Difference between revisions of "20.109(S22):Spring 2022 schedule"

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<font color=  #91b391 >'''SCHEDULE DETAILS:'''</font color><br>
 
<font color=  #91b391 >'''SCHEDULE DETAILS:'''</font color><br>
<font color=  #a6d5a5 >'''Lecture times:'''</font color>  <br>
+
<font color=  #91b391 >'''Lecture times:'''</font color>  <br>
 
*Tuesday (T) and Thursday (R) 11 - 12 pm ([https://mit.zoom.us/j/94815211031 Zoom access]; Meeting ID 948 1521 1031) <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=  #a6d5a5 >'''Laboratory section times:'''</font color>  <br>
+
<font color=  #91b391 >'''Laboratory section times:'''</font color>  <br>
 
*Tuesday (T) and Thursday (R) 1 - 4 pm ([https://mit.zoom.us/j/94585650880 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 - 4 pm ([https://mit.zoom.us/j/92289710115 Zoom access]) <br>
 
*Wednesday (W) and Friday (F) 1 - 4 pm ([https://mit.zoom.us/j/92289710115 Zoom access]) <br>
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| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_1.pdf|Slides]]  
 
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_1.pdf|Slides]]  
 
| [[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]
 
| [[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= #a6d5a5 >'''Orientation quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D1|Homework due]]
+
| <font color= #91b391 >'''Orientation quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D1|Homework due]]
 
|--
 
|--
 
| M1D2
 
| M1D2
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| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_4.pdf|Slides]]  
 
| [http://be.mit.edu/directory/leslie-mcclain LM] <br> [[Media:Sp21_Mod1_lecture_4.pdf|Slides]]  
 
| [[20.109(S21):M1D4 |Purify and sequence clone plasmids]] <br> [[Media:Sp21 M1D4 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| [[20.109(S21):M1D4 |Purify and sequence clone plasmids]] <br> [[Media:Sp21 M1D4 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
| <font color= #a6d5a5 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D4|Homework due]]
+
| <font color= #91b391 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D4|Homework due]]
 
|--
 
|--
 
| M1D5
 
| M1D5
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| [https://kdw-lab.mit.edu/members/sarah-cowles-research-interests/ Guest, SC] <br> [[Media:210316GuestLecture_SCCslides.pdf|Slides]]
 
| [https://kdw-lab.mit.edu/members/sarah-cowles-research-interests/ Guest, SC] <br> [[Media:210316GuestLecture_SCCslides.pdf|Slides]]
 
| [[20.109(S21):M1D7 |Analyze ligand titration curves]] <br> [[Media:Sp21 M1D7 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| [[20.109(S21):M1D7 |Analyze ligand titration curves]] <br> [[Media:Sp21 M1D7 bcm marked.pdf | T/R prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
| <font color= #a6d5a5 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D7|Homework due]]
+
| <font color= #91b391 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M1D7|Homework due]]
 
|--
 
|--
 
| colspan="6" |
 
| colspan="6" |
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| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M2L4 2021.pdf|Slides]]
 
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M2L4 2021.pdf|Slides]]
 
| [[20.109(S21):M2D4 |Analyze SMM data to identify putative small molecule binders]] <br> [[Media:Sp21 M2D4 bcm marked.pdf | T/R Prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
 
| [[20.109(S21):M2D4 |Analyze SMM data to identify putative small molecule binders]] <br> [[Media:Sp21 M2D4 bcm marked.pdf | T/R Prelab]] <br> [https://www.dropbox.com/sh/khcxnq9fyo68gvt/AACYdN42VVwvZ4WLUyp743_Na?dl=0 W/F prelab]
| <font color= #a6d5a5 >'''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>
+
| <font color= #91b391 >'''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>
 
|--
 
|--
 
|  
 
|  
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| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M2L7 2021.pdf|Slides]]
 
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M2L7 2021.pdf|Slides]]
 
| [[20.109(S21):M2D7 |Complete CETSA experiment and analyze data]] <br> [[Media:Sp21 M2D7 bcm marked.pdf| T/R Prelab]]<br> [[Media:Sp21_M2D7_lmm.pdf | W/F Prelab]]
 
| [[20.109(S21):M2D7 |Complete CETSA experiment and analyze data]] <br> [[Media:Sp21 M2D7 bcm marked.pdf| T/R Prelab]]<br> [[Media:Sp21_M2D7_lmm.pdf | W/F Prelab]]
| <font color= #a6d5a5 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D7|Homework due]]<br>
+
| <font color= #91b391 >'''Laboratory quiz'''</font color> <br> [[20.109(S21):Homework#Due_M2D7|Homework due]]<br>
 
|--
 
|--
 
| colspan="6" |
 
| colspan="6" |

Revision as of 16:04, 5 January 2022

20.109(S22): Laboratory Fundamentals of Biological Engineering

Sp17 20.109 M1D7 chemical structure features.png

Spring 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Metabolic engineering        M3: Project design       


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
W/F prelab
Laboratory quiz
Homework due
M1D5 R/F Mar 4/5 LM
Slides
Analyze clone sequences and choose clone to characterize
T/R prelab
W/F prelab
Homework due
T/W Mar 9/10 Student holiday
M1D6 R/F Mar 11/12 LM
Slides
Characterize clone ligand binding using flow cytometry
T/R prelab
W/F prelab
Homework due
M1D7 T/W Mar 16/17 Guest, SC
Slides
Analyze ligand titration curves
T/R prelab
W/F prelab
Laboratory quiz
Homework due
M2D1 R/F Mar 18/19 AK
Slides
Perform protein purification protocol
T/R prelab
W/F prelab
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
Slides
Assess purity and concentration of purified protein
T/R Prelab
W/F prelab
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
Slides
Prepare and scan small molecule microarray (SMM) slides
T/R Prelab
W/F prelab
Homework due
M2D4 R/F Apr 1/2 AK
Slides
Analyze SMM data to identify putative small molecule binders
T/R Prelab
W/F prelab
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
Slides
AI articles linked: here and here
Learn best practices for mammalian cell culture
T/R Prelab
W/F Prelab
Homework due
M2D6 R/F Apr 15/16 AK
Slides
Utilize cellular thermal shift assay (CETSA) to test putative small molecule binders
T/R Prelab
W/F Prelab
Homework due
T/W Apr 20/21 Student holiday
M2D7 R/F Apr 22/23 AK
Slides
Complete CETSA experiment and analyze data
T/R Prelab
W/F Prelab
Laboratory quiz
Homework due
M3D1 T/W Apr 27/28 AJ
Slides
Review IPC literature and examine structural characteristics
T/R Prelab
W/F Prelab
Homework due
M3D2 R/F Apr 29/30 AJ
Slides
Identify IPC mutations
T/R prelab
W/F prelab
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
Slides
Evaluate effect of mutations on IPC variants
T/R prelab
W/F prelab
Homework due
R/F May 6/7 Research proposal pitches
Develop Research proposal ideas and presentations
Prompts for discussion/homework
M3D4 T/W May 11/12 AJ
Slides
Design new IPC variant
T/R prelab
W/F prelab
Laboratory quiz
Homework due
R/F May 13/14 AJ
Slides
Mini-report due by 10 pm
T/W May 18/19 Research proposal presentations Blog post due Thu, May 20 at 10 pm
R May 20 Feedback session

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