Biology Dept.

DePauw University Spring 2010 
Instructor: Fornari

BIO 415 Lab
Molecular Genetics


R 9-11:50 AM in Olin 228A
Molecular Genetics 
& Bioinformatics Lab


The laboratory section of the course consists of both a research project and an Internet Web project. You will use most of the available laboratory periods to perform the experiments for your research project, and then collect, analyze and interpret the data in preparation of a formal laboratory report (same format as for the BIO 315 course lab). During the remaining lab sessions, you will construct an Internet Web page to completely dissect, in a molecular genetic sense, a human genetic disease.


RESEARCH PROJECT: Adopt a Chromosome *

The research project for this semester's Molecular Genetics course addresses specific questions about your own genes on a different chromosome for each lab group. The lab work requires that you master a few standard, molecular genetic techniques, and of course achieve a basic understanding of the relevant underlying concepts (what is the molecular, genetic, biochemical, and biological basis for a given technique?). Skillful use of these molecular techniques, coupled with an understanding of the underlying genetic and biochemical theory will ensure success in accomplishing the goals of the research project.

In this spirit then, it becomes necessary to incorporate the underlying genetic and biochemical theory of certain techniques into your laboratory work. In other words, simply "cook-booking" the lab will not be sufficient to earn you a decent grade for the research work you perform in the lab. You must also understand what you are doing, and why you are doing it, from biological, genetic and biochemical perspectives. Achieving these perspectives will require that you research the relevant scientific literature, especially when you are writing your final lab report. I will provide you with a more detailed description of your lab report requirements, along with criteria for grading, later in the semester.

*Each lab group "adopts" one or more chromosomes for the semester's lab and research work; you may also incorporate this chromosome and one of its disease genes into your web-project. Your responsibility here is to become thoroughly familiar with all aspects (physical, genetic, molecular, genomic) of this chromosome, including of course one or more disease genes carried on this particular chromosome. In keeping with my general pedagogical approach then, we are continuing to approach concepts and topics from a general perspective to a more specific one.

An important experimental task early in the semester will be to find or design primers for PCR fragments that contain SNP sites within your chosen genes on a your adopted chromosome(s). These PCR fragments should include not only SNP's but also possible mutations that are responsible for phenotypic changes. In this spirit then, we are continuing another, more specific pedagogical strategy to link genotype with phenotype, also one of the main goals of modern genetics.

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HTML INTERNET WEB PAGE PROJECT 

We will discuss  several genetic diseases in lecture, and  clearly demonstrate the new strategies that have become effective in isolating the genes for human diseases. Through such lecture discussions, you will see fully demonstrated the kind of analysis you should perform for your HTML page, and subsequent presentation to the class. I will provide you with a detailed description of the requirements for your disease gene project, along with criteria for grading. Please note that a full understanding of HTML script language is not required for you to successfully accomplish the project goals. Web pages may be completely constructed from auxiliary programs in most Web browsers, such as Netscape (the Composer program). In addition, both WordPerfect and MS Word allow you to convert text documents to HTML. Sample Disease Gene Projects.

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BIO 415  Laboratory Exercise Schedule

Lab

Excercises ( accompanied by detailed protocols in the BIO 415 I:/drive folder)

Feb.2

Orientation in Olin 228A; assignment to lab spaces, discussion of general lab procedures, safety rules, and equipment.

Feb.9

 Selection and ordering of primers for targeted genes 

Feb. 16

Collection hair/saliva samples, DNA isolations, and processing for proper storage.

Feb. 23

PCR's of isolated of genomic DNAs.  

March 2

 Exam #1 

March 9

  Analytical gel analysis of isolated DNA preparations.

March 16

Spectroscopic (Hitachi GeneSpecI) Analysis of PCR-DNA for concentration and purity.

March 23

DNA Sequencing of PCR products

March 30

 S P R I N G    B R E A K!!! 

April 6

Exam #2

April 13

Analysis of DNA sequencing results; genotyping SNP's

April 20

Open Lab: discussion of class results; start Web Projects

April 27

 Start Web Projects

May 4

 Exam #3

May 11
Disease Gene Presentations (see handout) 

May 18

Due date for Final Lab Report

Please note:

a lab fee of $20.00 is needed to cover the expense of some lab materials/copying fees. The Accounting Office will bill your DePauw student account (The lab fee is much less than the cost of a formal lab manual).

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Links to Molecular Genetics Sites

 The National Center for Biotechnology Information
OMIM Home Page -- Online Mendelian Inheritance in Man
 
 EMBL Nucleotide Sequence Database
 Molecular Biology Jump Station

 The Biology Project
Biology Web Site References
 Molecular Biology on the Web : Organisms Databases, Genome projects
 PCR Jump Station
 National Human Genome Research Institute (NHGRI)
 
 Virtual Genome Center
 Graphics Gallery


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