PLNT3140 INTRODUCTORY CYTOGENETICS    

This assignment is worth 5% of the course grade.

Due on UMLearn, Tuesday Oct. 24.

In most eukaryotes exposed to heat shock conditions (eg. 42°C), the synthesis of most proteins is shut down, but a new class of proteins, called heat shock proteins, is produced. For example, Figure 1 shows that transcripts for heat shock proteins hsp70, hsl93D and hsp22 are detectible in heat-shocked Drosophila cells but not untreated cells, while transcripts for actin and tubulin are seen only in untreated cells.
 

Figure 1. RNA gel blots using RNA from heat-shocked (H) or untreated flies (-). Hybridization probes are listed at top. Each band represents the mRNA for a gene.	Figure 2. Example of polytene chromosome showing heat shock puffs.

Fruit flies (Drosophila) were heat shocked, and cells were prepared from salivary glands, for cytogenetic analysis. At several sites on these polytene chromosomes, 'puffs' appear, in which one or more chromosome bands seem to be wider than the rest of the chromosome (Figure 2). These puffs are not seen in control flies that were not heat-shocked.

1) (3 points) Outline an experimental strategy to test the hypothesis that heat shock puffs correspond to loci encoding heat shock proteins. Include whatever controls are necessary. Since the entire Drosophila genome has been sequenced, you can assume that just about any gene you wish is available for use.

2) (2 points) Outline an experimental strategy that would tell you whether there were changes in chromatin structure at heat shock puffs.

Hints on experimental design and presentation:

1. Think carefully about the hypothesis you wish to test. Make sure that the experiment truely addresses the question. For example,  the experiment in Figure 1 tests both the hypothesis that some genes are activated by heat shock, and the hypothesis that some genes are down-regulated by heat shock.  Heat shock is the treatment, untreated flies are the control. As well, the expression of heat shock genes is compared with the expression of actin and tubulin as control genes.

2. Good experiments compare one thing with another ie. one or more treatments with a control.

3. Make sure experimental conditions are consistent between treatments and controls.

4. Try to imagine right at the start what form the results will take, and what they might look like. Will the results be an autoradiogram, a table of data, a micrograph? If your hypothesis is true, what might the results look like? If false, what might they look like? Although you can never really predict in advance what the results will be, this kind of advance planning is good for identifying treatments or controls that have been omitted, or other flaws in your strategy. It is possible that all you need to present for your answer is a set of results showing what the results might look like, in either case.

5. Neither of these answers needs to be long! Give me an overview of the strategy, and tell what the experiments prove.

6. These experiments can be done using one or more of the methods discussed in class.

Submitting your assignment

• Rename the template file something different from as2_report_template.docx.
  
• Make sure your assignment report includes your name, student number and UM email address.
• Feel free to include graphs, figures, tables, anything that gets your point across.
  
• Save your assignment report as a PDF file, and upload it to the PLNT3140 UMLearn dropbox site in the Assignment 2 folder. Files in word processing formats (.doc, .docx, .rtf, .odt) are NOT acceptable.

Note on grading: In assigning a grade, some consideration may be given to how the answer communicates your ideas. Keep in mind the following:

• Use precise and appropriate biological terms.
• Organization the ideas in your answer, so that a clear chain of logic is apparent. Formatting tools such as s subheadings or bullet points help to show the reader the structure of your ideas
  
• Ambiguity: Try to read your answers from the viewpoint of your reader. Are there several possible ways to interpret what you have said?
• Feel free to use figures or tables in cases where they will be useful get across your ideas.
  
• Your first step should NOT be to go into the literature and find papers on the topic. I want to see your interpretation of the data, not someone else's. All the information you need is given in this assignment.
• Be careful not to go beyond what the data is telling you. In other words, state only those conclusions that are actually supported by the data given here. It's perfectly legitimate to include sentences like "These results are consistent with what we know about glucocorticoid receptors...." but make it clear what you can actually conclude from this data, versus other points you wish to bring in.