BIOLOGY 50-05

RESEARCH IN MOLECULAR GENETICS

 

 

FALL 2002

SYLLABUS

 

Instructor: Mary Montgomery

 

MWF 2:20-3:20, R 8:30-11:40

 

Course Description: Collaborative research with a faculty member focused on understanding the molecular genetic mechanisms underlying animal development, the process whereby a single fertilized egg develops into a functional multicellular organism.  Extensive laboratory research, readings and discussion of the scientific literature related to the research area are undertaken.  A research project will be selected in consultation with the instructor.  Research will be geared toward elucidating the functions of genes involved in the earliest stages of animal development, and examining how the expression patterns and functions of such genes have evolved in different animal species.  Students will become familiar with several research techniques for isolating and manipulating DNA and RNA, “reverse” genetic methods for interfering with the functions of specific genes, and in situ methods that reveal where and when a gene is expressed, i.e. active or “on.”  Some lab and journal club meetings will be coordinated with Research in Molecular Genetics 50-07 in order to learn methods and/or discuss journal articles of mutual interest. 

Prerequisites: junior or senior standing, Biology 22 (Genetics) and Biology 23 (Cell Biology), and permission of the instructor.

 

Course Objectives:  Upon successful completion of this course, each student should be able to demonstrate the following competencies:

(1)  Comprehension and critical analysis of the primary literature.  Papers will be pulled from the fields of molecular genetics, evolution, and developmental biology, and from journals specializing in the publication of studies which combine aspects of all three of these disciplines.

(2)  Understanding of several methodologies used in molecular genetics, the rationale for choosing a particular method to approach a particular problem, and identification of appropriate controls for each method.

(3)  Demonstration of laboratory proficiency in several molecular genetic techniques, including methods for amplifying and cloning DNA, for analyzing gene expression, and for disrupting gene function.

(4)  Ability to “mine” genome databases, which includes performing database searches involving DNA sequences.and deciphering results of such searches.

(5)  Ability to use the scientific method to investigate a problem in molecular genetics, including communicating one’s findings in formal written scientific format.

(6)  Understanding the function of laboratory group meetings for exploration and refinement of ideas related to the investigation of a scientific problem.

 

How the course is organized:

 

The typical week will be organized as follows:

 

MON:       Lecture or discussion of the “Technique of the Week”

WED:        Journal club (discussion of a paper from the primary literature)

THURS:    In LAB, either learning new techniques or working on your research project

FRI:           Group meeting (presentation and discussion of results, plans for new experiments)

 

“Technique of the Week”

 

Each week we will learn/review a different technique commonly used in molecular genetics research.  I will lecture at many of these meetings, but each of you will be responsible for researching and presenting ONE technique during the course of the semester.  These presentations are expected to involve an explanation of how the technique works, what problems it is used to investigate, the appropriate controls that should be included when used, any advantages or drawbacks it offers/suffers from compared with other methods used to investigate similar problems, and some history to the development/discovery of the technique and/ or its application(s).     You will be able to add this technique to your virtual “Tool Bag” which will be posted on the course web page and added to each week.

 

Journal Club

 

Each week we will read and discuss one paper from the primary literature related to the research we will be undertaking in the lab.  Most weeks I will post a series of questions for you to think about as you read through the paper and should come to class prepared to discuss.  All of you are expected to contribute regularly to these discussions.  Each of you, however, will be responsible for LEADING the discussion for ONE paper during the course of the semester.  Together we’ll pick the paper for that week and then you will generate the list of questions to accompany critical analysis of the work represented in the article.

 

Group Meeting

 

Each week we’ll have a lab group meeting.  This is your opportunity to present to the rest of the group any results you’ve obtained since the previous gathering, and ideas you have for new experiments.  Other members of the lab can then think about your project and suggest ideas, which might include ideas for controls, ways to interpret your results, reasons for why an experiment might not have worked, ideas for future experimentation.  These will be informal in nature, but everyone is expected to contribute something every week. 

 

Thursday Lab

 

Thursday mornings are when the laboratory component of this course is scheduled.  Some weeks I will use the time to teach you a new technique; other weeks you will work independently on your project during this time.  You will be expected to supplement the time in lab on Thursday mornings with 3-6 additional hours during the week to finish experiments and procedures.  There is always some “down time” during lab, which you can use to e.g. read papers or prepare for group meeting.

 

 

Expectations and Evaluation:

 

During the course of the semester, I expect that you will

 

(1)  devote an average of 12-15 hours per week to work related to this course, with at least half that time taking place in the laboratory either mastering newly learned skills or working on your individual research project; 

(2)  participate in weekly journal clubs and lab group meetings;

(3)  lead a discussion of the primary literature one time during the semester;

(4)  respect the contributions of each member of the class during discussion meetings;

(5)  add to and maintain a virtual “Tool Bag”;

(6)  present one “technique of the week”;

(7)  maintain a detailed laboratory notebook;

(8)  maintain the laboratory in good working condition;

(9)  write up your findings for the semester as a formal scientific paper following the format used in the journal Genes and Development.

 

 

Your grade for the course will be determined by the following criteria:

 

“NC”:            If you fail to complete any of the following: writing and submission of your research paper; presentation of a “technique of the week”; lead a discussion of a paper from the primary literature; attend class regularly; demonstrate proficiency in two class laboratory techniques.

 

“D”: You fulfill the minimum requirements as outlined above, but either (1) you put in no additional hours in the lab beyond the scheduled R 8:30-11:40, and/or (2) your research paper does not meet minimal standards with regards to length, quality of writing, number and appropriateness of references, and/or presentation and analysis of results.

 

“C”: You fulfill the minimum requirements as outlined above, but either (1) you put in fewer than 3 additional hours in lab beyond the scheduled R 8:30-11:40, and/or (2) your research paper meets minimal standards but does not contain any original ideas or analysis, and/or (3) you attend group discussions but rarely if ever contribute to them.

 

“B”: You fulfill the minimum requirements as outlined above, and in addition (1) put in on average 3 or more hours in the lab in addition to the scheduled R 8:30-11:40, (2) submit a paper that meets minimal standards, contains few grammatical or spelling errors, contains a reasonable list of references, and demonstrates some original thinking either in the experimental question, design, or analysis, (3) contribute one or a few comments during group discussions each week, and (4) demonstrate proficiency in at least three class laboratory techniques.

 

“A”: You fulfill the minimum requirements as outlined above, and in addition (1) put in on average 4 or more hours in the lab in addition to the scheduled R 8:30-11:40, (2) submit a paper that meets minimal standards, contains no grammatical or spelling errors, contains an extensive list of references, and demonstrates original thinking in the experimental question, design, and/or analysis, (3) contribute several insightful comments during group discussions each week, and (4) demonstrate proficiency in at least four class laboratory techniques.