Biology: Gene Simulation


	This simulation presents you with a 5 part genetic puzzle that will allow you to generate mutations on the genetic pathway of Drosophila. To solve this puzzle you have five utilities you can use to experiement in order to generate the solutions. Five related concepts comprise the knowledge base to effectively ‘map’ characteristics onto the gene structure. These are: transmission complementation mapping between 2 known mutants, mapping between a known and unknown mutant biochemistry This mapping involves (1) dividing the chromosomes into smaller fragments that can be reproduced and characterized and (2) ordering (mapping) them to correspond to their respective locations on the chromosomes. After mapping is completed, the next step is to determine the base sequence of each of the ordered DNA fragments. The ultimate goal is to find all the genes in the DNA sequence and to develop ideas/tools for using this information in the study of drosophila and human biology and medicine. A genetic map describes the order of genes or other markers and the spacing between them on each chromosome. There are several different scales or levels of resolution. At the coarsest resolution are genetic linkage maps, which depict the relative chromosomal locations of DNA markers (genes and other identifiable DNA sequences) by their patterns of inheritance. Physical maps describe the chemical characteristics of the DNA molecule itself.

	installing the module
	directions Here are some things you need to know about running this module. For example, you may be required to install a Java plug-in, if you are prompted to do so please allow the installation or you will not be able to run the module. When the program starts, if asks whether you want to start a new Genetic Simulation or continue working on a previously started Genetic Simulation in a dialog box that looks like the one below. Click on "OK" to start the New Genetic Simulation. saving and typing in your seed number If you choose to start a new Genetic Simulation, it will generate a identification number for your session so that you can return and continue to work on the same experiment over time. You will be prompted to write this number down in a dialog box that looks like this: Obey this prompt and write down the number given to you. The next time you start using this program, select "Continue A Simulation" and then type in that same number into the "Seed:" text input box as shown below. Then click on "OK" to continue working on the Genetic Simulation already in progress. simulation registration Whenever you begin working on a new Genetic Simulation, you will be prompted to fill in a registration 'card' on-line. Simply type in your name and email address. The Genetic Simulation seed number will already be typed in for you. You need to fill out this registration 'card' so that your instructor can grade your assignment when you are finished working through the simulation. (top of section) (top of page)

	running the module
	Windows Java 2 plug-in enabled frames version Makes use of the java plug-in (requires a download if the plug-in is not installed). Works better than embedded plug-in version in low resolution environments. Windows Java 2 plug-in enabled embedded version Makes use of the java plug-in (requires a download if the plug-in is not installed).Works great in high resolution environments. Windows AWT version Use if you don't want to download the plug-in though I highly recommend downloading the plug-in and using on of the above options. Trust me. Macintosh version Mac users go here enough said. Internet Explorer users only thank you. (top of page)

	transmission module
	This utility will make crosses between homozygous mutant strains and wild type and then generate data based on the parental cross for two generations. Specify how many offspring are counted for each cross. You should assume that offspring from the F1 data generation are inbred to create the offspring in the F2 generation. (top of section) (top of page)

	complementation module
	This utility allows the user to make crosses between pairs of mutant strains. A complementation test allows one to determine if two mutations occur in the same gene or in different genes. Specify how many offspring are counted for each cross. You should assume that offspring from the F1 data generation are inbred to create the offspring in the F2 generation. (top of section) (top of page)

	mapping two known mutants module
	This utility is used to determine the distance among the genes of a genetic pathway by performing a genetic mapping cross between a strain of homozygous for an unknown mutation to a strain that carries a known mutation from Drosophila melanogaster. The known mutations are distributed across the four chromosomes of D. melanogaster. Specify the number of offspring that you can count in the F2 generation. (top of section) (top of page)

	mapping a known and unkown mutant module
	This utility is used to determine the distance among the genes of the genetic pathway by performing a cross between two strains to generate a heterozygote in the F1 generation. This may be done in one of two ways, either by crossing a fly that carries both mutations to a wild type fly or by crossing two strains that each carry a single mutation. The F1 double heterzygote is crossed to a strain that carries the two recessive mutations. Recombinant and parental offspring are counted in the F2 generation and the genetic map distance estimated as the fraction of recominant offspring divided by the total number of offspring. (top of section) (top of page)

	biochemistry module
	This analysis supplies each mutant strain with a metabolic intermediate that will allow the organism to grow or die. This matrix will allow you to determine the order that genes are expressed in the genetic pathway. If a metabolic allows a strain that carries a mutation to grow, then the gene functions acts on a substrate upstream of the metabolite. If a metabolite allows a strain that carries a mutation to (top of section) (top of page)