“A Week in the Life of …..”
Microbiology Final Exam, Spring 2017
This is a take-home, open note, open book, closed person exam. In other words, do not discuss anything about this test with your peers, other professors, etc.! If you have any questions at all, please come ask me. Any exams that resemble each other too closely will receive failing grades. Answer the following questions as completely as possible, but avoid writing more than 6 typed, double-spaced pages. In other words, aim for around ½ page per question. Some questions will take more space, others will take less.
You will be able to answer some of these questions using your textbooks, and others using your assigned external readings, but some questions will require deeper research. Cite all of your sources. Please place a literature-cited section at the end of this test (it will not be counted towards your page total). The exam is due via email no later than 5:00 pm, Saturday, May 7 (2016!). Good luck, and let the test begin!
You are (insert your microbe name here), and this is about to be a very busy week. You currently live in soils overlying the Centralia, PA mine fire. You spend your days looking for food, eating food, and reproducing. Life is good.
1)Are youGram positive or Gram negative or something completely different? Given this answer,describe your cell wall structure, including the names of any important cell wall components. You may draw a labeled picture, if you prefer (10 points)
2)Describe one type of adaptation that you most likely have in order to survive in Centralia’s thermophilic environment. (5 points)
You are having fun taking a steam bath in one of Centralia’s anthracite smokers when suddenly, with a great ‘whoosh,’ you, your neighbors and the surrounding soil are scooped up by a senior capstone research student, placed in a sterile tube and then put into a cooler full of crushed ice for the trip to the lab. Brrrr! You really wish you were a psychrophile. They’d love this kind of treatment.
3)What is a psychrophile? Describe one adaptation that psychrophiles use to thrive in icy environments. (5 points)
When the tube next opens, you have just enough time to register that you are now in a laboratory before you are unceremoniously dumped into a complex medium.
4)Why is a complex medium a good initial choice for growing up unknown bacteria? (5 points)
5)State one metabolic strategy that you normally utilize in order to get energy from your environment (Are you a phototroph, lithotroph or a chemotroph? Do you utilize aerobic respiration, anaerobic respiration, fermentation, etc.)? (5 points)
6)If you could help your captor design the perfect culture conditions for your continued survival, what would you say? List three culture conditions that you feel would make your complex medium even better for you, and justify those conditions using information from the literature. Make sure that you take into account your normal growth style (20 points)
The research student next takes around 1 mL of the liquid culture in which you are growing (you, fortunately, avoid being snagged, but some of your progeny are not so fortunate) and isolates genomic DNA from the sample for metagenomic analysis.
7)Which gene should the student use for this analysis, and why is this gene a good choice? (5 points).
“Drat!” the student exclaims a few days later. “The Phred scores are lousy! I shouldn’t use this data at all! ”
8)Describe what a Phred score is and why it is important to use sequence data with good Phred scores for phylogenetic analyses. What cutoff point would you use, and what does that cutoff point mean? (10 points)
9)The student repeats the analysis, and generates the data that you used in your Centralia Metagenomics Case Study. Look at the temperature and chemical composition of each of the original soil samples (refer to your class handouts if you can’t remember how to do this…not to your classmates!). Given what you know about your microbe’s biology, physiology and where it is normally found, would you expect to find it in any of the Centralia sites? Explain. (20 points)
Meanwhile, back in the flask, you are getting really bored and have decided to set up a biofilm on the side of the flask to pass the time.
10)Describe the steps by which you and your new best friends can form a biofilm (10 points).
While you are in the biofilm, you encounter a rather good-looking Streptococcuspyogenes that is willing to swap genetic information with you. How much fun can one small microbe have?
What a week! As the sun sets over the New Science Building you reflect on the variety of evolutionary adaptations that have made it possible for you to survive this week’s various twists and turns. Hrm, speaking of evolution, you wonder what that gene that Streptococcus just gave you actually does……?
11)Give one possibility and tell its possible impact on you, and on humanity (5 points).