840:153g/2008

Course Overview

This page is the PRELIMINARY homepage of the course titled "840:153g". Current version: Fall 2008! The page and course contents are still under development - please check back often!

We have 16 students in class which will work in teams of two throughout the semester. Each team will clone a hop (this is the name of the plant :-) gene, amplify it in E. coli and verify the integrity of a functional gene.

As a student, you have to select a gene from the NCBI database and clone the coding region only (no introns are allowed). In your team, you need to develop a strategy for cloning the gene, including a procedure for verification that you actually cloned the full coding region of the right gene. The approach must be written up in form of a research proposal and approved by the instructor before lab work can commence.

Your team will need to develop a website at OWW in which you describe your project (in form of the proposal). The project description should make up the first page of the online notebook. I also require that you write a DAILY online lab notebook (once lab work has started) for EACH and EVERY lab session. This online notebook must contain all procedures carried out during the lab session, including description and discussion of results. It should also contain a brief description of the steps you planned for the next session and material needed.

Students will be introduced to basic techniques in DNA cloning and protein analysis. The principles of gene cloning and DNA manipulation will be addressed from a practical view, with an emphasis on trouble-shooting and applications in agriculture and health care.

Upon completion of the course, you will

1. understand how gene sequences are translated into protein in different organisms
2. conceptually understand how to manipulate DNA and create recombinant proteins or modify protein expression
3. be able to identify, analyze, and functionally recombine DNA molecules

By taking this course, you will learn how to isolate, analyze, and clone DNA. You will have a broad overview over the most common procedures used in a molecular biology laboratory. You will be able design and carry out simple experiments, document and explain your results. You will have demonstrated that you developed skills in finding and using genomic information stored in public repositories, analyze and summarize your findings, and logically organize and present your data.

The Problem

Here is your story: "You just started your new job in a plant genetic engineering lab. The laboratory manager tells you that the business management department came up with a new gene sequence that has recently been published. The lab manager was asked to produce a GFP-tagged fusion-protein of it in E. coli that can be used in transgenic plants to track down its subcellular location. He just remembers the accession number of the gene but forgot what it was. He asks you to look up the gene in the database and tell him what it codes for (select your favourite hop gene here). Then he asks you as the new research assistant to make a suggestion how to clone it and to advise a detailed experimental strategy to do so. This is why he hired you 6 weeks ago. Since he has to leave for a conference overseas he cannot provide you any assistance until he is back in two weeks. But he expects you to develop a thorough experimental plant until he returns. The only help he can provide is the assistance of the new undergraduate student who started working in the lab just this week. However, since she is new in the lab she has no clue how to do proceed. You two therefore sit together developing an experimental strategy. And you know: when the lab manager is back he expects your plan to be ready to go. And there are you just two weeks left to get this done."

How to Start

Your first team task is to select a gene from hop you want to clone. Select a structural gene from the flavonoid pathway, a flavonoid transporter, or a transcription factor. Each team works on different gene and needs to provide the name of the gene and its accession number. After your selection has been approved by the instructor (by the end of the first week), you develop an experimental strategy to clone the gene and produce the protein.

You almost certainly will identify a couple of gaps in your knowledge that have to be addressed in order to perform this humongous task. Ask yourself (and your team member): What information (about the gene and the experimental procedures) do you need to know in order to clone it? Prepare a list of issues you need to address! Look for information in textbooks and the internet. Develop a plan! Please take into account that the first 2-3 weeks may indeed be spend developing an experimental strategy rather than working in the lab. If you wish, you can view this part as the combined lecture part of the course.

Getting Started with OWW

To get started with your online notebook, you have to apply for an account at OWW (which is free). Please write down your username and password from your confirmation email. After you obtained your account details, please go to the Project Page and start developing your project. There is help available on how to use this WIKI in the left-handed navigation pane and in the top menu bar.

Grading

A large and very important part of the class grade will be based on the online notebook. The notebook will be graded based on completeness, accuracy, and content. It will substitute for a paper lab notebook, although I strongly recommend to keep notes during each and every session (write down observations, calculations, remarks, etc.) The notebook has to be written at the day of the lab! No late entries (even 1 day) will be considered (the system we use gives time stamps !). Since each entry in OWW contains a time stamp and the name of user who writes it, this is very easy for me to monitor. Notebook writing is considered to be part of the work and therefore this work should be done during the lab. There will be lag times while experiments run and you should use those times for writing your notebook. The computer room is right next door.

Finally, I expect each group to clone their gene. If a group does not achieve it, the problems must be explained thoroughly in the notebook and evidence must be provided from the notebook that sufficient efforts have been undertaken to clone the gene. After all this is real science (none of the genes have been cloned) and there is no guarantee that any group will succeed. Therefore, keeping a good notebook is essential. The notebook will account for 40% of the grade and both partners receive the same grade for the notebook, weighed by a peer assessment. Both partners should therefore regularly take responsibility to develop a good notebook.

As the instructor, I will assign another 40% of the grade based everybody's individual contribution during class sessions (including preparation for class, discussion of experiments and results, timeliness, and teamwork). The remaining 20% will be given for the project presentation. One member of each team will give a midterm presentation (before spring break), the other member will give a final presentation (the week before finals). Both presentation should give an overview of what has been done - and achieved - in the project. It will be essential to provide experimental data and discuss them with classmates.

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