Biology 205 Fall 2002. Project Part 1: Using the Online MIM Database. 15 points.
Introduction:
In genetics online and other computer resources have become extremely important research tools. This exercise is the first of several designed to provide exposure to the main online resources related to genetics that you are likely to encounter as biologists. The goal of the project is to have you investigate these resources in the context of a genetically based problem. You may select a problem from the list below or after clearing it with me, do one of your own choosing. The strategy will be first to look at some of the general biology data bases to investigate what is known about the genetic basis for the problem, then focus on a specific gene believed to be linked with the problem you are investigating.
Your 'job' is to produce an online resource devoted to the genetics of your problem, ultimately focus on one or a few genes that appear to be connected in some way with the problem. This online resource will be published on the web to be shared with the rest of the students in the class. There is no written report per say. Material will be presented entirely online, but of course, citation of all work and use of primary resources, editing and spelling etc are all important. Most of you have probably never published on the web, but it is not that difficult and I will work with you individually through the technical details. For now you will need to be able to access a computer, use basic work procesing software (e.g. MS Word or Word Perfect), and use a browser such as Netscape, Opera or Internet Explorer. It does not matter what sort of computer you use as most and software today is cross platform. For instance at work I use a MacIntosh computer but at home have a Windows machine running Windows XP.
Today you will do the following:
Select a general problem or medical condition that is believed or known to involve genetics.
Access and surf the National Center for Biotechnology Website http://www.ncbi.nlm.nih.gov/.
Learn to use the Online MIM database and identify the types of information that can be obtained from this database.
Access and become familiar with guidelines for citing web material at http://owl.english.purdue.edu/handouts/research/r_docelectric.html.
Some possible topics including genetic disorders and other topics related to human genetics and health.
Procedure for this part of the exercise. Go to the National Center for Biotechnology Website http://www.ncbi.nlm.nih.gov/ and answer the following questions this web site.
1. What is bioinformatics and what are the main areas that bioinformatics deals with?
2. What are Expressed Sequence Tags and what can they be used to do?
3. What is an SNP and what are they used for?
4. What is BLAST and what sorts of information could you obtain using BLAST?
5. What is Plasmodium falciparum and in what Database would you look to find the sequence of its DNA?
6. What is Friedreich's ataxia and what is its mode of inheritance?
7. What does the are Orthologous sequences?
8. What is green fluorescent protein used for?
The gene MIM number
Name of the gene.
What chromosome the gene is on.
The normal function of the gene in the body.
The mode of inheritance of for the phenotype associated with the gene.
Animal 'models' used to study the gene.
Frequency of the allele asociated with the condition. Does the allele differ in frequency in different human populations?
List three recent(in the part two ears if possible) journal references to this gene where you might find more information about the gene. Make sure you give complete citations.
Due October . Please word process your report . Most of these can be found in your text as well, but rely on the OMIM data base for your information. Your report can be single spaced.
OMIM Home Page -- Online Mendelian Inheritance in Man
pgd 2/12/02