20.109(S24):Homework

Homework Submission Guidelines

• All homework assignments should be submitted to Canvas by 1:05p on the due date.
• 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'.
• 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: Drug discovery

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)
☐ Blood-borne Pathogen (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.

• Prepare for the first day of Module 1 by reading the M1 Project overview and the M1D1 Introduction.

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 M1D6. 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 confirmation digest (not the in-silico cloning!) and the protein purification steps you completed on M1D1 and M1D2, respectively.

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 M1D6. 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 scientific communication, data are represented as both figures and in text. For this homework you will craft a data figure using the SDS-PAGE and BCA assay results.

Use the checklist below to assist you as you complete this assignment:
☐ Did you format your images? (i.e. omit excess visual noise and empty space)
☐ Did you represent the data using an appropriate format (i.e. table or graph)?
☐ 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)?

• 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 M1D6. 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 M1D5

• In the previous homework you focused on the data portion of figures, for this homework you will draft a title and caption for the SDS-PAGE and BCA assay figure.

Use the checklist below to assist you as you complete this assignment:
☐ 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?
☐ Does your caption include any unnecessary information (such as methods or interpretation)?

• 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!

• 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 M1D6. 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

• In addition to data figures, scientists use experiment overview 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 craft an experiment overview schematic that shows the key steps used to purify MAX-6xHis.

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?

• 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 Koehler Laboratory.

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

• 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 M1D7

• 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. For this homework, complete the data slide for your protein purity and concentration 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 begin with a topic sentence and have the information necessary to interpret the figure?
☐ 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?

Due M1D8

• 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 Western blot results?
☐ What is the main conclusion for your SMM 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 to editing the text from M1D1 and M1D2, include the protocol you used to assess the purity and concentration of the expressed MAX-6xHis protein 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?