20.109(S20):Homework

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20.109(S20): Laboratory Fundamentals of Biological Engineering

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Spring 2020 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Screening ligand binding        2. Measuring gene expression        3. Engineering antibodies              


Module 1: Screening ligand binding

Due M1D1

  1. Review the Laboratory Orientation exercises to prepare for the Orientation quiz that you and your partner will complete together during your laboratory section.
  2. Before you can conduct experiments in the teaching laboratory you will need to complete the following online training offered through Environmental Health and Safety (EHS):
    • Emergency Preparedness (can be accessed from this link)
    • General Chemical Hygiene (can be accessed from this link)
    • General Biosafety (can be accessed from this link)
    • BBP and Hep. B form (can be accessed from this link)
    • If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but will need to print either 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.
  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 M1 Overview and the M1D1 Introduction.

Due M1D2

  1. Read through the webinair Keeping a Lab Notebook: Basic Principles and Best Practices provided by the National Institutes of Health. Though not all of the specifications will be adhered to in 20.109, please note the information on slide #9 as this is the basis of the rubric developed to grade your entries this semester.
  2. To prepare for your laboratory session, complete a template for your notebook entry according to the Laboratory notebook guidelines provided on the Assignment tab. You will use these guidelines for every notebook entry you complete in 20.109.
    • Click on the '+' symbol on the left menu bar
    • Click on More-->Template
    • In the "Create Template" dialog box, click "Manage Collections" in the lower left corner.
    • Click on "+ New Collection."
    • Name the collection appropriate (e.g. 20.109 Notebook Templates)
    • Create a new template within the newly created collection by typing in the name (e.g. Lab Notebook Entry Template) and press "Create Template."
    • Type in the categories or whatever reminders will help you fill out your lab notebook entry appropriately (It would be wise to base this on the guidelines set forth here)
    • Press "Update Information" to save your edits.
    • Now when you want to make a new entry for each lab day, you can make a new entry from this template (When you press the '+' symbol on the top menu bar near your project title, it will give you the option to create an entry from template).
  3. Use the Benchling template created above, to generate a page for M1D2.
    • To get a headstart on the laboratory exercises, complete the calculations required for the protein purification and include this in your notebook. Specifically for this homework assignment, calculate the volumes of stock IPTG and arabinose used to complete the induction step, and the volumes of imidazole you will add to the lysis buffer and DTT you will add to the SnapTag reaction. Stock concentrations can be found at the bottom of the wiki under the Reagents section.

Due M1D3

  1. Use the data collected from the confirmation digest to generate a figure for your Data Summary.
    • Carefully consider how to best present the data before you start and review the Data summary assignment guidelines.
    • 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. Often illustrations are useful when discussing experimental approaches in written communication outlets. Prepare a schematic diagram that depicts the TDP43-RRM12 protein, highlighting relevant domains and binding partners.
    • Think about what aspects of TDP43-RRM12 construct are most relevant to our experiment.
    • Schematics are figures and should have both a title and a caption.
  2. In addition to reporting your results in the M1 Data Summary, you will need to introduce your project. For this assignment, write topic sentences that will provide the reader with the information necessary for understanding your research. Your topic sentences should include references that you find to validate and support the statement. Please include between 4 and 7 topic sentences.
    • Review the Data summary assignment guidelines.
    • 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. At this point the references can be in any format you choose.
  3. 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.
    • 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.

Due M1D5

  1. In publications, the data are represented both in figures and in text. In a previous assignment you prepared a figure that illustrated the results of your confirmation gel digest. For this assignment you will use the data collected from the polyacrylamide gel and BCA assay to generate a figure and results sub-section for your Data summary.
    • Review the information provided in the Data summary assignment guidelines.
    • Carefully consider how to best present the data before you start. You can use 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.
    • Use the following questions to guide you as you prepare the bullet points for this section. Ideally each question will be addressed in 1-2 bullets.
      Sp17 20.109 results-interpretations bullets.png
  2. 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, work with your partner to write sub-sections that detail the protocols you completed on M1D2 and M1D3.
    • Only include the information relevant to the protein purification and evaluation procedures (ie NOT the confirmation digest).
    • Review your notes from prelab concerning how to present the information concisely and accurately.
  3. 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.
    • 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.

Due M1D6

  1. Schematics that show the experimental overview are helpful in describing the approach taken to answer a research question. Prepare a schematic diagram that depicts the experimental approach for Module 1. See the Module 1 overview page for an example, but do not simply copy this image!
    • Think about which steps are important to the overall goal of your approach and which are minor methods details that can be omitted.
    • Schematics are figures and should have both a title and a caption.
  2. In addition to the Data Summary, each student will individually complete a Mini-presentation that is focused on verbally describing the data and conclusions from 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.
    • Do not submit a script, but rather a bulleted outline of the information you will provide in your Mini-presentation.

Due M1D7

  1. The Data Summary will end with a section that highlights the importance and future applications of your project. For this assignment, you will outline this portion of your summary. At minimum, draft four potential Future works ideas that may be included in the Implications and Future Work section of the Data summary. This assignment is to be completed individually (not with lab partners).
  2. Use the feedback you received from the teaching faculty concerning the Materials and Methods draft you prepared for M1D5 to revise your text.
    • In addition, include the experimental protocols you completed that were relevant to the confirmation digest. As a reminder, these procedures were performed on M1D1 and M1D2.
    • This assignment should include the information relevant to the confirmation digest, protein purification and protein evaluation procedures.

Wrapping up M1

  1. The Data Summary draft is due Sunday, March 8th by 10 pm.
  2. The Mini-presentation is due Sunday, March 15th by 10 pm.
  3. The Data Summary revision is due Sunday, March 22nd by 10 pm.
  4. Please remember to contribute your reflections, comments, and ideas to the Class blog Monday, March 16th by 10 pm.

Module 2: Measuring gene expression

Due M2D1

  1. Prepare for the first day of Module 2 by reading the M2 Overview and the M2D1 Introduction.
  2. Carefully read the Wei et al. [| journal article] to prepare for an in-laboratory discussion.
    • Refer to Part 2 of M2D1 for more details concerning the questions that will be addressed during this discussion.

Due M2D2

  1. The oral communication assignment for this module is a Journal club presentation. The presentation dates are scheduled for M2D4 and M2D5. The slots for each presentation date are first-come-first-serve; however, you should consider your workload in the coming weeks when you reserve a date rather than simply choosing the later date to give yourself more time...or simply choosing the earlier date to get the assignment out of the way.
    • Reserve a slot to present on either M2D4 or M2D5 using the link above.
    • Review and reserve a journal article from the options provided, or submit your own selection to the teaching faculty for approval.
    • Be mindful when choosing your journal article as you will not be permitted to change your article without permission from the teaching faculty after M2D3!
  2. To help you prepare for the Journal Club presentation, you will craft a single slide using the data from the publication by XYZ et al. that was reviewed in the previous laboratory session. You will submit a powerpoint slide and an additional word document with the key information (in bullet points) you would delivery verbally if you were indeed presenting the information on your slide. Please keep the following in mind as you prepare this assignment:
    • Choose a single figure from the article to present on a slide.
    • Your slide should show the data and highlight the key finding(s).
    • Remember that you will provide information orally and therefore do not need to include everything on the slide.
    • The information should be clear and large enough to read.
    • Keep text to a minimum, but include necessary information.
    • The title should state the take-home message of the data that are shown.

Due M2D3

  1. As in Module 1, figures and captions will be important in your Research article; luckily, you have a lot of practice in crafting effective data images. Prepare one figure containing your choice of the RNA-seq data. Remember that your figure should include a title and caption!
  2. One key difference between the Data summary and Research article is that your associated results text will not include interpretation of the data shown in the figure, rather it will only be a verbal description of the image. For the one figure you crafted in Part #1 of this assignment, include a results section and separate discussion written in paragraph form according to the following guidelines:
    Sp18 20.109 results v discussion.png
    • Review the Research article assignment guidelines.
    • Please keep the following details in mind for the Results section:
      • Each sub-section should have a title that states the conclusion of that particular experimental step. In addition, each results paragraph should start with an overview, or introductory, sentence that motivates and introduces the experiment.
      • State the results of the experiment, minimizing any interpretation of the data.
      • End each results paragraph with a concluding sentence that provides a transition to the next experimental step when possible.
      • Each paragraph should only include one topic, but each sub-section may have more than one paragraph.

Due M2D6

  1. Though you practiced crafting a Methods section in module 1, this information was not included in your Data summary. In the Research article this information will be included and graded! For this assignment, you will write the initial sub-sections of your Methods section. This early draft should include the procedures completed M2D1 through M2D3 that are related to tissue culture (culturing / treating your cells and RNA purification -- omit the RNA-seq data analysis practice).
    • Review the Research article assignment guidelines.
    • Think carefully about the scope of each experimental step and how certain protocols can be combined or divided into coherent sub-sections.
    • Be sure that you write the procedures clearly and concisely, with enough detail so a non-109er can complete the experiment and find the necessary materials.
    • Avoid jargon and excess descriptive words.
  2. As in module 1, you will need to introduce your project in the Research article. For this assignment, write the first paragraph of your Introduction and for the remaining paragraphs, include topic sentences that provide an overview of the information you will include.
    • In addition to your first paragraph and the topic sentences, submit the references from which you obtained the information contained within your assignment.
    • You should include the title of the referenced article and a brief summary that informs the teaching faculty of why you chose that reference to support your statement(s).

Due M2D7

  1. For this assignment you will apply the skills you have developed in crafting methods sections to edit the methods section of a peer. Carefully read through the methods section of your classmate and comment on the following:
    • Is the information complete? Are any procedural steps absent? Is important information pertaining to any of the procedures missing?
    • Is the information clear? Are the procedural steps presented in an order that makes sense?
    • Are the sections divided and grouped appropriately?
    • Is the information presented in a way that can be followed by someone less familiar with the experimental procedure? Does the author use concentrations to convey amount?
    • Are the sections written in complete sentences?
    • Please note: for this assignment you will submit your typed comments as a separate document using the 'numbering method' employed by the teaching faculty. Please be specific in your comments to the author (use examples from the text to support your comments).

Due M2D8

  1. Outline all the figures you will create for your Research article. You do not need to actually generate the figures for this assignment. Rather, for each figure you plan to create, include one sentence that describes what the figure will show, one sentence that motivates the use of the figure in your research article and one sentence that will transition to the next figure. Remember your figures are the backbone to a well crafted story. It's not necessary to include every plot and graph you made in Mod2. Consider figure order carefully!

Wrapping up M2

  1. The Research article is due Sunday, April 19th by 10 pm.
  2. Please remember to contribute your reflections, comments, and ideas to the Class blog Monday, April 20th by 10 pm.

Module 3: Engineering biomaterials

Due M3D1

  1. Prepare for the first day of Module 3 by reading the M3 Overview and M3D1 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. 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 biological 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. This assignment is to be written as a team, not individually. 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.
    • Novelty of the approach.
    • 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 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 but please finalize your idea soon.

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, Benchling) 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 (cite your references)
      • sufficient context to understand the novelty of the project
      • 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
    • Specifically, 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.
  2. In lecture on Tuesday, April 28, you will pitch your idea with your laboratory partner so the teaching faculty can provide feedback that will help you polish your research proposal. Use this assignment to help you prepare this ~3 minute presentation of your potential idea!

Due M3D5

  1. For this module, you will also prepare a short 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.

Wrapping up M3

  1. The Research proposal presentation is due Thursday, May 7th or Friday, May 8th by 1 pm, according to your laboratory section.
  2. Please remember to contribute your reflections, comments, and ideas to the Class blog Saturday, May 9th by 10 pm.
  3. The Mini report is due Monday, May 11th by 10 pm.
  4. Please remember to contribute your reflections, comments, and ideas to the Class blog Tuesday, May 12th by 10 pm.
    • Note: only three blog posts are required for full credit.