BS934 Assignment 3

Biotechnology Lab Report

Task:

Describe in Scientific Paper Format (SPF) the experiments you performed for practical 3 (the last one involving PCR
BS934 Assignment 3
Please complete the assignment by yourself. We screen for plagiarism and collusion.
The assignment should be not more than 4 A4 pages, maximal word counts of each section as outlines below, font size 11 Ariel or Helvetica, single line spacing, without counting figure legends and references. Anything that is beyond these limits will be ignored.
Deadline for return of the assignment is 6th December 2022, 16:00.
————————————————————————————————————–Task:
Describe in Scientific Paper Format (SPF) the experiments that you performed for practical 3 (the last one involving PCR).
The assignment should have following elements:
1. Title (max 10 words)
2. Abstract: not more than 75 words (summarise what was done).
3. Introduction: Summarise the background and aims, 200 words max. You can extract this from the practical handbook. This should be very succinct, you can refer to the Scribble gene and what it does briefly and reference the relevant paper cited in the practical handbook. You can refer to CRISPR-Cas9 technology, but only briefly and again cite relevant literature.
4. Methods section (700 words max): describe in brief terms what has been done, like in a scientific paper. Everything should be written in past tense. Look at published papers how such methods are written. For example, look at what was in the practical handout:
“ DNA will be amplified using the following programme:

94 °C 5 min
94 °C 30 s
52 °C 30 s x 40 cycles
72 °C 30 s
72 °C 7 min”
Should become:
“PCR was performed with following parameters: initial denaturation: 94 °C 5 min, then 40 cycles of 94 °C 30 s, 52 °C 30 s, 72 °C 30 s followed by 72 °C, 7 min.”

Or:
“Carefully pipette off and discard as much liquid as you can, leaving the cell pellet”

Should become: “supernatant was removed”. And
“Using a P1000 carefully add 250 µl of your sample to the 1.5 ml microcentrifuge tube in the rack. This tube already contains 10 µl of PT-L2P DNA extraction buffer.”
Becomes:
“250 µl of the DNA sample was added to a tube containing 10 µl of PT-L2P DNA extraction buffer”.

This:
Add the following reagents to both tubes, in the order specified:
10 µl PCR product
7 µl sterile H2O (OR ADD 8 µl to tube N)
2 µl 10x digestion buffer
1 µl HaeIII restriction enzyme (DO NOT ADD enzyme to tube N)
Note: take your reaction mix and a pipette to a demonstrator who has the restriction enzyme stock on ice.
Should become:
“The DNA was digested using HaeIII restriction enzyme”.
This: “Incubate at 37ºC in a water bath for 1 hr” becomes: the sample was incubated 1 h, 37ºC.
Steps you did not do (preparation of bacterial plates) you do not need to describe.
You can use tables to summarise some protocol steps, but only use maximally 2.
You can also refer to manufacturer’s protocols (e.g. GeneJet) and not describe these in detail.
5. Results: 200 words max. Describe briefly what was done (summarise the methods steps in a few sentences) and what is seen on the gels, refer to the results figures (e.g., “..as shown in Figure 1..”.
6. Result Figures:
Generate result figures (Figures 1 and 2 of the two gels you ran) with legend from your results generated (uploaded on Moodle). Legend should be brief but clear, so it is obvious what is shown on the gel. You can include a figure that shows what was expected and compare the results in the Discussion. If you have images of the bacterial plates (blue/white screening) you can show that, but this is not necessary.

FIGURE PRESENTATION
Cut and paste/insert your gel images from Moodle into POWERPOINT, where you can label the gel. Save the labelled image as a jpeg or pdf to insert into your worksheet, label markers on your own gels (we used a 100 bp ladder).
Labelling gels: avoid any writing over the gel; do not try to label every size marker band; informative labelling makes the figure easier to understand than just numbering the tracks. (however, you can just number the lanes and then refer to the label numbers in the legend).
Figure legend must be below the figure and:
• must contain a number and brief title for the figure;
• should name the method (s, e.g. DNA separation by agarose gel electrophoresis) and have sufficient detail to enable the content of the figure to be understood without reading the text;
• should include a key to explain labelling if necessary;
• must NOT report, interpret or explain the results.
If you gel did not show the expected results (e.g., no band), still show it, as this will give you the opportunity to discuss what might have gone wrong in DISCUSSION. But you can also show the results from another student that gave expected results and compare. Or use someone else’s results, if you did not get any (if for some reason, your samples were not run, us results from someone else). If you combine images of two different gels or sections of gels, clearly indicate the two sections (do not splice gels together so it looks like it is one gel, this is image manipulation).
7. Discussion: 200 words max. How do the results compare with what was expected? Why might the experiment not have brought you the expected results, if this is the case?
8. References: Any references you deem necessary, including any protocols from manufacturers (e.g. GeneJet).
9. Assessment Criteria. These elements are not necessarily given equal weight in the overall assessment. (Marker: please highlight relevant comments.)
Elements Top distinction
>80% Distinction 70%-79% Merit 60%-69% Pass 50%-59% Fail <50% Low fail <40%
Completeness All sections completed. All sections completed. Almost all sections completed. Most sections completed Some sections not completed. Many / most sections not completed.
Quality of answers. All the info. required.
All accurate, relevant and concise. All important material, concise, few minor errors. Considerable content.
Minor errors, some irrelevant material. Reasonable info. content. Minor and some major errors. Some irrelevant material. Limited answers, and/or many major errors, not concise, some waffle. Little or no valid info.
Many errors, most material irrelevant and/or waffle.
Results.
(as appropriate) Very clearly, selectively & concisely described. Data correctly analysed & interpreted.
Tables and figures neat, accurate &, fully labeled.
Statistics correctly used, interpreted, & reported. Clearly & concisely described. Data correctly analysed & interpreted. Tables and figures neat, accurate & fully labeled.
Statistics correctly used, interpreted & reported. Mostly clearly & concisely described. Data generally well analysed; few misinterpretations.
Some omissions / errors in presentation of tables and figures.
Statistics mainly correctly used, interpreted, & reported. Generally clear, but difficult to identify key results.
Data analysis & interpretation satisfactory but some errors / omissions.
Significant errors in presentation of tables & figures.
Some errors in use, reporting & interpretation of statistics. Unclear, key results not identified. Many errors / omissions in data analysis & interpretation.
Many errors in presentation of tables & figures.
Major errors in use, reporting & interpretation
of statistics. No description of results.
Data not analysed; all key points missed or misinterpreted.
Tables and figures very poor or missing.
Statistics not used or totally inappropriate.
Understanding shown Excellent. Clearly evidenced. Substantial evidence. Some evidence. Limited and patchy. Little or none.

Presentation/
Quality of writing. Great clarity. Very concise. Entirely logical in structure. Negligible errors in spelling & grammar. Clear and concise. Generally very logical. Minimal errors in spelling & grammar. Usually clear and concise.
Only minor weaknesses in logic.
Few minor errors in spelling & grammar. Some lack of clarity and not concise.
Some lapses in logic.
Some errors in spelling & grammar. Lacks clarity, and not concise. Frequently illogical.
Many errors in spelling & grammar. Rambling, unclear. Difficult to understand. Illogical.
Very many errors in spelling & grammar.