20.109(F22):Homework

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20.109(F22): Laboratory Fundamentals of Biological Engineering

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Fall 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Project design       


Homework Submission Guidelines

  • When submitting assignments online, make sure that your section information, name, and assignment details are in the file name and included on the document itself. e.g. 'TR_ImaStudent_M1D1' Renaming the file in Stellar itself is not sufficient, as this does not actually affect the file name.
  • For group assignments, submit one copy of the homework and also include your section and team color. e.g. 'TR_Rainbow_M3D2'
  • Note: Some assignments may indicate a more specific naming scheme than this one. Follow that instead when applicable

Module 1: Genomic instability

Due M1D1

  • Review the Orientation and laboratory tour exercises to prepare for the Orientation quiz that you and your partner will complete together during at the start of the laboratory session.
  • Complete the following online training courses offered through Environmental Health and Safety (EHS):

Emergency Preparedness (access at this this link)
General Chemical Hygiene (access at this link)
General Biosafety (access at this link)
If you have completed EHS training in a UROP or in another laboratory class, you do not need to repeat the training. Instead submit the certificates of completion or your training record which can be found at "My Training Needs" on Atlas. To access, go to atlas.mit.edu then click the Learning Center tab on the left side of the screen.

Due M1D2

  • The major writing assignment in Mod1 is the Data summary. As part of this assignment you will provide details concerning the relevant background information important for understanding your project. In addition, you will use this information to motivate your specific research question.

To get you started, answer the questions below:
What is your research question?
What important problem is addressed by your research question?
What topics / concepts should be explained to ensure a reader understands why your research question is important?
What experiments / techniques will you use to answer your research question?
Hint: review the information provided on the M1 Project overview for help!

  • The BE Communication Lab is a great resource to keep in mind as you complete your assignments for 20.109. To familiarize you with this resource, you will receive homework points for meeting with a Fellow to discuss an assignment by M1D5. To schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.

Due M1D3

  • An important part of scientific research is documenting the details regarding how experiments were performed. To practice this skill, you will work with your laboratory partner to draft a methods section that details the procedures that you completed on M1D1 (specifically, Part 2 and Part 3) and M1D2.

Use the checklist below to assist you as you complete this assignment:
Do you have descriptive subsection headers in a logical order?
Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique?
Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.)
Do all reagents include manufacturer information in parentheses?
Are all abbreviations and acronyms written in full? (if this is the first use of the acronym)
Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty")
Are all mentions of tubes and water omitted?
Are the most flexible units used? (i.e. concentrations rather than volumes)
Is only information necessary to repeat the experiment included?
Are all descriptions concise and clear?


  • The BE Communication Lab is a great resource to keep in mind as you complete your assignments for 20.109. To familiarize you with this resource, you will receive homework points for meeting with a Fellow to discuss an assignment by M1D5. To schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.

Due M1D4

  • In addition to data figures, scientists use experimental schematics to illustrate the key steps of an experiment to better explain how the data were acquired. For this type of figure the important steps are represented using images and labels while the minor steps are omitted for clarity. To gain experience in this type of figure design you will work with your laboratory partner to craft an experimental schematic that shows the key steps used to complete the γH2AX experiment.

Use the checklist below to assist you as you complete this assignment:
Is your schematic correctly sized (legible, but no more than 1/2 of a 8.5x11" slide)?
Does your schematic include a title below the images that concisely states the figure purpose?
Does your caption concisely define all symbols, jargon, abbreviations, and other relevant information for the schematic?
Does your schematic include only the details needed to understand the main steps in the experiment?
Does your schematic include appropriate images that are not plagiarized from class materials or the wiki?
Is any text in the schematic concise and legible?

  • The major verbal assignment in Mod1 is the Research talk. As part of this assignment you will provide a brief, yet detailed, presentation of your results. For this homework, draft an outline of what you will verbally present for your Research talk.

Use the checklist below to assist you as you complete this assignment:
Did you introduce yourself? (No need to mention the class.)
Did you provide an impact statement to give broad context for your work?
Did you provide only appropriate background information to understand the project? (key scientific concepts, essential methods, etc...)
Did you indicate a clear hypothesis/research goal?
Did you discuss specific results using quantitative information?
Did you draw clear conclusions from those results?
Did you specify how those conclusions link back to your hypothesis and impact statement?
Hint: review the information provided on the Research talk page for help!

  • When tasked with preparing your science for written communication it is often helpful to review articles that present similar types of experiments and results. Through reading the literature that is related to your research you can better understand how to effectively present the data. To assist you in preparing your Data summary assignment, we will discuss a paper published from the Engelward Laboratory.

In preparation for this discussion, read the article and guidelines provided on the M1D4 wiki page.

Due M1D5

  • In scientific communication, data are represented as both figures and in text. For this homework you will craft a data figure from the γ-H2AX results you analyzed.

Use the checklist below to assist you as you complete this assignment:
Did you format your microscopy images? (i.e. more than just copying some microscopy images into your slide)
Does your figure include a take-home title below the image?
Does your figure include a caption with necessary details to interpret the figure?
Does your figure caption begin with a topic sentence if it has multiple panels?
Does your caption include any unnecessary information (such as methods or interpretation)?
Did you represent the data shown in your figure graphically (if appropriate)?
Is all text in the figure legible (especially axes)?
Is your figure correctly sized (legible, but no more than 1/3 of a 8.5x11" slide)?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!

  • Submit a short summary (1-2 paragraphs) concerning your meeting with a Fellow from the BE Communication Lab. Including your thoughts on the utility of your meeting and what you learned from the discussion. To schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked here to help your prepare for your meeting.

Due M1D6

  • Remember that for the Data summary you are presenting your results in an outline format to practice clear and concise writing. In addition, the Data summary is organized such that it is apparent what figures correspond to what text. Specifically, each data slide contains one figure and the bullets that explain the figure. The in-class exercise on M1D5 detailed how to present your results in your Data summary. For this homework, complete the data slide for your gamma-H2AX results.

Use the checklist below to assist you as you complete this assignment:
Did you include an appropriately sized and labeled data figure?
Do you have a concise conclusive title (one with a take-home message)?
Does your figure caption have the information necessary to interpret the figure?
Does your figure caption begin with a topic sentence if it has multiple panels?
Does the results section begin with a conclusive title? (This title should be different from the figure title.)
Do you begin the results by providing the overall goal of the experiment(s)?
Do you indicate your expected result?
Do you explain why your result would be correct or incorrect? (i.e. experimental controls)
Do you describe all of the data you show when indicating the result of your experiment? (i.e. all populations on a scatterplot, or all lanes on a gel)
Do you describe the data quantitatively?
Do you draw a conclusion based on the data?
Do you use your last sentence to transition to the next experiment?
Hint: you can find the information provided during the Comm Lab workshop on the Communication page for help!

Due M1D7

  • The final section of your Data summary will discuss the Implications & Future works of your research. In this section the main results are summarized and used to answer the research question. Also, experiments are proposed that will expand upon your results in an effort to address new research questions that are raised by your data.

To get you started, answer the questions below:
What is the main conclusion for your γ-H2AX results?
What is the main conclusion CometChip results?
How do the results answer your research question?
Did you observe any unexpected results or contradictory results?
What follow-up experiments (include at least two!) would be helpful in further addressing your research question?

  • Using feedback to improve your writing is an important step to developing your scientific communication skills. For this homework, work with your laboratory partner to incorporate the feedback you received to revise your methods draft. In addition, include the protocols you used on M1D3.

Use the checklist below to assist you as you complete this assignment:
Do you have descriptive subsection headers in a logical order?
Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique?
Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.)
Do all reagents include manufacturer information in parentheses?
Are all abbreviations and acronyms written in full? (if this is the first use of the acronym)
Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty")
Are all mentions of tubes and water omitted?
Are the most flexible units used? (i.e. concentrations rather than volumes)
Is only information necessary to repeat the experiment included?
Are all descriptions concise and clear?

Module 1: Drug discovery

Due M2D1

Due M2D2

  • The major verbal assignment in Mod2 is the Journal club presentation. As part of this assignment you will present a published, peer-reviewed research article to the class. For this homework, select and review an article for your presentation from the curated lists on the Journal club presentation assignment page. If you prefer, you can find your own paper and send it to the Instructors for approval.

Use the checklist below to assist you as you complete this assignment:
Reserve your article on the Journal article presentation page according to the directions provided under the 'Article selection' header.
Review the abstract and introduction for the selected article.
Submit a brief summary of the selected article that highlights why you think the research is interesting.

Due M2D3

  • For your Journal club presentation, you will only have 10 minutes to present a clear, cohesive story from the data in your selected research article. Given the number of figures in most research articles it is impossible to show all of the data from your paper in a short presentation. In this, it is important to identify which figures are the most important to the main conclusion(s) of the research article. For this homework, read through the paper you selected for the Journal Club presentation and choose the four figures that you think are most important in telling the story presented by the authors.

To get you started, answer the questions below:
What is the main conclusion of the paper?
What four figures are the most important in supporting the main conclusion? Why?
How do the figures work together to tell a story? How does this story lead you to the main conclusion of the paper?

  • The Journal club presentations will occur during the laboratory sessions on Tuesday, November 1st and Thursday, November 3rd for the T/R section and on Wednesday, November 2nd and Thursday, November 4th for the W/F section. Due to class size, presenters in each section will be divided between the two days by the Instructors.

To reserve a presentation date, email Noreen (nllyell@mit.edu) with which day you prefer to present and why. If one of the days becomes oversubscribed then slots will assigned using a lottery.

Due M2D4

  • Your slide deck will be important in your ability to effectively tell the story presented by the authors of your paper. For this homework you will draft a presentation slide using one of the data figures from the paper you selected that you want to discuss as part of your Journal club presentation. In addition, include a script for the verbal information that you will deliver when presenting the figure on your slide.

Use the checklist below to assist you as you complete this assignment:
Does the title of your slide convey a concise take-home message about the data shown?
Do you include data from a single figure of your paper?
Are you trying to include too much data on a single slide?
Is all the text from your data figure legible? (especially note the axes text and recreate it if necessary)
Is there a good balance between figures and text on the slide? (approximately half of each)
Does the text convey only key information?
Is your script concise? (i.e. Are you able to convey this information in approximately 1 minute?)
Does your script contain technically correct scientific information?
Is the information in your script directly relevant to the data on the slide?

Due M2D5

As part of your Research article, you will write a formal Introduction that includes the pertinent background information and motivation for your project. For this homework you will draft an outline of the Introduction.

Use the checklist below to assist you as you complete this assignment:
Do you begin with an impact statement to provide broad context for your project?
Does your first paragraph indicate the importance of work in this field of study?
Do your next outlined paragraphs provide necessary information to understand the specific aspects of your research? (i.e. information about disease, biological pathways, important experimental techniques)
Do you clearly state the knowledge gap in the field that your project will address?
Do you clearly state your hypothesis/research question?
Do you provide a preview of the key findings of this study? (or a placeholder indicating this will be included)
Does your outline follow a funnel structure where information begins broad and narrows to information increasingly specific to your project and results?
Does each topic/paragraph make a logical transition to the next topic?
Do you include references for background information?
Hint: review the information concerning how to write an Introduction provided on the Research article page for help!

Due M2D6

  • As in the Mod 1 Data summary, figures will be important in how you report your results for the Mod 2 Research article. For this homework, use the skills you developed throughout Mod1 to craft a data figure from the FKPB35 expression vector confirmation digest results. In addition to the figure include the text that will accompany your figure in the Results section of Research article.

Use the checklist below to assist you as you complete this assignment:
Did you include an appropriately sized and labeled data figure?
Do you have a concise conclusive title (one with a take-home message)?
Does your figure caption have the information necessary to interpret the figure?
Does your figure caption begin with a topic sentence if it has multiple panels?
Does the results section begin with a conclusive title? (This title should be different from the figure title.)
Do you begin the results by providing the overall goal of the experiment(s)?
Do you indicate your expected result?
Do you explain why your result would be correct or incorrect? (i.e. experimental controls)
Do you describe all of the data you show when indicating the result of your experiment? (i.e. all populations on a scatterplot, or all lanes on a gel)
Do you describe the data quantitatively?
Do you state the results objectively while omitting interpretation?
Do you use your last sentence to transition to the next experiment?
Hint: review the information concerning how to write text for the Results section provided on the Research article page for help!

  • The major written assignment in Mod2 is the Research article. In Mod1 you practiced writing a methods section with your laboratory partner. Now you will use this practice to write a methods section that will be included in the Research article. For this homework, you will begin working on the methods section of your Research article. Write a methods section that details the procedures that you completed on M2D1 (only the confirmation digest), M2D2, and M2D3.

Use the checklist below to assist you as you complete this assignment:
Do you have descriptive subsection headers in a logical order?
Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique?
Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.)
Do all reagents include manufacturer information in parentheses?
Are all abbreviations and acronyms written in full? (if this is the first use of the acronym)
Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty")
Are all mentions of tubes and water omitted?
Are the most flexible units used? (i.e. concentrations rather than volumes)
Is only information necessary to repeat the experiment included?
Are all descriptions concise and clear?
Hint: you should review the M1 methods homework and corresponding feedback for help!

Due M2D7

  • Figures serve many functions in scientific communication. In previous homeworks you crafted data figures and experiment schematics. Another type of figure is the research overview schematic, or visual abstract. In this type of figure only the important experiments / methods are represented to illustrate the workflow at a high-level.

Use the checklist below to assist you as you complete this assignment:
Is your schematic correctly sized (legible, but no more than 1/2 of a 8.5x11" page)?
Does your schematic include a title below the images that concisely states the figure purpose?
Does your caption concisely define all symbols, jargon, abbreviations, and other relevant information for the schematic?
Does your schematic include only the details needed to understand the main purpose/goal of the study?
Does your schematic include appropriate images that are not plagiarized from class materials or the wiki?
Is any text in the schematic concise and legible?

  • In the Discussion section of the Research article you will convey how the results of your experiments provide an answer to your research question. Consider how the data relate to the broader goal of your research project and how well the data support conclusions related to your research question.

To get you started, answer the questions below:
Were there any unexpected results? Is there a technical reason (i.e. an error in the setup or data collection)?
What follow-up experiment might you perform to clarify any unexpected results?
What are the limitations of your experimental approach? Is there another method that might better answer your research question? Is there another variable that should be tested to better answer your research question?
What next step experiment might you perform to further confirm your results?
Hint: review the information concerning how to write a Discussion provided on the Research article page for help!

Module 3: Research design

Due M3D1

  • The culminating major assignment in 20.109 is the Research proposal presentation. As part of this assignment you will present a novel research idea to the class. For this homework, consider what topics you might find interesting or what problems you might want to solve.

To get you started, answer the questions below:
What personal interests do you have that are related to the field of Biological engineering?
What core classes have you found to be the most interesting?
What concepts are of interest to you?
What techniques are of interest to you?
What types of problems (health-related, environment-related, technology-related, etc.) are of interest to you?

Due M3D2

  • For this homework, work with your co-investigator to develop your research question and to refine your Research proposal idea.

To get you started, answer the questions below:
What is your research question?
What is already known and how will your project advance what is already known?
What is the novel aspect of your project? Are you identifying something? Making something?
What types of techniques / experiments might you use to answer your research question?
How is your research proposal related to the field of Biological engineering?

Due M3D3

  • During your laboratory session, you will practice presenting your Research proposal idea to your classmates. The goal of this exercise is to give you a chance to relay your idea verbally to a new audience and also to provide an opportunity for you to receive feedback on your idea. For this homework, prepare a write-up of your proposal idea to get you ready for the in-class discussion exercise.

Use the checklist below to assist you as you complete this assignment:
Write a brief project overview that identifies the problem / idea you are addressing and your research question.
Clearly state your research question that will address this problem you've identified.
Describe what is currently known and how your project advances what is already known. Be clear on how your project is novel.
Include your project aims and the proposed methods / approaches that can be used to accomplish the proposed experiments.
Be sure your sources are appropriately cited!