BISC219/F12: Assignment Series2 Outline Summary

Assignment: Series 2 Outline & Summary/ Diagram & Explain Linkage Analysis

Your assignment due at the beginning of Lab 4 is in two parts. Part 1, worth 10pts., is to summarize the entire Series 2 project in classical (forward genetics). There are detailed directions that follow to help you break that part of the assignment into manageable parts. The goal of this part of the assignment is for you to have a complete and clear understanding of the broad topic, our investigative goals, and the experimental approach that we will use to accomplish this goals and answer our experimental questions. The second part of the assignment is to narrow your focus to the experimental design of our linkage analysis. You will explain in a narrative how the crosses you will set up are designed to answer the question, on which chromosome is the gene responsible for the aberrant phenotype observed in our mutant worms? In addition to the explanation, you will turn in a filled out template that shows your hypothesis about the outcome of the crosses you will set up in this part of our investigation.

Part 1( 10 points): Outline/ Summary of our Series 2 Classical (Forward Genetics) Investigation in C. elegans

Please construct a complete yet concise statement of the overall topic of investigation in Series 2 and the experimental question & goals of this classical (forward) genetics approach to understanding the structural and functional relationship between a gene and the product it encodes.

Construct and outline the entire experimental approach to achieving the our experimental goals in Series 2, including all of the following parts to our project: test for a true breeding mutant, linkage analysis to locate the gene associated with the mutation to a chromosome (any of the 6), mapping the mutation's location on a chromosome, complementation analysis to see if the mutation has been previously characterized, defining the gene sequence change responsible for the gene product change that is associated with the functional defect in the mutant through DNA sequence analysis and comparison with wild type gene sequence to find functionally significant sequences in a gene that encode important parts of the gene product, using bioinformatics (Wormbase or BLAST OR other public search engines) to find out if the proposed structurally/funcationally significant regions of the gene or gene product in C. elegans have homologs/orthologs in other species to broaden the context and significance of our findings. This outline can be done in outline form or as a flow-diagram.

Please use this outline to compose a summary in prose of how you will determine the gene and the exact location of the gene responsible for a particular mutant phenotype, how you will find the exact sequence change that is likely to be responsible for the abberrant phenotype, and if that gene or gene product change could be significant in other species. Note that this summary should NOT be a detailed list of exactly what you DO in lab in chronological order, but should, instead, be a brief summary of each part of the work that is included in our project. Imagine yourself trying to explain your project to someone who knows nothing about C. elegans genetics or about these mutant phenotypes. Grading Rubric found below.

Part 2 (5 points) Linkage Analysis :

Using the templates provided at Media:Series 2 Linkage Templates.pptx, construct a diagram of crosses that you will set up in the Linkage Testing part of Series 2. In the template, make sure to highlight the progeny that will be used to continue each step of the process of linkage testing. Include the expected results (genotype and phenotype) for both the outcross and self-fertilization progeny. Compose a narrative description that summarizes the rational for Linkage Testing as an important part of your overall Series 2 goals. Explain what you are looking for in the results of these crosses that will allow you to determine the linkage group to which your mutated gene of interest belongs. Grading Rubric found below.

Grading Rubrics

Assignment Part 1– 10 points
Series 2 summary of project

	At or Above Standard	Below Standard	Possible Points	Points Earned
Topic & Experimental Question	Constructed a clear, concise, and accurate description of the overall topic, the experimental question(s) and goals of the Series 2 investigation	Topic or experimental question(s)/goals missing, inaccurate, partially accurate; contains too much tangential information or is too simplified	2	__/2
Outline of Experimental Approach in Series 2: Classical or Forward Genetics	Constructed a complete, clear, concise, and accurate outline or flow diagram of ALL parts of Series2 including: test for true breeding, linkage testing to determine which chromosome the gene responsible for the mutation is found, mapping the mutation on a chromosome, complementation testing to determine if new mutation or previously characterized gene and mutation, DNA sequencing analysis & bioinformatics work to find structurally significant parts of the gene and functionally significant parts of the gene product, and to broaden the context and significance of the findings but a search for find homologs/orthologs.	Outline/diagram is missing elements, is inaccurate or partially inaccurate; contains too much tangential information or is too simplified.	4	__/4
Narrative summary of project	Constructed a clear, concise, accurate, and logically developed description of the experimental approach to locating and characterizing the gene and gene mutation responsible for a phenotypic alteration from wild type	Experimental analysis missing, inaccurate, partially accurate; contains too much tangential information or is too simplified, isn't logically developed	4	__/4
Total			10	__/10

Assignment Part 2 (5 Points)

Grading Rubric

Linkage Analysis

	At or Above Standard	Below Standard	Possible Points	Points Earned
Diagram of Crosses	All possible cross outcomes diagrammed accurately, completely, clearly, and concisely.	One or more possible crosses missing; one or more is inaccurate, information omitted , or did not include accurate predicted ratios of progeny for genotype and phenotype.	2.5	__/2.5
Narrative description of rational for crosses	Constructed a clear, concise, and accurate description of the rational for setting up the crosses described	Rational for crosses missing, inaccurate, partially accurate; contains too much tangential information or is too simplified, is unclear	0.5	__/0.5
Narrative description of Interpretation of Crosses	Constructed a clear, concise, and accurate description of how you will use the crosses to determine the linkage group to which your mutated gene belongs.	Interpretation of crosses missing, inaccurate, partially accurate, or unclear; contains too much tangential information or is too simplified.	2	__/2
Total			5	__/5