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Course Description and Goals

The Laboratory Notebook

Lab Reports

About Group Work

Student Assessment

Grading Scale

Class Time: Wed. 12:30-6:00 p.m.

Required: Student Lab Manual (supplements to be added as semester progresses)

Molecular Biology 312 is a laboratory course in recombinant DNA technology. In this course you will have the opportunity to perform many of the laboratory techniques currently in use in molecular biology research laboratories today. Furthermore, you will be performing these techniques as a natural consequence of undertaking a semester-long gene cloning and expression project. By completing the project, you will learn first hand how researchers bring a variety of techniques to bear on the resolution of a larger research problem. You will also experience the way in which the results of one experiment must be correctly interpreted to enable you to proceed to the next step in the project.

Unlike many classroom laboratory experiments, the project you will be undertaking this semester has never been done before. Your work here will be truly new, and the information that you collect has the potential to make a contribution to an ongoing research project. You will be cloning a yeast gene by PCR, setting up a system to allow expression of that gene in vitro (i.e. in a test tube as opposed to within cells) or in bacterial cells, and then using that system to express the protein your gene encodes. Each group will have a different construct to create. If all goes well, at the end of the semester we will use the proteins generated by each construct in protein interaction experiments which we will conduct as a class.

This project has been designed to complement and corroborate the work of the Lycan research lab here on campus, which is studying the yeast protein Yar1p and the proteins with which it interacts. By participating in this research in a classroom setting, you will get a taste of what day-to-day molecular biological research is like. Some of you may decide that you want to explore this research further, as an honors thesis project. (If you're interested in that option, be sure to come and talk with me about it!) More importantly, all of you will leave this semester with a more concrete idea of these techniques than you could obtain from a textbook. When you read about "gene cloning" or "PCR" or "recombinant DNA technology" in the newspaper or online, you will have a sense of what's involved in these new technologies.

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Over the semester you will generate a significant amount of original data. You will need to develop the habit of recording your data accurately and in sufficient detail to allow you (and me!) to interpret your work. This is particularly important in this laboratory, since you will be conducting original research. To get you started on this task, you have been provided with a 3-ring binder containing: 1) this lab syllabus and a tentative outline for the semester, 2) the first two weeks' worth of your lab manual (containing background and protocols for each experiment), 3) a set of appendices with information on some of the equipment and reagents we'll be using this semester, 4) a set of dividers, and 5) some notebook paper. (By the end of this week, please be sure to make your $5 contribution toward the cost of providing this manual. You may pay either me or Sharon.)

What you should do immediately: check to be sure that your notebook contains all of the above. Label and organize the dividers as you see fit. Finally (and very importantly!!) label the outside of your notebook with your name, "Bio312," and "Fall 2000."

What you should do before each lab: Review your notes and data from the previous week. With your lab members, complete your lab report and get it ready to bring to lab. Then, read through the background and protocol for the lab you'll be conducting. Make notes to yourself in the margin, highlight or underline sections of interest, etc. In your lab notebook (in the notebook paper section), make a flow-chart for yourself with an outline of the procedure. Make a xerox copy of this flow chart to turn in at the beginning of lab.

During lab: When you arrive, compare flow-charts with your group members to be sure you're all "on the same page." Turn in your group lab report and your individual flow-chart before lab begins. Distribute responsibilities within your group for the day's work. As you go, use your notebook to record any notes you take during the "lab lecture," changes you make to the written protocol, starting and ending times and actual temperatures for incubations, observations you make during the procedure, and any data you collect. Finally, before you leave for the day, use the department's xerox machine to make copies of any data tables, photographs, notes, etc. so that each group member leaves with a complete set.

After lab: Read through your notes to be sure they're correct, complete, legible, and interpretable. Look over the lab report questions and make notes to yourself about possible answers. Schedule a meeting with your group to complete your report and prepare for the next week.

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Despite the connection of this work with an ongoing research project, the primary goal of this laboratory is not the creation of a new set of protein expression constructs. The primary goal of this lab is for each of you to gain an understanding of a set of molecular biological techniques: their uses, limitations, interpretations, and underlying rationale. With that goal in mind, each lab will be followed by a set of questions to be answered and turned in each week as your group's lab report.

I do not intend these lab reports to be formal papers. The emphasis should be on thinking and on analysis, not on paragraph construction. Except for your final report (see below), your lab reports should simply answer the questions at the end of the protocol, in order. They should be typed on a word processor, spell-checked, proofread, and double spaced so that I can add comments. All graphs and tables required in the report can be added separately, either drawn on graph paper or done on computer. All the data that you use to generate a graph must be included as a table in your lab report. For example, if you graph the distances certain fragments migrated, you will need to include a table identifying each fragment and the distance migrated. (This wouldn't be included in a formal manuscript, but I need it to check your work.) In addition, all calculations that you do to answer the questions must be included and carefully labeled, either within the report or appended at the end.

Most of your lab reports will not require substantial writing revision, but they will require substantial data analysis. The analysis of your data should always be done in consultation with your lab partners. If you find that you are getting stuck, you may also wish to consult with me. You are more than welcome to do so&endash;I enjoy these discussions very much. However, you will need to plan ahead for this in order to use my office hours or arrange with me for another time. I will not be available on Wednesday mornings for these discussions, since I will be preparing for the coming lab. If you don't discover until Tuesday night that you are stuck and need help, you will be out of luck!

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By the beginning of the second week of Bio312, you will choose or be assigned to a small group of 2-3 students. These will be your colleagues for the semester. You will work together during the Wednesday afternoon lab sessions, and each week you will turn in a group lab report on the previous week's work. These reports will receive group grades.

The reasons for using group work in this laboratory are two-fold. First, the project you will be undertaking is ambitious and will be very challenging. It will be particularly challenging because most or all of the techniques you will be performing will be new to you, and because you have a limited time frame in which to work. Given these constraints, it would be close to impossible for any one person to succeed in isolation. Your colleagues are there to provide not only additional sets of hands but also additional brains to keep track of what you're doing and why. Second, professional science is a collaborative exercise. Scientists routinely design experiments, analyze data, and write papers in groups. They do this for the same reasons as yours&endash;the work is difficult and challenging, and a single person working alone is very unlikely to succeed. In his acceptance speech for the Nobel Prize for the structure of DNA, Francis Crick commented that the reason he and Watson had arrived at the solution, and Rosalind Franklin had not, is that he and Watson were each other's constant critic, challenging the other's ideas and thinking, while she was working alone.

For students and for professionals, working collaboratively presents special challenges. Some collaborations work very well and are maintained for years or decades. Others last for the duration of a single project, and still others are not productive at all. How can you make sure that your group works effectively together, and that you learn as much as possible from this course? Talk with your group about this. Chances are that each of you will have experiences from prior courses. What worked well for you in the past? What didn't work as well? What strategies could you employ from the beginning to improve your chances of succuss?

To help balance group and individual work, and to ensure that the grading is fair and an accurate reflection of the learning that must occur at the individual level, I have also included individually graded course components as follows:

• The most significant of these is the final exam. One quarter of your grade will be based upon your individual performance on this final, which is built directly on the work you have done in your group lab reports. This is a final for which you quite literally prepare all term, and students who have conscientiously contributed to their group's understanding and analysis of the data over the term always excel in this exam and students who do not, do not.
• You will also submit individual flow charts at the beginning of lab each week outlining the procedures for that week's lab. These flow charts will be graded for completion and accuracy, and you will use them at the beginning of each lab to compare notes with each other and create a group plan.
• Your lab notebook will be graded for completion and accuracy twice during the semester.
• A portion of your course grade is based on your participation. This will be based both on my assessment of what takes place on Wednesday afternoon and on your colleagues' assessment of your contributions outside of class. I will ask you to assess your and your colleagues' contributions on a formal basis at least twice during the semester.
• Finally, in situations where it becomes apparent that a student is not contributing equitably to a group's work, I reserve the right to adjust that student's overall course grade accordingly.

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Your course grade will be based on the number of points you earn over the course of the semester. Available points will be as follows:

Note: I would prefer not to use weekly lab quizzes, because I don't like the atmosphere they create. However, if it becomes apparent to me that students are arriving in lab unprepared, lab quizzes may become necessary to ensure that preparation. I'm open to other suggestions.

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So that you are not in competition with each other, your work will not be graded "on a curve," but strictly according to the scale above. The exception will be with the final exam. If I write an exam that is too difficult (i.e. one in which the mean score is below 75%), then I will adjust the exam scores upward so that the mean score is 75%.

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