Syllabus

Research Scope and Background: The Systems

Individual research projects in the Microbial Genetics Project Lab, during the Fall semester of 2003, focused on various species of Rhodococcus. Many bacteria within this genus can metabolize (break down) environmental pollutants and/or convert them to useful chiral molecules. These bacteria can also produce a wide range of useful molecules, including industrial chemicals (providing a "green chemistry" approach to their manufacture), and secondary metabolites such as antibiotics. Students were invited to explore how genes contribute to the useful properties of these bacteria.

Overview

The course consists of these three key components: lab work, oral presentations, and scientific writing. Since communication is an especially important component of scientific research, this course aims to improve your written and oral communication skills. Research activities "at the bench" occupy the bulk of your time; however, you are also responsible for making oral presentations to the class and for writing up your research results in a format suitable for publication in international scientific journals.

Laboratory

In this course, the teaching staff presents to you a series of questions that currently face the microbiology community. The instructors and teaching assistants then work with you to design a research strategy for answering these questions. Throughout the semester the staff coaches you through your work individually, helping you to design individual experiments, interpret your results, and to overcome technical challenges.

Oral Presentations

To foster the development of strong communication skills, you are required to make at least two formal oral presentations to the class during the semester. Students frequently use overhead projectors, Powerpoint presentations and/or other visual aids for these talks.

Presentation One: Journal Club

The first of these presentations will be in the form of a "journal club" In these presentations, you will read and report on articles from the primary research literature. The teaching staff will help you to identify 3-4 journal articles for this purpose that are relevant to your area of research. During the presentations, you will provide background information on the subject of the paper, providing context for the research to be described and explaining the questions that were addressed in the paper. You will describe the series of experiments described in the papers and show how the data were interpreted, presenting the authors' conclusions while commenting on the strengths and weaknesses of the papers. You are expected to describe the papers in such a way that they "tell the story" of how research in that particular field has evolved recently.

Presentation Two: Progress Report

The second formal presentation will be in the form of a "progress report," during which you will present to your classmates a synopsis of your own research activities. In these presentations, you are asked to describe the background of your research area, keeping in mind that not all of your classmates will be familiar with each other's specific projects. You will then describe your own experiments and whatever data you have collected to that point, interpreting your results as you go. You are also encouraged to discuss problems that you have encountered during your research, as well as your ideas for how to proceed in the future.

As with all aspects of this course, you are encouraged to discuss your ideas with the teaching staff as you prepare for your presentations. The staff also welcomes any requests for comments and feedback on your individual presentations.

Writing Requirements

Written communication has been the standard for disseminating scientific achievements and new knowledge for centuries. A lack of good writing skills would be a severe handicap for any scientist, regardless of skill at the bench. For this reason, students in Microbial Genetics Project Lab are required to take on a number of writing activities, culminating in a final paper that describes your own research.

In preparation for this final paper, you will complete two or three intermediate writing assignments, each of which will focus on the format and content of a specific portion of your final paper. Thus, the first of these assignments will likely focus on writing an Introduction. The next may focus on writing a Results section or a Materials and Methods section. The Writing Instructor and the rest of the teaching staff will coach you through these activities.

The final papers are written in the same format that microbiologists use throughout the world for publishing their own research results. Each paper is expected to contain:

• An introduction explaining the background and significance of your research area, reviewing the relevant literature and clearly stating the goals of the research to be described.
• Next, you will describe the experiments that were carried out and the data you collected in a 'Results' section. You will describe many of the procedural details of the experiments, however, in a separate section of the paper, entitled 'Materials and Methods,' which is often placed before the 'Results' section in a formal paper.
• This will be followed by a (hopefully) insightful discussion, in which you interpret your data, formulate models to explain your observations, and relate your own work to that of other researchers in the broader scientific community.

Grading Policy

Grading in this course is based on your performance in the areas summarized below.

Although students in this course typically work in groups of two, individual students are graded independently.

The most important theme in grading this course is whether you demonstrate an understanding and appreciation of the material in question.

• In the lab, do you understand why and how each experiment is being carried out?
• During oral presentations, have you carefully thought about the subject being presented and its implications
• Does your final paper demonstrate an understanding of not only the specific research project, but also how it fits into the greater body of knowledge in the scientific literature as a whole?

Progress, Skill, Effort, and Lab Notebooks (40%)

40% of the final grade will be based on how you perform in the laboratory. You do not necessarily have to complete your assigned research project, but you do need to demonstrate a basic level of competence and a genuine effort to extend the research as far as possible. Not everyone enters this course with the same level of laboratory research experience. The staff recognizes this and encourages you to "make the most" of your own skills. Your effort to expand your knowledge beyond the immediate need of the experimentation will be reflected favorably in this portion of the grade.

Also, you are expected to demonstrate good "team effort" -- working with your teammates to move the project forward. Everyone is expected to carry his or her share of the burden.

The Lab Notebook

In addition, you must keep a lab notebook. The notebook is very important as it is key to good experimental practice. Each lab partner should keep his or her own notebook, which will eventually contain all the data collected by the whole team. In this way each partner can consider the results independently.

Refer to the Lab Notebook Guidelines and Recommendations for specific information on how to use, keep, and maintain a viable lab notebook.

It is worth noting that the teaching staff is available, in part, to help you debug your experiments. Not being able to describe precisely what was done will make this task very difficult. The TAs will check the notebooks for completeness periodically. They must be current. You are responsible for having your previous day's entries completed every day.

Depending on the progress you make in your research project, future Project Lab students, UROPs, or graduate students may one day wish to pick up where you left off, trying to extend your findings even further. Alternatively, future researchers may be interested to learn how you solved a specific technical problem, how you carried out a certain experiment, or what protocol you used for a given assay. In any of these cases, scientists would need access to your lab notebook. To make this possible, you should plan on turning in your notebook (or a good photocopy of it) to the professor at the end of the semester.

Lab Hours and Attendance

You are expected to attend class every day during regular lab hours, 1 p.m. - 5 p.m.

You will receive a lower grade in this class if you do not show up on time. In the event of an emergency or illness, you must contact the Instructor or one of the TAs.

You may wish to stay after 5 p.m. on occasion. The TAs will stick around for a while after 5 p.m. so that students may complete the day's experiments. However, the TAs will not look favorably upon you if you need to work late because you did not arrive on time or wasted time during the normal hours.

Occasionally you may want come to the lab on weekends. Working in the lab at odd hours can be done, but only at the discretion of the TAs. The TAs will notify you of the hours when one of them will be in the lab. Under no circumstances will you be allowed to work in the lab when no member of the teaching staff is present.

Lab Meetings and Oral Presentations (20%)

On Monday and Friday of every week we will begin class with a group meeting in the afternoon. During this lab meeting we will discuss issues of general concern, explain protocols and strategies, and you will have the opportunity to hone your presentation skills through progress reports, journal clubs and other presentations.

For a journal club you will be asked to read papers from the primary literature that deal with a relevant topic. During the session we will discuss important issues raised by the papers, and come up with new experiments to address the problem.

You will also be asked to carry out a literature search dealing with your specific research projects early in the semester. The purpose of this exercise is:

• To ensure that you have a firm understanding of the background, principles and issues surrounding your projects
• To ensure that you gain experience in research-related literature searches
• To spark your creativity in finding alternate strategies to achieve your goals or to uncover new and interesting approaches to the central questions in each project, and
• To give you an opportunity to improve your presentation skills while working as part of a team.

Each group will also have ample opportunity to discuss your work with the entire class in lab meetings. We will discuss progress as a group and address common problems that arise.

Grades for the oral presentations will be based on your demonstration of a firm understanding of the subject in question, the clarity of the presentation, and the mechanics of the presentation itself (use of visual aids, speaking style, etc.).

Final Paper (25%)

You must submit a paper by the end of the term, describing the progress and results of your experiments in this course.

This paper should demonstrate a strong level of understanding of the topic researched during the semester, and should be based upon experimental data. It need not be an exhaustive description of everything that was done or attempted during the semester.

The best papers frequently discuss only two or three key experiments that occurred during the semester. For more information, see the description of "Writing Requirement" for this course. The paper must be turned in on time, in ses# 64. Late papers will be marked down.

Grades for the final paper will be based on your demonstration of a firm understanding of the subject in question, the clarity of the writing, and the mechanics of the presentation itself (use of figures, writing style, reference to published research, etc.).