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Friday, April 8, 2011

Bioinformatics for Fun

My new position at the University of Illinois involves creating online courses for the Online Master in Teaching Science-Biology degree. The first course up is one I'm creating about the Human Genome and Bioinformatics. While looking up information that might be useful for middle school and high school teachers, I found some great sites with games and stories about bioinformatics I thought I would pass along to you.

Bioinformatics is a field of study that helps biologists manage, store, and use massive amounts of biologic data, including information from DNA and protein sequences. To become a bioinformatician, one would have to know a bit of molecular biology and a lot of computer programming skills. This is a very hot field, so if you are good with computers and programming and are willing to learn molecular biology, you are almost guaranteed a career after some training.

In the meantime, I have found some very fun and easy ways to interact with biological data without being a bioinformatician or researcher. Each of these examples access very commonly used FREE databases. How can a member of the public access such high end scientific information for free? Because we pay for the research with your tax dollars! We pay for scientists to do the research and place the information on these websites to be available to you as well as other researchers. Knowing a little molecular biology yourself, you can learn more about diseases and how protein and DNA sequences are involved. We have a lot more to learn, but feel free to look on and interact as our knowledge grows.


Would you like to see your name in DNA? How can we do this? As we know, DNA is transcribed, or read, to become mRNA (messenger RNA). This mRNA is then translated by tRNA (transfer RNAs) to become a protein. This is the "central dogma" of biology. DNA always makes proteins, never sugars, carbohydrates or lipids. But those proteins can help the cells store, make and use the other products!

Proteins are long chains of amino acids. Amino acids can sometimes have long names such as "aspartic acid" and "threonine" so scientists came up with a way to shorten them. First, they made three letter nicknames such as asp or thr. Even that is quite long when reading some protein sequences, so they shortened them to individual letters such as A and D.

Did you know that the first amino acid to be discovered was from asparagus? In 1806, two French chemists isolated a compound from asparagus, which was subsequently named asparagine (Asn or N)! 

Since there are only about 21 standard amino acids, it is simple to assign a single letter of the alphabet to the amino acids. With a few letters left over, some letters won't have corresponding amino acids. 

We also know that each protein matches a three letter codon of DNA (or a few redundant codons), so we can, just for fun, translate your name to DNA and search all the protein sequences we have, and then tell you what protein your name is! deCODE is supported and created by EMBL-EBI (European Molecular Biology Laboratory- European Bioinformatics Institute)


Click on the above image, which will take you to the deCODE website, enter your name, your pet's name, your grandma's name...anything, and see what protein it becomes! Mine is similar to a protein called P46093iGPR4_HUMAN which is probably a G-protein coupled receptor (I recall that a GPCR crosses the entire cell membrane in eukaryotes, senses the environment and sends signals into the cells. It is a part of big superfamily of proteins with many different functions). To turn your name into protein, to DNA and back to protein takes quite a bit of computing power and is a fun way to see bioinformatics in action.

The nice thing about the deCODE exercise is it will tell you what it does at each step. Give it a try! 

The next item is an exciting way to interact with DNA sequences via ColdSpring Harbor Laboratory's online education website called Dolan DNA Learning Center.

Click on the Gene Boy image below and head to the website to "play" with it. You might also check out their other fantastic resources. I highly recommend this site if you want to learn how to manipulate DNA sequences. 


If you are a REAL gamer, then you simply must try FoldIt! Proteins are not just long strands of amino acids. Based on their chemistry, they tend to fold into fairly predictable shapes. By playing FoldIt, you may actually be able to help scientists predict how proteins are folded (possibly even the ones you found using your name). Click on the image below to go to a page where you can watch this well made video about how the game is played. I love that you can "Solve Puzzles for Science"!


Maybe instead of playing games, you happen to enjoy reading. There are two websites I suggest that are full of great stories about proteins that are important in our lives. The stories then connect you to the databases to tell you more about the disease, disorder or protein associated with those, if you care to explore.

First, I highly recommend the stories shared in "Protein Spotlight"  by Vivienne Baillie Gerritsen

Protein Spotlight is affiliated with the Protein Data Bank (PDB). The author has also written books with the stories about proteins, including one for children called Journey into a Tiny World that can be purchased for a small price (physical copy) or download for free (e copy). As the the website says, "This is the tale of two molecules - Globin and Poietin - who set out to save a little girl's life."  Be sure to check out PDB's Protein of the Month, too!

Another engaging story site is Coffee Break via NCBI (National Center for Biotechnology Information). As they say:

"Coffee Break is a resource at NCBI that combines reports on recent biomedical discoveries with use of NCBI tools....Each vignette also highlights the NCBI tools and resources used in the research process. These tools include PubMed, PubMed Central, Entrez Gene, and MapViewer.Coffee Break articles should be fun and informative reading for molecular biologists, clinicians, and students, and may serve as teaching aids for college and graduate students."

I do really enjoy both Protein Spotlight and Coffee Break!

Finally, I have a fun bioinformatics app on my iPhone. It is called "Molecules"  . This app is also a service of the Protein Data Bank listed above. I've had fun with it and most everyone is intrigued by seeing the 3D protein molecule images rotating on the screen.

These activities should keep most of you busy for a while.
Until next time,
Fri, April 8, 2011 | link 

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