle (such as might happen in a lecture course – especially in Biochemistry), but the overall process is summarized on the handout. For the final, make sure you know the definitions of the bold-faced terms in Appendix D.
Every semester about this time I get inquiries (all very similar, like a form letter) about the possiblity of doing extra credit with the hopes of a higher grade resulting from that. I can never go along with that. For one thing, it would not be part of the grading scheme indicated in the syllabus. Also – to make things fair and ethical – I would have to make the opportunity known much earlier to everyone if I did agree with that idea. This is a subject matter-oriented course, and as one can tell, your instructor considers that sacred. I do tend to ease up a little on the final grading scale, and AB's and B's are still very good, respectable grades. Most of you are getting A's on the unknowns. Also, there will be some extra credit things on the final.
Saturday, May 3, 2014
Questions from an old final exam are now posted here.
Following is a list of hints that can help in reviewing for the final (not necessarily in any particular order):
- Links to the old quiz questions and sample final exam are in the links box on the right. These are great for review, and they show that we don't ask about really trivial things (like differences between species, and color reactions). Answers are posted for all.
- You can go through the procedures in the manual, asking yourself "what did I do and why?" and especially noting the things in bold face.
- Appendices that are good to review are B, C, D (especially the bold-faced terms), F and G. There are some good summaries of various media we used in Appendix E, but don't memorize the ingredients!
- Also good are the introductions to the various experiments, especially Exps. 1 and 11C. It can be surprising to find that the introduction to Exp. 1 makes a lot more sense after your experience this semester, and the same goes for Appendix D.
- Remember the big deal we occasionally made about catabolic processes. These things are discussed in a very general way here. This page gives a more complete summary. (Both pages were passed out as a handout during the semester.) As for oxygen relationships, understanding the table on page 22 in the Exp. 5A introduction can help considerably. You would never have to memorize what specific organisms are associated these items, however.
- Don't memorize the colors of test reactions or what specific species do (such as in the identification tables for Experiments 7A and 14A). We did emphasize characteristics of certain groups (purple non-sulfur photosynthetic bacteria, enterics, and coliforms) and certain genera (the characteristics of Bacillus and Streptomyces and how each can produce a distinct type of cell besides the vegetative cell). As mentioned in a previous update, the characteristics of certain types of bacteria which led to our use of specific procedures and media to isolate them is here.
- If the terms genus and species are still confusing, read over Appendix H which includes some of the things that one is expected to retain from general biology courses. A strain is nothing more than an isolate that you know something about; never substitute "strain" for genus or species. Also never use media and bacteria as singular terms (which would be medium and bacterium). This is also pointed out in Appendix I in the guidelines for the lab reports!
- Be sure you can differentiate:
- isolate (the verb) vs. isolate (the noun)
- enrichment vs. isolation
- conjugation vs. recombination
- mutation vs. recombination
- cell vs. CFU vs. colony
- phage vs. PFU vs. plaque
- selective vs. differential media
- And always remember that when you define a term:
- Do not add a description (i.e., additional, irrelevant details) of an organism that goes along with that term.
- The definition should not be so broad as to include more than what the definition indicates. This is sometimes the case with antibiotic; see Exp. 10 for the actual definition. As another example, a phototroph is an organism that utilizes light in its energy production. Don't add any more! Sometimes we see while grading that phototrophs are defined as those that use carbon dioxide as a source of carbon. Utilization of CO2 goes along with the definition of autotroph. In Experiment 11B, we worked with the purple non-sulfur photosynthetic bacteria which utilize organic compounds as carbon source (which makes them heterotrophs) – and also electron donor (which makes them organotrophs).
- Examples and analogies really don't help much. These things along with excess specificity can really ruin a good definition. We can always do away with examples.
- Define the term according to how it is applied in this course!
- Keep the answers to "short answer" questions short. Itemize when you can. Please do not repeat the question as part of the answer.
Tuesday, April 29, 2014
Lab lecture notes for this week and last week (together) are now posted here.
You can sign up for an alternate time (given below) for the final exam in lab – this week or next week. I understand the need to spread out your finals according to the official policy that you can do so in case of a crowded schedule or other conflict. You don't have to email me or give a specific reason for taking it early. If you change your mind about a time you signed up for – or if you haven't signed up for an alternate time – just come at any of the scheduled times; there is no need to email me about that either. I would rather answer emails about subject matter.
Monday, April 28, 2014
Answers to Some Frequently-Asked Questions about the Lab Report
The Guidelines in Appendix I are indeed correct about the necessary shortness of the Materials and Methods section! Keep it short. When looking at published scientific papers (as I have mentioned in lab, and it is also suggested in Appendix I), you will see that a lot of methods in other papers are simply referred to and are not spelled out in further detail unless modifications were made. We can do the same in our reports by referring to the manual for the procedures. The published papers can also be helpful in determining what tense to use in the various sections (present, past, etc.).
By all means, do not have the manual as your only reference! Altogether, at least three would be nice, but two should be the minimum. When referencing the lab manual, as well as other things in book form, you would want to indicate author (or editor), title, year and publisher. Depending on the style of referencing, you would need to put these items in the appropriate order. One way of referencing the manual could be like this:
Lindquist, John (ed.). 2014. Microbiology 102 – General Microbiology Manual for Spring Semester. University of Wisconsin, Madison.
The referencing guidelines from the Helen C. White Library Writing Lab (mentioned in Appendix I and possibly useful for other courses as well) are downloadable on a pdf file here. For referencing, you can use whatever referencing format you are used to, as long as it is applied consistently.
Do not depend on Wikipedia for information! There is a lot of information in the introductions to the experiments! For example, page 107 is referred to in the introduction to Experiment 11A for an explanation about the medium used to isolate Streptomyces. Also, the introduction to Exp. 11C is basically a summary of soil microbiology. Realize that the CFUs you inoculate onto the plates have their origin in the soil – and that endospores can be CFUs! (See page 1 in the manual regarding the types of cells we encounter in the course.)
Regarding the characteristics of the organisms which we made use of (that is, "exploited") in the isolation process: Keep in mind that the lab report guidelines (Appendix I) indicate that these characteristics must be included in the introduction to the report. There is a good summary here, based on the introductions to the specific experiments. (Experiments 14A and 15A are included in this summary. As mentioned in a previous post, Exp. 15A can be substituted in place of 11A, 11B or 11C if those experiments did not work out well.)
How long should it be? There is no page limit. Most turned in over the years have been 4-6 pages. You can double-space if you like. In fact, I can insert comments easily in the blank space if you double-space. (Reminds me of writing papers in high school back when President Obama was a baby.)
Friday, April 25, 2014
Alternate Exam Times, Review Sessions, and More about the Lab Report
As I've mentioned in lab as early as February, we always accommodate individuals who have conflicts or too many final exams on a given day, and I have these alternate times available so far. Of course they would have to be taken in the lab, as our official lab location (which I haven't mentioned yet) would not be available at the alternate times.
·Wednesday, May 14 at 10:05 A.M. and 12:25 P.M.
·Thursday, May 15 at 10:05 A.M. and 12:25 P.M.
Not much is happening in lab during the last week (May 6-8), and we could easily have time for an hour-long review session in each section. We could also (or instead) have one at another time – perhaps Friday that week at a convenient time. That would be our last chance for such a review, as Finals Week starts the following Sunday.
Remember that you will be writing an individual report on your work in just one of the three parts of Experiment 11 – namely 11A, 11B and 11C. Guidelines are found in Appendix I (the last four pages of the manual), and perhaps you can start thinking seriously about it now if you haven't already. It doesn't work to start the day before it's due.
Note the strong recommendation in Appendix I to look over some actual scientific journal papers in Steenbock Library (or other libraries). This is not a requirement to use them as sources of information, but you can see how they are formatted – specifically how they handle tables, figures and references. You're not required to include figures, and you certainly can use the same format for tables that you find in the lab manual. For the tables of results, label them as Tables (not figures or charts), and for any illustrations you wish to provide (which would be optional), label them as Figures (not as photos).
If none of these experiments worked out satisfactorily for you, you can do a report on what you did in Experiment 15A and title it appropriately with "Enrichment and Isolation of Coliforms."
The deadline will be the end of the last week – specifically Friday, May 9 at 5PM. I can check the draft of your report, but that is best done in person – not via email. I will accept e-mailed reports, however.
A very old lab report that has some comments made by the grader is found here. Note that the writer of the report took sample collection seriously and did the exceptional thing by bringing in and testing three samples instead of one. Hardly anyone brought in a sample for anything this semester!
Use Wikipedia and encyclopedias with extreme caution. They are most valuable in indicating references that are reliable. Referencing a student lab report from this or another university would not be acceptable. The lab manual can certainly can be used and listed as a reference!
If you choose to do your lab report on Streptomyces (Experiment 11A) and are looking for references, there is one at Microbiology Bytes that is very popular but not well-written. It mentions that extracellular enzymes are commonly produced by Streptomyces which is correct. However, these enzymes are for breaking down molecules much larger than the compounds that are listed! Streptomyces uses extracellular enzymes to break down large macromolecules like cellulose, starch, chitin, complex proteins, and other such compounds in the process of biodegradation. Recall the concept of amylase in Experiment 7 and how an organism cannot utilize starch (as an energy source or for biosynthesis) unless it is broken down outside of the cell by extracellular enzymes. You will find much better Streptomyces references elsewhere.
If the terms genus and species are still confusing, read over Appendix H which includes some of the things that one is expected to retain from general biology courses. A strain is nothing more than an isolate that you know something about. Never substitute "strain" for genus or species. Also, a formal bacteriological report would never use media and bacteria as singular terms. Following Appendix H also pointed out in Appendix I in the guidelines for the lab reports!
Monday, April 21, 2014
A little more last-minute stuff about the quiz:
- Things to cover this week about Experiments 14A and 15A should not be on the quiz as we haven't gotten there yet, and they introduce a new anaerobic process called decarboxylation. That will be gone over this week for the first time.
- Need a quick review as to what is a strict aerobe and what is a facultative anaerobe? See the table on page 22 which is in Virtual Experiment 5A, and we have used those terms on occasion throughout the semester so far.
- Chemotroph and Phototroph are defined only by the general way they obtain energy: Chemotrophs obtain energy through chemical reactions; Phototrophs obtain it with the help of light. See the table on page 100 which is in Appendix C. (We didn't get into oxygenic phototrophy at all in our lab work.)
Monday, April 21, 2014
I will be in very late today as I am presently attending to car problems in Tomah, Wisconsin. In the meantime I may have occasional access to the internet.
Still questions about the light/dark test we did in Experiment 11B? Follow through the steps in the manual for Period 4. I made a point of reiterating those points as clearly as possible in the lab lecture notes for that week which are posted here.
Wednesday, April 16, 2014
The lab lecture notes are caught up through this week (Week 12), and their links are in the box on the right.
Regarding Virtual Experiment 10: A helpful diagram going along with this week's discussion of the Antibiotic Disk Sensitivity Test can be found here. It is also described in the Lab Lecture Notes for Week 12.
- Antibiotic D would be the antibiotic of choice if the diameter of the zone of inhibition around that disk is a certain minimum size (according to a table such as what is found on the Exp. 10 handout).
- Why should we not consider the possibility of using Antibiotic A? If the culture contained some cells that had gained resistance to Antibiotic A by mutation (those cells are indicated in red), their colonies would show up in the otherwise-clear area around the Antibiotic A disk. There would be no actual "zone of inhibition" after all, as the antibiotic would have no effect on these mutant cells which could possibly continue the infection.
Regarding the term "frequency" used in Virtual Experiment 8B: It is simply the proportion of "cells who did" to the total number of "cells who can (or are able to)" have a certain property. For example, if we have an equal number of donor and recipient cells (such as those in Exp. 8A) in a mixture of cells, the "recombination frequency" would never exceed 50%, as only the recipient cells could undergo recombination. As another example, if we have a culture of a strain of E. coli which contains 1000 cells, and one of the cells was found to be a mutant, then the "mutation frequency" would be 1 out of a thousand or 0.1%.
And regarding the "Enrichment/Isolation Experiments": A helpful review of the pertinant characteristics of the Experiment 11 and 15A organisms is included here.
You may need to review tube-to-tube transfers noting the link to the video.
Wednesday, April 9, 2014
Quiz No. 2 covers Experiments 8A, 8B, 10, 11 (all parts including 11D), 14A and 15A. Old questions from previous quizzes are now posted here, and the answers will be posted in the middle of next week. As before, the numbers of the questions correspond to the Experiment number in the manual, so you can skip the ones that would not be on the quiz.
Lab lecture notes for this week (Week 11) are finally posted, and they can be found here.
Let's have a review session for the final exam! It probably should not be during finals week, but I am up for one – or probably two to accommodate more that could come. Anything that could help understand the concepts better which would arise from these sessions can be posted on-line.
Tuesday, April 8, 2014
Note that you can bring in a sample to use in Experiment 17A which starts next week. What is required of a sample isn't much; see Period 1 for details.
Following are a few notes about on-line demonstrations associated with Experiments 14A and 15A:
- A "virtual demonstration" of selective-differential media for enterics is shown here.
- The membrane filtration method mentioned in Experiment 15A is basically where a water sample is run through a filter, and the filter is plated on a medium appropriate for the detection and isolation of a certain type of bacterium.
- An example: Twenty five ml of a water sample were passed through a filter with the bacteria being trapped on the surface of the filter. The filter was then placed on Experiment 14's Modified MacConkey Agar (which has indicators for lactose fermentation and hydrogen sulfide production). After 24 hours at 37°C, the black colonies seen here are of H2S+ bacteria whose colonies can then be counted and isolated.
- Likewise, fecal coliforms can be detected as lactose-fermenting colonies on a filter which was placed on a medium such as regular MacConkey Agar which was then incubated for 24 hours at 44.5°C (the incubation temperature we used for EC Broth).
- And the API-20E rapid method for enteric identification is shown here.
Monday, April 7, 2014
(updated from the April 3 posting)
The second problem set is provided as a pdf document here if you didn't pick it up in lab. Remember that it is due at the start of lab this coming week. For the first problem (as with other dilution plating problems), simply determine which colony count to use, and apply the correct dilution factor to calculate the answer. You always have Appendix C to refer to, and please do not confuse the terms "plated dilution" and "dilution factor"!
I have to be out of town until late Monday.
Monday, March 31, 2014
Lab Lecture Notes for this week (Week 10) are now posted. I have re-posted the Week 9 notes with corrected Period numbers for a couple of the experiments.
Be sure to look over the previous post (for March 27) which includes a link to the catabolism handout.
Thursday, March 27, 2014
The Second Take-Home Problem Set will be made available next week in lab, and it will be due one week later. Remember that it is indeed "bad form" to work on these problems together in lab. The problem set should be ready to hand in upon returning to lab next week. If you don't pick up a hard copy in lab, you will be able to download it next Thursday afternoon.
You can download the freshly-updated schedule for this semester here.
We will be starting another unknown next week with Experiment 14A, and the associated background handout is posted here. Remember that unknowns are not done in pairs or teams, and each person is given a particular one to work with. This exercise will be hassle-free if you streak well to achieve isolated colonies from which you can pick three pure cultures the following week! Note the series of photos on this week's handout which show five examples of bad streaking and one which successfully follows the preferred three-phase method described in Appendix B.
For Experiment 11B and the very interesting purple non-sulfur photosynthetic bacteria:
- Be sure to look ahead to Period 4 as we will be showing how the purple non-sulfur photosynthetic bacteria are "facultative phototrophs" – and what that means.
- At least some of the tubes we inoculated this week and put in the light will show H2 production. As you may learn elsewhere, these organisms are of interest in the field of alternative energy production. A short video I made a few semesters ago is posted here. It shows gas escaping out of a tube which contains a culture of purple non-sulfur photosynthetic bacteria that had been incubated in the light for 8-10 days. Hear the "pop" when the gas hits the Bunsen burner flame? That's how one can confirm hydrogen production in such tubes.
- Catching up on the on-line demonstration of phototaxis which I should have posted earlier: Here is a video of what happens to the purple non-sulfur bacterium Rhodospirillum rubrum when its light source is cut off for a half-second. The cells respond by reversing the direction of their movement, as if they think they have gotten into a dark environment and need to get back into the light.
- Why are they "non-sulfur"?
Note how we are working through the various ways organisms perform catabolism which is breaking down nutrients to obtain electrons and energy. The two sides of the Catabolism Handout which we made available a few weeks ago are here (page 1) and here (page 2).
Tuesday, March 25, 2014
Quite a bit to do in lab this week. Experiment 11C, Period 2 can actually be put off until next week, and we can save your plates (made last time) in the refrigerator until next week. By all means, do make the smears required for the various stains, but they can be saved until next week for staining and observing. (Remember: "Smears last forever.")
Good stuff is in the lab lecture notes which are now posted for this week (Week 9).
Monday, March 24, 2014
Welcome back from Break! Pretty short, wasn't it?
The lab lecture notes for the period before break (Week 8) are finally "finalized." This week's notes should be up (at least in rough form) soon.
Among a few other things this week, we will finish discussing the table on page 20 (in Week 8's notes); we have already gone through it for Experiment 11B. Also a few words are needed about the Lab Report which will be based on one of the parts of Exp. 11; note the Guidelines in the final appendix of the lab manual (pages 125-128).
As for Problem Set No. 2, that will be made available next week for handing in the following week. (The schedule has it earlier.)
Saturday, March 15, 2014
For when you get to them and work them through, the solutions to the problems in Virtual Experiment 8B are on-line here. Just a couple examples are given to help to explain the concepts and calculations of mutation frequency and recombination frequency. Our old Experiment 8 handout gives a lab-lecture's worth of explanatory material for what we are doing in both 8A and 8B.
Regarding the growth curve which is due the week after break: If you go here and click on the graph in the upper right, you can download a sheet of 3-cycle semilog paper if you didn't pick up any sheets in lab. You would need two sheets, as our data requires at least four cycles. That web page also discusses semilog paper in general.
Be sure to see what is coming up in lab 11 for the week after break. Also note that you will be writing a report on your work in one of the three parts of Experiment 11 – namely 11A, 11B and 11C. More about this when we get back!
Monday, March 10, 2014
Lab Lecture Notes for this week (Week 8) are posted here. Included is a reference that goes along with a demonstration of glucose media which we will attempt this week.
Saturday, March 8, 2014
Experiments 11A and 11C are being set up this coming week, using the same soil sample for both experiments. If you can find a soil sample to bring in, that would be very helpful; you can simply use a clean envelope to obtain the equivalent of a few tablespoons of soil. The dilutions and plating for Exp. 11A can be done first, and then (with an additional dilution blank) we can set up Exp. 11C. Directions in the manual are very clear and will involve a heating step in Exp. 11C.
For Experiment 11B, the three water samples we had last week were from the Yahara River in Madison, obtained February 4 and kept in the refrigerator until lab day.
Regarding Virtual Experiment 10: A handout will be provided in lab to replace the on-line images, and a helpful diagram that will go along with comments in lab is found here.
Thursday, March 6, 2014
A key for checking your Exp. 7 results page (page 34) is posted here.
- A link to photos of the cultures is given below the table on that page as well as a link to some added information (with photos) about Alcaligenes faecalis. So far, we don't have a similar page for Bacillus sphaericus which is also generally non-reactive (and "boring") in most of the tests we ran. Unlike most Bacillus species we come across, B. sphaericus is negative in the amylase test.
- Now you have a reliable data base to figure out a likely identification for your unknown which is due next week.
Wednesday, March 5, 2014
Lab Lecture Notes through this week (Week 7) are posted. See the links box on the right.
About Experiment 7 this week:
- A key to help you "tune up" your Exp. 7 results database (page 34) which you are filling out (as much as you can this week) will be posted late Thursday afternoon, and it includes some photos of the tube and plate reactions. Then you will have good results to figure out a likely identification for your unknown which due next week.
- On another website, the Differential Media pages explain (with color photos) some of the media we use in Experiments 6 and 7 – most notably Motility Medium, Glucose Fermentation Broth and Starch Agar. With Starch Agar and the amylase test, we are introduced to the concept of extracellular enzymes.
- 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 the growth curve experiment – a photo of which is here. Otherwise, the cultures we use in our various experiments (including those where we identify unknowns such as Exp. 7) tend to be typical strains of their species. Never confuse the terms "strain" and "species."
Saturday, March 1, 2014
As an important reminder, be sure to watch the tube-to-tube video again. Click here.
Monday, February 24, 2014
A reminder that the take-home problem set passed out last week (and also on-line) is due in lab this week. Remember that working on take-home items together in lab is really considered "bad form" as one might gather from the box under where you sign your name to it.
About the upcoming quiz:
- As hopefully already mentioned in lab, the format of the quiz is as follows: (1) multiple true-false questions (like most of the review questions), (2) matching items, (3) short answers, and (4) a couple very general dilution problems. We can include definitions of terms in the matching and short answer sections.
- The quiz concerns Experiments 1 through 7, and be sure to include the virtual labs and relevant appendices in your review – especially Appendix B, C and D. Appendix D is full of background material for things we have gone through in lab so far this semester. Pay special heed to the terms in bold-face. Don't worry about knowing any of page 105 for the coming quiz, as we have rarely asked questions about the sterilization of media or equipment on our quizzes and exams, and you are probably not seeing any in the sample quiz questions.
- The posted review questions can be a guide as to how deeply we may go into things. As we will not have gone into detail about the reactions we will observe in Period 2 of Experiment 7 (which will be on the day of the quiz), the only really relevant questions involving Exp. 7 are 7A, 7B and 7E. By all means do not memorize trivia such as the reactions and appearances of specific species or any specific formulations of media.
- We often ask questions in the quiz about aseptic technique. Review the videos which are both linked from this page. Also by now, you should be familiar with smear preparation and the use of the microscope which have reminders in recently-posted lab lecture notes.
Thursday, February 20, 2014
If you didn't pick up the Take-Home Problem Set in lab this week, we have it on-line as a pdf document here. Remember that having done the practice problems ("Virtual Experiment 4B") does help considerably. When figuring out the solution to problems that involve plates made from several different dilutions, keep in mind that we are cautioned (in Appendix C) to count the colonies only on plates that have between 30 and 300 colonies. (Too few colonies are not as statistically good, and crowded plates often are impossible to get an accurate count from.) Also, note how we handle the results from duplicate plates in the practice problems.
Tuesday, February 18, 2014
Here are some Review Questions (mostly taken from quizzes in previous semesters) to give you an idea of the kinds of questions we may ask in the in-lab Quizzes – the first of which comes in two weeks and will cover Experiments 1 through 7 and the relevant Appendices in the manual. The numbers by the questions refer to the experiment numbers.
Sunday, February 16, 2014
I now have reasonably-finalized lab lecture outlines through "week 6" on-line and listed in the "links box" on the right – including the one for the coming week ("week 5") which refers to a general handout on catabolism which is also on-line here.
The first "Take-Home Problem Set" will be put on-line for downloading on Thursday afternoon. Before then, they are being passed out at the end of each of the lab sessions this week. This problem set is to be worked on outside of lab and turned in first thing at the next lab session. Note the introductory directions at the top! Having done the practice problems in "Virtual Experiment 4B" will help considerably in doing these dilution problems.
Here's a hint that may help with the use of the microscope: With your marker, put a mark near the smear that you are going to be looking at. This mark should be easy to focus on, and the cells will be nearby. When you switch to the oil immersion lens, you only need to move it up or down (with the fine adjustment) no more than 1/3 turn. Also, make sure that the 10X lens is clean; a good rub with oil-free lens paper works best.
If the concepts of colony-forming units and scientific notation are troublesome, click here for CFUs and here for scientific notation. If you use Wikipedia to look up definitions of microbiological terms, you may find a lot of misleading information such as what you see for "colony-forming unit" (CFU). Appendix H in the manual can be helpful regarding terminology, including scientific names.
Friday, February 14, 2014
New Addition to update in red.
Here is the slightly revised schedule which reflects more correctly how the Virtual Experiments and "Items Due" fit in during the first several weeks.
For next week, be sure to have read Appendices C & D and worked on the practice problems of Virtual Experiment 4B. Note that there is a link to the solutions, and always feel free to ask about these problems (and other virtual items) in lab. Having done these practice problems will help considerably when doing the First Problem Set which will be available soon for turning in on the week of Feb. 25-27.
Also for next week's lab, read over Experiment 5C and note the special precautions about aseptic technique. We will have time to catch up on the endospore stain in Exp. 3A, Period 3.
Let's get Virtual Experiments 5A and 5B worked on by the end of February in time for the first quiz. These virtual experiments will make a lot more sense after you have read through Appendix D. We will apply the concept of "oxygen relationships" and relevant catabolic processes in various lab experiments throughout the semester including Experiment 7.
- Virtual Experiment 5A on Oxygen Relationships: The experiment in the Bacteriology Department's Virtual Manual that we use for this ("5-3") had to be improved, and it's presently posted for our course here. You will notice on page 23 (in our manual) a table for results titled "Oxygen Relationships and Related Physiological Processes." And you will also notice an "extra" introduction to the concept in the manual – in addition to the one on-line!
Virtual Experiment 5B:
- For media-making, we go to Experiment "5-2" in the Department's Virtual Manual which is here. There are no results to record; just read through the procedure.
- For the example of a requirement for a growth factor, we go to Experiment "5-4" in the Department's Virtual Manual which is here. The table for recording results is at the bottom of page 23. Hopefully soon (at least before the day of the quiz) we will go over the concept of siderophores in lab.
Friday, February 7, 2014
If you find you must miss a lab (due to sickness, interview, participation in an out-of-town athletic event, etc.), please note what we've written below about our attendance policy and e-mailing about what to make-up.
Regarding the coming week in lab (Week 4 on the schedule):
- Be sure to have read over Experiment 4A. Most of you have probably used pipettors in Chemistry to transfer specific amounts of solutions. We use them in our course to transfer suspensions aseptically. (Remember, bacteria are particles, and we could never consider a liquid containing bacteria or even viruses as being a solution.) As noted in Experiment 4A, we refer to page 95 in the appendix for some important points about the aseptic use of pipettors.
- With Experiment 1 (Period 3) and also Exp. 4A, we are getting into the concept of Dilution Theory. Note how we inoculated the soil and water samples into the plates this past week. Next week, we will take into account (1) the number of colonies on these plates, (2) the amount of sample we inoculated (which was 1 ml), and (3) the dilution of that sample; these things will be factored together to tell us how much these samples are "contaminated" with bacteria. Looking ahead to Period 3, you can see how this is done. It should be pretty straightforward, and you have already considered making dilutions in Chemistry utilizing the same principles.
- Appendix C explains the concept of dilution theory, and an easier-to-understand equivalent to this appendix which we have on the web is our first dilution plating page which is especially relevant to Exp. 1 (Period 3) and also our second dilution plating page which goes along with Exp. 4A in which we will be determining the number of colony-forming units per gram of hamburger!
- The "due date" for Virtual Experiment 4B can be extended into the following week. By then, dilution theory will make a lot more sense from what we are doing in lab. Again, for virtual experiments, there is not anything to hand in, and you can check your answers to the practice problems in Exp. 4B by following the link to the posted solutions.
I am sure that going through the videos again will make a lot more sense, considering how we did these techniques this week in lab. Two things to especially keep in mind: (1) not to let the caps and plugs lay on the table during the transfer of cultures and (2) never to have any tube open and upright in the test tube rack while making transfers. If the diagram on page 92 cannot be followed, it is perfectly OK to handle one tube at a time.
Notes you take during the lab lectures and all of the handouts you receive in lab can be inserted into the 3-ring binder which was recommended for your lab manual.
Monday, February 3, 2014
With much better weather it's great to be back in lab again. Regarding Appendices B, C and D in the "Items Due" column on the schedule, each of these appendices should be more appropriately placed with the following week, as they would make a bit more sense that way. (I had already mentioned reading Appendix B for this week, as it will be relevant for the microbiological techniques we will be doing in this week's lab.)
Wednesday, January 29, 2014
New Addition to update in red.
I've been getting a lot of emails about virtual labs and missing the first week.
I thought the Update for Wednesday, January 22 would have been simple and sufficient for Virtual Week and the "virtual lab experience." You can follow it step by step. A careful reading of that (and following through on the links) actually answers nearly all of the questions in the many emails I've been getting.
According to the schedule, Virtual Experiment 3B is associated with next week in lab, and we can get caught up with that in lab next week, as well as anything missed the first week in lab. Actually, what we are doing in lab in the next couple weeks includes things we touched on in the first week. In the "Items Due" on the schedule for next week, please make sure you have read Appendix B. Also, the introductions to Experiments 1, 2 and 3 and also the Gram Stain page on page 117.
If you happen to be without the manual next week (week "3" on the schedule), the equivalent material from the lab manual is here.
By the way, when you get to any website that we may link to for "Virtual Exp. 3B," please don't click "next"! Those "next" links are for individuals who are inching their way through that entire site and that's certainly not us.
What we are actually using for grading in the course is listed at the end of the syllabus. The Fall, 2013 syllabus was included in the manual by mistake, but it is identical to the Spring, 2014 syllabus which we meant to pass out as a handout.
Monday, January 27, 2014
It appears that I may have picked a good week to have our "virtual exercise" with no in-lab session at all this week. Lab manual and supply sales continue through this week. Note the Micro Club's schedule (also with email and website addresses), which is linked from an update on our website.
An hour or two on that should be enough, and we'll be ready to continue with our in-lab sessions the following week (Feb. 4-6). Remember for virtual experiments, there is nothing to hand in, and their substance will increase through the semester.
Presently I'm "stuck" in Rice Lake, Wisconsin because of the weather and roads and hopefully I'll be back some time Tuesday.
Wednesday, January 22, 2014
A reminder that there will be no in-lab session next week on January 28, 29 or 30. In its place we will have "Virtual Week." For this, please go here and check out a few things about the virtual side of our course. Also, there are some additional links to interesting websites that you may like to spend some extra time on.
The next in-lab session will be on February 4, 5 or 6. Hopefully by then, any registration difficulties will have been cleared up.
Regarding the Microbiology Club which some of you may have heard about already: They are in charge of manual and supply sales to the undergraduate courses, and anyone taking a Microbiology course is invited to join in on their meetings and activities. The Club's website is here, and they can be emailed at [email protected]
If somehow you missed getting the schedule for the manual and supply sales which continue the rest of this week and next, click here.
Tuesday, January 21, 2014
Lab Lecture notes for this week are now posted here.
Please note that next week is "Virtual Week." There will be no in-lab session. A link to the details is coming in an Update very soon.
For the following time that we meet in lab (Feb. 4, 5 or 6), please be sure to have read the following:
- The introductions to Experiments 1, 2 and 3.
- Appendix B.
- Page 117 which explains the Gram Stain.
Friday, January 17, 2014
Links to the syllabus and schedule for this semester are now in the "links box" on the right. You will also be getting hard copies in the lab.
If you are without the manual at our first meeting, we have a handout that will be available in the lab which covers the relevant material. It is also on-line here.
Monday, January 13, 2014
Welcome to the Microbiology 102 Website where we find it easy to post course announcements and links to relevant material on the web. These things are equivalent to Course News and Content found on Learn@UW. Eventually we will utilize Learn@UW for posting grades.
Information on obtaining the Lab Manual and other supplies for the semester will be provided by email soon. The syllabus and schedule will be posted on this site, and hard copies will be provided in lab.
Be advised that the course does indeed begin the first week of the semester. Also, the second week will be "virtual week" in which case there will be no in-lab session that week. Details will follow. It should be fun and interesting!
Going along with the Syllabus, here are some good things to know:
- Our attendance policy: We expect you to show up for every lab period, as your lab partner and your observations and understanding of the results and concepts of your experiments depend on it. Let us know if you cannot attend lab for sickness or any other reason. If you do miss a lab, please heed the following before e-mailing your instructor with questions about what material was missed and what to do about making it up: Consult the schedule and the manual regarding the lab material that was missed, and make sure that you see the results of the procedures that were done in your absence when you get back. We will often repeat important procedures in a coming lab period. We can save the things you inoculated and also afford the opportunity to start any "unknown" you missed getting on the day you were absent. And note that the Lab Lecture Notes will always be posted on-line (sooner or later, hopefully sooner).
Two unexplained absences in a row will tell us that you have dropped the course.
Getting your two credits-worth: Like any course, it is necessary to keep up with things right along. Before we had to convert to the present system where a number of laboratory experiments were converted to virtual exercises, the lab met the usual four hours a week during a regular semester for the two credits. Now, the course only meets once a week (for two hours) for the in-lab experiments. So – outside of the lab – you should plan on spending a good amount of time
We will be explaining more about what is expected for the virtual experiments in the coming weeks.
- reviewing things,
- looking ahead to the next lab period (according to the schedule), and
- working through the virtual experiments.
Our lab presentations (opening lecture with good stuff on the whiteboard), the on-line lecture notes (to "tune up" yours), and the updates and links (on this page) should help to amplify the schedule and clarify the subject matter. Hopefully, the experiments we do and their results should make sense – including what they mean in light of the "big picture" which we hope to develop as the semester continues.
- Our Bad Weather Policy for Microbiology 102: In case of inclement weather, especially when the roads are clogged and buses won't run, you should USE YOUR BEST JUDGEMENT about coming in or not. Unless the University publicizes the fact that it is closing down due to bad weather conditions, our course is still on, but do not feel that you must come in if it presents a possible danger. See our link to local weather conditions and forecast below.