miRNA Project Scientific Research Paper
We are continuing our authentic research experiment seeking to verify targets of miR-101 by analyzing the data from our qPCR runs.
You will demonstrate your understanding of the experiment by analyzing the data from the qPCR of your candidate gene and the appropriate controls.
All your writing for this report is individual. It must be in your own voice and your own ideas. Sources for information must be cited accurately using the CSE format. All drafts and final versions will be screened by Urkund for plagiarism, which is a serious academic offense. Unauthorized collaboration is a common problem in this class, so be original!
The Results
The Results is a statement of your data and statistical tests, observations and measurements, portrayed in tables and figures or graphs that allow the relationship between variables observed to be compared. It contains the visuals that display your data and a body of text that describe the data and trends (Knisley, 2017).
The Results section should begin with text that leads the reader through the data, pointing out trends and observations the writer feels are important, but not interpreting or drawing conclusions about the data, which belongs in the Discussion.
Insert the Tables after the paragraph where they are first mentioned for the convenience of your reader.
Tables are captioned above the table and describe where the data in the contents were gathered, any pertinent information about the treatment or experimental organisms not obvious from the column headings, and each replicate or criteria in rows. Tables present data in a way to make comparison of the numbers possible between different treatments or replicates, to show results of statistical tests or variance, or allow comparing lists of data. Knisely example:
The Discussion of a Scientific Research paper
Writing your first Discussion
Writing a coherent Discussion will probably be a challenge if you’ve never written one before, so follow the guidelines here in the Lab 8 post-lab, outlining what you need to include, then fill in your outline from your understanding.
- Relate your findings to research papers you either used in your Introduction (you probably should re-read it to remind you of what you proposed to do and why) or new papers about the context of your experiment.
- Why are your conclusions important? Write your ideas in rough form first, then go back and edit the details, add support from research papers on miRNA and gene expression or on your gene.
- Word choice is especially important in your Introduction and Discussion, where it must be clear and concise with no flowery phrases. If you feel challenged when writing for science, please view the following helpful video: Scientific Writing in Biology: Word Choice
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The Discussion
The Draft 2 guidelines provide details for your Draft 2, Title Results and Discussion, due 5 minutes before the beginning of the Lab 9 session, but here we will outline the basic requirements and purpose of a Discussion adapted from examples and Knisely’s Writing in Biology, 5th edition.
The discussion has the inverse of the organization of the Introduction. It begins with your specific hypothesis and your interpretation of your results, then relates those to the published literature or what is already known, and ends with the wider context; why your conclusions are important.
Knisely, 2017.
- Interpret the results of tests or experiments and controls in the context of your experimental question. Assess the quality of your data before drawing conclusions. Does the data support your hypothesis?
- Refer to the tables in your Results that support your statement by citing the graphic in the text.
- State the source of the error briefly when your results make it difficult to draw conclusions without a lot of explanation, especially if you are unsure of the reason. Human error, variability between different experimenters or replicates, or too small a sample size can all lead to an inability to make a convincing conclusion. These are all part of authentic research and can be corrected by repeating experiments.
- Careful of your language: Results don’t prove hypothesis, but can provide evidence that supports a hypothesis, or evidence that disagrees with a hypothesis. Be careful not to make strong conclusions since the scientific method only supports hypothesis until a large amount of evidence is gathered from multiple sources, the underlying mechanism is thoroughly investigated, or a newer study provides new information that disproves the existing theory.
- Persuade your reader that your interpretation is correct by referring to the data in your Results, leading them through the conclusions they should draw at each step of your analysis. If your evidence is strong and consistent, you can build your Discussion as a convincing argument to support your conclusion.
- Compare: Another way to convince your reader that your conclusions are correct is by comparing your findings to those of other researchers-do they agree with your conclusions? These can be papers with a similar hypothesis or who performed similar studies- not exactly the same, but comparable to some aspect of your experiment. Relating your study to others increases the credibility of your conclusions.
- Context: Finally, describe the context of your major finding. Suggest the next step- what would you do next? What could be the implications of your result in your subject area? How important is your finding?
- Tense: When referring to your Results or work from published studies, use the past tense when describing them. When you make statements about what is true or considered a scientific fact, use the present tense.
Examples from Knisely:
Past tense:
The initial velocity of the reaction was zero at temperatures between 60OC and 90OC (Figure 1).
Explanation: Past tense signifies that you are describing your own results.
Present tense:
At high temperatures, there is no enzymatic activity because the enzymes are denatured.
Explanation: Present tense signifies that these statements are generally valid and considered to be scientific fact.
Example
From Huang’s 2017 paper: 2017-Huang-miR101_FZD4_FZD6_TGFBR1_16420-39.pdf
Discussion
Introductory paragraph:
In this study, we discovered that the miR-101 level was reduced in the lungs of patients with IPF. miR-101 expression was regulated by the ETS transcription factor. Notably, miR101 reduced pulmonary fibrosis by inhibiting fibroblast proliferation and differentiation via the WNT5a/NFATc2 and TGF-/Smad2/3 pathways (Fig. 12).
Middle paragraph (relating project to the literature):
miR-101 was originally identified as a tumor suppressor, and its expression was reduced in many cancers due to genomic loss. miR-101 inhibited cell proliferation and invasion in cancer cells by targeting EZH2 (25) and inhibited autophagy and sensitized cancer cells to chemotherapeutic drug-induced cell death (26, 27). The effect of miR-101 on angiogenesis is contradictory, and both pro- and anti-angiogenic effects have been reported (28, 29). miR-101 enhanced LPS-induced pro-inflammatory cytokine production in macrophages via the activation of MAPK by targeting MAPK phosphatase-1 (30). Finally, miR-101 has been shown to inhibit liver and cardiac fibrosis (31, 32).
Final paragraph:
Emerging evidence suggests that suppressing up-regulated miRNAs or restoring the activities of the down-regulated miRNAs associated with disease could become a novel therapeutic strategy. Adeno-associated viruses have been used for the delivery of miRNAs in vivo to restore their activity; its therapeutic potential has been validated in a mouse model of lung carcinoma (35). Therapeutic delivery of miR-29 mimics by intravenous injections in the tail vein reversed pulmonary fibrosis in the bleomycin-induced mouse fibrosis model (14). In this study, adenovirus-mediated miR-101 lung delivery reduced the fibrotic changes in bleomycin-treated mouse lungs and also improved pulmonary function. Thus, miR-101 may be a potential therapeutic miRNA for the treatment of pulmonary fibrosis.
Questions to ask yourself:
- How does the discussion begin? Which writing strategy mentioned in our Discussion page did the author use? The others are equally good.
- Examine how concise the middle section, the relating your results to the work of others, reads. How should you explain the work of others? A single sentence in your own words can make the point of why you are mentioning another study. How does their result compare to your result? Does their study support your conclusion or does it contradict your study?
- Their final paragraph places their conclusion in context. How could your results be used? Make a suggestion for further studies or an application of your result in the disorder that you chose your candidate gene to affect.
Draft 2: Title, Results and Discussion- Individual
The authentic research experiment seeking to verify targets of miR-101 experiment is now complete.
Draft 2 will consist of your second version of the title, and the Results and Discussion (with References cited) of your scientific paper.
It is due by the beginning of your Lab 9. Your Tables will be completed, marked and returned to you with feedback before your submit Draft 2.
,The New parts of Draft 2 will be to write the narrative text of your Results section that describe your data Tables for your reader, and the Discussion which analyzes the Results.
You will submit it to the Draft 2 assignment dropbox in Brightspace by 5 minutes before your Lab 9. All submissions are screened by plagiarism software. No print copy needs to be submitted.
Before you submit your final version at the end of term, you will need to edit your drafts carefully to incorporate the TA feedback.
For the whole paper, you will follow the guidelines in the Student Handbook for Writing in Biology (Knisely, 2017). Also see the instructions that follow and the rubric for how your paper will be assessed.
All your writing for this report is individual. It must be in your own voice, and your own ideas. Sources for information must be cited accurately using the CSE format. All drafts and final versions will be screened by Urkund for plagiarism, which is a serious academic offence. Unauthorized collaboration is a common problem in this class, so be original!
WORKING TITLE
The title should:
- Be a concise description of your project
- include the name of your candidate gene, species and genus, method used to investigate your question, and now, your main result.
- a clear statement of your result or conclusion, if you could make one, not as a question.
- It should provide enough detail to allow someone interested in your topic to find your paper with a Google search.
- Make any changes or improvement suggested by your TA from your Draft1 feedback.
RESULTS
The Results are not limited by page or word limits. Key components referred to in the rubric are here:
Report the results of the experiment. Do not interpret or make conclusions about the results in this section. This section should objectively present the data you produced in the experiment and summarize your findings. Organize your results and data in a logical order:
- Start with a written description before the tables included in your results (Knisely, 2017, p.59-80). When describing results, refer to the appropriate table where supporting data can be found. Insert tables into your results.
- For each trial in your lab section for your candidate gene, you must present ALL the Cq values for all 3 or 4 replicates that also used your candidate gene primers.
- Do the DNA contamination check calculation for each data set and report the results.
- If no contamination is present, present the ∆Cq and ∆∆Cq values. You should analyze the data of ALL the teams that investigated your candidate gene. Tables must be formatted correctly with proper table titles following Knisely, 2017, p.62-64. For any missing data, use a dash or asterisk so it doesn’t look like an omission.
DISCUSSION
The purpose of a discussion is to analyze relationships among observed facts and to present your interpretation of the data. In your Discussion:
- Use at least two primary research articles (these may be the same as those used in your Introduction).
- 5-2 pages long when double-spaced with one-inch margins
- follow a logical order to develop your ideas
What should it include?
- Major Conclusions: Restate the hypothesis of the experiment and your prediction and make a succinct statement answering your experimental question (was your gene a target of miR-101?). Briefly describe the major conclusions of your experiment, by referring to specific results presented in graphs or tables. Your conclusion does not have to match your prediction.
- Discussion of Results
Interpret your results and discuss their meaning and conclusions. Refer to the relevant tables in your results section to support your conclusions. Are your results what you expected to see? Why or why not? Was your scientific rationale adequate to answer your question? Interpret results from your controls. Draw attention to outliers or problems in the data or recognize data that does not fit your hypothesis.
- Relate Findings to Literature Discuss your results as they relate to previous research in the literature. Compare the role of miR-101 and the role of your candidate gene (use references here to connect your results to other publications). Use in-text citations and use at least two primary research articles (or more if necessary). Do not use direct quotes – instead, compare the results from the published research to your own findings and discuss any similarities or differences you observe.
Propose what would be a logical next step to either confirm or disprove your results.
- Final Conclusion and Context Make a summary statement suitable for inclusion in an abstract. Can you draw any conclusions, and do you think your candidate gene is influenced by hsa-miR-101? What do your results mean (in the bigger picture)?
Optional (possible) discussion points to think about:
- The criteria you used to select your candidate gene
- The strength of the prediction (from miRDB) that your gene would be a target of miR-101
REFERENCES
Results sections usually do not include any citations to other work. It is meant to present your work only, with no interpretation, just the results of the tests.
For your Discussion:
- Include a reference list with your two primary research articles and any other sources you used.
- Look at your feedback for the references in Draft 1 and fix any problems.
- For how to format and cite your references, click on this CSE style guide link.
GRAMMAR, ORGANIZATION, WORDING, FORMAT
After you have written your text describing each table check for:
- Concise, organized and logical presentation, appropriate word choice, proofread with no spelling/grammatical errors.
- Name, B number and lab section in upper right-hand corner of first page (no cover page)
- Text double-spaced except for table captions, 11 or 12-pt Times New Roman, 1 inch margins, page numbers.
- Tables should be sequentially numbered, starting at 1. Tables not split over two pages. Table titles go above the table.
Rubric for Draft 2 – Title, Results, Discussion and References
RUBRIC (Same as in assignment dropbox):
| Criteria |
Excellent |
Very good |
Good |
Adequate |
Inadequate |
| Title |
5 points
Title conveys main point of experiment, and includes name of miRNA, candidate gene, species, method and result. |
4 points
Title mostly conveys main point of experiment, but one essential part is missing. |
3 points
Title mostly conveys main point of experiment, but two essential parts are missing. |
2.5 points
Point of experiment is difficult to determine by the title, three or more essential parts are missing. |
1 point
Point of experiment cannot be determined by the title. |
| Results |
20 points
Begins with narrative text, presents tables required, highlights key trends to reader and reports test results without biological interpretation. Tables have appropriately detailed captions and can stand on their own. |
17 points
Begins with narrative text, presents tables required, highlights key trends to reader and reports test results without biological interpretation. Small problems such as: interpreting Cq or delta Cq values before normalizing data, or brief table captions, or mistakes in data reporting or calculation. |
14 points
Begins with narrative text, presents most tables required, and reports test results without biological interpretation. Larger problems such as missing data, very brief narrative text, trends not explicitly mentioned, tables have very brief legends, or conclusions about hypothesis are briefly made. |
10 points
Three of the following: Minimal narrative text, tables minimal and mostly uninformative, trends not noted in text, tables lack captions, or makes conclusions about hypothesis. |
5 points
Major problems that leave reader uninformed; narrative text is lacking entirely, tables contain unclear and/or irrelevant information. e.g., “Results” contain no text, raw data are in a table w/ poor legend. |
| Discussion |
30 points
Presents most key components: supports or rejects hypothesis, formulates argument for conclusions referring back to biological rationale & by comparing with relevant findings in literature, evaluates experimental design, evaluates reliability of data, states implications of results, suggests next investigation steps, and ends paper with final conclusion. |
25 points
Presents many key components and has done a good job with the Discussion but -fails to clearly tie biological rationale from the Intro into the conclusions made OR has also included superfluous experimental problems OR another key component not well done |
20 points
Presents some key components but needs some improvement
e.g., clearly states that hypothesis is rejected or supported and develops a good argument that refers to the results and biological rationale, but fails to logically and objectively evaluate the experimental design and data reliability OR cites literature without relating to their results. |
15 points
Many key components are very weak or missing.
e.g., fails to explicitly reject or support hypothesis and so conclusions are vague and incompletely tied to rationale, literature is minimally cited, presents unranked list of problems instead of logical evaluation of design and data. |
10 points
Most key components are missing or very weakly done.
e.g., illogical conclusions made based on data, no ties to biological rationale are made, no literature cited, little to no evaluation of experimental design/data. |
| References |
5 points
Two primary research articles are cited within text in name, year format; references in final reference list are listed alphabetically and formatted using CSE guidelines. |
4 points
Two primary research articles are cited within text in name, year format; references in final reference list are listed alphabetically and formatted using CSE guidelines, but there are 1-2 errors. e.g., citations are done well but there are a few minor formatting errors in the final reference list. |
3 points
Two primary research articles are cited within text in name, year format; references in final reference list are listed alphabetically and formatted using CSE guidelines, for the most part, but there are consistent errors. OR a reference cited in the text does not appear in the final reference list OR a reference in the final list is not cited in the text. |
2.5 points
One required citation is missing OR citations are minimal within the text OR final reference list is largely incomplete and/or is not formatted appropriately. |
1 point
Information from outside source is presented but is consistently not cited; final reference list is missing. |
| Organization, wording, grammar |
10 points
Excellent organization and sentence flow, appropriate word choice; clear and concise explanations; no unnecessary repetition or irrelevant information, few to no grammatical errors. |
9 points
Organization was good with few to no problems, mostly clear and concise, wording awkward in a few places; minor unnecessary repetition, few grammatical errors. |
7.5 points
Organization somewhat problematic but can still follow thought progression e.g. explanation of methods in the results section; wording awkward at times; little unnecessary repetition; some grammatical errors or appears not to have been proofread. |
5 points
Problematic organization of some section resulting in loss of clarity; awkward wording at times; some unnecessary repetition; some grammatical errors. |
2.5 points
All poorly organized, interrupted flow of ideas leading to lack of clarity, can not follow thought progression, many grammatical errors. |
| Format |
5 points
Double-spaced text except table and figure legends, 11 or 12-pt Times New Roman or Gill Sans MT,, 1 inch margins, Name, B number and lab section in upper right-hand corner of first page, page numbers. Saved as .pdf |
4 points
Name, B number and lab section in upper right-hand corner of first page, missing one other requirement of formatting. |
3 points
Name, B number and lab section in upper right-hand corner of first page, missing two other requirements of formatting. |
2.5 points
Name, B number and lab section in upper right-hand corner of first page, missing three or more other requirements of formatting. |
1 point
Little attempt to format correctly. |
| Overall Score |
Level 5
63.25 or more |
Level 4
50.75 or more |
Level 3
37.75 or more |
Level 2
20.75 or more |
Level 1
0 or more |
