M465:ThinkingTime

January 7, 2013

Scientists in the field of environmental microbiology investigate the microbial organisms present in natural habitats such as lakes, streams, soils, oceans, and animal and plant hosts. How is this kind of microbiology different from traditional microbiology? Two important distinctions: 1) the focus, instead of on model clonal isolates, is on the community of microbes present and 2) the use of techniques that allow for the analyses of community function in situ. Today we will present you some background on microbial ecology and environmental microbiology – the techniques, the questions of interest, and how you can use one to answer the other. We will then focus on a case study of particular relevance to this course to get your mental juices flowing. After a short break, we will begin to teach you how to read a scientific paper, starting with some background literature specific to the farm habitats we will visit. As a final goal today we will form our groups for our research projects.

For some fun, check out the radiolab podcast of “Guts”
http://www.radiolab.org/2012/apr/02/

And here is a cute quiz on bacteria that are “good” -- test your microbe IQ!
http://science.howstuffworks.com/life/cellular-microscopic/bacteria-quiz.htm

January 9, 2013

We continue researching and reading background literature today with the goal of developing a hypothesis and some aims/methods you can use to address that hypothesis. At the beginning of class we will cover some basic techniques in detail (16S rRNA use, biolog plates, enrichment in media, antibiotic resistance, biofilms, etc). We will teach you how to access resources for scientific literature and how to keep track of your literature using EndNote. Make sure you download this software ahead of time (on your own laptops via http://iuware.iu.edu/).

We will also be providing you with a rubric and template that you will use for your draft proposals so that you get a sense of what we expect. These short proposals (less than 4 pages, double spaced, 12 pt font) should encapsulate your project for this semester but not be exhaustive. For example, we don’t require a complete methods section with protocols but would like a list of the techniques you’d use to answer the question. Along with the proposal you will also submit a reagent list and a timeline. These will help us have the tools available to help you answer your questions and will keep us on task throughout the semester.

Weird but true!: fecal transplants
http://science.howstuffworks.com/life/human-biology/fecal-transplant.htm

January 14, 2013

Today your draft proposals are due to your instructors at the end of the laboratory period. First, we will put our minds to work on another case study in the first half of class. The second half of class is dedicated to finishing your draft. Remember to schedule a time and date to meet with your instructors before heading out.

Case study: Bacteria in cystic fibrosis

January 16, 2013

Today your final proposals in written form are due at the end of class. During the first half of class you will present your hypothesis and your methods to your colleagues in the class via a short presentation (each group will present together). These presentations should be 10-15 minutes in length and should cover the motivation behind your proposed research (background, why anyone should care!), the hypothesis or question you are addressing, the methods you plan on using and the environments you plan to sample. The goal of this presentation is to 1) know what your classmates are investigating so that you may compare results/techniques during the semester and 2) be wowed by the breadth and depth of interesting projects that you can perform on just one farm!