BIOLOGY 023 - DEVELOPMENTAL BIOLOGY
SPRING 2000

Required Texts:

K. Kalthoff. Analysis of Biological Development. McGraw-Hill, Inc., 1996.

Leland G. Johnson. Patterns and Experiments in Developmental Biology (Second Edition). W.C. Brown Publishers, 1995

Cold Spring Harbor Laboratory Notebook

Other Texts

V.E. McMillan. Writing Papers in the Biological Sciences (Second Edition). (You should already own this book since it is required for all Biology courses in which you must write papers.

W.W. Mathews, and G. C. Schoenwolf. Atlas of Descriptive Embryology (Fifth Edition). Prentice Hall, Inc, 1998. (Optional)

CLASS FORMAT, OBJECTIVES AND GRADES

New knowledge is being added to basic principles at a very rapid rate in many sub-fields within the discipline of biology, developmental biology is one of these. Unlike some other rapidly evolving fields within biology, however, developmental biology is also a relatively old field of study. Consequently, to become reasonably well versed in developmental biology you need to learn a considerable amount of classic embryology as well as understand the more recently elucidated molecular genetic mechanisms that underlie the development of organisms. I have attempted to incorporate both the classic embryology and recent advances into both the lecture and the laboratory portions of this class. I expect students to learn the classic embryology that will be covered in lecture and the laboratory exercises. I also expect you to learn established molecular mechanisms (i.e. molecular mechanisms that are covered in your textbook) that underlie development.

Part of the lecture portion of the class will be devoted to discussion of primary literature. I expect you to read the assigned papers and to participate in class discussion. I expect to see progress in your ability to critically evaluate experimental data and the conclusions that scientists draw from their data. Because of the specialized and technical nature of many of the modern techniques used in developmental biology and because of their requirements in terms of time and equipment, we will be able to use only a limited number of these techniques in the laboratory portion of this class. Most of these techniques are general cell biological and molecular genetic techniques that are adapted to questions in developmental biology. Therefore, you will be able to learn them in an advanced cell and molecular biology laboratory class.

Lecture

The sequence and content of the lectures will follow basically that of the assigned text. Because of time constraints, we will not be able to cover all parts of the text nor will we be able to cover all topics in depth. You will be responsible only for those topics that we cover either in the lecture or the laboratory. Extra readings which are more current than your text will be assigned throughout the semester. You will also be responsible for these materials.

Lecture grades will be based on three exams (25 points each), preparation for class discussions of current literature (20 points) and a literature search and review (20 points).

For the exams you are responsible for all of the lecture material plus the background material for the experimental labs. Two of the exams will take place during regular class time on March 6 and April 3, The third exam will be during finals week on Monday, May 15 at 1:30 PM. There will be no make-up exams. There will be an optional cumulative final during finals week (Friday, May 19 at 12:50 PM). If you miss an regular exam you must take the cumulative final. If you do not miss any regularly scheduled exam you may opt to take the final, in which case, your best 3 test scores will be used to compute your grade.

I will assign reading from the primary literature 5-6 times during the semester. You will have a week to read these papers. We will then discuss them in class. I expect everyone to participate in the discussion. I may give a short quiz on the content of these papers before we begin the discussion. Your preparation for and participation in these discussions is worth 20 points, which is 10% of your final grade.

During this semester I also expect you to skim the current literature in search of interesting articles that are relevant to the topics that we have covered or will cover in class. This is much easier to do now than it used to be. Most journals have Web Sites that supply titles and abstracts of current and recent articles. Some of these sites also allow you to down load the full text of older articles. You should check the titles of all new issues of the following journals:

Development
http://www.biologists.com/Development

Developmental Biology
http://www.academicpress.com/db

Current Opinion in Genetics and Developmental Biology
http://www.biomednet.com/library/go_journal.exe?jcode=gen

Genes and Development
http://www.genesdev.org

Science
http://www.sciencemag.org

Nature
http://www.nature.com

In addition to keeping abreast of the current literature in developmental biology, you are required to submit a literature search and a limited review of a particular topic. The search need only cover the literature published in the last 3 years. The review involves a summary and critical evaluation of five of the papers in your bibliography. This paper should be about 10 double-spaced pages and is worth 20 points. More details about this assignment will be given in class. This assignment is due on Monday, April 24. A good place to search is Pub Med http://www.ncbi.nlm.nih.gov/PubMed

Laboratory

The laboratory sessions are an integral part of this course and you are required to attend. Missing more than 2 laboratory sessions will result in an automatic loss of 5 points from your lab grade for each laboratory missed. Each laboratory session has several parts - there is a lot to do each week. This means that: 1) you must come to laboratory prepared (i.e. read the laboratory manual and the laboratory handouts before arriving in laboratory and plan your time), 2) you must arrive on time and 3) you should expect to stay for the entire 3 hours most weeks. For many of the experiments you will also need to check your experimental preparations on Thursday and/or Friday. Although it is best for each of you to examine your preparations and collect your own data, I understand that this is not always possible. You will be working in groups of 2-3; you and your partners can share the responsibility for collecting data at these non-scheduled times. Pick partners with whom you can work well and with whom you can coordinate schedules.

Laboratory grades will be based on your laboratory notebook, one laboratory report, a practical exam and an experimental design project with an oral presentation.

Notebooks (50 points)

You must keep a laboratory notebook and you must keep it up-to-date. You must purchase the laboratory notebook that was ordered for this class or a similar one with removable carbon copies.

Notebook entries for each laboratory session should include:

1) the date,
2) the title of the experiment,
3) a brief statement about the purpose and design of the experiment and where appropriate a statement of the hypothesis and expected result,
4) an outline of the method and materials that is part of the laboratory instructions; more detailed notes of method are required for parts of the procedure that are not explicitly given in your laboratory manual or laboratory hand-out (for instance how dilutions are done, how much of a particular solution is added, exactly where you made an incision in an embryo, etc.; include the date and time that each experiment was done,
5) results including drawing, tables and graphs, include the date and time that each observation was made,
6) conclusions including explanations of the data, possible reasons for unexpected results and things you might do to improve the experimental design. Your conclusions should include answers to all of the questions that are embedded in the text of your manual and the laboratory hand-outs. Each entry should be dated.

The first two parts of your notes for each laboratory can and should be complete before the laboratory session begins. You should also write down an outline of the procedure for experiments BEFORE you come to lab.

Notebooks are important to me but it is the content, not the artistic quality, that I am interested in. I expect your notes to be thorough, legible and up-to-date. I don't expect them to be overly neat. Please do not waste your time re-copying your notebooks. Your notebooks are not expected to be any neater than mine - you are invited to inspect my laboratory notebook at any time. I will collect the carbon-copy of your notebooks - unannounced - several times during the semester. I will also collect them for grading at the end of the semester. All laboratory notes must be turned in no later than 5:00 PM on Monday, May 8. Notebooks are worth 50 points which is 25% of your final grade. Part of this grade will be an evaluation of your performance in the laboratory. This will be reflective of your degree of preparation and active participation in the experiments, not of your manual dexterity and success in manipulating tiny pieces of tissue.

Laboratory Reports (10 points)

You will also be required to hand in one formal laboratory report. This report should follow the format found in the required writing manual, Writing Papers in the Biological Sciences (Second edition). Reports should be about 10 double-spaced typed pages. Handwritten reports are not acceptable.

Papers may be written on any of the individual laboratory experiments or any logical combination of experiments. For example, you could write a laboratory report on the experiments that interfered with normal Xenopus gastrulation and axis formation. This would include the trypan blue, lithium and retinoic acid experiments. I am assigning only one laboratory report because all of you should know how to write these reports at this point in your college careers. I expect that all of these papers will be done correctly. I will ask you to re-write your paper numerous times if it is not done correctly. Points will be subtracted from your grade for this assignment for each re-write. Therefore, if you don't know how to write a laboratory report you should talk to me BEFORE you hand in this report.

You may hand in this report at any time on or before April 12 (with the exception of reports on the Drosophila Plasmid Rescue experiments that will be due on April 26). One point will be deducted for each day a paper is late. Since you can choose the papers you write there is no excuse for writing a paper with no results. For example, if your embryos do not survive a particular experimental manipulation, you should not choose to write a paper on that particular experiment - wait until you have better results to report. (I expect that you will have some failed experiments. This is OK. It is not OK if all of your experiments fail). I would be glad to read early drafts of these papers.

Practical Exam (10 points)

There will be a short practical covering the slides of the frog and chick embryo on Wednesday, May 10.

Experiment Design and Oral Presentation (15 points)

During laboratory Session on May 3 you will be carrying out experiments that you and your laboratory partners design. You will receive more details about this later in the semester. You should start thinking and talking with your lab partners about possible experiments immediately. We will spend time in lab on March 29 and April 5 planning these experiments. Each group will meet with me between April 5 and April 12 to make final plans for their experiment. On Wednesday, May 10, you and your laboratory partners will present your experiment, including your hypothesis, experimental design, procedures, results and conclusions, to the class. Presentations will be followed by a question and answer period. The design and execution of your experiment plus your presentation plus your participation in the discussion of other presentations will be worth 15 points.

Laboratory Rules

Each student must clean up his/her bench space at the end of each laboratory session.

Absolutely no dissecting tools that have "seen" fixative" are to be brought into the laboratory.

No food or drink is allowed in the laboratory at any time.

Final point accumulation of > or = 180 will be result in a grade of at least an A-
Final point accumulation of > or = 160 will be result in a grade of at least a B-
Final point accumulation of > or = 140 will be result in a grade of at least a C-
Final point accumulation of > or = 120 will be result in a grade of at least a D-

Click here for the COURSE OUTLINE.