Difference between revisions of "20.109(S21):Spring 2021 schedule"

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Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used 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 the experiments and techniques used in biological engineering. Though there is not enough time 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.
  
 
<font color=  #d1b217 >'''SCHEDULE DETAILS:'''</font color><br>
 
<font color=  #d1b217 >'''SCHEDULE DETAILS:'''</font color><br>
 
<font color=  #d1b217 >'''Lecture times:'''</font color>  <br>
 
<font color=  #d1b217 >'''Lecture times:'''</font color>  <br>
*Tuesday (T) and Thursday (R) 11 - 12 pm ([ Zoom access)] <br>
+
*Tuesday (T) and Thursday (R) 11 - 12 pm ([https://mit.zoom.us/j/94815211031 Zoom access]; Meeting ID 948 1521 1031) <br>
 
<font color=  #d1b217 >'''Laboratory section times:'''</font color>  <br>
 
<font color=  #d1b217 >'''Laboratory section times:'''</font color>  <br>
*Tuesday (T) and Thursday (R) 1 - 5 pm ([ Zoom access]) <br>
+
*Tuesday (T) and Thursday (R) 1 - 4 pm ([https://mit.zoom.us/j/94585650880 Zoom access]) <br>
*Wednesday (W) and Friday (F) 1 - 5 pm ([ Zoom access]) <br>
+
*Wednesday (W) and Friday (F) 1 - 4 pm ([https://mit.zoom.us/j/92289710115 Zoom access]) <br>
  
 
{| border=1px
 
{| border=1px
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|  
 
|  
 
| T/W Feb 16/17   
 
| T/W Feb 16/17   
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[ Slides]]
+
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp21 Orientation lecture students.pdf |Slides]]
| [[20.109(S21):Laboratory tour | Orientation and laboratory tour]]<br>
+
| [[20.109(S21):Laboratory tour | Orientation and laboratory tour]]<br> [https://www.dropbox.com/s/wkgflfcdyegxtg8/Sp21_M0D0_bcm.pdf?dl=0 T/R prelab] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
|
 
|
 
|--
 
|--
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| M1D1
 
| M1D1
 
| R/F Feb 18/19  
 
| R/F Feb 18/19  
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
+
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_1.pdf|Slides]]
| [[20.109(S21):M1D1 |In silico cloning library]]
+
| [[20.109(S21):M1D1 |Generate scFv library]] <br> [[Media:Sp21 M1D1 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| <font color= #d1b217 >'''Orientation quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D1|Homework due]]
 
| <font color= #d1b217 >'''Orientation quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D1|Homework due]]
 
|--
 
|--
 
| M1D2
 
| M1D2
 
| T/W Feb 23/24   
 
| T/W Feb 23/24   
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
+
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_2.pdf|Slides]]
| [[20.109(S21):M1D2 |Enrich candidate clones from library using FACS]] <br>
+
| [[20.109(S21):M1D2 |Enrich candidate clones from library using FACS]] <br> [[Media:Sp21 M1D2 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| [[20.109(S21):Homework#Due_M1D2|Homework due]]
 
| [[20.109(S21):Homework#Due_M1D2|Homework due]]
 
|--
 
|--
 
| M1D3
 
| M1D3
 
| R/F Feb 25/26   
 
| R/F Feb 25/26   
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
+
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_3.pdf|Slides]]
| [[20.109(S21):M1D3 |Harvest candidate clone plasmids from library]] <br>
+
| [[20.109(S21):M1D3 |Harvest clone plasmids from library]] <br> [[Media:Sp21 M1D3 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| [[20.109(S21):Homework#Due_M1D3|Homework due]]
 
| [[20.109(S21):Homework#Due_M1D3|Homework due]]
 
|--
 
|--
 
| M1D4
 
| M1D4
 
| T/W Mar 2/3
 
| T/W Mar 2/3
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
+
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_4.pdf|Slides]]
| [[20.109(S21):M1D4 |Purify plasmids and sequence clones]] <br>
+
| [[20.109(S21):M1D4 |Purify and sequence clone plasmids]] <br> [[Media:Sp21 M1D4 bcm marked.pdf | T/R prelab]]
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D4|Homework due]]
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D4|Homework due]]
 
|--
 
|--
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| R/F Mar 4/5
 
| R/F Mar 4/5
 
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
 
| [http://be.mit.edu/directory/leslie-mcclain LM] <br>  
| [[20.109(S21):M1D5 |Analyze clone sequence and choose clone to characterize]] <br>
+
| [[20.109(S21):M1D5 |Analyze clone sequences and choose clone to characterize]] <br>
 
| [[20.109(S21):Homework#Due_M1D5|Homework due]]
 
| [[20.109(S21):Homework#Due_M1D5|Homework due]]
 
|--
 
|--
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| R/F Mar 18/19
 
| R/F Mar 18/19
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D1 |Placeholder ]] <br>
+
| [[20.109(S21):M2D1 |Perform protein purification protocol]] <br>
 
| [[20.109(S21):Homework#Due_M2D1|Homework due]]
 
| [[20.109(S21):Homework#Due_M2D1|Homework due]]
 
|--
 
|--
 
|  
 
|  
| <font color = 999999>T/W Mar Mar 23/24 </font color>
+
| <font color = 999999>T/W Mar 23/24 </font color>
 
|  
 
|  
 
| <font color = #0d368e>'''Student holiday'''</font color>
 
| <font color = #0d368e>'''Student holiday'''</font color>
|  
+
| [[20.109(S21):Data Summary| <font color =  #b3251c>'''Data Summary draft due'''</font color>]] Wed, Mar 24 at 10 pm <br>
 
|--
 
|--
 
| M2D2
 
| M2D2
 
| R/F Mar 25/26
 
| R/F Mar 25/26
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D2 |Placeholder ]] <br>
+
| [[20.109(S21):M2D2 |Assess purity and concentration of purified protein ]] <br>
| [[20.109(S21):Homework#Due_M2D2| Homework due]] <br> [[20.109(S21):Data Summary| <font color =  #b3251c>'''Data Summary draft due'''</font color>]] XXX at 10 pm<br>[ Blog post due] XXX at 10 pm
+
| [[20.109(S21):Homework#Due_M2D2| Homework due]] <br> [[20.109(S21):Mini-presentation| <font color =  #b3251c>'''Mini-presentation due'''</font color>]] Sun, Mar 28 at 10 pm <br>[http://app.slack.com/client/T01KU1VLZQB/C01KQNPD3UM Blog post due] Mon, Mar 29 at 10 pm
 
|--
 
|--
 
| M2D3
 
| M2D3
 
| T/W Mar 30/31
 
| T/W Mar 30/31
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D3 |Placeholder ]] <br>  
+
| [[20.109(S21):M2D3 |Prepare and scan small molecule microarray (SMM) slides]] <br>  
 
| [[20.109(S21):Homework#Due_M2D3|Homework due]]
 
| [[20.109(S21):Homework#Due_M2D3|Homework due]]
 
|--
 
|--
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| R/F Apr 1/2
 
| R/F Apr 1/2
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D4 |Placeholder ]] <br>
+
| [[20.109(S21):M2D4 |Analyze SMM data to identify putative small molecule binders]] <br>
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D4|Homework due]]<br>[[20.109(S21):Mini-presentation| <font color =  #b3251c>'''Mini-presentation due'''</font color>]] XXX at 10 pm
+
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D4|Homework due]]<br>[[20.109(S21):Data Summary| <font color =  #b3251c>'''Data Summary revision due'''</font color>]] Sun, Apr 4 at 10 pm <br>
 
|--
 
|--
 
|  
 
|  
Line 117: Line 117:
 
|  
 
|  
 
| [[20.109(S21):Journal club presentation| <font color =  #b3251c>'''Journal club presentations'''</font color>]]
 
| [[20.109(S21):Journal club presentation| <font color =  #b3251c>'''Journal club presentations'''</font color>]]
| [ Blog post due] XXX at 10 pm
+
| [http://app.slack.com/client/T01KU1VLZQB/C01KQNPD3UM Blog post due] Sat, Apr 10 at 10 pm
 
|--
 
|--
 
| M2D5
 
| M2D5
 
| T/W Apr 13/14
 
| T/W Apr 13/14
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D5 |Placeholder ]]
+
| [[20.109(S21):M2D5 |Learn best practices for mammalian cell culture ]]
 
| [[20.109(S21):Homework#Due_M2D5|Homework due]]<br>
 
| [[20.109(S21):Homework#Due_M2D5|Homework due]]<br>
 
|--
 
|--
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| R/F Apr 15/16
 
| R/F Apr 15/16
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D6 |Placeholder ]] <br>
+
| [[20.109(S21):M2D6 |Utilize cellular thermal shift assay (CETSA) to test putative small molecule binders]] <br>
 
| [[20.109(S21):Homework#Due_M2D6|Homework due]]<br>
 
| [[20.109(S21):Homework#Due_M2D6|Homework due]]<br>
 
|--
 
|--
Line 140: Line 140:
 
| R/F Apr 22/23
 
| R/F Apr 22/23
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
 
| [http://be.mit.edu/directory/angela-koehler AK] <br>  
| [[20.109(S21):M2D7 |Placeholder ]] <br>
+
| [[20.109(S21):M2D7 |Complete CETSA experiment and analyze data]] <br>
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D7|Homework due]]<br>
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D7|Homework due]]<br>
 
|--
 
|--
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| M3D1
 
| M3D1
 
| T/W Apr 27/28
 
| T/W Apr 27/28
| [https://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
+
| [http://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
| [[20.109(S21):M3D1 |Placeholder ]] <br>
+
| [[20.109(S21):M3D1 |Review inverse pericam (IPC) cloning strategy ]] <br>
 
| [[20.109(S21):Homework#Due_M3D1|Homework due]] <br>
 
| [[20.109(S21):Homework#Due_M3D1|Homework due]] <br>
 
|--
 
|--
 
| M3D2
 
| M3D2
 
| R/F Apr 29/30
 
| R/F Apr 29/30
| [https://be.mit.edu/directory/alan-p-jasanoff AJ]<br>  
+
| [http://be.mit.edu/directory/alan-p-jasanoff AJ]<br>  
| [[20.109(S21):M3D2 |Placeholder ]] <br>
+
| [[20.109(S21):M3D2 |Examine IPC mutations ]] <br>
| [[20.109(S21):Homework#Due_M3D2|Homework due]] <br> | [[20.109(S21):Research article| <font color =  #b3251c>'''Research article due'''</font color>]]  XXX at 10 pm <br> [ Blog post due] XXX at 10 pm
+
| [[20.109(S21):Homework#Due_M3D2|Homework due]] <br> [[20.109(S21):Research article| <font color =  #b3251c>'''Research article due'''</font color>]]  Sun, May 2 at 10 pm <br> [http://app.slack.com/client/T01KU1VLZQB/C01KQNPD3UM Blog post due] Mon, May 3 at 10 pm
 
|--
 
|--
 
| M3D3
 
| M3D3
 
| T/W May 4/5
 
| T/W May 4/5
| [https://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
+
| [http://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
| [[20.109(S21):M3D3 |Placeholder ]] <br>
+
| [[20.109(S21):M3D3 |Prepare expression system and purify IPC variants ]] <br>
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M3D3|Homework due]]<br>
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M3D3|Homework due]]<br>
 
|--  
 
|--  
Line 171: Line 171:
 
| M3D4
 
| M3D4
 
| T/W May 11/12
 
| T/W May 11/12
| [https://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
+
| [http://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
| [[20.109(S21):M3D4 |Placeholder ]] <br>
+
| [[20.109(S21):M3D4 |Evaluate effect of mutations on IPC variants ]] <br>
 
| [[20.109(S21):Homework#Due_M3D4|Homework due]]
 
| [[20.109(S21):Homework#Due_M3D4|Homework due]]
 
|--
 
|--
 
| M3D5
 
| M3D5
 
| R/F May 13/14
 
| R/F May 13/14
| [https://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
+
| [http://be.mit.edu/directory/alan-p-jasanoff AJ] <br>  
| [[20.109(S21):M3D5 |Placeholder ]] <br>
+
| [[20.109(S21):M3D5 |Design new IPC variant ]] <br>
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color ><br> [[20.109(S21):Homework#Due_M3D5|Homework due]]
 
| <font color= #d1b217 >'''Laboratory quiz'''</font color ><br> [[20.109(S21):Homework#Due_M3D5|Homework due]]
 
|--
 
|--
Line 185: Line 185:
 
|  
 
|  
 
| [[20.109(S21):Research proposal presentation| <font color =  #b3251c>'''Research proposal presentations'''</font color>]]
 
| [[20.109(S21):Research proposal presentation| <font color =  #b3251c>'''Research proposal presentations'''</font color>]]
| [ Blog post due] XXX at 10 pm
+
| [http://app.slack.com/client/T01KU1VLZQB/C01KQNPD3UM Blog post due] Thu, May 20 at 10 pm
 
|--
 
|--
 
| colspan="6" |
 
| colspan="6" |
Line 191: Line 191:
 
|  
 
|  
 
| R May 20
 
| R May 20
|
+
| <font color =  #0d368e>'''Feedback session'''</font color> <br>
| <font color =  #0d368e>'''Feedback session'''</font color> <br>  
+
| [[20.109(S21):Mini-report | <font color =  #b3251c>'''Mini-report due'''</font color>]] XXX at 10 pm <br>
+
| [[20.109(S21):Mini-report | <font color =  #b3251c>'''Mini-report due'''</font color>]] Mon, May 24 at 10 pm <br>
 
|}
 
|}
 
</div>
 
</div>

Revision as of 21:59, 2 March 2021

20.109(S21): Laboratory Fundamentals of Biological Engineering

Sp21 banner image v2.png

Spring 2021 schedule        FYI        Assignments        Homework        Communication |        Accessibility

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


Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used in biological engineering. Though there is not enough time 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:

  • Tuesday (T) and Thursday (R) 11 - 12 pm (Zoom access; Meeting ID 948 1521 1031)

Laboratory section times:

MODULE DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Feb 16/17 NLL
Slides
Orientation and laboratory tour
T/R prelab
W/F prelab
M1D1 R/F Feb 18/19 LM
Slides
Generate scFv library
T/R prelab
W/F prelab
Orientation quiz
Homework due
M1D2 T/W Feb 23/24 LM
Slides
Enrich candidate clones from library using FACS
T/R prelab
W/F prelab
Homework due
M1D3 R/F Feb 25/26 LM
Slides
Harvest clone plasmids from library
T/R prelab
W/F prelab
Homework due
M1D4 T/W Mar 2/3 LM
Slides
Purify and sequence clone plasmids
T/R prelab
Laboratory quiz
Homework due
M1D5 R/F Mar 4/5 LM
Analyze clone sequences and choose clone to characterize
Homework due
T/W Mar 9/10 Student holiday
M1D6 R/F Mar 11/12 LM
Characterize clone ligand binding using flow cytometry
Homework due
M1D7 T/W Mar 16/17 LM
Analyze ligand titration curves
Laboratory quiz
Homework due
M2D1 R/F Mar 18/19 AK
Perform protein purification protocol
Homework due
T/W Mar 23/24 Student holiday Data Summary draft due Wed, Mar 24 at 10 pm
M2D2 R/F Mar 25/26 AK
Assess purity and concentration of purified protein
Homework due
Mini-presentation due Sun, Mar 28 at 10 pm
Blog post due Mon, Mar 29 at 10 pm
M2D3 T/W Mar 30/31 AK
Prepare and scan small molecule microarray (SMM) slides
Homework due
M2D4 R/F Apr 1/2 AK
Analyze SMM data to identify putative small molecule binders
Laboratory quiz
Homework due
Data Summary revision due Sun, Apr 4 at 10 pm
T/W Apr 6/7 Journal club presentations
R/F Apr 8/9 Journal club presentations Blog post due Sat, Apr 10 at 10 pm
M2D5 T/W Apr 13/14 AK
Learn best practices for mammalian cell culture Homework due
M2D6 R/F Apr 15/16 AK
Utilize cellular thermal shift assay (CETSA) to test putative small molecule binders
Homework due
T/W Apr 20/21 Student holiday
M2D7 R/F Apr 22/23 AK
Complete CETSA experiment and analyze data
Laboratory quiz
Homework due
M3D1 T/W Apr 27/28 AJ
Review inverse pericam (IPC) cloning strategy
Homework due
M3D2 R/F Apr 29/30 AJ
Examine IPC mutations
Homework due
Research article due Sun, May 2 at 10 pm
Blog post due Mon, May 3 at 10 pm
M3D3 T/W May 4/5 AJ
Prepare expression system and purify IPC variants
Laboratory quiz
Homework due
R/F May 6/7 Research proposal pitches
Develop Research proposal ideas and presentations
M3D4 T/W May 11/12 AJ
Evaluate effect of mutations on IPC variants
Homework due
M3D5 R/F May 13/14 AJ
Design new IPC variant
Laboratory quiz
Homework due
T/W May 18/19 Research proposal presentations Blog post due Thu, May 20 at 10 pm
R May 20 Feedback session
Mini-report due Mon, May 24 at 10 pm