Using Your Computer Skills to Explore DNA
Genomics is an excellent area of research for students who are good with computers. If you are comfortable navigating somewhat complicated websites and enjoy manipulating and downloading computer files, then genomics might be a good fit for you.
So what exactly is genomics? Genomics is the study of the entire set of an organism's genes (or the genes of multiple organisms) and their functions, using techniques such as mapping, sequencing, analyzing and modeling. Genomics aims to look at all genes together as a complex and dynamic system. Specialists in genomics hope that their discoveries will lead to innovative new ways to design diagnostic tests as well as therapies to treat diseases. Check out some of the topics that are featured in the Project Ideas below:
- Using computer programs to identify, visualize, and analyze DNA sequences
- Using computational tools to investigate the causes of genetic diseases or to study the evolution of species
- Comparing human and animal DNA sequences to infer how closely related we are to those animals
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All animals have a genome, but do they all have genome projects? Find out which animals are currently having their genomes sequenced and how much we know already. Whose genomes are already finished? Whose genomes are just getting started? Find out by doing some simple bioinformatics data digging!
Humans are complex creatures, but do we have the biggest genome? All living things, from humans to worms to bacteria have genomes. In this experiment you will compare the genome sizes of different organisms to find out who has the smallest and the largest genomes. Where will we fit in?
Some characteristics, like the shape of your hairline, whether your earlobes are attached or detached, and whether or not you have freckles, are inherited from your parents. In this science project you'll see how writing these characteristics onto a family tree can help you determine how they are inherited.
This is a project about the "molecular alphabet" of DNA. With just four "letters," it manages to keep track of the plan for an entire person, and keep a complete copy in nearly every cell. This project will help you start learning this new alphabet.
Fingerprints are used as reliable identification because each person's fingerprints are unique. But are these unique patterns created randomly or are they influenced by genetics?
Have you ever tried to pack a suitcase? If so, you know that no matter how hard you try, there is a limit to the amount you can cram in, which means if you have more stuff, you need a bigger suitcase! Do you think the same principle applies to DNA in a cell? Does an animal with a bigger genome need a larger cell nucleus to store its DNA? Try this science project and find out!
Imagine that a biologist arrived at your big family reunion and had no idea who were sisters, cousins, aunts, uncles, etc., but tried to sort it out by how all of you look. Just based on how you look, would s/he be able to guess whether the kid standing next to you is your sister or your cousin? The biologist might be able to make some good guesses this way, but by using samples of your family's DNA, s/he could construct your whole family tree. In this project, you'll use a Web-based computer program to help make a "human family tree." (For a more advanced project, see "The Tree of Life – II".)
Finding a cure for cancer is one of scientists' greatest challenges today. But first, they have to study and understand the disease. In this science project, you will explore the software available on the Cancer Genome Anatomy Project (CGAP) website and use bioinformatics tools to identify genes whose level of expression is higher in cancer tissue.
Did you ever wonder about your ancient ancestors? Who they were? Where they came from? In this science project, you will investigate the secrets of your distant past as revealed by your DNA. In order to obtain a sample for DNA analysis, you will scrape a soft swab inside your mouth to collect cheek cells. The cheek cell sample will be sent to a lab for processing, and the results of the analysis will be sent to you. Based on the genetic markers in your DNA, the ancient clan that your ancestors belonged to will be identified. The resources you receive back will introduce you to your ancient ancestors and allow you to explore their migrations.
Find out the real explanation for why your parents are so weird! Here is a project that lets you explore "the net" to find out why your "DNA blueprint" is so important to health and disease. In this project you will use methods that bioinformatics and biotech scientists perform on a daily basis to decipher the human genome in their efforts to diagnose and treat genetic diseases.
Remember going to the doctor and getting vaccine shots? It's no fun getting poked with a needle, but fortunately, a vaccine gives you protection against a serious illness for years to come. But what about the flu vaccine? How come there's a new one every year? This project will show you why.
Native plants are important for both ecological and medicinal reasons. However, most native plants are not very well studied. One way to know more about these plants is to understand which other species of plants they are most closely related to. In this science project you will sequence part of the chloroplast genome from a native plant and use this information to determine its evolutionary relationship to other species of plants. If the plant you chose has not been sequenced before, you can contribute your data to GenBank—the public gene sequence data bank—for scientists worldwide to see and use!
Imagine that a biologist arrived at your big family reunion and had no idea who were sisters, cousins, aunts, uncles, etc., but tried to sort it out by how all of you look. Just based on how you look, would s/he be able to guess whether the kid standing next to you is your sister or your cousin? The biologist might be able to make some good guesses this way, but by using samples of your family's DNA, s/he could construct your whole family tree. In this project, you'll use Web-based computer programs and some background research to make your own evolutionary tree for a group of your choice. (For a more basic project, see "The Tree of Life – I".)
The DNA in our cells contains our "blueprints," but it's the proteins in our cells that do most of the work. The Human Genome Project has allowed us to start reading the blueprints, but we still don't understand what most of the proteins do. This is a fairly advanced project that explores ways of identifying the function of unknown proteins.
Terms, Concepts and Questions to Start Background Research
The National Human Genome Research Institute (NHGRI) created the Talking Glossary of Genetic Terms to help people without scientific backgrounds understand the terms and concepts used in genetic research. http://www.genome.gov/glossary.cfm
Resources
- Scientists, enabled by the Human Genome Project, are churning out an unprecedented volume of data on human chromosomes and the tens of thousands of genes residing on them, many associated with genetic disorders. These data, and many Web sites on human genetic disorders, are freely accessible on the Internet. Gene Gateway is a collection of guides and tutorials designed to help students and other novice users get started with some of the resources that make these data available to the public. Here you can find detailed introductions to six different types of genomics-related research tools:
- Gene and Protein Database Guide,
- Bioinformatics Tools,
- Genetic Disorder Guide,
- Sample Profiles of Genes and Genetic Disorders,
- Chromosome Viewer,
- Evaluating Medical Information on the Web.
http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/.
- This webpage has a table comparing genome sizes for different organisms:
Kimball, J.W., 2006. "Genome Sizes," Kimball's Biology Pages [accessed March 23, 2006] http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html.
