GENERAL GUIDELINES Formatting: Papers must be typed, including tables and figure

GENERAL GUIDELINES
Formatting:
Papers must be typed, including tables and figures. Text should be 1 ½ spaced. Font should be a simple, easily legible text (e.g. Times New Roman) and font size should be 12 and you must use standard margins.
Papers should be organized to conform to a traditional scientific journal format, with the following sections (in the following order) for the peer reviewed lab report:
TITLE PAGE (Title and Name)
RESULTS (in sub sections)
DISCUSSION (not subsections but in paragraph form)
Content:
This paper will cover labs 2, 3, 4, and 5, including the SnapGene exercise. The “Results” section of your paper should be subdivided into titled subsections by experiment in order, NOT by lab session/week.
All of the relevant information for that experiment should be included in that subsection including data and text describing the data..
The “Discussion” should NOT be sub-sectioned, although it should flow in the same order as the data were presented in in the previous sections.
A key element of a good paper is that it is appropriately formatted and structured, as well as well organized and easy to follow. These components will be included in the assessment of your paper, and therefore are part of your grade.
Audience:
While writing this paper, assume the reader is a scientist who is not taking BIOL101L. You can assume they are generally familiar with all of the techniques utilized- meaning you are not to explain what a restriction digest is or how it works, for example. Having said that, this reader does not know specifically what you did in your experiments- therefore you must specifically describe your experimental results and interpretive discussion. Do NOT write this paper as if your audience is the TA or the instructor, or a fellow classmate in BIOL101L.
Nomenclature and Abbreviations:
You will be held to some conventional nomenclature rules in 101L. The most relevant are:
Names of organisms should be italicized, genus capitalized and species lowercase, and fully spelled out at first mention in the text (e.g. Escherichia coli).
Names or organisms may be abbreviated after first mention in the text, so long as the abbreviation has been defined in parentheses at first mention- e.g. Escherichia coli (E. coli). Abbreviations include capital first letter genus followed by a period, and fully spelled out species. Still italicized.
While genetic nomenclature differs for different model organisms, for the purposes of 101L, names of genes should be lower-case and italicized (e.g. egfp), protein products are NOT italicized and in upper-case (e.g. EGFP)
If abbreviations are to be used in the text, they must be defined at first mention- e.g. Luria Broth (LB) or transformation 1 (T1).
Metric units should be abbreviated appropriately.
SPECIFIC GUIDELINES, BY SECTION
TITLE PAGE
A descriptive title that conveys the overall focus of the paper and (generally) how it was done. Do not simply list the methods you used. Mention the class or type of experiments used. Do a PubMed search and take a look at the research article titles you see in the results list.
Author name
Section (Tuesday AM or Wednesday PM, for example)
TA’s name
Page break before starting the next section.
RESULTS should be organized by subsection headings:
Ligation:
Transformation:
DNA Purification:
Restriction Digest:
PCR:
SnapGene including proposed digest:
In each subsection of the “Results” section, you are responsible for presenting the data and results for that experiment. You aim to do this concisely, in the context of your specific objective for that experiment, and without interpreting your results (that is what the “Discussion” section is for).
You are expected to both SHOW (using tables and figures) and DESCRIBE (in your text) your results here, but DO NOT interpret your results or discuss what they mean in the results section. A reader should be able to use the written section to (nearly) recreate your figures and should be able to figure out the most important data points in your written section by looking at the figures. In short, the two parts, show and describe, should be almost independent of one another.
For each experiment, you will need to provide of the following as you SHOW and DESCRIBE the data:
SHOW THE DATA: Your analyzed data (not necessarily your raw data) collected in an experiment should be presented in a simple, well-labeled table or figure. Tables are generally good for simplifying presentation of a large amounts of numerical data (i.e. colony counts on transformation plates, and nanodrop concentrations) and figures include anything that is not presented in a table (i.e. gel photographs, SnapGene plasmid map, etc.).
Formatting tables and figures:
– Table and figures must be named and numbered in the order in which they appear. Figures and tables are numbered separately.
Each table must have a table number and a descriptive title that includes a useful description of either the specific objective or result of the experiment, and what data is being presented in the figure. This should be 2-3 sentences maximum.
– Each figure must have a title and caption that includes a useful description of either the specific objective or result of the experiment, and what data is being presented in the figure. This should be 2-3 sentences maximum. You should also provide info on what samples are in which lane. Either in the caption or in a table adjacent to the figure that contains the lane numbers and the samples in each lane.
For example: [TITLE]“Figure 1: Confirmation of the presence of NUP2 gene in pUC19 vector by restriction digest. [CAPTION]1.2% agarose gel showing the results of single, double and no-enzyme control digests of recombinant and non-recombinant plasmids with EcoRI and SmaII.”
The following title is inappropriate: “Week 3 restriction digest results gel.”
– Specifically for gel photographs: images should be cropped so as to limit the area presented to focus on the data (crop out empty spaces, but retain the entire ladder and lanes that include results). You should label 3-5 ladder band sizes that are relevant to the sizes of bands included in the results. DO NOT paste an image of the NEB 1kb ladder next to your gel image- it is not appropriate. As part of the gel photo itself, label the contents of each lane.
– Tables and figures, with their titles and captions, should be included within the text of the results section.
– Tables and figures should be of proportional and reasonable size (not too small to read and not bigger than needed). There may be more than one table or figure per page if space allows. Any one table or figure must fit on one page along with its title and caption.
DESCRIBE THE DATA: You must also include in this section of the paper, an independent written description of the data, in words; i.e. a paragraph describing the data to the reader, with a reference to the result in the table or figure included. A good way to approach this is to begin with stating the objective of the experiment, and then present the key pieces of data that the reader should notice in the figures; you need to point out these data and describe what the data ARE (but, again, don’t interpret what they mean yet).
For example: “A restriction digest was used to confirm the presence of the NUP2 gene in the pUC19 recombinant plasmid. Recombinant and non-recombinant plasmids were subject to three digest conditions: no-enzyme control, single digest with SmaII and double digest with EcoRI and SmaII. The no-enzyme controls for both plasmids showed supercoil bands corresponding to non-linearized plasmid DNA (Figure 1, lanes 1 and 4). Single digest of the recombinant plasmid produced a 7kb fragment (Figure 1, lane 5), and single digest of the non-recombinant plasmid produced a 6kb band (Figure 1, lane 2). Double digest of the non-recombinant plasmid produced one band at ~6kb (Figure 1, lane 3). Double digest of the recombinant plasmid produced 2 bands; one at 1kb, and one at 6kb (Figure 1, lane 6).”
NOTICE: That I just stated my results, I did not interpret them (i.e. I did not state my expectations, compare my results to my expectations, or interpret what my results mean in the context of the experimental objective). For controls, it is OKAY to state they behaved as expected (or didn’t) because that validates your assay and is why they exist. Your discussion around interpreting the behavior of your controls (and whether your assay is valid and trustworthy) and your results is meant for the “Discussion” section. Also notice that I did this concisely, and not in story-telling fashion where I am merely “reading the gel image to you” from left to right, lane by lane. I presented it all in the most organized way to avoid over-redundancy. I am highlighting key data with my words, in context with the experiments. Your reader can LOOK at the gel themselves, that’s why you made a figure!
Here is some of the key data to describe in the “Results” section and show in the Figures and Table section after the Discussion. Again, don’t interpret or draw conclusions from your data in this section– you’ll do that in the “Discussion” section.
Ligation: show the gel of the ligation in a well annotated figure and describe the results in the context of the experimental objective in the text (i.e. identify the samples and controls and describe their results- the number of bands and their sizes, pointing out any important differences you’d like to bring to the reader’s attention).
Transformation: show the number of colonies that grew on each plate in a well annotated table and include your calculated transformation efficiency. Do NOT make a figure of the transformation plate photos.
Miniprep: show the concentration and purity ratios for each of your minipreps in a table and briefly describe the result in the context of the experimental objective in the text.
Restriction digest: show the digest gel in a well annotated figure and describe the results in the context of the experimental objective in the text (i.e. identify the samples and controls and describe their results- the number of bands and their sizes, pointing out any important differences you’d like to bring to the reader’s attention).
PCR: show the gel in a well annotated figure and describe the results in the context of the experimental objective in the text (i.e. identify the samples and controls and describe their results- the number of bands and their sizes, pointing out any important differences you’d like to bring to the reader’s attention). Also, be sure to state the exact size of the expected PCR product using your two primers, for a recombinant plasmid that you determined in the SnapGene exercise.
Include an image of the recombinant plasmid map from your SnapGene exercise and a table of the restriction digest you designed including enzymes and potential single and double digest results.
Aim to limit yourself to one, concise paragraph for each experiment in each subsection. A good way to begin this paragraph is to state the objective of the experiment in the first sentence, followed by the results. Be sure to reference your tables and figures (see above example).
DISCUSSION (no subsection headings)
In the “Discussion” section, you should interpret the results of each of your experiments. Your objective here is to translate what the results of each experiment mean to you in the context of your research- to draw conclusions in line with your objectives/hypotheses.
Again, aim to limit yourself to one, concise paragraph to discuss conclusions for each experiment. Remember NOT to subsection the “Discussion” section with sub-titles, and instead be sure to present each paragraph in the same order as the data were presented in the “Results” section. At the end of the “Discussion” section, include one final conclusions paragraph, where you relate your overall results for each clone analyzed to the overall objective (i.e. Did you achieve what you set out to in this research? Do you feel confident in your results to confirm that? Remember our goal!!).
I suggest framing a “Discussion” section paragraph in the following way (i.e. as answers to the following questions, in complete sentences):
What was the specific objective of this experiment?
What was your expectation/prediction for your key result(s)? Why? State your reasoning.
Did your controls behave in an unexpected manner that cause you to question the validity of your results? Explain. (Remember that positive and negative controls help support your arguments.)
What did your data show you with respect to your key result(s)? This is BRIEF- DO NOT REPEAT YOUR RESULTS SECTION TEXT!
Did your data/results behave in an unexpected manner, or is there a lack of result? Explain.
If yes to one of the above, state ONE SPECIFIC source of error or explanation that makes sense with what your results actually show. Note: merely saying “human error” is NOT APPROPRIATE. This should include a statement of what you expected to get.
If yes to one of the above, propose a simple solution or follow up experiment.
What is your final conclusion regarding your key data from this experiment? Is your data inconclusive? Explain your reasoning.
Warning: Many novice writers mistakenly write the “Discussion” section so it reads like a complete copy and paste of the “Results” section. Be sure you understand clearly the different objectives of these two separate sections of a scientific paper. Remember that scientific writing is meant to be as concise as possible with very little redundancy. Meaning- if you said it in one section, you’re NOT supposed to say it all again in another section. “Methods” is for methods, “Results” is to show results, and “Discussion” is to discuss your results. Your language should be very different in each section, even though you’re talking about all of the same experiments in each- you’re just approaching them from a different perspective or lens in each section in a highly organized way! Carefully compare the example text in the “Results” section with the “Discussion” example text below about the same experiment…
Peer review:
Your paper will be assessed by your peers for structure, formatting and accuracy as described in these guidelines, as well as data presentation and interpretation. Use these guidelines throughout writing your draft, and as a final checklist before uploading your paper.
Final grading by TAs:
Inclusive in those categories are assessments for spelling, grammar and scientific nomenclature. Similarly, students are assessed on their scientific reasoning and critical thinking skills in the interpretation of the data. Points will be deducted if students are not able to appropriately reason through an explanation. Again, use these guidelines throughout writing your draft, and as a final checklist before uploading your paper.