Microbial Ecology:
Assignments & Announcements
1/7/09 See you next week!
1/12/09 A schedule of lectures, reading assignments, and exams has been posted here
1/16/09 A copy of the textbook is now on 2-hr reserve in the library. I also put a copy of another book on reserve: 'Manual of Environmental Microbiology', from which we'll periodically have reading assignments.
1/21/09 Please take a look at this journal article, on use of rDNA analysis in microbial ecology: http://aem.asm.org/cgi/content/abstract/64/3/871
(You should be able to access it from on campus, since UI is a member institution for this publisher) Read the abstract and introduction, briefly skim the methods and results, and read the discussion.
2/2/09 As mentioned in lecture today, it has been suggested that the relatively high G+C content in DNA of some thermophiles is an adaptation to high temperatures (e.g., see page 295 in the textbook). There is also evidence to the contrary, e.g. the following article (completely optional, I'm just listing this one in case anyone's interested in reading more about this) Hurst, LD. and Merchant, AR. High Guanine-Cytosine Content is Not an Adaptation to High Temperature: A Comparative Analysis amongst Prokaryotes Proceedings: Biological Sciences, 268(466) 493-497, 2001.
2/2/09 Here are review questions for Exam 1. I will add a few more questions to the list tomorrow and/or Wednesday, so please check back to make sure you have the full list! But meanwhile, these are to get started. For our review session in class on Wednesday, 2/11, please bring TWO TYPED COPIES of the questions with your answers to class: one to hand in, and one to keep and make notes or corrections on during the review session. The copy you turn in will be worth 10% of your grade on the first exam. I won't grade them per se, you'll get the full 10 points just for turning it in, but please do your best for your own benefit!
2/4/09 Several more review questions have been added to the list, make sure you include these in your study and turn them in also! The list is now complete, and no more questions will be added for this exam cycle!
2/10/09 Here are some sample questions that are typical of what might show up on the exam! You don't need to turn these in. If you are comfortable with the review question answers, it should be pretty easy to come up with correct answers for these sample questions. We can discuss them on Wednesday in class.
2/12/09 As promised, here is an example of the type of multiple choice question that sometimes shows up on my exams.
2/24/09 ASSIGNMENT! Here is a spreadsheet exercise, as promised, on the subject of population growth modeling. Due in class on Wednesday, March 4. Please don't procrastinate, if you start early you will have at least a couple class sessions (Friday, Monday) in which to ask questions!
IMPORTANT NOTE: Thanks to
those who discovered a typo in the
logistic growth formula on the spreadsheet exercise. I’ve
corrected that formula, and also changed the
exponential growth formula to make the results easier to compare.
Please do the assignment using the
corrected formulas, sorry about the inconvenience!
I’ve extended the due date until Friday of next week.
2/27/09 Leafcutter ants and their fungal (and bacterial) associates are briefly mentioned in today's lecture. Here's where some of those photos came from, please take a look and read the accompanying text:
http://www.blueboard.com/leafcutters/what.htm#7
3/4/09 Here are review questions for Exam 2. For our review session in class on Wednesday, 3/11, please bring TWO TYPED COPIES of the questions with your answers to class: one to hand in, and one to keep and make notes or corrections on during the review session. The copy you turn in will be worth 10% of your grade on the second exam (just like last time). These questions will be all you need to turn in next week, but I will be adding a few more questions by the weekend, which we can also discuss during the review session. UPDATE: the additional questions are now appended to the original list
3/30/09 Reading assignment! Note: this Friday's lecture (4/3) will focus on the subject of 'bioterrorism', and will include tie-ins to other microbial ecology topics including microbe-animal interactions, microbe-plant interactions, epidemiology, environmental biotechnology, etc. The following five on-line readings should be looked at before Friday's lecture (they're mostly pretty short):
1) The Resurgence of Infectious Diseases http://www.thefreelibrary.com/The+resurgence+of+infectious+diseases-a017312938
2) PBS, Frontline, 'Plague War' episode (read the FAQs section, at least)http://www.pbs.org/wgbh/pages/frontline/shows/plague/
3) Third Generation Biotechnology: A First Look http://www.issues.org/25.1/sagoff.html
4) Biotech Regulation (response to the Third Generation Biotechnology article): http://www.issues.org/25.2/forum.html (scroll down to 'Biotech Regulation')
For each set of organisms, consider the three pairwise species interactions within the set (e.g., Pilobolus x cow, cow x Dictyocaulus, Pilobolus x Dictyocaulus) How would you characterize each interaction, using the list of 8 interactions we discussed in class back in late February (neutralism, commensalism, etc...) ? (Grazing may be considered to be a type of predation). You don't need to turn this in, but please go through the exercise and be able to justify your answers. You will probably want to do a little internet research for more background on these interactions, there's plenty out there! Please expect to see a variation of this question on the next exam!
4/16/09 Notes on "Intimate Strangers: Unseen Life on Earth" videos: we've now watched 3 of the 4 videos in this series ("Tree of Life", "Dangerous Friends, Friendly Enemies", and "Keepers of the Biosphere". We'll watch the final one ("Creators of the Future", about applied microbial ecology including antibiotics & plasmids, genetic engineering, bioremediation, microbial detection), on Wednesday May 6. To refresh your memory, especially about how the material in each of these videos relates to topics we've covered in lectures and reading, check out this website: http://www.pbs.org/opb/intimatestrangers/index.html
4/16/09 A comment related to bioremediation and some other topics: as you look through the course syllabus, it's apparent that we don't spend a great deal of time specifically on bioremediation, and a couple of people have asked about this. A few points about that: bioremediation is one of the better known practical applications of microbial ecology (there are many more: e.g., microbial pest control, epidemiology of animal & plant diseases, organic vs. conventional agriculture, waste treatment, biofilms, biomass production etc. etc.) In our allotted time, the primary goal of this course is to gain an appreciation of the scope of this vast subject, and a grounding in the ecological fundamentals that govern microbial contributions to our planet (and maybe other ones). You'll notice that the textbook devotes a large number of pages to bioremediation and biodeterioration; I think to a large extent that reflects the professional specialties of the two authors (check out the back cover of the book). I spend much of my own research time on microbial pest control, and wish we could spend more class time on that, but sadly we can't. But as you progress in any of these more specialized areas, I think you may find the material from this course surprisingly relevant, at least other students have told me that! Here are a few of those more specialized courses that I recommend (there are others): EnvE WS-J419/J519 Hazardous Waste Treatment; BAE 433/533 Bioremediation; BAE 432/532 Bioreactor Design and Theory; PlSc 415 Plant Pathology; Geol 418/518 Geomicrobiology, etc. Thanks for reading my mini-essay!
4/16/09 In lecture (Friday or Monday) we will be briefly discussing another tool to add to our microbial ecologist's toolbox: DGGE analysis. There's a very short paragraph about DGGE in the textbook (p. 195), please read that and also read the information here for a more detailed explanation. If you can read it before Friday, all the better: http://www.microbe.com/dgge-overview.html and: http://www.microbe.com/how-does-dgge-work.html
4/27/09 Take-Home Assignment #2: we have one more take-home assignment, it will be worth approximately 1/4 of your "class participation" grade (the first take-home assignment, which I will return by Wednesday, is also worth 1/4, and actual class participation will be worth the other 1/2). This assignment is due in class (or before) on Friday, May 8 (the last day of class). Details here
4/27/09 Swine flu epidemic in the news: as microbial ecologists, you know more about this emerging problem than most people do (think: disease triangle, host/parasite population interaction, epidemiology, epidemic/endemic disease, disease control, microbial diversity, etc.) Keep up on this disease and what's going on with it, over the next couple of weeks, we'll have a related question or two on the final exam!
4/29/09 Notes on the "class participation" 20% of your course grade for MMBB/Soil 425: the syllabus says this: "class participation" = attendance + constructive interaction, especially when we have guest lectures and/or graduate student presentations, plus occasional take-home exercises. Here's how the numbers work out: of that 20%, 1/4 is your grade on the first take-home assignment, 1/4 is your grade on the second take-home assignment, and 1/2 is the "constructive interaction" part. For the latter, here are the approximate numbers I'll use (100-point scale): 93= almost always in class unless prior notice, and constructive questions/comments; 90= almost always in class, not much to say; 86= usually there; 82= often not there; 78= very often not there. Some variation possible because I especially value your participation for the student presentations! Email me if you have a question or concern about where you fall on this scale.
5/1/09 Here are review questions for Exam 4. Please turn in answers at our review session next Friday (5/8).
By Tuesday of next week, I will also post some questions related to the student presentations and associated handouts, some of these will show up on the exam but you don't need to hand in the answers ahead of time.
5/5/09 A couple of notes on the spreadsheet exercise: A couple of notes: "log" in the formula means log base 10, so use that instead of natural log in your spreadsheet. Actually, the value of C (2.3) is just a constant to relate back to natural log. Don't mix up n (number of individuals in a given species) with N (total number of individuals in all species).
5/6/09 Here are questions related to the four grad presentations, please review them for the final exam! Thanks again to Tom, Malcolm, David, and Stephanie for the great presentations!
5/14/09 An answer key for the final exam is posted here. If you have a question about any of these answers, please email me. Final grades have been posted, the derivation of the semester grade is as explained above and in the posted syllabus. Again, please email me with any questions or concerns! If you want to get your final exam, let me know and we can arrange for you to pick it up.
5/14/09 Final post of the semester! Thanks for taking Microbial Ecology with me, and I hope you have a great summer! -Guy