Cell Biology
Chemical Ecology
Biol. Problems


Course Overview and Objectives

NOTE: Registration for this course requires advanced approval by the instructor.

The Biological Problems course (BIO485) is intended as an opportunity for you investigate a research question by applying the ideas and skills gained from previous coursework. This requires gathering existing information about your subject (i.e. a literature review), the collection and interpretation of relevant laboratory data, and then dissemination of what you discover via a formal reporting mechanism (written paper, oral presentation, or poster presentation).

The most common difficulty that students have is deciding what question to address; not a surprising problem given that the world is full of interesting stuff. While I would like to give you as much freedom as possible in planning and developing your own experience for the course, my responsibility is to help you have a productive experience in which you can see the organizational structure and a progression of your work. Therefore, when developing a topic to explore in the course, you must keep in mind whether or not,

  1. we have the facilities to conduct the experiments, and
  2. your lab advisor (i.e. me) has the training and background to effectively advise you when things get messy.

To guide you in your preferences, a descriptive list of potential projects is included in the next section. These are projects that I am interested in either because they are relevant for curriculum development or they pertain to my research interests. They cover most things microbial with a strong emphasis on the techniques of analytical chemistry or biochemistry.

The importance of advanced planning…

At this point in your career, you have undoubtedly realized that the block plan forces you to be ready to move on any class project from day 1; there is simply no time to waste pondering what you might like to work on. This is especially true here because lab work always takes 10 times longer than you initially anticipate, and the 3½ weeks for this course are going to be gone before you even know it. Therefore, it is imperative that you plan for this course before the block starts. The outcome of this initial planning should be:

  1. A clearly stated objective or hypothesis.
  2. A list of the materials needed and procedures to be developed or followed.
  3. A tentative work plan.

The importance of prior planning is also important when considering grades for this course. Because the primary objective in the course is for you to have a productive research experience, I am expecting you to have a clear direction of what to do on the first day of class. Not having a clear goal in mind severely limits your chances of being productive in the course and thus makes it very difficult to earn the “A” grade.

      Project Suggestions

The list below is simply some likely candidate projects I think are worth pursuing; however, these are not the only projects that worth considering. Nevertheless, devising your own project may force you into being your own best resource when problems arise. In other words, choosing a subject or project that I don’t know anything about makes me less helpful to you.

Isolating chemical compounds from bacteria
      This type of project involves using chromatographic methods (HPLC, GC/MS, and column chromatography) for detecting and isolating chemical compounds from bacterial cultures. I have been looking at two biologically active chemical compounds, and at this point, we know the compounds exist but have no idea what their structures are. In order to determine their structures, they first must be isolated; therefore, developing part (of all) of an isolation procedure will directly impact future progress in understanding the chemistry of these bacteria. Furthermore, the bacterial species are known to produce a variety of natural products, so there is always the possibility that you might find something else interesting.

Urease as an indicator of soil quality
      Studying the bacterial enzyme urease allows you a choice of experimental methods to work with—anything from isolating soil microbes with urease activity to characterizing urease variants by electrophoresis. I am interested in this system because urease is linked to soil nitrogen cycling and is used as an indicator of soil quality. The agricultural applications of urease and the variety of tools to study it make this an attractive system to use in our biology and biochemistry curriculum.

Computer modeling of cellular metabolism
      If you are less enthusiastic about wet labs, this is an interdisciplinary project aimed at devising a semi-quantitative model describing the flow of glucose through the metabolic pathways in a cell. This will require you to map out the metabolism and regulatory controls of glucose catabolism and then enter that map into modeling program. In a sense, you will be constructing a virtual cell that can be used to test ideas about metabolic regulation, but more importantly, it provides others with a way to visualize how the parts of glucose metabolism are connected and controlled by feedback loops.

Enzyme assays using nitrophenyl acetate
      This is a project involves the development of a colorimetric assay to compare the catalytic properties of enzymes and small organic compounds and then use this assay to detect enzyme activity in vegetables. To develop the assay, you will need to demonstrate quantitative differences between several enzyme and organic catalysts. You will also need to search the literature to identify likely vegetables that possess esterase or protease activity and then test them experimentally to see if you can demonstrate that they do. The intent is to develop a robust method and experiment that we can use in the introductory biology course.