From Course Wiki
Revision as of 18:11, 6 November 2018 by Josephinebagnall (Talk | contribs)

Jump to: navigation, search
20.109(F18): Laboratory Fundamentals of Biological Engineering

Fa18 20109 banner image.png

Fall 2018 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Measuring genomic instability        2. Modulating metabolism        3. Engineering biomaterials              

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. (TR section: Alternatively, screen capture your training record/certificate of completion and turn it in electronically as a PDF on Stellar)
  3. Sign up for a Benchling account. 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 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).
    • For additional help, review the prelab and the entry you generated with the teaching faculty for M1D1.
  3. To prepare for the laboratory on M1D2, make a new notebook page for M1D2 based on the template you just created.

Due M1D3

  1. Use the data collected for the cell loading experiments to generate a figure for your Data Summary.
    • Recall the pointers given by the teaching faculty during prelab!
    • 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.
    • During class on M1D3, the BE Communication Lab Instructors will host a workshop to provide information on how your first attempt at figures / captions can be improved. You will have until 10 pm on M1D3 to submit a revised version of this assignment and receive up to half of the points deducted on your draft.
  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 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 3 and 7 topic sentences. These sentences should be a draft of the first sentence from each new paragraph in your background and motivation section.
    • Carefully consider the Background and Motivation suggestions provided for the Data Summary.
    • 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.
  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

  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, work with your laboratory partner to draft a methods section that details the protocols you completed on M1D1 through M1D3. You can omit non-experimental details such as the 'Research cell lines' exercise.
    • Be sure to read the methods information provided on the Research article assignment tab for a general description of the information / details that should be included.
  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.

Due M1D6

  1. Use the feedback you received from the teaching faculty concerning the Materials and Methods draft you prepared for M1D5 to revise your text. This is to be done with your lab partner(s).
    • In addition, include the experimental protocols you completed through M1D4 (just what pertains to the CometChip!) in this revised assignment.
  2. In addition to the Data Summary, each student will individually (not with your lab partners) 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.
    • You should not submit a script, but rather a bulleted outline of the information you will provide in your Mini-presentation.
  3. In class, we will discuss a journal article paper. Read through the assignment details on the M1D6 page.

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 draft this portion of your summary. At minimum, draft a response to the four potential topic bullets listed under the Implications and Future Work content guidelines. This assignment is to be completed individually (not with lab partners).

Wrapping up M1

  1. The Data Summary draft is due by 10 pm on Wednesday, October 10th for both sections.
  2. The Mini-presentation is due by 10 pm on Saturday, October 13th for both sections.
  3. The Data Summary revision is due by 10 pm on Saturday, October 20th for both sections.
  4. Please remember to contribute your reflections, comments, and ideas to the class blog within 24 h of submitting the Data Summary draft.

Module 2: Manipulating Metabolism

Due M2D1

  1. Prepare for the first day of Module 2 by reading the module overview and the day one introduction.

Due M2D2

  1. The oral communication assignment for this module is a Journal club presentation. The presentation dates are scheduled for M2D4 and M2D6. 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 M2D6 to give yourself more time...or simply choosing M2D4 to get the assignment out of the way.
    • Reserve a slot to present on either D4 or D6 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.
  2. To help you prepare for the Journal Club presentation, you will craft 1-2 slides using this article by Ji. et al. to present the data from Figure 2. Submit a copy on Stellar for grading, and note that you should also hang on to a copy for a BE Communication Lab workshop later next week. Please keep the following in mind as you prepare this assignment:
    • 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.
    • 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. One difference between the Data summary and Research article is that your associated results text will be written in paragraphs rather than bullet points. For this assignment, prepare a figure and caption with your digest confirmation agarose gel image. In addition, include a results narrative according to the information provided within the Results section on the Research article page. Please keep the following details in mind:
    • 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.
  2. Prepare for the journal article in-lecture discussion by carefully reading the paper and discussion questions sent by the teaching faculty via email.

Due M2D5

  1. 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 according to the information provided in the Introduction section of the on the Research article page. For the remaining paragraphs that will form your Introduction, 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).
  2. Often illustrations are useful when discussing experiment approaches in written communication outlets. Prepare a schematic diagram that depicts your experimental approach/design for increasing ethanol or acetate production of MG1655 e. coli.
    • Think about images or graphics that represent the overall goal of your approach; leaving out minor methods details.
    • Remember, schematics are figures and should have titles and captions.
  3. Write a Discussion section that interprets the data represented by your digest confirmation agarose gel figure / caption / results according to the information provided in the Discussion section of the Research article page.

Due M2D7

  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. This early draft should include the procedures completed M2D1 (part 4) through M2D5 according to the information provided within the Materials and methods section of the Research article page. For M2D1, only include methods for the confirmation digest, and do not include methods regarding the in silico portion.
    • 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.

Due M2D8

  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 may submit your typed comments as a separate PDF document using the manual 'numbering method' employed by the teaching faculty. Alternatively, you may submit a digitally highlighted and commented PDF. Please be specific in your comments to the author (use examples from the text to support your comments).

Wrapping up M2

  1. The Research article is due by 10 pm on Monday, November 12th for both sections.
  2. Please remember to contribute your reflections, comments, and ideas to the class blog by 10pm on November 2nd (regarding journal club) and November 13th (regarding research article).

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. 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 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
      • 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
    • 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.
  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.

Due M3D5

  1. Read the Introduction section 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.

Wrapping up M3

  1. The Research proposal presentation slides are due on Stellar by 1 pm on Thursday, Dec 6th or Friday, Dec 7th according to your laboratory section.
  2. The Mini-report is due by 10 pm on Monday, Dec 10th for both sections.
  3. Please remember to contribute your reflections, comments, and ideas to the class blog before 10 pm on Saturday, Dec 8th.