20.109(S21):Homework

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20.109(S21): Laboratory Fundamentals of Biological Engineering

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Spring 2021 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Antibody engineering        M2: Drug discovery        M3: Protein engineering       


Module 1: Antibody engineering

Due M1D1

  1. 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.
  2. Though you will not be completing experiments in the laboratory this semester, please complete the following online training offered through Environmental Health and Safety (EHS). First, it is important that you learn best practices this semester and safety is a major part of this. Second, the training certifications do not expire and will be valid when are able to return to campus for UROP work!
    • 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.
  3. Download Benchling onto your computer. You will use this program to maintain your laboratory notebook for the semester.
  4. Prepare for the first day of Module 1 by reading the M1 Project overview and the M1D1 Introduction.

Due M1D2

  1. In lab, we will discuss a paper relevant to the material presented in Module 1.
  2. 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 notebook entries this semester.
  3. 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."
    • Give the collection an appropriate name (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 Laboratory notebook guidelines provided as this will ensure the Instructors are able to find the information for grading purposes.
    • 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).
    • See the example entry below for further guidance.
    • Use the Benchling template created above, to generate a Laboratory notebook page for M1D2.
      Fa20 notebook entry template.png

Due M1D3

  1. In scientific communication, data are shown both as figures and in text. For this homework use the data analyzed from the FACS experiment to craft a figure from the dot plot provided for your Data summary. Specifically, it is most useful to create a figure from the final scatterplot used to select the scFv library sort, plotting yeast analyzed by FITC-A (AF488) vs. APC-A (AF647).
    • Carefully consider how to best represent the raw data. How will you label the data to ensure it is clear to a reader?
    • Relabel or remove excess text from analysis software that's not helpful to the figure.
    • Remember that all figures must include a title and caption.
    • Review the prelab slides for suggestions and guidance!
  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. Please review the document linked here to help your prepare for your meeting.

Due M1D4

  1. The major writing assignment in Module 1 is the Data summary. As part of this assignment you will provide details concerning the the motivation for your research and background information relevant to your research. To help you prepare, in this homework you will draft topic sentences that provide the reader with the information necessary for understanding your project. A topic sentence is the first sentence of a paragraph and states and provides context for the subsequent statements in the paragraph.
    • Write 4-5 topic sentences that will be the outline for the Background and Motivation section of your Data summary.
    • Each topic sentence should be supported by a reference from the literature (peer reviewed articles only!). Include the full citation for each article used as a reference and a short description of the key finding(s) in each article.
    • Review the Data summary assignment page and prelab slides for suggestions and guidance!
  2. As part of the major writing assignment in Module 2, you will document the details of the experiments performed in a Methods section. To help you prepare for this task, and to provide you feedback early on, you will draft the Module 1 methods. For this homework, work with your laboratory partner to draft a methods section that details the procedures that were described on M1D2 and M1D3.
    • Review the prelab slides for suggestions and guidance!
  3. 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. Please review the document linked here to help your prepare for your meeting.

Due M1D5

  1. 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.
    • You must 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.
  2. In scientific communication, data are shown both as figures and in text. For this homework use the FACS figure you have previously created to write the corresponding bullets for your Data summary.
    • Carefully consider how to best represent the data before you start. Will you summarize the results in an image / table? How will you organize the data to ensure it is clear to a reader?
    • Remember that all figures must include a title and caption.
    • Use the questions below to organize the information that should be included in the bullets.
    • Review the prelab slides for suggestions and guidance!
      M1D5 HW description.jpg

Due M1D6

  1. Figures serve many functions in scientific communication. In the previous homework you crafted a figure to represent the results of an experiment. Figures are also useful in illustrating the experimental approach, or overview, of a research project. In this type of figure the important experimental steps are represented to highlight the workflow at a high-level. For example, an important plasmid could be represented in a schematic but the specific details around building the plasmid would not be included.
    • For this homework craft an overview schematic that illustrates the research demonstrated in Module 1.
    • This figure should not be organized according to the wiki like the instructor's chronological overview schematic.
    • Please note, schematics are figures and should have both a title and a caption.
    • Review the prelab slides for suggestions and guidance!
  2. The major verbal assignment in Module 1 is the Mini-presentation. The Mini-presentation is a short, verbal description of the key components / results of your research project. Furthermore, this assignment is an 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. You should not submit a script, but rather a bulleted outline of the information you will provide in your oral presentation.
    • Review the Mini-presentation assignment page and prelab slides for suggestions and guidance!

Due M1D7

  1. The final section of your Data summary will discuss the Implication and Future works of your project. In this section the main findings of the research are summarized and used to answer the research question. Also, experiments are proposed that will expand upon the results in an effort to further answer the research question or perhaps address a new research question raised by your research.
    • For this homework, provide a bulleted outline of your Implication and Future works section.
    • This assignment should include your summarized results and outline two proposed future experiments.
    • You should include placeholders for addressing your research question and results not yet analyzed.
    • Topics or proposed future experiments that draw from previous published literature must include the full citation for each article used as a reference.
    • Review the Data summary assignment page and prelab slides for suggestions and guidance!
  2. Incorporate the feedback you received from the Instructors to revise the Methods draft homework you submitted M1D4. As before, work with your laboratory partner to complete this homework.
    • In addition, include the experimental procedures that were discussed M1D4, M1D5, and M1D6 in this revised assignment.

Wrapping up M1

  1. The Data Summary draft is due by 10 pm on Wednesday, March 24th.
  2. The Mini-presentation is due by 10 pm on Sunday, March 28th.
  3. The Data Summary revision is due by 10 pm on Sunday, April 4th.
  4. Please remember to contribute your reflections, comments, and ideas to the Class blog before 10 pm on Monday, March 29th.

Module 2: Drug discovery

Due M2D1

  1. Prepare for the first day of Module 2 by reading the M2 Project overview and the M2D1 Introduction.

Due M2D2

  1. The major verbal assignment in Module 2 is the Journal club presentation. For this assignment you will present a published, peer-reviewed research article. To help you get an early start, in this homework you will select an article to present. If needed, you can take a few extra days to review the articles before making a decision on which to present; however, all selections must be finalized by M2D4. At which time you will need permission from the Instructors to change your article selection.
    • Review the selection of articles suggested by the Instructors and reserve an article according to the directions.
    • If you prefer, submit an article you would like to present for approval. Please note, the article should be related to the content in Module 2.
    • Review the Journal club presentation assignment page for article suggestions and guidance!
  2. In the previous module you crafted data figures and overview schematics. For this homework you will practice another type of figure, an experimental schematic. Unlike an overview schematic, an experimental schematic focuses on the major steps used in for a single method / procedure. Though the focus is to highlight steps of a method, it is still best to omit minor details. For example, performing a ligation reaction would be represented, but the amount of ligase used would not be included.
    • For this homework craft an experimental schematic that illustrates the protein purification procedure.
    • Please note, schematics are figures and should have both a title and a caption.
    • Review the prelab slides for suggestions and guidance!

Due M2D3

  1. The major writing assignment in Module 2 is the Research article. As part of this assignment you will provide the pertinent background information for your research in the Introduction section. To help you prepare, in this homework you will draft an outline with the information necessary for introducing your project to a reader.
    • Write the first paragraph of your Introduction in full sentences (with citations!)
    • For each subsequent paragraph that will be part of your Introduction, provide a topic sentence. In addition, provide the citation for each topic sentence.
    • Include a short summary (~2 sentences) for each of the citations used in your Introduction.
    • Review the Research article assignment page and prelab slides for suggestions and guidance!
  2. In class, you will discuss a paper relevant to the material presented in Module 2 with your laboratory partner.
    • To prepare for the this discussion, review the article and exercise details (both are provided on the M2D3 page).
    • To practice crafting visuals for the Journal club presentation, prepare a slide that illustrates the key result(s) shown in Figure 1 of the paper. Keep the following in mind as you prepare this assignment:
      • The title should state the take-home message of the data that are shown.
      • Your slide(s) should show the data and highlight the key finding(s).
      • The information should be clear and large enough to read.
      • Keep text to a minimum.
    • In addition to the slide, submit an outline of the information that you would provide verbally to accompany the slide during a presentation of the paper.

Due M2D4

  1. As part of the Research article, you will write a Methods section that details the experimental protocols employed in your research. For this homework, draft a methods section that details the procedures that were used on M2D1, M2D2, and M2D3.
    • Review the prelab slides for suggestions and guidance!

Due M2D5

  1. Use the protein purity and concentration data to craft a figure, results, and discussion text for your Research article. The Research article is organized such that the results are described in the Results section and interpreted in the Discussion section.
    • For this homework, include 1-2 paragraphs that describe the data shown in the figure(s) for the Results section and include 1-2 paragraphs that interpret the data shown in the figure(s) for the Discussion section.
    • Carefully consider how to best include the data before you start. How will you represent the data? How will you organize the data to ensure it is clear to a reader?
    • Remember that all figures must include a title and caption.
    • Use the questions below to organize the information that is included in the Results and the information that is included in the Discussion.
    • Review the Research article assignment page and prelab slides for suggestions and guidance!
Sp18 20.109 results v discussion.png

Due M2D6

  1. For this homework 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, you should submit your typed comments as a separate document using the 'numbering method' employed by the Instructors.

Due M2D7

  1. As part of the Research article, you will summarize the key findings from your research in a Discussion section. In this section, the results from all of the experiments are tied together such that a cohesive, main conclusion is presented that either supports or refutes the research goal. In addition, the implications of the research are described in the context of the literature that already exists. How do your results expand what is already known? Why is this important? Lastly, experiments are proposed that will expand upon the results in an effort to further answer the research question or perhaps address a new research question raised by your research.
    • For this homework, provide an outline of your Discussion section and propose two future experiments.
      • For help with potential next step binding experiments, please review Prof. Koehler's lecture slides for M2D4
    • Where relevant, include citations!
    • Review the Research article assignment page and prelab slides for suggestions and guidance!

Wrapping up M2

  1. The Research article is due by 10 pm on Sunday, May 2nd.
  2. Please remember to contribute your reflections, comments, and ideas to the Class blog before 10 pm on Saturday, April 10th AND before 10 pm on Monday, May 3rd.

Module 3: Protein engineering

Due M3D1

  1. Prepare for the first day of Module 3 by reading the M3 Project overview and the M3D1 Introduction.

Due M3D2

  1. The major verbal assignment in Module 3 is the Research proposal presentation. For this assignment you will develop and present a novel research idea with your laboratory partner. To help you get an early start, in this homework each partner will individually describe five recent (within the last 5 years) articles that they find interesting.
    • Submit a short summary (3-5 sentences) and the citation information for each article.
    • The topics addressed in the articles can be related to any aspect of biological engineering.
    • While reviewing the literature, consider which topics / ideas have open questions that can be addressed in your Research proposal presentation.
    • Review the Research proposal presentation assignment page for suggestions and guidance!

Due M3D3

  1. With your co-investigator (laboratory partner), discuss the topics that you each identified. For this homework, work with your laboratory partner to develop a research question that you are interested in pursuing for the Research proposal presentation. Provide a short write-up that describes your idea. Include information concerning the following:
    • What is your research goal?
    • What is the current state of the field (what is already known)?
    • How might your proposal advance what is already known?
    • How might you accomplish this research goal? What will you need to develop or test?
    • Is your research goal appropriate for this assignment? Can the work be completed in a reasonable amount of time with non-infinite resources?
    • Please note, the idea you submit for this homework is not the idea you have to use for the Research proposal presentation. It is okay to change directions or pursue a different research question if something more interesting is discovered during your preparations. With that, it may be easier to finalize your idea sooner rather than later.

Due M3D4

  1. Consider the feedback you and your co-investigator received during the Research proposal pitches and begin to refine your research plan. For this homework, work with your laboratory partner to prepare a more complete write-up that includes details regarding your idea. Include the following information:
    • Brief project overview.
    • Sufficient background information for the audience to understand the importance and novelty of your research.
    • Statement that addresses the research problem and goal.
    • Details regarding the project aims, including possible methods and technologies that will be used to complete the proposed experiments.
    • Alternate experiments / methods / technologies in case unexpected results are observed.
    • Relevant references with complete citations.

Due M3D5

  1. The major writing assignment in Module 3 is the Mini-report. In this assignment you will provide a description of the data analysis you completed to study the effects of mutating residues in IPC. For this homework, work with your laboratory partner to prepare an outline of your Mini-report. Include the following information:
    • List the key topics that will be addressed / explained in the Background and Approach section.
    • List the figures that will be included and provide a brief description of how the data will be presented in the figures. Also, include a statement concerning the interpretation of the data represented in each figure.
    • Review the Mini-report assignment page for guidance!

Wrapping up M3

  1. The Research proposal presentation is due by 1 pm on Tuesday, May 18th or Wednesday, May 19th, according to you laboratory section.
  2. The Mini report is due by 10 pm on Monday, May 24th.
  3. Please remember to contribute your reflections, comments, and ideas to the Class blog before 10 pm on Thursday, May 20th.
    • Note: only three blog posts are required for full credit.