Cloning of Brachyury from SW480 cells

Please use the word template supplied for you write up.
Save the template to your computer then rename it with your Banner number, and report 2014. An example file name: 0000000 Report 2014.

Abstract (10%)
No more than 200 words.
The key to writing a good abstract is to break it down into 5 key sentences, and then use these to structure the abstract. The sentences should contain key information ?abstracted? from each section of your finished report.
1. The first sentence. This should introduce the overall topic, state the problem you tackled or the key research question you asked. Build on it, and focus on one key question within that topic. If you can?t summarize your report into one key question, then you don?t yet understand what you?re trying to write about! Keep working at this step until you have a single, concise (and understandable) question.
2. The second sentence. This should be derived from literature review/introduction. It should summarize why nobody has adequately answered the research question before. Your introduction will cover some/all of what?s been previously published in the literature about this research topic. Boil this information down to one key sentence. Don?t try to cover all the various ways in which people have tried or even succeeded; explain how this particular research/project is unique, and is required to fill a ?gap? nobody else has successfully completed yet. You can phrase the sentence such as ?previous groups have not (include your unique research)??.
3. The third sentence. This should come from the project experimental plan. It should explain how you tackled the research question. What was the idea/plan? What was the overall intention you introduced in sentence 2?
4. The fourth sentence This should also come from the results. State how you go performed the research. What experiments did you do? This is likely to be the longest sentence, but don?t overdo it! ? still just one sentence that you could read aloud without having to stop for breath. Remember, the word ?abstract? means a summary of the main ideas with most of the minute detail left out.
5. The fifth sentence This should come from the discussion. It should state what the key impact of the research is. This should include the the overall outcome of the experiments but must also include a summary of the implications/conclusions can you draw from the research. Why should other people care about your ?result’? What could they do with this research?
Introduction (10%)
No more than 1000 words.
Your introduction must cover some/all of what?s been previously published in the literature about the research topic. It should also give ?background? information on the experimental procedures being used and a brief overview of the overall experimental plan. The introduction MUST be correctly and well referenced with current relevant literature from peer reviewed scientific journals. In this report you should ?introduce?
1. Brachyury
2. Restriction digest cloning
3. Blue/white selection
Material and Methods (no mark, formative feedback only)
You should write up the material and methods for Week 1 Day 2: Preparation of plasmid for restriction digest cloning. Remember try to use the past imperfect tense.

Results (30%)
No more than 2000 words.
The results should contain a number of sections, each related to a specific overall aim. You should decide how many sections should be presented and how best to structure and order these to enable a logical progression through, the experiments we performed, to the final end ?result? we achieved.

Each section you produce must contain…
A short explanatory section explaining the overall aim of the procedures for the particular result section
Text explaining fully processed results data for the particular result section
Figure(s) and/or table(s) presenting data to support the text and be referred to from the text

The results sections MUST contain at least the following figures and tables.
1. RNA extraction figure: This figure should have 2 parts. Part A will be your data from the group agarose gel image result of Week 1 Day 4. Part B will be an image from the Experion data for your lane/well.
2. Plasmid and Brachyury Preparation results: This figure should have 2 parts Figure 2(A) and (B). I have prepared an example for you in the template. Figure 2 (A) contains the image of the pBlueScript sk+ plasmid after EcoRI digestion, phosphatase treatment and gel purification. (B) should be your OWN set of results from your group image. You must ‘crop’ this image down to include your 4 lanes: 1) the Easy ladder, 2) the Acin PCR lane, 3) the Brachyury PCR lane and finally 4) the Brachyury PCR purified lane.
3. Colony PCR results: This figure should be your OWN set of results from your group image. You must ‘crop’ this image down to include your 1 lanes: 1) the Easy ladder, 2) colony 1 PCR, 3) colony 2 PCR 4) colony 3 PCR 5) colony 4 PCR
4. Plasmid Map(s) figure: This will be a produced from the results of your plasmid purification and plasmid maps for the plasmid you purified
Each figure must be presented on a single page, NOT within the text sections of the results.
Each figure must have a suitable title (above the figure) and legend (below the figure).
Legends must provide a key to the data the figure presents and note any key points from the data.
Each figure must be capable of ‘standing alone? i.e. the reader should not have to refer back to the main text for information to interpret the figure data.

These data for the tables should be fully processed from the Excel class data files NOT just a reprint of the Excel spreadsheet.
They must contain a statistical analysis of the data (standard deviations and average) and contain your own particular data set(s).
1. Table 1: Class plasmid preparation data from Week 1 Day 2.
2. Table 2: Class total RNA concentration data (Qubit and your own Experion data) and class cDNA data.
3. Table 3: Class transformation results data.

Discussion (30%)
No more than 1000 words.
The discussion MUST be correctly and well referenced with current relevant literature from peer reviewed scientific journals. The discussion should have 3 sections.
1. Section 1: Discuss the final results you obtained for each stage. Clearly explain the main findings from each section and how one results section lead on to the next, highlighting any issues that may have affected your results and/or progression from one stage to the next stage. i.e. create a logical progression of the ?flow? of the whole experiment from start to finish.
2. Section 2: You should then come to a final conclusion discussion point as to the success or otherwise of the entire experiment. What conclusions can you draw from the project and the final result?
3. Section 3: Finally you should discuss what would you and/or other researches could/should do next with your findings. Discuss what?s been previously beeb published in the literature about this research topic. State what the key impact of your results in relation to these previous findings is. Why should other people care about your ?result? and what could you or they do to further this research.
Suitability for publication in a peer reviewed scientific journal (20%)
This assessment will judge the quality of the data presented; how clear and easily interpreted are the figures and tables, the level of scientific English used in the report and the referencing quality/quantity in the report and final bibliography.
1. Presentation quality of the data:
o All figures must be presented as outlined in the guidelines and the template document. All figures must be fully processed with key data clearly annotated/outlined. Annotations (e.g. arrows, numbers etc) must not obscure figure data.
3. Scientific English:
o You?re writing this thesis/report for scientists, who expect to read accurate unambiguous scientific English. Sentences like ?the band is bright? or ?I saw a fat band in the gel? are examples of poor scientific English. Band 1 displayed a higher intensity relative to band 2, indicating it contained a higher concentration of DNA? is an example of higher quality scientific English. If, for example, you can attach figures to the intensity, even better.
5. Quality/quantity of referencing and final bibliography
o For research to pass ‘peer review? and be published in a quality journal, the paper presenting it must contain sufficient current relevant background literature to support the experimental plan, and set the research findings and final discussion/conclusions into context. Without such referencing you will not be able to publish your research in a quality journal.

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