Difference between revisions of "20.109(F24):Homework"

Homework Submission Guidelines

• All homework assignments will be submitted via [ Canvas].
• For homework submissions, be sure to include your section, name, and assignment details in the file name and include your name on the actual document.
• For partner homework assignments, submit one copy of the homework with your section and team color in the file name and on the actual document.

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 required online training courses that are listed below and offered through Environmental Health and Safety (EHS). If you have completed any of the EHS training modules as part of a UROP or in another laboratory class, you do not need to repeat the training. For this homework, submit proof of completion by screen capturing the certificate or your training record. Your training records can be found at "My Training Needs" on Atlas (go to atlas.mit.edu then click the Learning Center tab on the left side of the screen).

☐ Emergency Preparedness (access at this this link)
☐ General Chemical Hygiene (access at this link)
☐ General Biosafety (access at this link)

Due M1D2

• The major written communication assignment in Mod 1 is the Data summary. In Data summary you will provide a detailed outline for your experimental results. To introduce your research, you will write a Background & Motivation section that gives the context for your results and motivates your specific research goal / question. For this homework, you will get a start on the Background & Motivation section by completing the template (attached here).

Use the following resources for assistance:
☐ Review the M1D1 lecture and M1D1 prelab slides.
☐ Read the information included on the Mod 1 Project page.

Due M1D3 - UPDATE CHECKLIST ACCORDING TO PRELAB EXERCISE

• An important part of scientific research is documenting the details regarding how experiments were performed. To practice this skill, you will draft a methods section that details the procedures that you completed on M1D1 (only Part 2 and Part 3) and M1D2. For this homework, work with your laboratory partner to build from the in-class activity to complete the write-up of the methods used for the γH2AX experiment.

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?

Due M1D4

• Experimental schematics 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. For this homework, work with your laboratory partner to complete the experimental schematic you started as part of the in-class exercise for the γH2AX experiment.

Use the checklist below to assist you as you complete this assignment:
☐ Is your schematic appropriately sized (small as possible, but large enough to be legible)?
☐ Does your schematic include only the steps needed to understand how the data were generated from the experiment?
☐ Does your schematic include images that convey how the output relates to what was measured?
☐ Is the text in the schematic clear and legible?

• When researching methods useful to your research or when preparing your science for written communication, it is often helpful to read published literature. As discussed in the prelab lecture, you will use two methods to assess DNA damage: the γH2AX assay and the CometChip. Before we begin the CometChip experiment, you will read an article from the Engelward Laboratory to familiarize yourself with the procedure and assay. For this homework, read the following article: CometChip: A high-throughput 96-well platform for measuring DNA damage in microarrayed human cells. Journal of Visualized Experiments. (2014) 92: 1-11.

Answer the questions below to prepare for an in-class discussion of the article:
☐ How does the CometChip estimate the level of DNA damage within cells?
☐ List two issues / problems with the comet assay?
☐ List two improvements provided by the CometChip assay?

Due M1D5

• Data figures are used to present the results from key experiments to a reader. To ensure the reader is able to interpret the results, the data must be presented with clearly and accurately. For this homework, use the guidelines from the M1D4 prelab to draft the data figure for your γH2AX results.

Use the checklist below to assist you as you complete this assignment:
☐ Is your figure appropriately sized (small as possible, but large enough to be legible)?
☐ Are the separate data representations within the figure defined with panel labels?
☐ Are the microscopy images clearly labeled and absent of visual noise?
☐ Is the graphical representation of your data clearly labeled and absent of visual noise?

• The major verbal communication assignment in Mod 1 is the Research talk. In this assignment you will provide a detailed presentation of your γH2AX results. For this homework, you will get a start on the script for your Research talk by completing the template (attached here).

Use the checklist below to assist you as you complete this assignment:
☐ Did you discuss your results using quantitative descriptions of relevant comparisons (i.e. fold change or percent difference)?
☐ Did you clearly state the conclusion from the results?
☐ Did you specify how the conclusion relates back to your research question / goal?

Due M1D6

• The experimental schematic and the data figure that you crafted for the γH2AX results will be one of the powerpoint slides included in your Data summary. To give you an opportunity to practice in presenting your results according to the guidelines for the Data summary you will submit the powerpoint slide for your γH2AX results. For this homework, work with your laboratory partner to complete the powerpoint slide you started as part of the in-class exercise for the γH2AX experiment.

Use the checklist below to assist you as you complete this assignment:
☐ Did you include appropriately sized figures at the top of the slide?
☐ Is the text formatted correctly for the caption and for the Results & Interpretations?
☐ Is the writing coherent and absent of excess wordiness?

Due M1D7

• The final section in your Data summary will discuss the Implications & Future works of your research. This section summarizes your key data and ties the results to your specific research goal / 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. For this homework, you will get a start on the Implications & Future works section by completing the template (attached here).

Use the following resources for assistance:
☐ Review the M1D6 prelab slides.
☐ Read the information included on the Mod 1 Project page.

• 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 from the teaching team to revise your methods section. In addition, include the protocols you used on M1D3.

Use the checklist below to assist you as you complete this assignment:
☐ Is the information organized such that each subsection is a complete description of the steps used to accomplish a specific experiment?
☐ Does each subsection have a specific header?
☐ Does each subsection beg]). <p style="margin-left:100px;"> Use the following resources for assistance:
☐ Review the M1D6 prelab slides.
☐ Read the information included on the [[20.109(F24):Module 1| Mod in parentheses?
☐ Are all abbreviations and acronyms written in full?
☐ Are all 20.109-specific details omitted?
☐ 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?