20.109(F19): Research article

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20.109(F19): Laboratory Fundamentals of Biological Engineering

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Fall 2019 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Measuring genomic instability        2. Modulating metabolism        3. Testing chemical probes              


The culminating assignment for Module 2 will be a research article in which you describe your metabolic engineering investigation. The term research article (as opposed to laboratory report) is meant to indicate your growing maturity as scientific writers, and our growing expectations of you. Your Module 2 paper should approach the quality of the primary scientific literature (excepting its lack of experiment repetition), especially with respect to explaining rather than merely documenting your observations.

The target audience for this report is a scientifically literate reader who is unfamiliar with your specific field. Thus, you can assume rapid comprehension – but not a priori knowledge – of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.

Writing a "research article" versus a "lab report"

A quick but unscientific survey of several journal's "instructions for authors" shows some common themes that are worth considering here. For instance, the instructions from JCB say:
"To warrant publication in the JCB, a manuscript must provide novel and significant mechanistic insight into a cellular function that will be of interest to a general readership. Manuscripts containing purely descriptive observations will not be published."
Similarly, the instructions from MCBstate:
"MCB is devoted to the advancement and dissemination of fundamental knowledge concerning the molecular biology of eukaryotic cells, of both microbial and higher organisms. In most cases, reports that emphasize methods and nucleotide sequence data alone (without experimental documentation of the functional significance of the sequence) will not be considered."

Clearly the goal of published research is not merely to catalog or describe observations but to collect the information into some coherent story that advances general understanding and provides insights that others can use. This is the critical difference between a "lab report" which primarily describes your observations and the "research article" you'll write which invites you to share the insights your data gives. Here you must frame your results to address a larger question that's of general interest to the community. Many of the format instructions that applied to a lab report also apply to your research article, but keep in mind how the intention of the two written assignments differs.

Be sure to review the 20.109 statement on collaboration and integrity as you proceed.


You will complete this assignment individually.

As you prepare your assignment be sure to review the resources provided on the Communication tab.

Please submit your completed Research article due by Mon, Nov 11 at 10 pm on Stellar, with filename Name_LabSection_RA.doc (for example, NoreenLyell_TR_RA.doc).

Formatting and length guidelines

  • Your main document (excluding figures) should be/have
    • .docx or .pdf (preferred)
    • 12-point font
    • with 1-inch margins
    • double-spaced (except the abstract)
    • Figures can be made in a separate drawing program (such as PowerPoint), and can either be embedded or submitted as a separate document.
  • Not counting figures/title/abstract, report length should not exceed 14 pages. The following rough division is recommended:
    • Introduction: 2-3 pages
    • Materials and methods: 3-4 pages
    • Results: 3-4 pages (not including figures)
    • Discussion: 2-3 pages

Content considerations

Title, List of authors, and Abstract

The title, list of authors, and abstract do not count toward the 14-page limit and should all be on the first page of the submitted document.


The title should be short (no more than about 10 words), interesting, and it should describe what you discovered in your research. Avoid very broad titles (e.g., 'DNA recombination'), and try to specify your own unique result within the limited space, while still maintaining readability of your title.

List of authors

Indicate that you are the primary author of the report by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed.


The abstract serves as a condensed version (~250 words) of your research article, from background (both context and motivation) to key results to implications for the future. By convention, it should be single-spaced and not include citations.

The importance of a good abstract cannot be overstated, since computers generally index only the words in a paper's title and abstract, and these may be the only parts that many people read. The abstract may also be the way a journal's editor decides whether to send your paper out for peer review or reject it as uninteresting or not relevant.

The title and abstract will account for 10% of the final grade for this assignment.


The introduction will start on the second page. As you write your introduction, recall the idea of an hourglass structure. The information you use to set up the investigative question in your introduction should be supported by appropriate citations. Any details you found in another researcher's work should be cited.

The introduction provides a framework for the story you are about to tell, and thus serves two main purposes. For one, you must provide sufficient background information for a reader to understand the forthcoming results. Just as importantly, you must motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interesting future applications.

Most introductions are "funnel"-shaped in terms of content:

  • Opening paragraph(s): most general, "big picture" paragraph(s). Here you should introduce the reader to the broader context of your experiment and motivate why your research is important. The best introductions tell a coherent story rather than present a dense but unconnected list of facts.
  • Middle of introduction: "zooming in" somewhat. Once the reader has a frame for thinking about your research, you can present background information in more depth and motivation with more specificity.
  • Wrapping up: most specific, a description of your particular investigation. Here you should make your overall methodology clear without getting into minute detail. In many journals, the introduction concludes with a brief preview of key findings and their implications (2-3 sentences total).

Please pay close attention to the feedback you received from the teaching faculty on your homework assignments as you prepare your introduction (as well as the rest of the report). Also, you may find that the BE Communication Lab is a terrific resource for providing comments on your Introduction. If the Comm Lab peer tutors (a scientifically literate audience) understand your motivation for the study -- you are in good shape!

The introduction will account for 10% of the final grade for this assignment.


The methods section should include all procedures used in Module 2, though you should assume your audience is scientifically literate and somewhat familiar with each procedure. Remember that the methods should be divided into sub-sections that do not necessary correspond to the order in which the experiments were completed in laboratory.

You should include all information required for an independent investigator to repeat your experiments. Use subsection headings to allow readers to quickly identify experiments of interest to them (e.g., "Protein conjugation to hydrogels" or "Cell culture and fluorescent labeling"). When commercially available kits were used, it is sufficient to cite the name of the kit and say that it was used according to the manufacturer's protocol. The key to a good methods section is developing your judgment for what information is essential and what is extraneous.

Note that the methods section should be written in the past tense, since your experiments are complete at the time you are writing your paper. This section should also be written in complete sentences and paragraphs, not in bullet point form.

Important things to consider:

  • Do not use volumes, instead include the final concentrations
  • Include the manufacturer information for kits
  • Be concise and clear in your description of the procedures

The methods section will account for 20% of the final grade for this assignment.


The purpose of the Results section is to present your data in a relatively unbiased way, but with some guiding framework. Begin with a short description of the goal and strategy of your overall experiment, and then delve into specific subsections that describe each piece of the work.

Titled subsections help support your high-level narrative and make dense papers easier to read. Effective subsections are organized by functional content, not by order in which the experiments were completed. For example, two successive titles might be "Conjugating lymphoid tissue-associated adhesion proteins to hydrogels" and "T cell migration in protein-coated hydrogels." Less helpful titles for the same content would be "Hydrogel-protein reaction" and "Microscopy and velocity analysis."

To write the Results section, use the figures and tables as a guide. One approach is to start by outlining the points of what you found by going slowly through each part of the figures. Then take the points and group them into paragraphs, and finally order the points within each paragraph. Present the data as fully as possible, including stuff that does not quite make sense at first glance. Ultimately, each subsection should begin with an overview sentence that motivates and introduces the present experiment and end with a sentence stating the primary conclusion reached from that experiment. Subsection headings and figure caption titles can also emphasize the conclusion. The overview and/or concluding sentences should also provide a transition to the previous/next piece of data when possible. Within a subsection, be sure to stick to one topic per paragraph; subsections will generally require a few paragraphs each.

Note that verbs in the results section are in the past tense and passive form. Only established scientific knowledge is written about in the present tense: "the world is round" is an example. You cannot presume that your own data are part of the body of established scientific knowledge. Thus, when you describe your own results, use the past tense: "a band of 1.3 kb was seen," for example. There are exceptions to this general rule, such as "Table 3 shows the sizes of the DNA fragments in our preparation" or "In a 1991 paper, Ebright and coworkers used PCR to mutagenize DNA," which are both acceptable statements.

In most research endeavors, you will collect more data than you ultimately publish. In the spirit of writing a research article, in this assignment you should present only essential data that come together to tell your scientific story. The suggested list of figures below is meant to provide guidance rather than a check-list.

Potential results:

Schematics / Diagrams

  • Depiction of your design strategy for gRNA target
  • Experimental overview


  • Digestion confirmation of pdCas9
  • Sequencing confirmation of pgRNA_target
  • Colorimetric assay results for fermentation product measurements

Tables / Text

  • Comparisons of gRNA_target effects on fermentation products

The results section will account for 50% of the final grade for this assignment.


This section should incorporate all the good practices described in the Module 1 Data summary, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before to inform your analysis in the discussion. You should also propose specific future experiments and otherwise show that you deeply understand the meaning and significance of your results; for example, if you have a hypothesis about why a particular transcript increased in response, consider what follow-up experiments you might try. You may also want to consider how the experiments can be improved; for example, what additional controls might be useful to include. In addition to drawing conclusions from your own data, you are expected to spend some time considering your classmates’ data.

The purpose of the Discussion section is to interpret and contextualize your data. You should begin by reiterating the purpose of your research and your major findings. Then you might do any or all of the following: connect your findings to other research (published or that of your peers); describe any ambiguities and sources of error in the data, and suggest future experiments to resolve uncertainties; explain where you expect your work may lead, and suggest specific experiments for extending your findings; describe any conceptual or technical limitations of the research. Finally, you should explain the significance of your findings to basic science research and/or to engineering applications. As with previous sections, the discussion should have a clear organization and narrative flow, whether or not you use subsections.

The discussion will account for 10% of the final grade for this assignment.


References are generally used in the Introduction and Discussion sections to support any claims that are not common knowledge. Include only those references that pertain to the question at hand. Journals vary considerably in their preferred format for the reference list. For this class, you should list the references alphabetically by the first author's last name. Include all the authors, the title, the name of the journal in which it was published, the year of publication, the volume number, and page numbers. Please carefully follow the punctuation and format requirements.

Your references should be provided at the end of your Research article in the following format:

Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 1991; 252:809-817.

In the body of your report, this article would be cited as follows:

"The crystal structure of the Zif268-DNA complex has been solved (Pavletich 1991)."

If two or more articles can be cited for this finding, then they are listed alphabetically, separated by a comma.

See also the MIT libraries information on citing sources, here.

Evaluation criteria

The Research article will be graded by Dr. Noreen Lyell with input from Dr. Leslie McClain and Dr. Becky Meyer using the following criteria:

Section Goal Evaluation
Excellent Good Needs improvement
Title To give content information to reader
  • Engaging
  • Appropriate
  • Not enough content information or too much
Abstract To concisely summarize the experimental question, general methods, major findings, and implications of the experiments in relation to what is known or expected.
  • Key information is presented completely and in a clear, concise way
  • All information is correct
  • Organization is logical
  • Captures any reader's interest
  • Sufficient information is presented in proper format
  • Would benefit from some reorganization
  • Understandable with some prior knowledge of experiment
  • Some key information is omitted or tangential information is included
  • Some information is misrepresented
  • Some implications are omitted
  • Incorrect format is used
Introduction To identify central experimental questions, and appropriate background information. To present a plausible hypothesis and a means of testing it.
  • Relevant background information is presented in balanced, engaging way
  • Your experimental goals and predictions are clear and seem a logical extension of existing knowledge
  • Writing is easy to read
  • All background information is correctly referenced
  • Relevant background information is presented but could benefit from reorganization
  • Your experiment is well described and a plausible hypothesis is given
  • With some effort, reader can connect your experiments to background information
  • Writing is understandable
  • Background information is correctly referenced
  • Background information is too general, too specific, missing and/or misrepresented
  • Experimental question is incorrectly or not identified
  • No plausible hypothesis is given
  • Writing style is not clear, correct or concise
  • References are not given or properly formatted
Materials & methods To describe procedures correctly, clearly, and succinctly.
  • Sufficient for another researcher to repeat your experiment
  • Procedures could be pieced together with some effort
  • Procedures incorrectly or unclearly described or omitted
Results To present your data using text AND figures/tables.
  • Text tells story of your major findings in logical and engaging way
  • Figures and tables are formatted for maximum clarity and ease of interpretation
  • All figures and tables have numbers, titles and legends that are easy for the reader to follow
  • Text presents data but could benefit from reorganization or editing to make story easier for reader
  • Text includes interpretation of results that is better suited for discussion section
  • Figures and tables are formatted to be clear and interpretable
  • All figures and tables have numbers, titles and legends
  • Text omits key findings, inaccurately describes data, or includes irrelevant information
  • Text difficult to read due to style or mechanics of writing
  • Text difficult to read due to logic or organization
  • Figures and tables missing information, improperly formatted or poorly designed
  • Figures and tables have inadequate or missing titles or legends
Discussion To evaluate meaning and importance of major findings
  • Appropriate conclusions drawn from findings
  • Connections made between experimental findings
  • Connections made between findings and background information
  • Future directions considered
  • Writing is compelling
  • Appropriate conclusions drawn from findings
  • Experimental limitations considered
  • Writing is clear
  • Conclusions omitted, incorrectly drawn or not related to hypothesis.
  • Relationship between experimental findings and background information is missing or incorrectly drawn
  • Writing style and mechanics make argument difficult to follow
References To give credit to foundational work (on which your own study is based)
  • Complete list of reliable sources, including peer-reviewed journal article(s)
  • Properly formatted in body of report and in reference section
  • Adequate list of reliable sources
  • With minor exceptions, properly formatted in body of report and in reference section
  • List is incomplete or includes sources not cited in body of report
  • List includes inappropriate sources
  • List not properly formatted
  • References not properly cited in body of report

The language usage in your Research article will also be considered using the following criteria:

Writing style and mechanics Evaluation
Excellent Needs improvement
  • Appropriate for audience
  • Consistent passive or active voice
  • Too simple or too advanced
  • Irregular use of passive and active voice
Word choice
  • Concise
  • Precise
  • Vocabulary (scientific and otherwise) used correctly
  • Avoids contractions and informal wording
  • Verbose
  • Ambiguous, vague, or incorrect
  • Scientific or other vocabulary misused
  • Informal/colloquial tone
  • Sentences and paragraphs well-structured
  • Clear topic for each paragraph and clear transitions between topics
  • Punctuation correct or only minor errors
  • Grammar correct or only minor errors
  • Spelling correct
  • Sentences repetitive or awkward
  • Ideas haphazardly arranged, logic connecting them not clear, paragraphs not focused on one topic each
  • Periods, commas, colons and semicolons misused
  • Significant number of run-on sentences, sentence fragments, misplaced modifiers, subject/verb disagreements
  • Significant number of spelling errors
Scientific format
  • Past tense for describing new findings
  • Present tense used for accepted scientific knowledge and figure legends
  • All sections included and properly formatted
  • Misleading verb tenses
  • Some sections missing
  • Abstract not single-spaced
  • Figures missing legends
  • References not properly formatted

  • You can find parts of this text in an on-line collection of instructional materials used in the Purdue University Writing Lab (http://owl.english.purdue.edu). Other parts are inspired by "How to Write and Publish a Scientific Paper" from Oryx Press by Robert A. Day (ask to borrow a copy from the teaching faculty) or are based on the research and teaching experiences of the teaching faculty.
  • You may also wish to read the article Writing Readable Prose, published in 2006 by the EMBO journal. The authors make a strong case for the role that writing (good or bad) can play in your career development, and the article also explains some elements of clear writing.

Helpful hints

Crafting a cohesive story

  • Your data (Results and Figures) are the heart of your paper. Begin by assembling and understanding these sections as clearly as possible. Then you can write the framing material (introduction and discussion), while compiling relevant references. The final revision is best written once you have all your results. You should generally write the abstract last, once you have a big picture understanding of every element of your investigation. As for the methods section, it can help to write it in short pieces day-by-day, while the procedures are fresh in your mind.
  • The first draft is a record of your ideas; the second draft is a crafted presentation of them. Draft as much of your report as possible early on, so you have the opportunity to revise it before submission. Even better, outline the content and high-level organization of your paper before you even begin drafting.

Representing the data

  • Some readers begin by scanning the figures, so these and their captions should provide a self-explanatory overview of your data. Decide what the data show, then create figures that highlight the most important points of your paper.
  • Tables are used to present text or repetitive numerical data. Graphs or illustrations, collectively called figures, are used to present numerical trends or comparisons, raw data (like a picture of a gel), or a model that explains your work.
  • All tables and figures must have numbers, titles, and captions. Include legends only if they are useful in clarifying the data.
  • When you prepare your figures and tables, keep in mind that it is significantly more expensive for journals to publish figures and tables than text, so try to present the data in a way that is worthy of such added expense. The table below is an example of an ineffective table, where the information could be presented clearly and concisely in one sentence, such as: "In ten experiments carried out at 24°C, ion flow was detected only in the presence of cortical cells."
 Temperature		Repeats		Cortical cells		Ion flow
 24°C			5		+			+
 24°C			5		-			-
  • What should you do when two independent pieces of data suggest two very different conclusions about your overall experiment? The one thing you should not do is state that both conclusions are correct, in different parts of the paper, and hope that the reader will ignore the discrepancy! As a scientist, you must take a holistic view of your analyses. Is there any way to reconcile the two results? Is one method more trustworthy, or is there another indication to favor one conclusion over the other? If you have no way of determining which result is correct with your present data, can you propose future experiments to distinguish more conclusively?

Organizing the details

  • Captions to the figures and tables explain the elements that appear in the illustration. Interpretations about the data are NOT included in the captions. As you write your first draft, you might state the point of the figure or table in a short simple sentence. In later drafts, make sure each element of the figure or table is explained. Your figure captions should be written in the present tense, since you are explaining elements that still exist at the time that you are writing the paper.
  • The readability of your paper can be substantially improved by its organization. Well-chosen subsection titles provide the reader with a distillation of the high-level points you want to emphasize. Be sure to summarize major points - if you do this right, you will feel like you are repeating yourself too much! Each major section of the report should be more or less stand-alone, that is, understandable without having to read the rest of your paper. Be sure to work from big to small to big (from broad points to details and back) throughout your paper. Finally, limit paragraphs to one topic, splitting up longer linked ideas as needed.
  • One difficult task for budding scientific writers is determining what goes in a Results vs. a Discussion section. Even at the professional level, different scientific journals may have different expectations for how much interpretation is appropriate in the Results. A good rule of thumb in most contexts is to draw technical conclusions in the Results, but save scientific conclusions for the Discussion. An alternative framework that should yield similar writing choices is to focus on relatively certain conclusions in the Results, and save more speculative (but still supported!) conclusions for the Discussion.
    • Example of a technical conclusion: "Sequence alignment revealed that both mutants exhibited mutations in at least one of the expected sites and thus were consistent with the possible nucleotide changes that could occur with the library used."
    • Example of a scientific conclusion: "A previously reported model proposes that the OmpR-P phosphatase reaction occurs by hydrolysis rather than direct phosphotransfer from H557 (Hsing 1997). Our mutant is consistent with a change to the structure of EnvZ that facilitates this hydrolysis reaction, thus increasing phosphatase activity while concurrently reducing kinase activity."