modencode.sciencemag.orgmodENCODE | modENCODE Education Suppplement

-- modENCODE Home Introduction -- Drosophila C. elegans Transcription Chromatin Genomics Bioinformatics Glossary Q&A -- Navigation [Teacher's Guide] [Site Authors/Contributors] Model Organisms and Modern Biology An educational portal from the modENCODE Project The Modules Module 1: Model Organisms in Biology Why we study flies and worms to learn about humans -- and what we've learned so far. [More info] Drosophila >> The lowly fruit fly -- easy to grow and maintain, with giant chromosomes and some surprising genetic similarities to humans -- has been at the core of biological research for more than 100 years. C. elegans >> Adult C. elegans worms have precisely 959 cells, move through a rapid life span, are transparent at every stage, and share many similarities with humans -- which has made them ideal for studies of cell death, development, and aging. Module 2: Model Organisms and Gene Expression How studies of the fly and the worm, and a large scientific project, have shed light on the ways genes drive biological processes. [More info] Transcription Regulation >> How do genes "know" when they're needed -- when to turn on and when to turn off? Part of the answer lies in a class of proteins called transcription factors. Chromatin >> To fit into the nucleus, DNA must be packaged up with proteins called histones into chromatin, and that packaging creates different patterns of modifications of the genome. Module 3: The Role of Computers and Technology Increasingly, biology is not just about doing benchtop experiments, as scientist rely on computers and cutting-edge techniques to generate and make sense of massive data sets. [More info] Genomics >> Sequencing a genome used to take years of painstaking work. New "parallel-processing" and "high-throughput" techniques have slashed that time to months or even days -- and dramatically expanded the horizons of molecular biology. Bioinformatics >> The volumes of data churned out by modern sequencing techniques require sophisticated computer analysis to find patterns in the data. That's spawned a new field combining biology and computer science -- bioinformatics. [Image credits] Welcome to a look at how some rather common invertebrate organisms can lead to some very uncommon insights into human biology, health, and disease. By drilling down into the three modules on this Web site, you will: Explore the significance of two classic model organisms , the fruit fly ( Drosophila melanogaster ) and the roundworm ( Caenorhabditis elegans ), in studies of human biology and conditions ranging from alcoholism to aging. Investigate how genes are activated, transcribed, and translated into proteins that do the biological heavy lifting in cells and systems -- and how the six feet of DNA in each of your cells is packed to fit into a microscopic nucleus. Find out how new technologies and the use of computers to crunch massive amounts of data are creating new frontiers and growth areas in the biological sciences. The site examines these topics through the lens of a highly successful recent example of international scientific collaboration -- the Model Organism Encyclopedia of DNA Elements (modENCODE) project. About modENCODE The instructions to create and maintain a living organism are recorded by the sequence of bases in its DNA . In recent years scientists have decoded the sequences of the genomes (all the DNA within each cell) of many organisms, including humans. But what are the instructions encoded in the sequence of a genome and how do these thousands of genetic instructions work together to create a multicellular organism? Our understanding of the language of DNA is only rudimentary, and we can only partly read its instructions. What are our genes and how do they result in cells as different as a muscle cell and a nerve cell? The answer lies in differences in gene expression -- the amazingly intricate work of turning genes on and off and regulating their action within cells. Understanding the instructions in a genome and how they are used to make an organism is the core purpose of the ENCODE (Encyclopedia of DNA Elements) and modENCODE (model organism ENCODE) projects, which aim to define all of the functional elements in the human and the worm and fly genomes. This includes precisely defining the genes that code for proteins and non-coding RNAs, and identifying functionally important elements that direct gene expression, DNA replication, and chromosome inheritance. The two model organisms, the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans , that are the focus of modENCODE have been central to understanding the biology of multicellular organisms. The use of worms and flies in modENCODE has allowed the study of tens of thousands of individual genes in the living organisms, as well as cells in tissue culture. The ability to manipulate these animals experimentally allows any conclusions to be tested directly. The project has relied on some cutting-edge lab methods to examine those many genes in many different stages of the life cycle and has exploited powerful computing techniques to make sense of it all. That makes this project a great place to start looking at how and why scientists use simple organisms to study the intricate world of gene expression, how technology is shaping and reshaping biology as a science (and as a career), and how this work ultimately informs the study of complex human traits and diseases. Let's Get Started! Within each section of this site, you will find case studies, laboratory results, videos, exercises, and assessment questions. Work through the two sections in each of the three modules, completing the assessments before moving on to the next section. (Your teacher will let you know whether these will be graded assignments or self-assessment exercises.) The modules can be completed in any order, but we strongly suggest that you move through them in the order presented. You'll find in-line pop-ups to give further information on unfamiliar terms, as well as a comprehensive glossary you can consult at any point. So let's dive in, and start by finding out what fruit flies and roundworms can tell us about ourselves . . . Contributors Following are some of the people who contributed to this Web site. Sarah C R Elgin, Washington University in St. Louis, MO Cheryl Bailey, Univeristy of Nebraska - Lincoln and Howard Hughes Medical Institute James Bedard, University of the Fraser Valley, BC Martin Burg, Grand Valley State - Michigan Jennifer Roecklein-Canfield, Simmons College, MA Christopher Jones, Moravian College, PA Nighat Kokan, Cardinal Stritch University, WI Susan Parrish, McDaniel College, MD Cathy Silver Key, North Carolina Central University Philip Meneely, Haverford, PA Bob Waterston, University of Washington Michelle Smith, University of Maine Valerie Reinke, Yale, CT Roger Alexander, Yale, CT Gidi Shemer, University of North Carolina Kelly Hogan, University of North Carolina Peter Park, Harvard, Boston, MA Ivy McDaniel, UC Berkeley Sue Celniker, UC Berkeley Ben Brown, UC Berkeley Rebecca Lowdon, NIH/ MD Trupti Kawil, Stanford Barry Starr, Stanford Caroline Kelly, NHGRI Laura Zahn, AAAS/ Science , San Diego, CA Melissa McCarthy, AAAS/ Science , Washington, DC More Info Terms Model Organisms Model organisms are animals (or plants, or fungi, or bacteria) that scientists have found convenient to use in the lab. Animals that are: easy and inexpensive to keep, eat cheap food, are small and hardy, have well-characterized mutations (for example, mutations that lead to certain disease symptoms) for genetic studies, and breed easily, with short generation times make good model organisms. A few organisms meeting these criteria are now used by many scientists. In this module, we explore two model organisms that were used for modENCODE studies -- the fruit fly Drosophila melanogaster and the worm Caenorhabditis elegans . Both organ...