20.109(S17): Research article

Overview

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 Manuscripts containing purely descriptive observations will not be published."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.

Logistics

• You will complete this assignment individually.

• Be sure to review the class late policy.

Method of submission

Please submit your completed research article on Stellar, with filename LastName_LabSection_Mod2.doc (for example, Samson_TR_Mod2.doc).

Date of submission: April 22nd

Your Research Article is due by April 22nd at 10pm.

Formatting expectations

• 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.

Length guidelines

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

Remember that it is important to be concise and clear in scientific writing.

Content guidelines

Begin by reading the general guidelines for scientific writing. A few notes specific to the Module 2 Research article are below.

Title and Abstract

The title and abstract do not count toward the 14-page limit and should both be on the first page of the submitted document. The introduction will start on the second page.

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

Introduction

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.

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.

Methods

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.

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.

Potential figures

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.

Schematics / Diagrams

• Schematic of HR and NHEJ pathways with key proteins / products highlighted
• Experimental overview

Figures

• Western blot analysis of DLD-1 and BRCA2- cell lines
• Quantitative PCR results for p21 transcript levels
• Viability data from NHEJ and PARP inhibitor experiment
• RNA-seq analysis with heat maps / PCA

Tables / Text

• Genes identified from RNA-seq analysis as upregulated / downregulated

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

Discussion

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 to etoposide treatment, 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. For example, it would be good to compile all of the data available from the cell viability assay to improve your statistical analysis.

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

Evaluation

A rubric for the Research article can be found on the general guidelines for scientific writing. The research article will be graded by Dr. Noreen Lyell with input from Dr. Leslie McClain and Dr. Maxine Jonas.