Nagivate To


Research

The research at Drexel is part of the G K-12 program.  This is part of a grant from the National Science Foundation to include high school students in research being done in the field of mathematics, science, technologies, and engineering.

While participating in the 5-week program I’ve helped Dr. Youngmoo Kim and Dr. Gail Rosen develop labs for high school students.  These labs ranged from having students pick out a voice in a crowd of people to using matlab to use DNA forensics science to identify the perpetrator of a crime. My college, Dr. Bo Dirnbach, will explain Dr. Youngmoo Kim’s work.  I will explain Dr. Gail Rosen’s work.


DNA Overview


Deoxyribonucleic Acid (DNA) is the building block of an organism.  The structure is a double helix (think of a twisted ladder), and contains base pairs.  These pairs are adenine (A), guanine (G), thymine (T), and cytosine (C).  These bases come together to form genes.  

A gene can vary in function.  Some determine what color eyes you have, some help combat disease.  Each gene can vary in length from several hundred to several million base pairs long.  While everyone’s DNA is unique, and it is a mixture of the DNA from your parents, everyone’s DNA is 99.9% the same.  Since the DNA chain is so long (if you take all the DNA contained in one cell and laid it out on the ground, it would be almost 2 meters in length)

There are two types of DNA in a cell: the nuclear DNA, which is a mixture of both parents, and mitochondrial DNA (or mDNA), which is inherited only from your mother. The sex-determining chromosome for men (the Y of the XY) is inherited only from the father.  

Mutations can occur at any point in the DNA strand.  When DNA is copied, sometimes there is an error in the copying:
Original Sequence:     A-A-C-T-G-A-A-G…
Mutated Sequence:     A-T-C-T-G-A-A-G…
Analyzing these mutations in people is where the focus of the research is being done. This mutation is helpful in determining lineage, hereditary, and can even help track the migration of the human species.
Completely different strands of DNA (such as the genome’s of Humans and chimps) can be analyzed to find out how long ago they shared a common ancestor.  

 

DNA Trees

Currently, you can compare two different sets of genomes, and based on the number of common genes in the genome, you can determine how long ago their genomes parted.

At the National Center for Biotechnology Information website, they have a program called “BLAST”.  This program will scan the Genome of several organisms and produce an evolution tree.  The program can be submitted by any developer who can create a new program more accurate than what is currently being used.  


So far they have developed a program using the program Matlab.  Matlab is high-level computer program that allows you to quickly perform math operations much quicker than a traditional graphing calculator, and even programming languages.  

A program was written:


This specific program will compare the evolution tree of the German Neanderthal, Russian Neanderthal, European Human, Mountain Gorilla of Rwanda, and the Chimp Troglodytes.  Our program produced the following tree:
 

The tree shows the evolutionary distance (normalized) between the 5 different animals.  

The table shows that the German & Russian Neanderthal are the closest related.  The next closest related are the European Human and the Neanderthals, which is followed by the Gorilla.  

 

Other G K-12 Labs:

Introduction to Bio-Informatics:

In this lab experiment students will extract specific gene sequences from Humans as well as similar genes from different animals and compare them.

The first gene they will look at is the gene responsible for synthesizing and manufacturing Vitamin C in humans, dogs, and Pigs.  Dogs do not need to get Vitamin C from an external source, but humans do.  In dogs, the gene that produces Vitamin C is called GULO, in humans a similar gene is called GULO-P (the P stands for pseudo since humans cannot produce their own Vitamin C).  We will see through the analysis of these genes that humans and pigs are more similar than humans and dogs.

1: Extract the GULO Gene: The NCBI webpage can do this for us.

2: Protein Translation: The students will enter the DNA sequence into their proteins.

3: BLASTing the Gene.  The BLAST (Basic Local Alignment Search Tool) is a software program that will analyze the protein structure of a gene, and compare it to similar genes in other animals. 

For the purposes here, we will compare in Humans to that in a pig.



Now we will choose the Gene's with the highest Max Indent.

After we analyze the result we see that a human and a pig's GULO gene is 86% similar.


If you do a similar process with a dog, the results are lower!  Only 70% of the sequence is the same.


The iRobot Lesson

This is another lab where I worked with one of Dr. Gail Rosen graduate students to develop a lesson to get high school students involved in engineering.

 


Documents

 TitleOwnerCategoryModified DateSize (Kb) 
Research Poster (old ppt)Peter Konstantopoulos 8/5/2008592.90Download
Research PosterPeter Konstantopoulos 8/5/20081,307.65Download

  

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