Difference between revisions of "20.109(S20): Spring 2020 schedule"

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Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.
 
Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.
  
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<font color= #00BFFF >'''SCHEDULE DETAILS:'''</font color><br>
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<font color= #01A9DB >'''SCHEDULE DETAILS:'''</font color><br>
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<font color= #00BFFF >'''Lecture times:'''</font color>  T/R 11 - 12 pm (32-124)  <br>
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<font color= #01A9DB >'''Lecture times:'''</font color>  T/R 11 - 12 pm (56-154)  <br>
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<font color= #00BFFF >'''Laboratory section times:'''</font color>  T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)<br>
+
<font color= #01A9DB >'''Laboratory section times:'''</font color>  T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)<br>
  
 
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{| border=1px
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|  
 
|  
 
| T/W Feb 4/5   
 
| T/W Feb 4/5   
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp20 Orientation lecture formatted.pptx| Orientation lecture]]
−
| [[20.109(S20):Laboratory tour | Orientation and laboratory tour]]
+
| [[20.109(S20):Laboratory tour | Orientation and laboratory tour]] <br> [[Media:Sp20 M0D0 bcm.pdf | Lab Orientation Prelab]]
 
|
 
|
 
|--
 
|--
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| 1
 
| 1
 
| R/F Feb 6/7  
 
| R/F Feb 6/7  
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L1 2020.pdf| M1D1 lecture]]
−
| [[20.109(S20):In silico cloning and confirmation digest of protein expression vector(Day1) |In silico cloning and confirmation digest of protein expression vector]]<br>
+
| [[20.109(S20):Complete in silico cloning and induce TDP43 protein expression (Day1) |Complete in silico cloning and induce TDP43 protein expression]]<br>[[Media:Sp20 M1D1 nll marked.pdf| T/R prelab]]<br> [[Media:Sp20 M1D1 bcm.pdf | WF Prelab]]
−
| <font color= #00BFFF>'''Orientation quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D1| Homework due]]
+
| <font color= #01A9DBF>'''Orientation quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D1| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 2
 
| 2
 
| T/W Feb 11/12   
 
| T/W Feb 11/12   
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L2 2020.pdf| M1D2 lecture]]
−
| [[20.109(S20):Purify protein for secondary assays(Day2) |Purify protein for secondary assays]]<br>
+
| [[20.109(S20):Purify TDP43 protein (Day2) |Purify TDP43 protein]]<br>[[Media:Sp20 M1D2 nll marked.pdf| T/R prelab]]<br>[[Media:Sp20 M1D2 bcm marked.pdf| W/F prelab]]
 
| [[20.109(S20):Homework#Due_M1D2| Homework due]]
 
| [[20.109(S20):Homework#Due_M1D2| Homework due]]
 
|--
 
|--
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| 3
 
| 3
 
| R/F Feb 13/14   
 
| R/F Feb 13/14   
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L3 2020.pdf| M1D3 lecture]]
−
| [[20.109(S20):Analyze small microarray data (Day3) | Analyze small molecule microarray (SMM) data]]<br>
+
| [[20.109(S20):Assess purity and concentration of TDP43 protein (Day3) | Assess purity and concentration of TDP43 protein]]<br> [[Media:Sp20 M1D3 nll marked.pdf| T/R prelab]] <br>[[Media:Sp20 M1D3 bcm marked.pdf | WF Prelab]]
 
| [[20.109(S20):Homework#Due_M1D3| Homework due]]
 
| [[20.109(S20):Homework#Due_M1D3| Homework due]]
 
|--
 
|--
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| 4
 
| 4
 
| R/F Feb 20/21
 
| R/F Feb 20/21
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L4 2020.pdf| M1D4 lecture]]
−
| [[20.109(S20):Evaluate protein purity and concentration (Day4) |Evaluate protein purity and concentration]]<br>
+
| [[20.109(S20):Perform small molecule microarray (SMM) with TDP43 protein (Day4) |Perform small molecule microarray (SMM) with TDP43 protein]]<br>[[Media:Sp20 M1D4 nll marked.pdf| T/R prelab]] <br> [[Media:Sp20 M1D4 bcm marked.pdf | WF prelab]]
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D4| Homework due]]
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D4| Homework due]]
 
|--
 
|--
 
| 1
 
| 1
 
| 5
 
| 5
 
| T/W Feb 25/26  
 
| T/W Feb 25/26  
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L5 2020.pdf| M1D5 lecture]]
−
| [[20.109(S20):Test protein activity using peptidyl-prolyl cis-trans isomerase assay (Day5) |Test protein activity using peptidyl-prolyl cis-trans isomerase assay]]<br>
+
| [[20.109(S20):Scan SMM slides to identify binders of TDP43 protein (Day5) |Scan SMM slides to identify binders of TDP43 protein]]<br>[[Media:Sp20 M1D5 nll marked.pdf| T/R prelab]] <br> [[Media:Sp20 M1D5 bcm marked.pdf | WF prelab]]
 
| [[20.109(S20):Homework#Due_M1D5| Homework due]]
 
| [[20.109(S20):Homework#Due_M1D5| Homework due]]
 
|--
 
|--
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| 6
 
| 6
 
| R/F Feb 27/28
 
| R/F Feb 27/28
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L6 2020.pdf| M1D6 lecture]]
−
| [[20.109(S20):Confirm ligand binding using differential scanning fluorimetry assay (Day6) |Confirm ligand binding using differential scanning fluorimetry assay]]<br>
+
| [[20.109(S20):Analyze SMM data (Day6) |Analyze SMM data]]<br>[[Media:Sp20 M1D6 nll marked.pdf| T/R Prelab]] <br> [[Media:Sp20 M1D6 bcm marked.pdf | WF Prelab]]
 
| [[20.109(S20):Homework#Due_M1D6| Homework due]]
 
| [[20.109(S20):Homework#Due_M1D6| Homework due]]
 
|--
 
|--
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| 7
 
| 7
 
| T/W Mar 3/4
 
| T/W Mar 3/4
−
| [http://be.mit.edu/directory/angela-koehler AK]<br>
+
| [http://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M1L7 2020.pdf| M1D7 lecture]]
−
| [[20.109(S20):Complete data analysis (Day7) |Complete data analysis]]<br>
+
| [[20.109(S20):Examine TDP43 binders for chemical features (Day7) |Examine TDP43 binders for chemical features]]<br>[[Media:Sp20 M1D7 nll marked.pdf| T/R prelab]] <br> [[Media:Sp20 M1D7 bcm marked.pdf | WF Prelab]]
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D7| Homework due]]
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M1D7| Homework due]]
 
|--
 
|--
 
| colspan="7" |
 
| colspan="7" |
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| 1
 
| 1
 
| R/F Mar 5/6
 
| R/F Mar 5/6
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
+
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Sp20 M2D1Lecture nll.pdf| M2D1 lecture]]
−
| [[20.109(S20):Practice tissue culture techniques and prepare cells for RNA purification (Day1)| Practice tissue culture techniques and prepare cells for RNA purification]]<br>
+
| [[20.109(S20):Prepare cells for RNA purification and practice RNA-seq data analysis methods (Day1)| Prepare cells for RNA purification and practice RNA-seq data analysis methods]]<br>[[Media:Sp20_M2D1_LMMmarked.pdf| T/R prelab]]<br>[[Media:Sp20_M2D1_bcm_marked.pdf| W/F prelab]]
−
| [[20.109(S20):Homework#Due_M2D1| Homework due]]
+
| [[20.109(S20):Homework#Due_M2D1| Homework due]]<br> [[20.109(S20): Data Summary| <font color=#B40404>'''Data summary draft due'''</font color>]] Sun, Mar 8 at 10 pm<br>
 
|--
 
|--
 
| 2
 
| 2
 
| 2
 
| 2
 
| T/W Mar 10/11
 
| T/W Mar 10/11
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[[Media:Lecture 300311 for posting.pdf| M2D2 lecture]]
−
| [[20.109(S20):Etoposide treat cells for RNA purification (Day2)| Etoposide treat cells for RNA purification]]<br>
+
| [[20.109(S20):Treat cells with etoposide and analyze RNA-seq data (Day2)| Treat cells with etoposide and analyze RNA-seq data]]<br>[[Media:Sp20_M2D2_LMMmarked.pdf| T/R prelab]] <br> [[Media:Sp20 M2D2 bcm marked.pdf | WF Prelab]]
−
| [[20.109(S20):Homework#Due_M2D2| Homework due]]<br> [[20.109(S20): Data Summary| <font color=#FF0000>Data summary draft due</font color>]] Mon, Mar 11 at 10 pm<br>
+
| [[20.109(S20):Homework#Due_M2D2| Homework due]]
 
|--
 
|--
 
| 2
 
| 2
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| R/F Mar 12/13
 
| R/F Mar 12/13
 
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br>  
 
| [http://be.mit.edu/directory/ernest-fraenkel EF] <br>  
−
| [[20.109(S20):Purify RNA and practice RNA-seq data analysis methods (Day3)| Purify RNA and practice RNA-seq data analysis methods]]<br>
+
| [[20.109(S20):Purify RNA from etoposide-treated cells and and generate cDNA (Day3)| Purify RNA from etoposide-treated cells and generate cDNA]]<br>[[Media:Sp20_M2D3_LMMmarked.pdf| T/R prelab]] <br> [[Media:Sp20 M2D3 bcm marked.pdf | WF Prelab]]
−
| [[20.109(S20):Homework#Due_M2D3| Homework due]] <br> [[20.109(S20): Mini-presentation| <font color=#FF0000>Mini-presentation due</font color>]] Sat, Mar 16 at 10 pm<br>[https:// Blog post due] Sun, Mar 17 at 10 pm <br>
+
−
|--
+
−
| 2
+
−
| 4
+
−
| T/W Mar 17/18
+
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
+
−
| [[20.109(S20):Analyze RNA-seq data and prepare for quantitative PCR experiment (Day 4)| Analyze RNA-seq data and prepare for quantitative PCR experiment]]<br>
+
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D4| Homework due]]
+
−
|--
+
−
| 2
+
−
| 5
+
−
| R/F Mar 19/20
+
−
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
+
−
| [[20.109(S20):Perform quantitative PCR experiment and explore additional RNA-seq datasets (Day5) | Perform quantitative PCR experiment and explore additional RNA-seq datasets]]<br>
+
−
| [[20.109(S20):Homework#Due_M2D5| Homework due]]
+
−
|--
+
 
|  
 
|  
−
|
 
−
| T/W Mar 24/25
 
−
| 
 
−
| <font color = #FACC2E>'''Spring vacation'''</font color>
 
−
| [[20.109(S20): Data Summary| <font color=#FF0000>Data summary revision due</font color>]] Mon, Mar 25 at 10 pm
 
 
|--
 
|--
−
|  
+
| colspan="7" |   <center><font color = #0f688c > '''First, we hope that you are all well and taking care of yourselves!!  Second, we want to welcome you all back to the Sp20 semester of 20.109!!  This will be an interesting endeavor for all of us and we have done / are doing our best to provide you all a positive experience.  In that, several changes and modifications have been made to the remainder of the schedule.  Please review the details below and, as always, feel free to share feedback...now more than ever we need your ideas to improve 20.109 and ensure a rewarding outcome for everyone!  A summary of the remote teaching strategy is linked [[Media:Sp20 Remote teaching strategy.pdf |here]].'''</font color></center>
−
|
+
−
| R/F Mar 26/27
+
−
| 
+
−
| <font color = #FACC2E>'''Spring vacation'''</font color>
+
−
|
+
 
|--
 
|--
 
| 2
 
| 2
 
| 6
 
| 6
 
| T/W Mar/Apr 31/1
 
| T/W Mar/Apr 31/1
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[https://www.google.com/url?q=https%3A%2F%2Fmit.zoom.us%2Fj%2F348659452&sa=D&ust=1585502144595000&usg=AFQjCNG0iLNO3f-D3L837sTrvXtzc-0Vtw Zoom access]<br> [https://mit.zoom.us/rec/share/_elkEKzgsUVOS9bK9EbfCqwMAdr0aaa81CQZ-6ZZzgnAyffHAkkaD9A1zV9ugqQ M2D6 video] <br> [[Media:Module 2 Lecture 200331 for posting FINAL.pdf| M2D6 slides]]
−
| [[20.109(S20):Design cell viability experiment and complete RNA-seq data analysis (Day6)| Design cell viability experiment and complete RNA-seq data analysis]]<br>
+
| [[20.109(S20):Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment (Day 6)| Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment]]<br>
 +
[https://mit.zoom.us/s/613303093 T/R Zoom access], [https://mit.zoom.us/rec/share/xuxzd6Pt81JOU5GRx1HOd6sKN4PUaaa8hiAd8_UPzh2x3oo4anGmidcVM1e7r_wV?startTime=1585674840000 T/R prelab video], [[Media: Sp20_M2D6_LMM.pdf| T/R prelab slides]] <br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/tM4pNrPa20BLAc_q9kz5e5E4RpbZX6a80SJK8vMNmU3q7wz67l-FelmAozaxutO8 W/F prelab video], [[Media:Sp20 M2D6 bcm unmarked.pdf| W/F prelab slides]]
 
| [[20.109(S20):Homework#Due_M2D6| Homework due]]  
 
| [[20.109(S20):Homework#Due_M2D6| Homework due]]  
 
|--
 
|--
Line 143: Line 118:
 
| 7
 
| 7
 
| R/F Apr 2/3
 
| R/F Apr 2/3
−
| Comm Lab<br>
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[https://www.google.com/url?q=https%3A%2F%2Fmit.zoom.us%2Fj%2F348659452&sa=D&ust=1585502144595000&usg=AFQjCNG0iLNO3f-D3L837sTrvXtzc-0Vtw Zoom access]<br>[https://mit.zoom.us/rec/share/_Y9sPey3z1hJGKPXxU_jBPINFbq6X6a82yIZqPdbxBrHLdTbyLEevSHmJxUKTViR M2D7 video] <br> [[Media:Lecture 3 RNA-Seq for posting.pdf| M2D7 slides]]
−
| [[20.109(S20):Journal club presentations (Day7 and 8)| Journal club I presentations]]<br>
+
| [[20.109(S20):Perform qPCR experiment and continue RNA-seq data analysis (Day7) | Review qPCR experiment and complete statistical analysis]]<br>[https://mit.zoom.us/s/613303093 T/R Zoom access], [https://mit.zoom.us/rec/share/x957aLbX0k5LQYnW7U3zWfAgEam4X6a81yge-KBZyElN1gM40LtpSxUi5hxSORtt?startTime=1585847490000 T/R prelab video], [[Media: Sp20_M2D7_LMM.pdf| T/R prelab slides]] <br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/48NRJqHu02hLGNLp7l3dfbQZPYXieaa81XMY_6APnU9RluvDKvaXQfF3qkRJ1bu_ WF prelab video], [[Media:Sp20 M2D7 bcm UNMARKED.pdf | WF prelab slides]]
−
| [https:// Blog post due] Sat, Apr 6 at 10 pm <br>
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br>[[20.109(S20):Homework#Due_M2D7| Homework due]]<br>[[20.109(S20): Data Summary| <font color=#B40404>'''Data summary revision due'''</font color>]] Sat, Apr 4 at 10 pm <br>[https://be20109s20.blogspot.com/ Blog post due] Mon, Apr 6 at 10 pm <br>
 
|--
 
|--
 
| 2
 
| 2
 
| 8
 
| 8
 
| T/W Apr 7/8
 
| T/W Apr 7/8
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
+
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>[https://www.google.com/url?q=https%3A%2F%2Fmit.zoom.us%2Fj%2F348659452&sa=D&ust=1585502144595000&usg=AFQjCNG0iLNO3f-D3L837sTrvXtzc-0Vtw Zoom access]<br>[https://mit.zoom.us/rec/share/7MVRHeGgxnxIUtbA1EPCZekTPonfT6a8hiUdrPALn0vGNKg00SKcZRoEF2p4I905 M2D8 video]<br>[[Media:Lecture 4 transcriptional regulation FINAL to post.pdf|M2D8 slides]]
−
| [[20.109(S20):Journal club presentations (Day7 and 8)| Journal club II presentations]]<br>
+
| [[20.109(S20):Examine qPCR results and complete data analysis (Day8) | Complete RNA-seq data analysis]]<br>[https://mit.zoom.us/s/613303093 T/R Zoom access],[https://mit.zoom.us/rec/share/4eNSHo7f6U5IUp31-HyEaLAxAbnuX6a8g3ce_aZcnhqsCwkfQw9Zcc7oyKPL4gnH?startTime=1586279524000 T/R prelab video], [[Media: Sp20_M2D8_LMM.pdf ‎| T/R prelab slides]]<br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/38FbIoD3qntJTI3wuALwSP4FOL3Leaa8gXUbrvZeyUomVGcB1C_E7a6zsXa-GRJa W/F prelab video], [[Media:Sp20 M2D8 bcm unmarked.pdf‎| WF prelab slides]]
−
|
+
| [[20.109(S20):Homework#Due_M2D8| Homework due]]
 +
|--
 +
| 2
 +
| 9
 +
| R/F Apr 9/10
 +
| BE Comm Lab<br> [https://mit.zoom.us/j/714801029 Zoom access]<br>[https://mit.zoom.us/rec/share/-sFoLIrpyDpOf4mdyGHQeJdiMLW9T6a80SZN_PQPmhlGwu5gvM4N--6ZxpDuu6oO M2D9 video]
 +
|Prepare M2 Major assignments: Journal club presentation and Research article<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [https://mit.zoom.us/rec/share/zMFfNLvUx35LQZXm81HEV7EgIKP7eaa82iIc86YEy0yWAbiNrz9HLzjA-hDoo1R4 T/R prelab video], [[Media:Sp20 M2D9Prelab nll.pdf|T/R prelab slides]]<br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/4_xXILPO2GdLWYXQsFzUCvYcE73rT6a8gCka_fQEzkbSJypqfq7CeIAspEvXlPKZ  W/F prelab video], [[Media:Sp20 M2D9Prelab nll.pdf|W/F prelab slides]]
 +
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D9| Homework due]] <br> [[20.109(S20):Journal club presentations (Day4 and 5)|<font color=#B40404>'''Journal club presentation due'''</font color>]] Sat, Apr 11 at 10 pm <br>[https://be20109s20.blogspot.com/ Blog post due] Mon, Apr 13 at 10 pm <br>
 
|--
 
|--
 
| colspan="7" |
 
| colspan="7" |
Line 158: Line 140:
 
| 3
 
| 3
 
| 1
 
| 1
−
| R/F Apr 9/10
+
| T/W Apr 14/15
−
| [http://be.mit.edu/directory/ernest-fraenkel EF]<br>
+
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>[https://mit.zoom.us/s/613303093 Zoom access]<br>[[Media:Sp20_Mod3_lecture 1.pdf|M3D1 slides]]<br>[https://mit.zoom.us/rec/share/_egpI63800VLSa_fxVz5ZK1iAbrUX6a81yMbrvtexUgATJB4EXCPChegA1vEGO9u?startTime=1586876971000 M3D1 video]
−
| [[20.109(S20):Complete data analysis (Day9)| Complete data analysis]]<br>
+
| [[20.109(S20):Enrich candidate clones using fluorescence-activated cell sorter (FACS) (Day1)| Enrich candidate clones using fluorescence-activated cell sorter (FACS)]]<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [https://mit.zoom.us/rec/share/4Z0oEY6s_WJJZ43S9UPvYKIfFKLvX6a80CNMrPJbzhlG5xmsEUZbnQpncq4-uB8Z T/R prelab video], [[Media:Sp20 M3D1 nll.pdf|T/R prelab slides]]<br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/w-xIM4383W5OT9LXxmPeYvAeWYTqX6a81SAf8vFfmBq0uu3N_aBsQAOdLlVV3XbI W/F prelab video], [[Media:Sp20 M3D1 bcm unmarked.pdf | WF prelab slides]]
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M2D9| Homework due]] <br>  
+
| [[20.109(S20):Homework#Due_M3D1| Homework due]] <br>
 +
|--
 +
| 3
 +
| 2
 +
| R/F Apr 16/17
 +
| BE Comm Lab<br>[https://mit.zoom.us/j/714801029 Zoom access]<br>[https://mit.zoom.us/rec/share/vO4sCK3R13lLQLPz92_FfqdmMMfGT6a81SFM8_YEzxlVVanXWhZYdlr9o1t1XnjW M3D2 video]
 +
| [[20.109(S20):Harvest candidate clones  (Day2) |Harvest candidate clones and prepare for sequencing]]<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [https://mit.zoom.us/rec/share/xeNpF6qhy2xJBavK6WXScZ8vN5_feaa8hClN-fALyxkSLXnS-p3m-4ygYoUueYQP T/R prelab video], [[Media:Sp20 M3D2 nll.pdf|T/R prelab slides]]<br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/5-lMFazw7k9OE7Pv1WCHWo0sNYW6eaa8hyZIrvUNnRq4XRYFKqIql9nUCBDsmA_Z  W/F prelab video], [[Media:Sp20 M3D2 bcm unmarked.pdf | WF prelab slides]]
 +
| [[20.109(S20):Homework#Due_M3D2| Homework due]] <br>  
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| T/W Apr 16/17
+
| T/W Apr 21/22
 
|
 
|
 
| <font color = #FACC2E>'''Patriots' day holiday'''</font color>
 
| <font color = #FACC2E>'''Patriots' day holiday'''</font color>
−
|
+
| [[20.109(S20): Research article| <font color=#B40404>'''Research article due'''</font color>]] Mon, Apr 20 at 10 pm <br> [https://be20109s20.blogspot.com/ Blog post due] Tue, Apr 21 at 10 pm
 
|--
 
|--
 
| 3
 
| 3
−
| 1
 
−
| R/F Apr 18/19
 
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>
 
−
| [[20.109(S20):Growth of phage-based active (cathode) material (Day1) | Grow phage-based active (cathode) material]]<br>
 
−
| [[20.109(S20):Homework#Due_M3D1| Homework due]] <br> [[20.109(S20): Research article| <font color=#FF0000>Research article due</font color>]] Sat, Apr 20 at 10 pm <br> [https:// Blog post due] Sun, Apr 21 at 10 pm
 
−
|--
 
 
| 3
 
| 3
−
| 2
+
| R/F Apr 23/24
−
| T/W Apr 23/24
+
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>[https://mit.zoom.us/s/613303093 Zoom access]<br>[[Media:Sp20_Mod3_lecture 2.pdf|M3D3 slides]]<br>[https://mit.zoom.us/rec/share/vPEkMOnSyXNLWKeRzhDuB6MfQ6viX6a80yFM-PNZzBx2cnJ6YG_9C7zvCKKs4QjS?startTime=1587654517000 M3D3 video]
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>
+
| [[20.109(S20):Identify clones to characterize  (Day3) |Identify clones to characterize]]<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [https://mit.zoom.us/rec/share/9dcuKu-v2m9JRp3f2EzuUYkuJ638eaa81HIZ-_IIzh2hRtewr_XwzEtoM7qdju7B?startTime=1587661822000 T/R prelab video], [[Media:Sp20 M3D3 nll.pdf|T/R prelab slides]] <br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/upBYIPLp3EdOYaPStlmcRP9_BsP5X6a8hHAcrvYPzZq5X1fC51L1AqfP8gZyNX0?startTime=1587748234000 W/F prelab video], [[Media:Sp20 M3D3 bcm.pdf | WF Prelab slides]] <br>
−
| [[20.109(S20):Purify phage-based active (cathode) material (Day2) | Purify phage-based active (cathode) material]]<br>
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M3D3| Homework due]] <br>
−
| [[20.109(S20):Homework#Due_M3D2| Homework due]]
+
 
|--
 
|--
−
| 3
 
 
|  
 
|  
−
| R/F Apr 25/26
 
 
|  
 
|  
−
| <font color = #FACC2E>'''Lecture, but no laboratory'''</font color>
+
| T/W Apr 28/29
−
|
+
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>[https://mit.zoom.us/s/613303093 Zoom access]<br>[[Media:Sp20_M3L3_slides_handout.pdf|Apr28 slides/handout]]<br>[https://mit.zoom.us/rec/share/3dRJJbHQ1mpORq_wuGeCY4czEo7IX6a8gyRI-KVfyRtzNY-7ruAaJPIHg-M7mN8F?startTime=1588086584000 Apr28 video]
−
|--
+
| Research proposal pitches, will be delivered by each team during laboratory time <br> [https://mit.zoom.us/j/137247921 T/R Zoom access]<br>[https://mit.zoom.us/j/735216560 W/F Zoom access]
−
| 3
+
|
−
| 3
+
−
| T/W Apr/May 30/1
+
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>
+
−
| [[20.109(S20):Construct cathode with phage-based active material (Day3)| Construct cathode with phage-based active material]]<br>
+
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M3D3| Homework due]]
+
 
|--
 
|--
 
| 3
 
| 3
 
| 4
 
| 4
−
| R/F May 2/3
+
| R/F Apr/May 30/1
−
| [http://be.mit.edu/directory/angela-belcher AB]<br>
+
| [http://be.mit.edu/directory/leslie-mcclain LM]<br>[https://mit.zoom.us/s/613303093 Zoom access]<br>[[Media:Sp20_M3L4.pdf|M3D4 slides]]<br>[https://mit.zoom.us/rec/share/zP5QF7Pu6XJOXYnQ8mPgaJAYQIW6T6a8hyQYq6cEzEfHjTEa-Gql4TCi8MxquSrH?startTime=1588259394000 M3D4 video]
−
| [[20.109(S20):Visualize phage nanowires using TEM (Day4)| Visualize phage nanowires using transmission electron microscopy]]<br>
+
| [[20.109(S20):Characterize clone by titration using flow cytometry (Day4)|Characterize clone by titration using flow cytometry ]]<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [ T/R prelab video], [[Media:Sp20 M3D4 nll.pdf|T/R prelab slides]] <br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/zMdNAZXR8HxLR9Kd826cZoF6HIjleaa8gSYXrqFfyxxkaqhSmmOHldJDtxTRw4MN  WF prelab video], [[Media:Sp20 M3D4 bcm unmarked.pdf | WF prelab slides]]
 
| [[20.109(S20):Homework#Due_M3D4| Homework due]]
 
| [[20.109(S20):Homework#Due_M3D4| Homework due]]
 
|--
 
|--
 
| 3
 
| 3
 
| 5
 
| 5
−
| T/W May 7/8
+
| T/W May 5/6
−
| [http://be.mit.edu/directory/angela-belcher AB]
+
| Guest, SC<br>[https://mit.zoom.us/s/613303093 Zoom access]<br>[[Media:200505_SCC_guestLecture_notPublic.pdf|M3D5 Slides]]<br>[https://mit.zoom.us/rec/share/4-5FK4Gh0XxITJ314xCYQekQEqrieaa80XdI-vJeyF_vwbqD09tY0wQ323CJNEo?startTime=1588691427000 M3D5 video]
−
| [[20.109(S20):Assemble and test batteries (Day5) | Assemble and test batteries ]]<br>
+
| [[20.109(S20):Analyze titration curves (Day5) |Analyze titration curves ]]<br>[https://mit.zoom.us/j/137247921 T/R Zoom access], [ T/R prelab video], [[Media:Sp20 M3D5 nll.pdf|T/R prelab slides]]<br> [https://mit.zoom.us/j/735216560 W/F Zoom access], [https://mit.zoom.us/rec/share/vOtbdbje63pOQoWKxRjzevQZAd7FT6a82nMYq_tfzx6w7ESzcewfbUI6OAqq7ZSF  W/F prelab video], [[Media:Sp20 M3D5 bcm unmarked.pdf | WF prelab slides]]
−
| <font color= #00BFFF>'''Laboratory quiz'''</font color> <br> [[20.109(S20):Homework#Due_M3D5| Homework due]]
+
| <font color= #01A9DB>'''Laboratory quiz'''</font color> <br>[[20.109(S20):Homework#Due_M3D5| Homework due]]
 
|--
 
|--
 
|  
 
|  
 
|  
 
|  
−
| R/F May 9/10
+
| R/F May 7/8
 
|
 
|
−
| [[20.109(S20):Research proposal presentation | Research proposal presentations]]
+
| [[20.109(S20):Research proposal presentation | <font color=#B40404>'''Research proposal presentations'''</font color>]], will be delivered by each team during laboratory time<br> [https://mit.zoom.us/j/137247921 T/R Zoom access]<br>[https://mit.zoom.us/j/735216560 W/F Zoom access]
−
| [https:// Blog post due] Sat, May 11 at 10 pm
+
|
 
|--
 
|--
 
|
 
|
 
|
 
|
−
| T May 14
+
| T May 12
 
|  
 
|  
−
| <font color = #FACC2E>'''Feedback and celebratory lunch'''</font color>
+
| <font color = #FACC2E>'''Feedback session, lunch will be rescheduled!'''</font color>
−
| [[20.109(S20): Mini-report | <font color=#FF0000>Mini-report due</font color>]] Mon, May 13 at 10 pm <br>
+
| [[20.109(S20): Mini-report | <font color=#B40404>'''Mini-report due'''</font color>]] Mon, May 11 at 10 pm <br>[https://be20109s20.blogspot.com/ Blog post due] Tue, May 12 at 10 pm
 
|}
 
|}
 
</div>
 
</div>

Latest revision as of 21:02, 6 May 2020

20.109(S20): Laboratory Fundamentals of Biological Engineering

Sp20 banner image v2.png

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


Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. Though there is not time enough to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

SCHEDULE DETAILS:
Lecture times: T/R 11 - 12 pm (56-154)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)

MODULE DAY DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Feb 4/5 NLL
Orientation lecture 		Orientation and laboratory tour
Lab Orientation Prelab
1 1 R/F Feb 6/7 AK
M1D1 lecture 		Complete in silico cloning and induce TDP43 protein expression
T/R prelab
WF Prelab 		Orientation quiz
Homework due
1 2 T/W Feb 11/12 AK
M1D2 lecture 		Purify TDP43 protein
T/R prelab
W/F prelab 		Homework due
1 3 R/F Feb 13/14 AK
M1D3 lecture 		Assess purity and concentration of TDP43 protein
T/R prelab
WF Prelab 		Homework due
T/W Feb 18/19 President's day holiday
1 4 R/F Feb 20/21 AK
M1D4 lecture 		Perform small molecule microarray (SMM) with TDP43 protein
T/R prelab
WF prelab 		Laboratory quiz
Homework due
1 5 T/W Feb 25/26 AK
M1D5 lecture 		Scan SMM slides to identify binders of TDP43 protein
T/R prelab
WF prelab 		Homework due
1 6 R/F Feb 27/28 AK
M1D6 lecture 		Analyze SMM data
T/R Prelab
WF Prelab 		Homework due
1 7 T/W Mar 3/4 AK
M1D7 lecture 		Examine TDP43 binders for chemical features
T/R prelab
WF Prelab 		Laboratory quiz
Homework due
2 1 R/F Mar 5/6 NLL
M2D1 lecture 		Prepare cells for RNA purification and practice RNA-seq data analysis methods
T/R prelab
W/F prelab 		Homework due
Data summary draft due Sun, Mar 8 at 10 pm
2 2 T/W Mar 10/11 EF
M2D2 lecture 		Treat cells with etoposide and analyze RNA-seq data
T/R prelab
WF Prelab 		Homework due
2 3 R/F Mar 12/13 EF
Purify RNA from etoposide-treated cells and generate cDNA
T/R prelab
WF Prelab
First, we hope that you are all well and taking care of yourselves!! Second, we want to welcome you all back to the Sp20 semester of 20.109!! This will be an interesting endeavor for all of us and we have done / are doing our best to provide you all a positive experience. In that, several changes and modifications have been made to the remainder of the schedule. Please review the details below and, as always, feel free to share feedback...now more than ever we need your ideas to improve 20.109 and ensure a rewarding outcome for everyone! A summary of the remote teaching strategy is linked here.
2 6 T/W Mar/Apr 31/1 EF
Zoom access
M2D6 video
M2D6 slides 		Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) experiment

T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides

Homework due
2 7 R/F Apr 2/3 EF
Zoom access
M2D7 video
M2D7 slides 		Review qPCR experiment and complete statistical analysis
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, WF prelab video, WF prelab slides 		Laboratory quiz
Homework due
Data summary revision due Sat, Apr 4 at 10 pm
Blog post due Mon, Apr 6 at 10 pm
2 8 T/W Apr 7/8 EF
Zoom access
M2D8 video
M2D8 slides 		Complete RNA-seq data analysis
T/R Zoom access,T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, WF prelab slides 		Homework due
2 9 R/F Apr 9/10 BE Comm Lab
Zoom access
M2D9 video 		Prepare M2 Major assignments: Journal club presentation and Research article
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides 		Laboratory quiz
Homework due
Journal club presentation due Sat, Apr 11 at 10 pm
Blog post due Mon, Apr 13 at 10 pm
3 1 T/W Apr 14/15 LM
Zoom access
M3D1 slides
M3D1 video 		Enrich candidate clones using fluorescence-activated cell sorter (FACS)
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, WF prelab slides 		Homework due
3 2 R/F Apr 16/17 BE Comm Lab
Zoom access
M3D2 video 		Harvest candidate clones and prepare for sequencing
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, WF prelab slides 		Homework due
T/W Apr 21/22 Patriots' day holiday Research article due Mon, Apr 20 at 10 pm
Blog post due Tue, Apr 21 at 10 pm
3 3 R/F Apr 23/24 LM
Zoom access
M3D3 slides
M3D3 video 		Identify clones to characterize
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, WF Prelab slides
Laboratory quiz
Homework due
T/W Apr 28/29 LM
Zoom access
Apr28 slides/handout
Apr28 video 		Research proposal pitches, will be delivered by each team during laboratory time
T/R Zoom access
W/F Zoom access
3 4 R/F Apr/May 30/1 LM
Zoom access
M3D4 slides
M3D4 video 		Characterize clone by titration using flow cytometry
T/R Zoom access, [ T/R prelab video], T/R prelab slides
W/F Zoom access, WF prelab video, WF prelab slides 		Homework due
3 5 T/W May 5/6 Guest, SC
Zoom access
M3D5 Slides
M3D5 video 		Analyze titration curves
T/R Zoom access, [ T/R prelab video], T/R prelab slides
W/F Zoom access, W/F prelab video, WF prelab slides 		Laboratory quiz
Homework due
R/F May 7/8 Research proposal presentations, will be delivered by each team during laboratory time
T/R Zoom access
W/F Zoom access
T May 12 Feedback session, lunch will be rescheduled! Mini-report due Mon, May 11 at 10 pm
Blog post due Tue, May 12 at 10 pm
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