Difference between revisions of "20.109(F16):Homework"

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==Module 1: Protein engineering==
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==Module 1: Measuring Genomic Instability==
  
 
===Due M1D1===
 
===Due M1D1===
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#Review the [[20.109(F16):Lab tour| lab orientation exercises]] to prepare for the lab orientation quiz that you and your partner will complete together during your laboratory section.
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#Complete the required EHS training on-line.
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#*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 [http://ehs.mit.edu/site/training MIT's Environmental Health and Safety page], from any computer that has your MIT certificate on it.
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#*From the EHS training page select the second button labeled "I have EHS training requirements for an academic subject."
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#*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.
 +
#*<b>You must print the certificates of completion (or your training record) to turn in at the start of your laboratory section.</b>
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#Download [https://benchling.com/signin# Benchling] onto your computer.  This program will serve as your laboratory notebook for the semester.
 +
#Prepare for the first day of Module 1 by reading the [[20.109(F16):Module 1 | module overview]] and the [[20.109(F16):Prepare comet chips (Day1) | day one introduction]].
  
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# Review the [[20.109(F16):Lab tour| lab orientation exercises]] to prepare for the lab practical that you and your partner will take together next time.
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===Due M1D2===
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# Complete the required EHS training on-line.
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#The laboratory exercises will take the full laboratory session to complete.  To ensure you are prepared, please carefully read through the information provided on the [[20.109(F16):Test comet chip loading variables (Day2)| M1D2]] page.
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#*There are two web-based training modules required for 20.109.  They are '''Chemical Hygiene Training''' and '''Managing Hazardous Waste'''. ''Chemical Hygiene'' includes 7 sections and 6 quizzes with an estimated completion time of 1 hour, while ''Managing Hazardous Waste'' has one quiz and should take somewhat less time to complete. Both courses can be accessed through [http://ehs.mit.edu/site/training MIT's Environmental Health and Safety page], from any computer that has your MIT certificate on it.  
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#To further prepare for the long laboratory session, complete a template for your notebook entry according to the [http://engineerbiology.org/wiki/20.109(F16):Communication#Laboratory_notebook_guidelines Laboratory notebook guidelines] provided on the Communication page.
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#*<b>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 hand in.</b>
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#*For additional help, see the template for your M1D2 notebook entry below.
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#*From the EHS training page select the second button labeled “I have EHS training requirements for an academic subject.” 
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[[Image:Fa16 due M1D2 notebook template.png|thumb|center|700px|'''Notebook entry template.''']]
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#*Your summary page (“My EHS Training") should show ''Chemical Hygiene'' and ''Managing Hazardous Waste'' as requirements for 20.109.  Click on the purple button “Go to Web Classes” right above the training requirements section. You may stop and start the web-based courses as many times as you need to complete them; the software keeps track of your progress in the course.
+
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#*<b>Print the certificates of completion (or your training record) to turn in next time.</b>
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#Open an Evernote account at [http://evernote.com '''this link''']. We recommend downloading Evernote to your computer versus operating from the web based application (although both work). You can also download Evernote to your smart phone for ease of uploading pictures and data. You should make a notebook that will be utilized as your lab notebook. Give it a name with the following convention: 20.109(F16)_Name and share that notebook with your lab instructor(s) and TA.
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#Complete the student registration/questionnaire from [[20.109(F16):Student registration and questionnaire | '''this link''']] to turn in next time. Click on the "edit" tab of this page, then copy the "source code" you see to your user page, fill out the form, and print it. You do not need to keep the information on your user page after printing it.
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#Prepare for the first day of Module 1 by reading the [[20.109(F16):Module 1 | module overview]] and [[20.109(F16):DNA engineering using PCR (Day1) | day one introduction]].
+
  
 
===Due M1D3===
 
===Due M1D3===
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+
#Use the data collected for the cell loading experiments to generate a figure for your [[20.109(F16): Assignments| M1 Data Summary]].
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#Sketch the expected product from the PCR you performed on M1D1.  
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#*Review the information provided by the BE Communication Lab workshop on M1D2.
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#*You may work on paper or electronically. Either way, prepare a schematic rather than detailing each base.  
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#*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.
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#*Clearly indicate the 5' and 3' end of each DNA strand.
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#*All figures '''must include a title and a caption'''.
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#*Be sure to reflect every new feature that you have introduced (e.g., restriction site) or deleted.
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#*'''Please note:''' only use the cell loading data to craft your figure and caption for this assignment, in other words do not include the growth rate information.
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#*What is the expected size of the PCR product?
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#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.
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#Following the directions in Part 4 of M1D2, prepare a plasmid map in ApE of the clone you are trying to create in lab. Print the graphic map with all singly present restriction sites shown.
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#*You must schedule your appointment online at the [https://be.mit.edu/communicationlab BE Communication Lab] homepage.  Click "Make an appointment" at the top right corner of the screen.
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#*Hint: You may choose to show fewer restriction sites in your Module 1 summary.
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#*Using your map, calculate the fragment sizes expected for each double digest below. '''Please show your work.'''
+
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#**''EcoRV'' and ''XbaI''
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#**''BamHI'' and ''XhoI''
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#*Use the skills you learned from the BE Communications instructors to write a title and caption for your plasmid map figure.
+
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#In Module 2, you will document your experiments in a written methods section that will be part of a larger report. To help you prepare, as well as give you feedback early on, you will draft portions of the Module 1 methods. For this assignment, write a draft of the Methods concerning PCR and DNA digestion. Be sure to read the Materials and Methods section [[Guidelines_for_writing_up_your_research | guidelines at this link]] before you begin; doing so may save you some effort.
+
  
 
===Due M1D4===
 
===Due M1D4===
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+
#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 [[20.109(F16):Prepare comet chips (Day1)| M1D1]] and [[20.109(F16):Test comet chip loading variables (Day2)| M1D2]].  
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#You will document the work you do during Module 1 in a [[20.109%28F16%29:_DNA_engineering_summary | '''DNA engineering summary''']]. To help you pace your work, as well as give you feedback early on, you will draft small portions of the summary as homework assignments. For M1D4, you should document your experimental outcomes.
+
#*Be sure to read the [http://engineerbiology.org/wiki/20.109(F16):Communication#Written_communication_guidelines  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.
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#*Begin by reading, under [[20.109%28F16%29:_DNA_engineering_summary#Logistics | Logistics]], ''Guidelines on Formatting and Length''. Next, skim the [[20.109%28F16%29:_DNA_engineering_summary#Content_Guidelines | Content Guidelines]], paying particular attention to those relevant for M1D3.
+
#As a reminder, you should meet with a Fellow in the BE Communication Lab by M1D5 to discuss an assignment.
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#*You should present both the purification gel and the recovery gel, each in a well-labeled figure with an appropriate figure caption. Be sure to follow our written guidelines as well as the suggestions presented by your writing instructor during class.
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#*You must schedule your appointment online at the [https://be.mit.edu/communicationlab BE Communication Lab] homepage.  Click "Make an appointment" at the top right corner of the screen.
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#*Below the figures, interpret the outcomes in concise language. Consider reviewing [[media:Poster Best Practices pages 30 31.pdf | these slides]] from the BE Communication Lab to learn how to turn bulky sentences into succinct bullets. It's also okay to use complete sentences when they more clearly make your point
+
−
#*Please see [[media:SampleF14_Mod1_DataSummary.pdf‎ | this example]] for a suggested layout.
+
−
#To prepare for the lab session, calculate the amounts of DNA you will use in the ligation by following the steps below.
+
−
#*Separately calculate the concentration of backbone and of insert based on the recovery gel posted on today's Talk page. Refer to the [https://www.neb.com/products/n3232-1-kb-dna-ladder NEB marker] definitions to estimate the ''ng'' of DNA in each lane, and refer to your notebook/protocol for the relevant volume basis. Note that the ''ng'' listed are for 10 &mu;L of ladder (and you loaded 20 &mu;L of ladder).
+
−
#*You may convert the mass concentration to a molar concentration, using the fact that a typical DNA base is 500 g/mol. This conversion will mostly cancel out between the insert and the backbone, except for the difference in number of bases. Feel free to either omit steps that will cancel if you are comfortable doing so, or to keep them if you follow the lab math better that way.
+
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#*Ideally, you will use 50-100 ng of backbone in the upcoming ligation. Referring to the mass concentration, what volume of DNA will this amount require?
+
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#*Ideally, you will use a 4:1 '''''molar''''' ratio of insert to backbone. Referring to the molar concentrations, how much insert do you need per &mu;L of backbone?
+
−
#*A 15 &mu;L scale ligation should not include more than 13.5 &mu;L of DNA. If your backbone and insert volumes total to greater than this amount, you must (1) scale down both DNA amounts, using less than 50 ng backbone and/or (2) stray from the ideal 4:1 molar ratio. You may ask the teaching faculty for advice during class if you are unsure what choice is best, but make and submit an initial ligation plan for now.
+
  
 
===Due M1D5===
 
===Due M1D5===
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+
#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.
−
#Complete Part 5 of the M1D4 protocol.
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#*Be sure to read the [http://engineerbiology.org/wiki/20.109(F16):Communication#Written_communication_guidelines  Introduction information] within the Written communication guidelines section of the Communication page before you begin; doing so will save you some time and effort.
−
#In addition to reporting your results in the DNA engineering summary, you will need to introduce your project.  For this assignment, write topic sentences for the paragraphs that will be included in the [http://openwetware.org/wiki/20.109%28F16%29:_DNA_engineering_summary#Background_and_motivation:_potential_topics_and_figures 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.
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#*Carefully consider the [http://engineerbiology.org/wiki/20.109(F16):_M1_Data_Summary#Background_and_Motivation:_potential_topics_and_figures Background and Motivation] suggestions provided for the M1 Data Summary.
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#*Review the [http://Introduction general guidelines] for writing up an introduction to your research.
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#*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.  
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#*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.
+
#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.
−
#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 [http://openwetware.org/wiki/20.109%28F16%29:Module_1 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.
+
#*You must schedule your appointment online at the [https://be.mit.edu/communicationlab BE Communication Lab] homepage. Click "Make an appointment" at the top right corner of the screen.
  
 
===Due M1D6===
 
===Due M1D6===
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+
#The M1 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.  
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#Revise your earlier draft of the Methods section, just through M1D2, applying the feedback you received.
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#*Be sure to read the [http://engineerbiology.org/wiki/20.109(F16):Communication#Written_communication_guidelines  Discussion information] within the Written communication guidelines section of the Communication page before you begin; doing so will save you some time and effort.
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#*Prepare the rest of your Methods section (through M1D5) in outline form. Start by considering what methods may be logically grouped together. Please submit:
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#*Carefully consider the [http://engineerbiology.org/wiki/20.109(F16):_M1_Data_Summary#Implications_and_Future_Work:_potential_topics Implications and Future Work] suggestions provided for the M1 Data Summary.
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#**sub-section titles
+
#In addition to the M1 Data Summary, each student will individually complete a [[20.109(F16): M1 Mini-presentation | 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.
−
#**topic sentences for each sub-section
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#*You should not submit a script, but rather a bulleted outline of the information you will provide in your Mini-presentation.
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#**bulleted lists of the individual methods that will be included in each section
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#Review the [[20.109(F15):Guidelines for working in the tissue culture facility| tissue culture guidelines]] in preparation for M1D6, when you will set up the culminating experiment of this module!
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−
#Lastly, consider the following questions concerning the transformation experiment:
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−
#*Imagine that your EGFP positive control turns up 200 colonies. What is the transformation efficiency under these conditions, in colony-forming units (CFU) per &mu;g 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.
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===Due M1D7===
 
===Due M1D7===
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#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: <br>
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#Use the feedback you received from the teaching faculty concerning the Materials and Methods draft you prepared for M1D4 to revise your text.
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#*'''Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death'''<br>'' EMBO J'' 15 January 1998<br> E Sonoda, M S Sasaki, J M Buerstedde, O Bezzubova, A Shinohara, H Ogawa, M Takata, Y Yamaguchi-Iwai, and S Takeda M <br> [http://doi.org/10.1093/emboj/17.2.598 URL]
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#*In addition, include the experimental protocols you completed through M1D3 in this revised assignment.
−
#In addition to the DNA engineering summary, each student will individually complete a [[20.109%28F16%29:_DNA_engineering_presentation | 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:
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#Complete the in-class summary of the H2AX assay results according to the [http://engineerbiology.org/wiki/20.109(F16):Data_analysis_(Day7) assignment description] provided on the M1D7 page.
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#*topic sentence that introduces the big picture
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#*Please note: you will have time to complete this assignment during your laboratory section and it is not due until 10 pm on M1D7!
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#*key results
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#*take-home message
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===Wrapping up M1===
 
===Wrapping up M1===
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#The [[20.109(F16): DNA engineering summary| DNA engineering summary draft]] is due by '''5 pm on Saturday, March 12th''' for both sections.
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#The [[20.109(F16): M1 Data Summary| Data Summary draft]] is due by '''5 pm on Wednesday, October 12th''' for both sections.
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#The [[20.109(F16): DNA engineering presentation| DNA engineering mini-presentation]] is due by '''10 pm on Tuesday, March 15th or Wednesday, March 16th''' according to your laboratory section.
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#The [[20.109(F16): M1 Mini-presentation| Mini-presentation]] is due by '''10 pm on Saturday, October 15th''' for both sections.
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#The [[20.109(F16): DNA engineering summary| DNA engineering summary revision]] is due by '''5 pm on Monday, March 28th''' for both sections.
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#The [[20.109(F16): M1 Data Summary| Data Summary revision]] is due by '''5 pm on Monday, October 24th''' for both sections.
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#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] within 24 h of submitting the DNA engineering summary revision.
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#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] within 24 h of submitting the Data Summary revision.
  
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==Module 2: System engineering==
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==Module 2: Manipulating Metabolism==
  
 
===Due M2D1===
 
===Due M2D1===
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#Prepare for the first day of Module 2 by reading the [[20.109(F16):Module 2 | module overview]] and the [[20.109(F16):Complete in silico cloning (Day1) | day one introduction]].
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 +
===Due M2D2===
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#The oral communication assignment for this module is a [[20.109(F16):Journal club II (Day 6)| 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.
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#*Reserve a slot to present on either D4 or D6 using the link above.
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#*Review and reserve a journal article from the options provided, or submit your own selection to the teaching faculty for approval.
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#To help you prepare for the Journal Club presentation, you will craft a single slide using [[Media:Fa16 dueM2D2 HW.pptx |this information]] from a publication by G. J. Pickering. Submit a hard copy at the start of your laboratory section and have an electronic copy that you can edit during the BE Communication Lab workshop.  Please keep the following in mind as you prepare this assignment:
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#*Your slide should show the data and highlight the key finding(s).
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#*The information should be clear and large enough to read.
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#*Keep text to a minimum.
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#*The title should state the take-home message of the data that are shown.
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 +
===Due M2D3===
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#As in module 1, figures and captions will be important in your [[20.109(F16): Research article| 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 in the Results section of the [http://engineerbiology.org/wiki/20.109%28F16%29:Communication#Written_communication_guidelines general guidelines for scientific writing] on the Communication page.  Please keep the following details in mind:
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#*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.
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#*State the results of the experiment, minimizing any interpretation of the data.
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#*End each results paragraph with a concluding sentence that provides a transition to the next experimental step when possible.
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#*Each paragraph should only include one topic, but each sub-section may have more than one paragraph.
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#Prepare for the journal article in-class exercise by carefully reading the paper and discussion questions posted in [[20.109(F16):Generate_gRNA_plasmid_(Day3)#Part_4:_Journal_article_discussion| Part 4 of M2D3]].
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 +
===Due M2D5===
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#As in module 1, you will need to introduce your project in the [[20.109(F16): Research article |Research article]].  For this assignment, write the first paragraph of your Introduction according to the information provided in the Introduction section of the [http://engineerbiology.org/wiki/20.109%28F16%29:Communication#Written_communication_guidelines general guidelines for scientific writing] on the Communication page.  For the remaining paragraphs that will form your Introduction, include topic sentences that provide an overview of the information you will include.
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#*In addition to your first paragraph and the topic sentences, submit the references from which you obtained the information contained within your assignment.
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#*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).
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#Often illustrations are useful when discussing experiment approaches in written communication outlets. Prepare a schematic diagram that depicts your experimental approach for Module 2.  See the [[20.109(F16):Module 2| Module 2 overview]] page for an example, but do '''not''' simply copy this image!
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#*Think about which steps are important to the overall goal of your approach and which are minor methods details that can be omitted or should be added.
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#*Remember, schematics are figures and '''should have captions'''.
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#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 [http://engineerbiology.org/wiki/20.109%28F16%29:Communication#Written_communication_guidelines general guidelines for scientific writing] on the Communication page.
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 +
===Due M2D7===
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#Though you practiced crafting a Methods section in module 1, this information was not included in your Data summary.  In the [[20.109(F16): Research article |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 M2D2 through M2D5 according to the information provided in the Materials and methods section of the [http://engineerbiology.org/wiki/20.109%28F16%29:Communication#Written_communication_guidelines general guidelines for scientific writing] on the Communication page.
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#*Think carefully about the scope of each experimental step and how certain protocols can be combined or divided into coherent sub-sections.
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#*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.
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#*Avoid jargon and excess descriptive words.
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===Due M2D8===
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#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:
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#*Is the information complete?  Are any procedural steps absent?  Is important information pertaining to any of the procedures missing?
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#*Is the information clear?  Are the procedural steps presented in an order that makes sense?
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#*Are the sections divided and grouped appropriately?
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#*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?
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#*Are the sections written in complete sentences?
 +
<!--
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#*Use the rubric linked [here] to guide your review. 
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-->
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#*'''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).
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===Wrapping up M2===
 
===Wrapping up M2===
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#The [[report| research article]] is due by '''5 pm on Monday, April 18th''' for both sections.
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#The [[20.109(F16): Research article | Research article]] is due by '''5 pm on Sunday, November 20th''' for both sections.
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#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] before 5pm on Tuesday, April 19th.
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#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] within 24 h of submitting the Research article.
  
 
==Module 3: Biomaterials engineering==
 
==Module 3: Biomaterials engineering==
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===Due M3D2===
 
===Due M3D2===
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#The primary assignment for this experimental module will be for you to develop a [[20.109(F16):Research proposal presentation |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.
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#The primary assignment for this experimental module will be for you to develop a [[20.109(F16):Research proposal presentation |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.
 
#*'''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.
  
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#*Can your proposal be carried out in a reasonable amount of time and with non-infinite resources?  
 
#*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.
 
#*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.
+
#*'''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===
 
===Due M3D4===
−
#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).  
+
#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:
 
#*Keep in mind that your presentation to the class will ultimately need:
 
#**a brief project overview
 
#**a brief project overview
Line 117: Line 146:
 
#**predicted outcomes if everything goes according to plan and if nothing does
 
#**predicted outcomes if everything goes according to plan and if nothing does
 
#**needed resources to complete the work
 
#**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 [http://openwetware.org/wiki/Yeast_rebuild “yeast rebuild”] or the [http://openwetware.org/wiki/T7.2 “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.
+
#*'''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.'''  
−
#For this module, you will also prepare a short [[20.109(F16): Biomaterials engineering report| 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.  
+
 
 +
#For this module, you will also prepare a short [[20.109(F16): Biomaterials engineering mini-report| 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.
 
#*Review the assignment details and carefully consider the questions specified within the evaluation criteria as you craft the Background and Approach section.
  
Line 126: Line 156:
  
 
===Due (after) M3D5===
 
===Due (after) M3D5===
−
#The [[20.109(F16): Biomaterials engineering report | Biomaterials engineering mini-report]] is due by '''10 pm on Thursday, May 5th or Friday, May 6th''' according to your laboratory section.
+
#The [[20.109(F16): Biomaterials engineering mini-report | Mini-report]] is due by '''10 pm on Monday, Dec 12th''' according to your laboratory section.
  
 
===Wrapping up M3===
 
===Wrapping up M3===
−
#The [[20.109(F16):Research proposal presentation| Research proposal presentation]] slides are due on Stellar by '''1 pm on Tuesday, May 10th or Wednesday, May 11th''' according to your laboratory section.
+
#The [[20.109(F16):Research proposal presentation| Research proposal presentation]] slides are due on Stellar by '''1 pm on Thursday, Dec 8th or Friday, Dec 9th''' according to your laboratory section.
 
#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] before 11am on Saturday, May 14th.
 
#Please remember to contribute your reflections, comments, and ideas to the [http://be20109f16.blogspot.com/ 20.109 class blog] before 11am on Saturday, May 14th.

Latest revision as of 21:26, 30 November 2016

20.109(F16): Laboratory Fundamentals of Biological Engineering

Engelward PNAS 2006.png

Schedule Fall 2016        Announcements        Assignments        Homework        Communication
       1. Measuring Genomic Instability        2. Manipulating 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.
  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 M1D2

  1. The laboratory exercises will take the full laboratory session to complete. To ensure you are prepared, please carefully read through the information provided on the M1D2 page.
  2. To further prepare for the long laboratory session, complete a template for your notebook entry according to the Laboratory notebook guidelines provided on the Communication page.
    • For additional help, see the template for your M1D2 notebook entry below.
Notebook entry template.

Due M1D3

  1. Use the data collected for the cell loading 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.
    • Please note: only use the cell loading data to craft your figure and caption for this assignment, in other words do not include the growth rate information.
  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

  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.
    • Be sure to read the Introduction information within the Written communication guidelines section of the Communication page before you begin; doing so will save you some time and effort.
    • Carefully consider the Background and Motivation suggestions provided for the M1 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. 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. The M1 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.
    • Be sure to read the Discussion information within the Written communication guidelines section of the Communication page before you begin; doing so will save you some time and effort.
    • Carefully consider the Implications and Future Work suggestions provided for the M1 Data Summary.
  2. In addition to the M1 Data 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.
    • You should not submit a script, but rather a bulleted outline of the information you will provide in your Mini-presentation.

Due M1D7

  1. Use the feedback you received from the teaching faculty concerning the Materials and Methods draft you prepared for M1D4 to revise your text.
    • In addition, include the experimental protocols you completed through M1D3 in this revised assignment.
  2. Complete the in-class summary of the H2AX assay results according to the assignment description provided on the M1D7 page.
    • Please note: you will have time to complete this assignment during your laboratory section and it is not due until 10 pm on M1D7!

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: 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 a single slide using this information from a publication by G. J. Pickering. Submit a hard copy at the start of your laboratory section and have an electronic copy that you can edit during the BE Communication Lab workshop. Please keep the following in mind as you prepare this assignment:
    • Your slide 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 in the Results section of the general guidelines for scientific writing on the Communication 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-class exercise by carefully reading the paper and discussion questions posted in Part 4 of M2D3.

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 general guidelines for scientific writing on the Communication 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 for Module 2. See the Module 2 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 or should be added.
    • Remember, schematics are figures and should have 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 general guidelines for scientific writing on the Communication 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 M2D2 through M2D5 according to the information provided in the Materials and methods section of the general guidelines for scientific writing on the Communication page.
    • 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 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).

Wrapping up M2

  1. The Research article is due by 5 pm on Sunday, November 20th for both sections.
  2. Please remember to contribute your reflections, comments, and ideas to the 20.109 class blog within 24 h of submitting the 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 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 Mini-report is due by 10 pm on Monday, Dec 12th according to your laboratory section.

Wrapping up M3

  1. The Research proposal presentation slides are due on Stellar by 1 pm on Thursday, Dec 8th or Friday, Dec 9th 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.
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