20.109(F16):Homework

Module 1: Measuring Genomic Instability

Due M1D1

1. Review the lab orientation exercises to prepare for the lab orientation quiz that you and your partner will complete together during your laboratory section.
2. Complete the required EHS training on-line.
   • There are two web-based training modules required for 20.109: Chemical Hygiene Training includes 7 sections and 6 quizzes with an estimated completion time of 1 hour and Managing Hazardous Waste has one quiz and should take less time to complete. Both courses can be accessed through MIT's Environmental Health and Safety page, from any computer that has your MIT certificate on it.
   • From the EHS training page select the second button labeled "I have EHS training requirements for an academic subject."
   • Your summary page ("My EHS Training") should show Chemical Hygiene and Managing Hazardous Waste as requirements. Click the purple button "Go to Web Classes" above the training requirements section. You may stop and start the web-based courses as many times as you need; the software keeps track of your progress in the course.
   • If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need to print out your training record to submit.
   • You must print the certificates of completion (or your training record) to turn in at the start of your laboratory section.
3. Download Benchling onto your computer. This program will serve as your laboratory notebook for the semester.
4. Prepare for the first day of Module 1 by reading the module overview and the day one introduction.

Due M1D3

1. Use the data collected for the cell loading and doubling time experiments to generate a Figure for your M1 Data Summary.
   • Review the information provided by the BE Communication Lab workshop on M1D2.
   • Carefully consider how to best present the data before you start. You can use the CometChip images or any graphs or tables you generate from the data; however, it is best not to show the same data set in numerous forms unless you are highlighting specific aspects of each representation.
   • All figures must include a title and a caption.
2. 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.
   • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen.

Due M1D4

1. In Module 2, you will document the details of your experiments in a written methods section as part of the Research Article. To help you prepare for this task, and to give you feedback early on, you will draft portions of the Module 1 methods. For this assignment, write a methods sub-section that details the protocols you completed on M1D1 and M1D2.
   • Be sure to read the Materials and Methods information within the Written communication guidelines section of the Communication page before you begin; doing so will save you some time and effort.
2. As a reminder, you should meet with a Fellow in the BE Communication Lab by M1D5 to discuss an assignment.
   • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen.

Due M1D5

introduction bullets mini-presentation outline -- assign comm lab visit day 3

1. In addition to reporting your results in the M1 Data Summary, you will need to introduce your project. For this assignment, write topic sentences for the paragraphs that will be included in the background and motivation section of your data summary for module 1. Your topic sentences should include references that you find to validate and support the statement. At this point the references can be in any format you choose. Please include between 3 and 7 topic sentences.
   • Review the general guidelines for writing up an introduction to your research.
   • In addition to the topic sentences, submit a list of your references. You should include the title of the referenced article and a brief summary of the article that includes why you chose that reference to support your topic sentence.
2. Submit a short written summary (1-2 paragraphs) concerning your meeting with a Fellow from the BE Communication Lab. Consider including your thoughts on the utility of your meeting and what you learned from the discussion.
   • You must schedule your appointment online at the BE Communication Lab homepage. Click "Make an appointment" at the top right corner of the screen.

1. Complete Part 5 of the M1D4 protocol.

1. Prepare a schematic diagram that describes your study of homologous recombination -- the diagram should include information about the construction of your plasmid system and (at this point) a rough idea of how you will use the system to study DNA damage. See the schematic overview on the Module 1 homepage, but make sure that your diagram is presents your own thoughts and ideas (i.e. do not just copy that diagram!). Note: schematic diagrams require figure captions.

Due M1D6

write result/discussion bullets in-class assignment for gamma H2AX

1. Revise your earlier draft of the Methods section, just through M1D2, applying the feedback you received.
   • Prepare the rest of your Methods section (through M1D5) in outline form. Start by considering what methods may be logically grouped together. Please submit:
     • sub-section titles
     • topic sentences for each sub-section
     • bulleted lists of the individual methods that will be included in each section
2. Review the tissue culture guidelines in preparation for M1D6, when you will set up the culminating experiment of this module!
3. Lastly, consider the following questions concerning the transformation experiment:
   • Imagine that your EGFP positive control turns up 200 colonies. What is the transformation efficiency under these conditions, in colony-forming units (CFU) per μg of DNA? Be sure to carefully consider how much DNA ended up on the plate.
   • If you found an equal number of colonies on your "bkb + ligase" plate and your "bkb + insert + ligase" plate, what DNA would you predominantly expect to isolate from the "bkb + insert + ligase" colonies, plasmid with insert or plasmid without insert? In 2-3 sentences, explain how plasmid without insert could end up being recovered here -- which experimental step(s) failed, and how?
   • Note: These questions are not to be turned in but they should help prepare you to interpret the results you will collect and to analyze and frame your data for the DNA engineering summary.

Due M1D7

rewrite methods

1. During M1D7 each group will meet with Dr. Engelward to discuss one of the background papers for this module. To prepare for this discussion read the following article:
   
   • Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death
     EMBO J 15 January 1998
     E Sonoda, M S Sasaki, J M Buerstedde, O Bezzubova, A Shinohara, H Ogawa, M Takata, Y Yamaguchi-Iwai, and S Takeda M
     URL
2. In addition to the DNA engineering summary, each student will individually complete a mini-presentation that is focused on the data generated in Module 1. The mini-presentation (or 'elevator pitch') is your opportunity to practice your oral communication skills before the Journal Club presentation in Module 2. For this assignment, prepare an outline for your mini-presentation. Be sure to include the following:
   • topic sentence that introduces the big picture
   • key results
   • take-home message

Wrapping up M1

1. The Data Summary draft is due by 5 pm on Wednesday, October 12th for both sections.
2. The Mini-presentation is due by 10 pm on Saturday, October 15th for both sections.
3. The Data Summary revision is due by 5 pm on Monday, October 24th for both sections.
4. Please remember to contribute your reflections, comments, and ideas to the 20.109 class blog within 24 h of submitting the Data Summary revision.

Module 2: System engineering

Due M2D1

read intro information

D2 (possibly date for M1 revision) sign up for JC paper

D3 gel image figure with caption, title, written out results, discussion

D4: journal club

D5: schematic / introduction in full sentences

D6: journal club

D7: methods writeup due

D8: peer edit of classmate methods -- typed

Wrapping up M2

1. The | research article is due by 5 pm on Monday, April 18th for both sections.
2. Please remember to contribute your reflections, comments, and ideas to the 20.109 class blog before 5pm on Tuesday, April 19th.

Module 3: Biomaterials engineering

Due M3D1

1. Prepare for the first day of Module 3 by reading the module overview and day one introduction.

Due M3D2

1. The primary assignment for this experimental module will be for you to develop a research proposal and present your idea to the class. For next time, please describe five recent findings that could potentially define an interesting research question. You should hand in a 3-5 sentence description of each topic, in your own words, and also formally cite an associated reference from the scientific literature. The topics you pick can be related to any aspect of the class, i.e. DNA, protein, or biomaterials engineering. During lab next time, you and your partner will review the topics and narrow your choices, identifying one or perhaps two topics for further research.
   • Please note: for this assignment, you do not need to have a novel research idea completely sketched out; you simply have to describe five recent examples of existing work that you find interesting. However, you can start to brainstorm how to expand those topics into something new if you want to get ahead of the game.

Due M3D3

1. Discuss the potential research topics you prepared for the previous assignment with your co-investigator (your lab partner) and write a paragraph concerning the research question you would like to pursue for your research proposal. Please include 2-3 sentences that introduce your topic and a brief discussion of your potential plan. Consider the following as you discuss your potential research topics:
   • Your interest in the topic.
   • The availability of good background information.
   • Your likelihood of successfully advancing current understanding.
   • The possibility of advancing foundational technologies or finding practical applications.
   • Can your proposal be carried out in a reasonable amount of time and with non-infinite resources?
   • Take advantage of downtime in lecture and lab to discuss your research ideas with Prof. Belcher and the teaching faculty.
   • Please note: The idea you submit for this assignment does not have to be the idea you present at the end of Module 3. It is okay if you change directions and decide to pursue other research questions during the process of developing your proposal.

Due M3D4

1. Consider the feedback you and your co-investigator received in the peer review exercise and begin to refine your research proposal by sharing a page (i.e. wiki, Googledoc, Evernote) to collect your ideas and resources (you can do this on one page with your partner or split the effort and each turn in an individual page).
   • Keep in mind that your presentation to the class will ultimately need:
     • a brief project overview
     • sufficient background information for everyone to understand your proposal
     • a statement of the research problem and goals
     • project details and methods
     • predicted outcomes if everything goes according to plan and if nothing does
     • needed resources to complete the work
   • You can organize your wiki page along these lines or however you feel is most helpful -- check out the ���yeast rebuild��� or the ���T7.2��� wiki pages on OpenWetWare for examples of research ideas in process. For this assignment, please submit a printed copy of your research page, making sure it defines your general topic (background and significance), your specific idea (research gap and general approach), and two or more references you've collected and summarized. Keep in mind that your idea may still change - if you come up with something that you like better later on, that's fine.
2. For this module, you will also prepare a short Biomaterials engineering mini-report with your partner. To get you started, work with your laboratory mate to prepare an outline of the Background and Approach section for this assignment. Keep in mind your background should reference previous scientific work so there should also be a works cited or references section to this outline.
   • Review the assignment details and carefully consider the questions specified within the evaluation criteria as you craft the Background and Approach section.

Due M3D5

1. Read the introductory material for M3D5, and then, based on the mass of the cathode you constructed, determine the number of mA to apply in order to fully discharge the battery in 10 hours. Use the loading factor of 17.8 mA/g, a value that is in accordance with cathodes tested during the pilot experiments for this module, and assume 63% of the mass you measured for the nanowires is active material in the cathode.
   • Remember, when you generated your cathode material your composition was 70% active material (nanowires), 25% Super P, and 5% PTFE. You also need to account for the proportion of phage in your active material, which we will assume is 10%. With these values taken into account, your cathode is composed of 63% active material.

Due (after) M3D5

1. The Biomaterials engineering mini-report is due by 10 pm on Thursday, May 5th or Friday, May 6th according to your laboratory section.

Wrapping up M3

1. The Research proposal presentation slides are due on Stellar by 1 pm on Tuesday, May 10th or Wednesday, May 11th according to your laboratory section.
2. Please remember to contribute your reflections, comments, and ideas to the 20.109 class blog before 11am on Saturday, May 14th.