Overall format:

Page 1 Picture of the agarose gel.

Page 2-4 Analysis of the results.

Page 5 Reference list if necessary.

Worth a total of 20 marks (13.5 % of final mark):
--10 marks for the results section (Page 1) (3.5% of final mark)
--100 marks for analysis of the results (Page 2-4) (10 % of final mark)

RESULTS

Every member of the group is required to perform his or her own restriction enzyme digestion of the plasmid. This is an individual results mark. Therefore, the first page of your assignment will be a picture of your group's gel with the lane digested by you indicated.

Marks	For what?
5	Preparation of DNA. No DNA 0 marks, DNA 5 marks
3	Restriction enzyme digestion (individual mark) (No marker or uncut DNA 2 marks lost, partial digestion 1 mark lost
2	DNA sequence (0 for no DNA sequence, 1 mark lost for less than 100 bases of readable sequence, and 2 full marks received for greater than 100 bases of readable sequence).

ASSIGNMENT: ANALYSIS OF RESULTS

Example assignment

Analysis of the results: 100 marks.

Layout of pages 2-4

Top of page two must show the raw sequence you recieved. This sequence must be annotated with the start and stop of the clipped sequence you used for your analysis. This sequence may be presented in a smaller but readable font.

Three page maximum description of your analysis and conclusions. 12 point font; 1.5 line spacing;1 inch margins; figures included. You may have a maximum of one page of figures that must be referred to in the report text. This must be individual work; no collaboration. Plagarism is an academic offence that will be reported directly to the Dean of Science, which will result in a fail in the course.

EXPECTATIONS FOR THE ANALYSIS.

I have very high expectations for your analysis. Students find this assignment to be one of the hardest they have experienced. You must remember that you have been taught the structure of a gene, the flow of genetic information at least twice maybe even 3-4 times at university. In this assignment you are expected to know and apply this knowledge. This assignment is rooted in the teaching paradigm: learning by doing. It becomes very evident in your report whether you truly understand what you are doing, or whether you are merely pushing buttons blindly. If you do not understand what a gene is and Blast analysis (you did Blast in Biology 281b), then it is time that you break open that text book, read and absorb.

Remember I will perform an analysis of all the sequences. I usually spend 15-20 minutes per sequence. If I can find more in 15-20 minutes than you do, do not expect a passing grade for the assignment. Expect to spend 5-10 hours or more on the analysis, you will mostlikely go down many blind alleys before finding something interesting. This is an open ended assignment; what you get out of it depends what you put in to it.

You must do the analysis on the DNA sequence that you determined with your group or that was assigned to your group. If you do an analysis of DNA sequences from another group, you will be given a mark of zero for the assignment.

A limited list of expectations for the analysis of the results to help guide you:

1. Perform the basic BLAST analyses.

2. You are expected to have read the content in the help page for BLAST provided on the Blast home page, particularly the FAQs and how Blast works. What is a low complexity sequence is something you should know?

3. What is the oreintation of your cDNA in the vector?

4. Explain clearly what you did and what you found. Don't bore me with non-relevent detail.

5. Where is it located in the genome? Is this important?

6. Has the EST been sequenced before? How many times?

7. Does your EST have the same structure as the other ESTs (Alternative splicing).

8. If you have a duplicate gene, which copy is your mRNA expressed from? Why?

9. If your EST overlaps with another EST sequence, can you walk along the mRNA to increase the amount of DNA sequence for analysis? What did this tell you?

10. Do not show me the output of the Blast program with out your interpretation of its meaning. If you don't know what it is telling you, it will not recieve any marks.

11. How does it align with the honeybee genomic sequence? The intron/exon structure of the gene that can be concluded from your sequence.

12. Does the mRNA encode a protein? What is the function of the protein? Metabolism, transcription factor, signal transduction, etc.?

13. Use pictures to illustrate your points.

IF YOU HAVE DONE A GOOD JOB WITH THE ABOVE TASKS YOU CAN EXPECT A MARK OF 60-70 PERCENT. REMEMBER THE ABOVE IS A LIMITED LIST OF EXPECTATIONS, EVERY EST WILL HAVE THEIR OWN PROPERTIES AND CONSEQUENTLY THEIR OWN EXPECTATIONS.

TO GET A STELLAR MARK I EXPECT THAT YOU SHOW INDEPENDENCE AND THE ABILITY TO EXPLORE. THERE IS NO PRESCRIBED TEMPLATE TO FOLLOW HERE, AS THAT IS THE NATURE OF EXPLORATION.

14. To get more than 60-70 marks you will have to explore the web for other information about the gene that you have not been asked.
------------For example, what do we know about the role of the gene in other organisms?

------------Are there any publications on the honeybee gene in honeybees?

15. All published information must be cited and referenced properly; otherwise, you are committing plagarism. A reference list may be included as page 5.

16. Every spelling mistake will result in a 5 mark reduction.

17. Every basic grammatical mistake will result in a 5 mark reduction. These mistakes include, but are not limited to, the following: sentence fragments; subject verb agreement; dangling modifiers; unbalanced constructions; inappropiate word usage; incorrect punctuation; improper paragraphing; etc.. If you are not familar with these mistakes, buy a book that explains basic English grammar.