Difference between revisions of "20.109(F20): Fall 2020 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.
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<font color=#0d368e>'''SCHEDULE DETAILS:'''</font color><br>
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<font color=#0d368e>'''Lecture times:'''</font color>  T/R 11 - 12 pm  <br>
 +
<font color=#0d368e>'''Laboratory section times:'''</font color>  T/R 1 - 5 pm or W/F 1 - 5 pm <br>
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 +
{| border=1px
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|'''MODULE'''
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|'''DAY'''
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|'''DATE'''
 +
|'''LECTURER'''
 +
|'''LABORATORY EXPERIMENTS'''
 +
|'''ASSIGNMENTS'''
 +
|--
 +
|
 +
|
 +
| R/F Sept 5/6 
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br> [[Media:Fa19 Orientation lecture STUDENTS.pdf| Orientation slides]]
 +
| [[20.109(F19):Lab tour | Orientation and laboratory tour]]<br>[[Media: Fa19_MOD0_LMMmarked.pdf| Prelab T/R]]<br>[[Media:Fa19 MOD0 nll marked.pdf| Prelab W/F]]
 +
|
 +
|--
 +
| colspan="7" |
 +
|--
 +
| 1
 +
| 1
 +
| T/W Sept 10/11
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Practice cell culture and begin sub-nuclear foci assay (Day1)| Learn optimal methods for culturing mammalian cells and initiate repair foci analysis experiment]]<br>[[Media:M1D1_Fa19_LMmarked.pdf| Prelab T/R]]<br>[[Media:Fa19 M1D1 bcm.pdf| Prelab W/F]]
 +
| <font color=#298A08>'''Laboratory orientation quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D1|Homework due]]
 +
|--
 +
| 1
 +
| 2
 +
| R/F Sept 12/13 
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Treat cells for gamma-H2AX (Day2)| Perform cell exposures for repair foci experiment and perform high-throughput genome damage pilot]]<br>[[Media:M1D2_Fa19_LMMmarked.pdf| Prelab T/R]]<br> [[Media:M1D2 Fa19 bcm marked.pdf| Prelab W/F]]
 +
| [[20.109(F19):Homework#Due_M1D2|Homework due]]
 +
|--
 +
| 1
 +
| 3
 +
| T/W Sept 17/18 
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Complete gamma-H2AX assay and prepare CometChip (Day3)| Perform immunofluorescence assay for repair foci and optimize high-throughput genome damage assay]]<br>[[Media:M1D3_Fa19_LMmarked.pdf| Prelab T/R]] <br> [[Media:M1D3 Fa19 bcm marked.pdf| Prelab W/F]]
 +
| [[20.109(F19):Homework#Due_M1D3|Homework due]]
 +
|--
 +
|
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|
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| R/F Sept 19/20
 +
| Comm Lab
 +
| <font color =  #0101DF>'''Lecture, but no laboratory'''</font color><br><font color = 999999>Career fair student holiday</font color><br>
 +
|
 +
|--
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| 1
 +
| 4
 +
| T/W Sept 24/25
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Load cells into CometChip and apply treatments (Day4)| Perform immunofluorescence imaging for repair foci and expose cells for high-throughput genome damage assay]]<br>[[Media:M1D4_Fa19_LMmarked.pdf| Prelab T/R]] <br> [[Media:M1D4 Fa19 bcm marked.pdf|Prelab W/F]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D4|Homework due]]
 +
|--
 +
| 1
 +
| 5
 +
| R/F Sept 26/27
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Complete CometChip experiment (Day5)| Quantify repair foci via network algorithm and complete high-throughput genome damage assay]]<br>[[Media:Fa19 M1D5 Dushan ver2.pdf|Dushan's Talk]]<br>[[Media:M1D5_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D5 Fa19 bcm.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M1D5|Homework due]]
 +
|--
 +
| 1
 +
| 6
 +
| T/W Oct 1/2
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Image CometChip (Day6)| Perform quantitative image analysis for the high-throughput genome damage assay]]<br>[[Media:M1D6_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D6 Fa19 bcm marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M1D6|Homework due]]
 +
|--
 +
| 1
 +
| 7
 +
| R/F Oct 3/4
 +
| [http://be.mit.edu/directory/bevin-p-engelward BE]
 +
| [[20.109(F19):Practice statistical analysis methods and complete data analysis (Day7)| Complete data analysis and apply statistical methods]]<br>[[Media:M1D7_Fa19_LMmarked.pdf|TR Prelab]] <br> [[Media:M1D7 Fa19 bcm.pdf | WF Prelab]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M1D7|Homework due]]
 +
|--
 +
| 2
 +
| 1
 +
| T/W Oct 8/9
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D1 lecture slides v2.pdf| Lecture slides]]
 +
| [[20.109(F19):Complete in silico cloning of pdCas9 (Day1)| Complete in silico cloning of pdCas9]]<br>[[Media:M2D1_Fa19_LMmarked.pdf|TR Prelab]]<br> [[Media:M2D1 Fa19 bcm marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M2D1| Homework due]]<br>
 +
|--
 +
| 2
 +
| 2
 +
| R/F Oct 10/11
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D2 lecture slides v2.pdf|Lecture slides]]
 +
| [[20.109(F19):Design gRNA sequence for CRISPRi (Day2)| Design gRNA sequence for CRISPRi]]<br>[[Media:M2D2_Fa18_SPmarked.pdf|TR Prelab]]<br>[[Media:Fa19 M2D2 CYK marked.pdf|WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M2D2|Homework due]]
 +
|--
 +
|
 +
|
 +
| <font color = 999999>T/W Oct 15/16</font color>
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|
 +
| <font color = 999999>Columbus day holiday</font color>
 +
| [[20.109(F19): Data Summary| Data Summary draft due]] Mon, Oct 14 at 10 pm<br>[https://be20109f19.blogspot.com/ Blog post due] Fri, Oct 18 at 10 pm
 +
|--
 +
| colspan="7" |
 +
|--
 +
| 2
 +
| 3
 +
| R/F Oct 17/18
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa18 M2D3 figures.pptx| Article Figures]]<br>[[Media:Fa19 M2D3 paper discussion slides.pdf| Lecture slides]]
 +
| [[20.109(F19):Generate gRNA plasmid (Day3)| Generate gRNA plasmid]]<br> [[Media:M2D3_Fa18_LM_SP_edit.pdf | TR Prelab]]<br> [[Media:Fa19 M2D3 bcm marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M2D3|Homework due]]<br>[[20.109(F19): Mini-presentation| Mini-presentation due]] Sat, Oct 19 at 10 pm
 +
|--
 +
| 2
 +
| 4
 +
| T/W Oct 22/23
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D4 lecture slides.pdf|Lecture slides]]
 +
| [[20.109(F19):Journal club presentation (Day4 and 6)| Journal club I]]
 +
|
 +
|--
 +
| 2
 +
| 5
 +
| R/F Oct 24/25
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D5 lecture slides v2.pdf| Lecture slides]]
 +
| [[20.109(F19):Confirm gRNA sequence in pgRNA (Day5)| Confirm gRNA sequence in pgRNA]]<br> [[Media: M2D5_Fa19_LMmarked.pdf | TR Prelab]]<br> [[Media:Fa19 M2D5 cyk marked.pdf | WF Prelab]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D5|Homework due]]<br>[[20.109(F19): Data Summary| Data Summary revision due]] Sat, Oct 26 at 10 pm
 +
|--
 +
| 2
 +
| 6
 +
| T/W Oct 29/30
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D6 lecture slides.pdf|Lecture slides]]
 +
| [[20.109(F19):Journal club presentation (Day4 and 6) | Journal club II]]
 +
|
 +
|--
 +
| 2
 +
| 7
 +
| R/F Oct/Nov 31/1
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>[[Media:Fa19 M2D7 lecture slides.pdf| Lecture slides]]
 +
| [[20.109(F19):Induce CRISPRi system (Day7)| Induce CRISPRi system]]<br> [[Media: M2D7_Fa19_LM.pdf | TR Prelab]] <br> [[Media:Fa18 M2D7 bcm marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M2D7|Homework due]]<br>[https://be20109f19.blogspot.com/ Blog post due] Fri, Nov 1 at 10 pm
 +
|--
 +
| 2
 +
| 8
 +
| T/W Nov 5/6
 +
| [http://be.mit.edu/directory/noreen-lyell NLL]<br>
 +
| [[20.109(F19):Measure_fermentation_products_(Day8) | Measure fermentation products]]<br> [[Media: M2D8_Fa19_LMmarked.pdf | TR Prelab]] <br> [[Media:Fa19 M2D8 bcm marked.pdf | WF Prelab]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M2D8|Homework due]]
 +
|--
 +
| colspan="7" |
 +
|--
 +
| 3
 +
| 1
 +
| R/F Nov 7/8
 +
| [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L1 2019.pptx|Lecture slides]]
 +
| [[20.109(F19):Prepare for cellular thermal shift assay (Day1)| Prepare for cellular thermal shift assay]]<br> [[Media:Fa19 M3D1 prelab slides nllmarked.pdf| TR Prelab]] <br> [[Media:Fa19 M3D1 bcm marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M3D1|Homework due]] <br>
 +
|--
 +
|
 +
|
 +
| <font color = 999999>T/W Nov 12/13</font color>
 +
|
 +
| <font color = 999999>Veterans' day holiday</font color>
 +
| [[20.109(F19): Research article| Research article due]]  Mon, Nov 11 at 10 pm <br>[https://be20109f19.blogspot.com/ Blog post due] Tue, Nov 12 at 10 pm
 +
|--
 +
| 3
 +
| 2
 +
| R/F Nov 14/15
 +
| [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L2 2019.pptx|Lecture slides]]
 +
| [[20.109(F19):Incubate with ligand and apply heat treatment for protein denaturation (Day2)| Incubate with ligand and apply heat treatment for protein denaturation]]<br>[[Media:Fa19 M3D2 prelab slides nllmarked.pdf|TR Prelab]] <br> [[Media:191115 prelab CYK marked.pdf | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M3D2|Homework due]]<br>
 +
|--
 +
| 3
 +
| 3
 +
| T/W Nov 19/20
 +
| [https://be.mit.edu/directory/angela-koehler AK]<br> [[Media:20109 Struntz Lecture 2019.pdf| Lecture slides]]
 +
| [[20.109(F19):Begin Western blot analysis (Day3)| Begin Western blot analysis]]<br>[[Media:Fa19 M3D3 prelab slides nllmarked.pdf|TR Prelab]] <br> [[Media:Fa19 M3D3 bcm.pdf | WF Prelab]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D3| Homework due]]
 +
|--
 +
| 3
 +
| 4
 +
| R/F Nov 21/22
 +
| [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L4 2019.pdf| Lecture slides]]
 +
| [[20.109(F19):Complete antibody staining for Western blot analysis (Day4)| Complete antibody staining for Western blot analysis]]<br> [[Media:M3D4 Fa19 bcm marked.pdf | TR Prelab]] <br> [[Media:M3D4WF Fa19 bcm marked.pdf  | WF Prelab]]
 +
| [[20.109(F19):Homework#Due_M3D4|Homework due]]
 +
|--
 +
|
 +
|
 +
| T/W Nov 26/27
 +
|
 +
| <font color =  #0101DF>'''Lecture: research proposal pitch, but no laboratory'''</font color>
 +
|
 +
|--
 +
|
 +
|
 +
| <font color = 999999>R/F Nov 28/29</font color>
 +
|
 +
| <font color = 999999>Thanksgiving holiday</font color>
 +
|
 +
|--
 +
| 3
 +
| 5
 +
| T/W Dec 3/4 
 +
| [https://be.mit.edu/directory/angela-koehler AK]<br>[[Media:20109 M3L5 2019.pdf| Lecture slides]]
 +
| [[20.109(F19):Data analysis and assignment preparation (Day5)| Data analysis and assignment preparation]]<br>[[Media:Fa19 M3D5 prelab slides nllmarked.pdf| TR Prelab]] <br> [[Media:Fa19 M3D5 bcm marked.pdf | WF Prelab]]
 +
| <font color=#298A08>'''Laboratory quiz'''</font color><br>[[20.109(F19):Homework#Due_M3D5|Homework due]]
 +
|--
 +
|
 +
|
 +
| R/F Dec 5/6
 +
|
 +
| [[20.109(F19):Research proposal presentation| Research proposal presentations]]
 +
| [https://be20109f19.blogspot.com/ Blog post due] Fri, Dec 6 at 10 pm
 +
|--
 +
| colspan="7" |
 +
|--
 +
|
 +
|
 +
| T Dec 10
 +
|
 +
| <font color =  #0101DF>'''Feedback and celebratory lunch'''</font color>
 +
| [[20.109(F19): Mini-report | Mini-report due]] Mon, Dec 9 at 10 pm <br>
 +
|}
 +
</div>

Revision as of 15:58, 10 July 2020

20.109(F20): Laboratory Fundamentals of Biological Engineering

Fa20 banner image v2.png

Fall 2020 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Metabolic 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 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
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm

MODULE DAY DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
R/F Sept 5/6 NLL
Orientation slides 		Orientation and laboratory tour
Prelab T/R
Prelab W/F
1 1 T/W Sept 10/11 BE Learn optimal methods for culturing mammalian cells and initiate repair foci analysis experiment
Prelab T/R
Prelab W/F 		Laboratory orientation quiz
Homework due
1 2 R/F Sept 12/13 BE Perform cell exposures for repair foci experiment and perform high-throughput genome damage pilot
Prelab T/R
Prelab W/F 		Homework due
1 3 T/W Sept 17/18 BE Perform immunofluorescence assay for repair foci and optimize high-throughput genome damage assay
Prelab T/R
Prelab W/F 		Homework due
R/F Sept 19/20 Comm Lab Lecture, but no laboratory
Career fair student holiday
1 4 T/W Sept 24/25 BE Perform immunofluorescence imaging for repair foci and expose cells for high-throughput genome damage assay
Prelab T/R
Prelab W/F 		Laboratory quiz
Homework due
1 5 R/F Sept 26/27 BE Quantify repair foci via network algorithm and complete high-throughput genome damage assay
Dushan's Talk
TR Prelab
WF Prelab 		Homework due
1 6 T/W Oct 1/2 BE Perform quantitative image analysis for the high-throughput genome damage assay
TR Prelab
WF Prelab 		Homework due
1 7 R/F Oct 3/4 BE Complete data analysis and apply statistical methods
TR Prelab
WF Prelab 		Laboratory quiz
Homework due
2 1 T/W Oct 8/9 NLL
Lecture slides 		Complete in silico cloning of pdCas9
TR Prelab
WF Prelab 		Homework due
2 2 R/F Oct 10/11 NLL
Lecture slides 		Design gRNA sequence for CRISPRi
TR Prelab
WF Prelab 		Homework due
T/W Oct 15/16 Columbus day holiday Data Summary draft due Mon, Oct 14 at 10 pm
Blog post due Fri, Oct 18 at 10 pm
2 3 R/F Oct 17/18 NLL
Article Figures
Lecture slides 		Generate gRNA plasmid
TR Prelab
WF Prelab 		Homework due
Mini-presentation due Sat, Oct 19 at 10 pm
2 4 T/W Oct 22/23 NLL
Lecture slides 		Journal club I
2 5 R/F Oct 24/25 NLL
Lecture slides 		Confirm gRNA sequence in pgRNA
TR Prelab
WF Prelab 		Laboratory quiz
Homework due
Data Summary revision due Sat, Oct 26 at 10 pm
2 6 T/W Oct 29/30 NLL
Lecture slides 		Journal club II
2 7 R/F Oct/Nov 31/1 NLL
Lecture slides 		Induce CRISPRi system
TR Prelab
WF Prelab 		Homework due
Blog post due Fri, Nov 1 at 10 pm
2 8 T/W Nov 5/6 NLL
 Measure fermentation products
TR Prelab
WF Prelab 		Laboratory quiz
Homework due
3 1 R/F Nov 7/8 AK
Lecture slides 		Prepare for cellular thermal shift assay
TR Prelab
WF Prelab 		Homework due
T/W Nov 12/13 Veterans' day holiday Research article due Mon, Nov 11 at 10 pm
Blog post due Tue, Nov 12 at 10 pm
3 2 R/F Nov 14/15 AK
Lecture slides 		Incubate with ligand and apply heat treatment for protein denaturation
TR Prelab
WF Prelab 		Homework due
3 3 T/W Nov 19/20 AK
Lecture slides 		Begin Western blot analysis
TR Prelab
WF Prelab 		Laboratory quiz
Homework due
3 4 R/F Nov 21/22 AK
Lecture slides 		Complete antibody staining for Western blot analysis
TR Prelab
WF Prelab 		Homework due
T/W Nov 26/27 Lecture: research proposal pitch, but no laboratory
R/F Nov 28/29 Thanksgiving holiday
3 5 T/W Dec 3/4 AK
Lecture slides 		Data analysis and assignment preparation
TR Prelab
WF Prelab 		Laboratory quiz
Homework due
R/F Dec 5/6 Research proposal presentations Blog post due Fri, Dec 6 at 10 pm
T Dec 10 Feedback and celebratory lunch Mini-report due Mon, Dec 9 at 10 pm
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