http://measurebiology.org/w/api.php?action=feedcontributions&user=Noreen+Lyell&feedformat=atomCourse Wiki - User contributions [en]2024-03-28T10:14:50ZUser contributionsMediaWiki 1.22.3http://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-19T15:14:57Z<p>Noreen Lyell: </p>
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<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
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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 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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> [[Media:Sp24 M2L1.pdf| Lecture slides]] <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> [[Media:Sp24 M2D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M2D1 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:20170602-GeorgeSun for 20.109 sp 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> [[Media:Sp24 M2D2 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M2D2 nll.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:Sp24 L2 AMB.pdf | Lecture slides]]<br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> [[Media:Sp24 M2D3 nll.pdf|TR prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-19T15:14:30Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> [[Media:Sp24 M2L1.pdf| Lecture slides]] <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> [[Media:Sp24 M2D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M2D1 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:20170602-GeorgeSun for 20.109 sp 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> [[Media:Sp24 M2D2 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M2D2 nll.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:Sp24 L2 AMB.pdf | Lecture slides]]<br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> [[Media:Sp24 M2D3 nll.pdf|TR prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M2D3_nll.pdfFile:Sp24 M2D3 nll.pdf2024-03-19T15:13:46Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-14T15:11:36Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> [[Media:Sp24 M2L1.pdf| Lecture slides]] <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> [[Media:Sp24 M2D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M2D1 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:20170602-GeorgeSun for 20.109 sp 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> [[Media:Sp24 M2D2 nll.pdf|TR prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M2D2_nll.pdfFile:Sp24 M2D2 nll.pdf2024-03-14T15:11:03Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-14T15:09:26Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> [[Media:Sp24 M2L1.pdf| Lecture slides]] <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> [[Media:Sp24 M2D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M2D1 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> [[Media:20170602-GeorgeSun for 20.109 sp 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:20170602-GeorgeSun_for_20.109_sp_2024.pdfFile:20170602-GeorgeSun for 20.109 sp 2024.pdf2024-03-14T15:08:56Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Class_data20.109(S24):Class data2024-03-12T17:44:53Z<p>Noreen Lyell: /* Module 1: Drug discovery */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
<br />
==Module 1: Drug discovery==<br />
<br />
Please find uploaded data for Mod 1 in the Dropbox folder linked [https://www.dropbox.com/scl/fo/gahf236k8x4azmy577ntw/h?rlkey=1s0gplfcjsdh54fmvkl1hpbc0&dl=0 here].<br />
<br />
<br />
Please find the SMM screen results [[Media:Screen results.csv | here]].<br />
<br />
<br />
Please find the EMSA results [https://www.dropbox.com/scl/fo/zd7u15wwjmscxzrnt9hkp/h?rlkey=5k8nwwpg80apvurbk5y1746eh&dl=0 here].<br />
<br />
<br />
'''DSF results:'''<br />
<br />
<center><br />
{| border="1"<br />
|-<br />
| <br />
| Replicate #1<br />
| Replicate #2<br />
| Replicate #3<br />
| Average T<sub>m</sub><br />
|-<br />
| '''TR Orange'''<br />
|-<br />
| DMSO<br />
| 45.57<br />
| 45.57<br />
| 47.10<br />
| 46.08<br />
|-<br />
| Small molecule #1<br />
| 45.57<br />
| 35.38<br />
| 45.57<br />
| 42.17<br />
|-<br />
| Small molecule #6<br />
| 44.55<br />
| 46.08<br />
| 45.06<br />
| 45.23<br />
|-<br />
| Small molecule #9<br />
| 45.06<br />
| 46.59<br />
| 46.08<br />
| 45.91<br />
|-<br />
| Small molecule #10<br />
| 43.53<br />
| 45.06<br />
| 45.57<br />
| 44.72<br />
|-<br />
| '''TR Yellow'''<br />
|-<br />
| DMSO<br />
| 48.12<br />
| 47.61<br />
| 49.13<br />
| 48.29<br />
|-<br />
| Small molecule #2<br />
| 48.62<br />
| 46.59<br />
| 44.55<br />
| 46.59<br />
|-<br />
| Small molecule #10<br />
| 47.61<br />
| 47.61<br />
| 47.61<br />
| 47.61<br />
|-<br />
| Small molecule #11<br />
| 44.55<br />
| 45.57<br />
| 44.55<br />
| 44.89<br />
|-<br />
| Small molecule #13<br />
| 47.10<br />
| 47.10<br />
| 49.13<br />
| 47.78<br />
|-<br />
| '''TR Green'''<br />
|-<br />
| DMSO<br />
| 43.02<br />
| 45.06<br />
| 45.06<br />
| 44.37<br />
|-<br />
| Small molecule #2<br />
| 43.02<br />
| 47.10<br />
| 45.57<br />
| 45.23<br />
|-<br />
| Small molecule #6<br />
| 46.08<br />
| 49.65<br />
| 46.08<br />
| 47.27<br />
|-<br />
| Small molecule #9<br />
| 44.04<br />
| 45.06<br />
| 46.59<br />
| 45.23<br />
|-<br />
| Small molecule #10<br />
| 46.08<br />
| 45.57<br />
| 48.62<br />
| 46.76<br />
|-<br />
| '''TR Blue'''<br />
|-<br />
| DMSO<br />
| 47.11<br />
| 45.08<br />
| 44.06<br />
| 45.42<br />
|-<br />
| Small molecule #1<br />
| 48.64<br />
| 48.64<br />
| 44.06<br />
| 47.11<br />
|-<br />
| Small molecule #2<br />
| 46.60<br />
| 47.11<br />
| 43.56<br />
| 45.76<br />
|-<br />
| Small molecule #4<br />
| 46.60<br />
| 44.57<br />
| 43.56<br />
| 44.91<br />
|-<br />
| Small molecule #10<br />
| 47.62<br />
| 44.57<br />
| 44.06<br />
| 45.42<br />
|-<br />
| '''TR Pink'''<br />
|-<br />
| DMSO<br />
| 47.11<br />
| 44.57<br />
| 44.57<br />
| 45.42<br />
|-<br />
| Small molecule #1<br />
| 46.10<br />
| 46.60<br />
| 45.08<br />
| 45.93<br />
|-<br />
| Small molecule #2<br />
| 45.59<br />
| 46.10<br />
| 47.62<br />
| 46.43<br />
|-<br />
| Small molecule #10<br />
| 47.11<br />
| 44.06<br />
| 45.57<br />
| 45.25<br />
|-<br />
| Small molecule #11<br />
| 45.08<br />
| 44.06<br />
| 44.06<br />
| 44.40<br />
|-<br />
|}<br />
</center><br />
<br />
<br />
<center><br />
{| border="1"<br />
|-<br />
| <br />
| Replicate #1<br />
| Replicate #2<br />
| Replicate #3<br />
| Average T<sub>m</sub><br />
|-<br />
| '''WF Red'''<br />
|-<br />
| DMSO<br />
| 47.05<br />
| 44.51<br />
| 35.86<br />
| 42.47<br />
|-<br />
| Small molecule #3<br />
| 45.53<br />
| 46.55<br />
| 46.04<br />
| 46.04<br />
|-<br />
| Small molecule #4<br />
| 46.55<br />
| 47.05<br />
| 45.53<br />
| 46.38<br />
|-<br />
| Small molecule #5<br />
| 43.49<br />
| 47.06<br />
| 46.55<br />
| 45.70<br />
|-<br />
| Small molecule #8<br />
| 45.02<br />
| 46.55<br />
| 45.53<br />
| 45.70<br />
|-<br />
| '''WF Orange'''<br />
|-<br />
| DMSO<br />
| 44.02<br />
| 45.55<br />
| 46.05<br />
| 45.21<br />
|-<br />
| Small molecule #1<br />
| 43.09<br />
| 46.56<br />
| 46.56<br />
| 45.40<br />
|-<br />
| Small molecule #2<br />
| 44.53<br />
| 45.04<br />
| 44.53<br />
| 44.77<br />
|-<br />
| Small molecule #10<br />
| 45.04<br />
| 46.56<br />
| 45.04<br />
| 45.55<br />
|-<br />
| Small molecule #13<br />
| 46.05<br />
| 44.53<br />
| 44.53<br />
| 45.04<br />
|-<br />
| '''WF Yellow'''<br />
|-<br />
| DMSO<br />
| 43.50<br />
| 46.04<br />
| 45.53<br />
| 45.02<br />
|-<br />
| Small molecule #2<br />
| 44.52<br />
| 46.04<br />
| 45.53<br />
| 45.36<br />
|-<br />
| Small molecule #10<br />
| 44.52<br />
| 46.04<br />
| 48.59<br />
| 46.38<br />
|-<br />
| Small molecule #11<br />
| 46.04<br />
| 45.02<br />
| 47.57<br />
| 46.21<br />
|-<br />
| Small molecule #13<br />
| 44.01<br />
| 43.50<br />
| 45.02<br />
| 44.18<br />
|-<br />
| '''WF Green'''<br />
|-<br />
| DMSO<br />
| 45.04<br />
| 43.51<br />
| 43.00<br />
| 43.85<br />
|-<br />
| Small molecule #2<br />
| 46.05<br />
| 46.05<br />
| 46.56<br />
| 46.22<br />
|-<br />
| Small molecule #9<br />
| 46.05<br />
| 45.04<br />
| 46.05<br />
| 45.71<br />
|-<br />
| Small molecule #10<br />
| 45.04<br />
| 45.04<br />
| 45.04<br />
| 45.04<br />
|-<br />
| Small molecule #13<br />
| 44.53<br />
| 47.07<br />
| 44.54<br />
| 45.38<br />
|-<br />
| '''WF Blue'''<br />
|-<br />
| DMSO<br />
| 46.04<br />
| 44.52<br />
| 43.50<br />
| 44.685<br />
|-<br />
| Small molecule #5<br />
| 45.02<br />
| 43.50<br />
| 45.02<br />
| 45.70<br />
|-<br />
| Small molecule #9<br />
| 47.06<br />
| 47.06<br />
| 45.02<br />
| 46.38<br />
|-<br />
| Small molecule #10<br />
| 48.08<br />
| 45.02<br />
| 44.01<br />
| 45.70<br />
|-<br />
| Small molecule #13<br />
| 45.53<br />
| 43.50<br />
| 44.01<br />
| 44.35<br />
|-<br />
| '''WF Pink'''<br />
|-<br />
| DMSO<br />
| 44.01819<br />
| 46.46263<br />
| 45.54488<br />
| 45.3419<br />
|-<br />
| Small molecule #5<br />
| 46.05378<br />
| 45.03598<br />
| 47.58047<br />
| 46.22341<br />
|-<br />
| Small molecule #9<br />
| 45.03598<br />
| 46.56268<br />
| 45.54488<br />
| 45.71451<br />
|-<br />
| Small molecule #10<br />
| 44.01819<br />
| 46.56268<br />
| 44.52709<br />
| 45.0360<br />
|-<br />
| Small molecule #13<br />
| 44.01819<br />
| 44.52709<br />
| 46.05378<br />
| 44.86635<br />
|-<br />
| '''WF Purple'''<br />
|-<br />
| DMSO<br />
| 47.05<br />
| 43.50<br />
| 42.99<br />
| 44.51<br />
|-<br />
| Small molecule #5<br />
| 45.53<br />
| 47.06<br />
| 45.53<br />
| 46.04<br />
|-<br />
| Small molecule #9<br />
| 42.98<br />
| 46.04<br />
| 48.59<br />
| 45.87<br />
|-<br />
| Small molecule #10<br />
| 44.51<br />
| 45.02<br />
| 46.55<br />
| 45.36<br />
|-<br />
| Small molecule #13<br />
| 46.04<br />
| 43.50<br />
| 46.04<br />
| 45.19<br />
|-<br />
|-<br />
|}<br />
</center><br />
<br />
<br />
<center><br />
{| border="1"<br />
|-<br />
| <br />
| Replicate #1<br />
| Replicate #2<br />
| Replicate #3<br />
| Average T<sub>m</sub><br />
|-<br />
| '''WF Teal'''<br />
|-<br />
| DMSO<br />
| 45.54<br />
| 45.54<br />
|43.00<br />
| 44.69<br />
|-<br />
| Small molecule #1<br />
| 47.07<br />
| 46.05<br />
| 44.53<br />
| 45.88<br />
|-<br />
| Small molecule #2<br />
| 44.53<br />
| 45.04<br />
| 45.54<br />
| 45.04<br />
|-<br />
| Small molecule #10<br />
| 46.56<br />
| 46.56<br />
| 47.07<br />
| 46.73<br />
|-<br />
| Small molecule #11<br />
| 47.07<br />
| 46.56<br />
| 44.53<br />
| 46.05<br />
|-<br />
|}<br />
</center><br />
<br />
==Module 2: Protein engineering==<br />
<br />
Please find uploaded data for Mod 2 in the Dropbox folder linked [[https://www.dropbox.com/scl/fo/pfoqp6ndpzt3kt6kbgbdv/h?rlkey=6sp3sw3rds01y2xv9qyqc9t2o&dl=0 here]].<br />
<br />
====T/R====<br />
<br />
<center><br />
{| border=1px<br />
|'''Team'''<br />
|'''Peptide sequence'''<br />
|'''DNA sequence for peptide'''<br />
|-<br />
|TR orange<br />
| <br />
| <br />
|-<br />
|TR yellow<br />
| <br />
| <br />
|-<br />
|TR green<br />
| <br />
| <br />
|-<br />
|TR blue<br />
| <br />
| <br />
|-<br />
|TR pink<br />
| <br />
| <br />
|}<br />
</center><br />
<br />
====W/F====<br />
<br />
<center><br />
{| border=1px<br />
|'''Team'''<br />
|'''Peptide sequence'''<br />
|'''DNA sequence for peptide'''<br />
|-<br />
|WF red<br />
| <br />
| <br />
|-<br />
|WF orange<br />
| <br />
| <br />
|-<br />
|WF yellow<br />
| <br />
| <br />
|-<br />
|WF green<br />
| <br />
| <br />
|-<br />
|WF blue<br />
| <br />
| <br />
|-<br />
|WF teal<br />
| <br />
| <br />
|-<br />
|WF pink<br />
| <br />
| <br />
|-<br />
|WF purple<br />
| <br />
| <br />
|}<br />
</center></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-12T16:24:15Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> [[Media:Sp24 M2L1.pdf| Lecture slides]]<br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> [[Media:Sp24 M2D1 nll.pdf| TR prelab slides]]<br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M2D1_nll.pdfFile:Sp24 M2D1 nll.pdf2024-03-12T16:22:34Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-11T18:46:56Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR & WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-07T19:32:22Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8v2 nll.pdf| TR prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M1D8v2_nll.pdfFile:Sp24 M1D8v2 nll.pdf2024-03-07T19:31:57Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-07T17:51:38Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D7 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> [[Media:Sp24 M1D8 nll.pdf| TR prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M1D8_nll.pdfFile:Sp24 M1D8 nll.pdf2024-03-07T17:51:03Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-07T17:35:24Z<p>Noreen Lyell: /* Part 1: Image EMSA experiment */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with 5 mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add 5 mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add 5 &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with 5 mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix 0.12 mL of Substrate A with 0.12 mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your membrane, then use a pipet to transfer all of the 0.24 mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes at room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**10X Detection wash buffer<br />
**10X Blocking buffer<br />
**Streptavidin-HRP conjugate<br />
**Substrate A<br />
**Substrate B<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-07T16:03:40Z<p>Noreen Lyell: /* Protocols */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with 5 mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add 5 mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add 5 &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with 3 mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix 0.12 mL of Substrate A with 0.12 mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your membrane, then use a pipet to transfer all of the 0.24 mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes at room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**10X Detection wash buffer<br />
**10X Blocking buffer<br />
**Streptavidin-HRP conjugate<br />
**Substrate A<br />
**Substrate B<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-06T19:39:14Z<p>Noreen Lyell: /* Part 1: Image EMSA experiment */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with 5 mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add 5 mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add 5 &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with 5 mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix 0.12 mL of Substrate A with 0.12 mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your membrane, then use a pipet to transfer all of the 0.24 mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes at room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**10X Detection wash buffer<br />
**10X Blocking buffer<br />
**Streptavidin-HRP conjugate<br />
**Substrate A<br />
**Substrate B<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-05T15:31:16Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[Media:Sp24 M1D7 nll.pdf| TR prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-05T15:30:58Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> [[File:Sp24 M1D7 nll.pdf| TR prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M1D7_nll.pdfFile:Sp24 M1D7 nll.pdf2024-03-05T15:30:27Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-04T23:07:55Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L7 2024 .pptx| Lecture slides]]<br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> <br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/File:20109_M1L7_2024_.pptxFile:20109 M1L7 2024 .pptx2024-03-04T23:07:19Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Homework20.109(S24):Homework2024-03-04T17:51:53Z<p>Noreen Lyell: /* Due M1D8 */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
<br />
==Homework Submission Guidelines==<br />
<br />
* All homework assignments should be submitted to [https://canvas.mit.edu/courses/24927 Canvas] by 1:05p on the due date.<br />
* When submitting assignments online, '''make sure that your section information, name, and assignment details are in the file name''' and included on the '''document itself'''. e.g. 'TR_ImaStudent_M1D1'. <br />
* For group assignments, submit '''one''' copy of the homework and also include your section and team color. e.g. 'TR_Rainbow_M3D2'<br />
* ''Note:'' Some assignments may indicate a more specific naming scheme than this one. Follow that instead when applicable<br />
<br />
==Module 1: Drug discovery==<br />
<br />
===Due M1D1===<br />
<br />
*Review the [[20.109(S24):Laboratory tour| Orientation and laboratory tour exercises]] to prepare for the Orientation quiz that you and your partner will complete together during at the start of the laboratory session.<br />
*Complete the following online training courses offered through Environmental Health and Safety (EHS):<br />
<p style="margin-left:100px;"> <br />
<font color=red>'''&#9744;'''</font color> Emergency Preparedness (access at this this [http://be-ehs.mit.edu/epp-training link]) <br><br />
<font color=red>'''&#9744;'''</font color> General Chemical Hygiene (access at this [http://web.mit.edu/training/course.html?course=EHS00100w&sys=PS1 link]) <br><br />
<font color=red>'''&#9744;'''</font color> General Biosafety (access at this [http://web.mit.edu/training/course.html?course=EHS00260w&sys=PS1 link]) <br><br />
<font color=red>'''&#9744;'''</font color> Blood-borne Pathogen (access at this [http://atlas.mit.edu/atlas/Main.action?tab=home&sub=group_training&sapSystemId=PS1 link]) ,<br><br />
<font color=red>'''&#9744;'''</font color> If you have completed EHS training in a UROP or in another laboratory class, you do not need to repeat the training. Instead submit the certificates of completion or your training record which can be found at "My Training Needs" on Atlas. To access, go to atlas.mit.edu then click the Learning Center tab on the left side of the screen. <br> <br />
</p style><br />
<br />
*Prepare for the first day of Module 1 by reading the [[20.109(S24):Module_1#Module_1:_drug_discovery| M1 Project overview]] and the [[20.109(S24):M1D1#Introduction |M1D1 Introduction]].<br />
<br />
===Due M1D2===<br />
<br />
*The major writing assignment in Mod1 is the [[20.109(S24):Data Summary| Data summary]]. As part of this assignment you will provide details concerning the relevant background information important for understanding your project. In addition, you will use this information to motivate your specific research question. <br />
<p style="margin-left:100px;"> <br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> What is objective / goal of this module? <br><br />
<font color=red>'''&#9744;'''</font color> What important problem is addressed by your research question? <br><br />
<font color=red>'''&#9744;'''</font color> What topics / concepts should be explained to ensure a reader understands why your research question is important? <br><br />
<font color=red>'''&#9744;'''</font color> What experiments / techniques will you use to answer your research question? <br><br />
<font color=red>'''&#9744;'''</font color> Hint: review the information provided on the [[20.109(S24):Module 1#Overview | M1 Project overview]] for help! <br><br />
</p style><br />
<br />
*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 M1D6. To schedule your appointment online at the [http://be.mit.edu/communicationlab BE Communication Lab] homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked [[Media:20109 Comm Lab Appointment.pdf| here]] to help your prepare for your meeting.<br />
<br />
===Due M1D3===<br />
<br />
*An important part of scientific research is documenting the details regarding how experiments were performed. To practice this skill, you will '''work with your laboratory partner''' to draft a methods section that details the confirmation digest (not the in-silico cloning!) and the protein purification steps you completed on [[20.109(S24):M1D1 | M1D1]] and [[20.109(S24):M1D2 | M1D2]], respectively. <br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Do you have descriptive subsection headers in a logical order? <br><br />
<font color=red>'''&#9744;'''</font color> Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique? <br><br />
<font color=red>'''&#9744;'''</font color> Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.) <br><br />
<font color=red>'''&#9744;'''</font color> Do all reagents include manufacturer information in parentheses? <br><br />
<font color=red>'''&#9744;'''</font color> Are all abbreviations and acronyms written in full? (if this is the first use of the acronym) <br><br />
<font color=red>'''&#9744;'''</font color> Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty") <br><br />
<font color=red>'''&#9744;'''</font color> Are all mentions of tubes and water omitted? <br><br />
<font color=red>'''&#9744;'''</font color> Are the most flexible units used? (i.e. concentrations rather than volumes) <br><br />
<font color=red>'''&#9744;'''</font color> Is only information necessary to repeat the experiment included? <br><br />
<font color=red>'''&#9744;'''</font color> Are all descriptions concise and clear? <br><br />
<br />
</p style><br />
<br />
*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 M1D6. To schedule your appointment online at the [http://be.mit.edu/communicationlab BE Communication Lab] homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked [[Media:20109 Comm Lab Appointment.pdf| here]] to help your prepare for your meeting.<br />
<br />
===Due M1D4===<br />
<br />
*In scientific communication, data are represented as both figures and in text. For this homework you will craft a data figure using the SDS-PAGE and BCA assay results.<br />
<br />
<p style="margin-left:100px;"><br />
Use the checklist below to assist you as you complete this assignment:<br><br />
<font color=red>'''&#9744;'''</font color> Did you format your images? (i.e. omit excess visual noise and empty space) <br><br />
<font color=red>'''&#9744;'''</font color> Did you represent the data using an appropriate format (i.e. table or graph)? <br><br />
<font color=red>'''&#9744;'''</font color> Is all text in the figure legible (especially axes)? <br><br />
<font color=red>'''&#9744;'''</font color> Is your figure correctly sized (legible, but no more than 1/3 of a 8.5x11" slide)? <br><br />
<br />
</p style><br />
<br />
*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 M1D6. To schedule your appointment online at the [http://be.mit.edu/communicationlab BE Communication Lab] homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked [[Media:20109 Comm Lab Appointment.pdf| here]] to help your prepare for your meeting.<br />
<br />
===Due M1D5===<br />
<br />
*In the previous homework you focused on the data portion of figures, for this homework you will draft a title and caption for the SDS-PAGE and BCA assay figure.<br />
<br />
<p style="margin-left:100px;"><br />
Use the checklist below to assist you as you complete this assignment:<br><br />
<font color=red>'''&#9744;'''</font color> Does your figure include a take-home title below the image? <br><br />
<font color=red>'''&#9744;'''</font color> Does your figure include a caption with necessary details to interpret the figure? <br><br />
<font color=red>'''&#9744;'''</font color> Does your figure caption begin with a topic sentence? <br><br />
<font color=red>'''&#9744;'''</font color> Does your caption include any unnecessary information (such as methods or interpretation)? <br><br />
<br />
</p style><br />
<br />
*The major verbal assignment in Mod1 is the Research talk. As part of this assignment you will provide a brief, yet detailed, presentation of your results. For this homework, draft an outline of what you will verbally present for your Research talk.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Did you introduce yourself? (No need to mention the class.) <br><br />
<font color=red>'''&#9744;'''</font color> Did you provide an impact statement to give broad context for your work? <br><br />
<font color=red>'''&#9744;'''</font color> Did you provide only appropriate background information to understand the project? (key scientific concepts, essential methods, etc...) <br><br />
<font color=red>'''&#9744;'''</font color> Did you indicate a clear hypothesis/research goal? <br><br />
<font color=red>'''&#9744;'''</font color> Did you discuss specific results using quantitative information? <br><br />
<font color=red>'''&#9744;'''</font color> Did you draw clear conclusions from those results? <br><br />
<font color=red>'''&#9744;'''</font color> Did you specify how those conclusions link back to your hypothesis and impact statement? <br><br />
<br />
<font color=red>'''&#9744;'''</font color> Hint: review the information provided on the [[20.109(S24):Research talk | Research talk]] page for help! <br><br />
<br />
</p style><br />
<br />
*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 M1D6. To schedule your appointment online at the [http://be.mit.edu/communicationlab BE Communication Lab] homepage. Click "Make an appointment" at the top right corner of the screen. Please review the document linked [[Media:20109 Comm Lab Appointment.pdf| here]] to help your prepare for your meeting.<br />
<br />
===Due M1D6===<br />
<br />
*In addition to data figures, scientists use experiment overview schematics to illustrate the key steps of an experiment to better explain how the data were acquired. For this type of figure the important steps are represented using images and labels while the minor steps are omitted for clarity. To gain experience in this type of figure design you will craft an experiment overview schematic that shows the key steps used to purify MAX-6xHis. <br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment:<br><br />
<font color=red>'''&#9744;'''</font color> Is your schematic correctly sized (legible, but no more than 1/2 of a 8.5x11" slide)? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include a title below the images that concisely states the figure purpose? <br><br />
<font color=red>'''&#9744;'''</font color> Does your caption concisely define all symbols, jargon, abbreviations, and other relevant information for the schematic? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include only the details needed to understand the main steps in the experiment? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include appropriate images that are not plagiarized from class materials or the wiki? <br><br />
<font color=red>'''&#9744;'''</font color> Is any text in the schematic concise and legible? <br><br />
<br />
</p style><br />
<br />
*Submit a short summary (1-2 paragraphs) concerning your meeting with a Fellow from the BE Communication Lab. Including your thoughts on the utility of your meeting and what you learned from the discussion. To 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. Please review the document linked [[Media:20109 Comm Lab Appointment.pdf| here]] to help your prepare for your meeting.<br />
<br />
===Due M1D7===<br />
<br />
*Remember that for the Data summary you are presenting your results in an outline format to practice clear and concise writing. In addition, the Data summary is organized such that it is apparent what figures correspond to what text. Specifically, each data slide contains one figure and the bullets that explain the figure. For this homework, complete the data slide for your protein purity and concentration results.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Did you include an appropriately sized and labeled data figure? <br><br />
<font color=red>'''&#9744;'''</font color> Do you have a concise conclusive title (one with a take-home message)? <br><br />
<font color=red>'''&#9744;'''</font color> Does your figure caption begin with a topic sentence and have the information necessary to interpret the figure? <br><br />
<font color=red>'''&#9744;'''</font color> Does the results section begin with a conclusive title? (This title should be different from the figure title.) <br><br />
<font color=red>'''&#9744;'''</font color> Do you begin the results by providing the overall goal of the experiment(s)? <br><br />
<font color=red>'''&#9744;'''</font color> Do you indicate your expected result? <br><br />
<font color=red>'''&#9744;'''</font color> Do you explain why your result would be correct or incorrect? (i.e. experimental controls) <br><br />
<font color=red>'''&#9744;'''</font color> Do you describe all of the data you show when indicating the result of your experiment? (i.e. all populations on a scatterplot, or all lanes on a gel) <br><br />
<font color=red>'''&#9744;'''</font color> Do you describe the data quantitatively? <br><br />
<font color=red>'''&#9744;'''</font color> Do you draw a conclusion based on the data? <br><br />
<font color=red>'''&#9744;'''</font color> Do you use your last sentence to transition to the next experiment? <br><br />
<br />
</p style><br />
<br />
*When tasked with preparing your science for written communication it is often helpful to review articles that present similar types of experiments and results. Through reading the literature that is related to your research you can better understand how to effectively present the data. To assist you in preparing your Data summary assignment, we will discuss a paper published from the Koehler Laboratory. <br />
<br />
<p style="margin-left:100px;"> <br />
<font color=red>'''&#9744;'''</font color> In preparation for this discussion, read the article and guidelines provided on the [[20.109(S24):M1D7#Part_3:_In-class_paper_discussion| M1D7]] wiki page. <br><br />
<br />
</p style><br />
<br />
===Due M1D8===<br />
<br />
*The final section of your Data summary will discuss the Implications & Future works of your research. In this section the main results are summarized and used to answer the research question. Also, experiments are proposed that will expand upon your results in an effort to address new research questions that are raised by your data.<br />
<br />
<p style="margin-left:100px;"><br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> What is the main conclusion for your DSF results? <br><br />
<font color=red>'''&#9744;'''</font color> What is the main conclusion for your EMSA results? <br><br />
<font color=red>'''&#9744;'''</font color> How do the results answer your research question? <br><br />
<font color=red>'''&#9744;'''</font color> Did you observe any unexpected results or contradictory results? <br><br />
<font color=red>'''&#9744;'''</font color> What follow-up experiments (include at least two!) would be helpful in further addressing your research question? <br><br />
</p style><br />
<br />
*Using feedback to improve your writing is an important step to developing your scientific communication skills. For this homework, '''work with your laboratory partner''' to incorporate the feedback you received to revise your methods draft. In addition to editing the text from M1D1 and M1D2, include the protocols you used to assess the purity and concentration of the expressed MAX-6xHis protein on [[20.109(S24):M1D3| M1D3]]. <br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Do you have descriptive subsection headers in a logical order? <br><br />
<font color=red>'''&#9744;'''</font color> Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique? <br><br />
<font color=red>'''&#9744;'''</font color> Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.) <br><br />
<font color=red>'''&#9744;'''</font color> Do all reagents include manufacturer information in parentheses? <br><br />
<font color=red>'''&#9744;'''</font color> Are all abbreviations and acronyms written in full? (if this is the first use of the acronym) <br><br />
<font color=red>'''&#9744;'''</font color> Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty") <br><br />
<font color=red>'''&#9744;'''</font color> Are all mentions of tubes and water omitted? <br><br />
<font color=red>'''&#9744;'''</font color> Are the most flexible units used? (i.e. concentrations rather than volumes) <br><br />
<font color=red>'''&#9744;'''</font color> Is only information necessary to repeat the experiment included? <br><br />
<font color=red>'''&#9744;'''</font color> Are all descriptions concise and clear? <br><br />
<br />
</p style><br />
<br />
==Module 2: Protein engineering==<br />
<br />
===Due M2D1===<br />
<br />
*Prepare for the first day of Module 2 by reading the [[20.109(S24):Module_2#Module_2:_protein_engineering| M2 Project overview]] and the [[20.109(S24):M2D1#Introduction |M2D1 Introduction]].<br />
<br />
===Due M2D2===<br />
<br />
*The major verbal assignment in Module 2 is the Journal article presentation. As part of this assignment you will present a published, peer-reviewed research article to the class. For this homework, select and review an article for your presentation from the curated lists on the Journal article presentation assignment page. If you prefer, you can find your own paper and send it to the Instructors for approval.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Reserve your article on the [[20.109(S24):Journal article presentation|Journal article presentation]] page according to the directions provided under the 'Article selection' header. <br><br />
<font color=red>'''&#9744;'''</font color> Review the abstract and introduction for the selected article. <br><br />
<font color=red>'''&#9744;'''</font color> Submit a brief summary of the selected article that highlights why you think the research is interesting. <br><br />
<br />
</p style><br />
<br />
===Due M2D3===<br />
<br />
*For your Journal article presentation, you will only have 10 minutes to present a clear, cohesive story from the data in your selected research article. Given the number of figures in most research articles it is impossible to show all of the data from your paper in a short presentation. In this, it is important to identify which figures are the most important to the main conclusion(s) of the research article. For this homework, read through the paper you selected for the Journal article presentation and choose the four figures that you think are most important in telling the story presented by the authors.<br />
<br />
<p style="margin-left:100px;"><br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> What is the main conclusion of the paper? <br><br />
<font color=red>'''&#9744;'''</font color> What four figures are the most important in supporting the main conclusion? Why? <br><br />
<font color=red>'''&#9744;'''</font color> How do the figures work together to tell a story? How does this story lead you to the main conclusion of the paper? <br><br />
<br />
</p style><br />
<br />
*The Journal article presentations will occur during the laboratory sessions on Tuesday, 2nd and Thursday, April 4th for the T/R section and on Wednesday, April 3rd and Thursday, April 5th for the W/F section. Due to class size, presenters in each section will be divided between the two days by the Instructors. <br />
<br />
<p style="margin-left:100px;"> <br />
<font color=red>'''&#9744;'''</font color> To reserve a presentation date, email Becky (rcmeyer@mit.edu) with which day you prefer to present and why. If one of the days becomes oversubscribed then slots will assigned at random. <br><br />
<br />
</p style><br />
<br />
===Due M2D4===<br />
<br />
*Your slide deck will be important in your ability to effectively tell the story presented by the authors of your paper. For this homework you will draft a presentation slide using one of the data figures from the paper you selected that you want to discuss as part of your Journal club presentation. In addition, include a script for the verbal information that you will deliver when presenting the figure on your slide.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Does the title of your slide convey a concise take-home message about the data shown? <br><br />
<font color=red>'''&#9744;'''</font color> Do you include data from a single figure of your paper? <br><br />
<font color=red>'''&#9744;'''</font color> Are you trying to include too much data on a single slide? <br><br />
<font color=red>'''&#9744;'''</font color> Is all the text from your data figure legible? (especially note the axes text and recreate it if necessary) <br><br />
<font color=red>'''&#9744;'''</font color> Is there a good balance between figures and text on the slide? (approximately half of each) <br><br />
<font color=red>'''&#9744;'''</font color> Does the text convey only key information? <br><br />
<font color=red>'''&#9744;'''</font color> Is your script concise? (i.e. Are you able to convey this information in approximately 1 minute?) <br><br />
<font color=red>'''&#9744;'''</font color> Does your script contain technically correct scientific information? <br><br />
<font color=red>'''&#9744;'''</font color> Is the information in your script directly relevant to the data on the slide? <br><br />
<br />
</p style><br />
<br />
===Due M2D5===<br />
<br />
As part of your Research article, you will write a formal Introduction that includes the pertinent background information and motivation for your project. For this homework you will draft an outline of the Introduction.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Do you begin with an impact statement to provide broad context for your project? <br><br />
<font color=red>'''&#9744;'''</font color> Does your first paragraph indicate the importance of work in this field of study? <br><br />
<font color=red>'''&#9744;'''</font color> Do your next outlined paragraphs provide necessary information to understand the specific aspects of your research? (i.e. information about disease, biological pathways, important experimental techniques) <br><br />
<font color=red>'''&#9744;'''</font color> Do you clearly state the knowledge gap in the field that your project will address? <br><br />
<font color=red>'''&#9744;'''</font color> Do you clearly state your hypothesis/research question? <br><br />
<font color=red>'''&#9744;'''</font color> Do you provide a preview of the key findings of this study? (or a placeholder indicating this will be included) <br><br />
<font color=red>'''&#9744;'''</font color> Does your outline follow a funnel structure where information begins broad and narrows to information increasingly specific to your project and results? <br><br />
<font color=red>'''&#9744;'''</font color> Does each topic/paragraph make a logical transition to the next topic? <br><br />
<font color=red>'''&#9744;'''</font color> Do you include references for background information? <br><br />
<br />
<font color=red>'''&#9744;'''</font color> Hint: review the information concerning how to write an Introduction provided on the [[20.109(S24):Research_article#Introduction | Research article]] page for help! <br><br />
<br />
</p style><br />
<br />
*As in the Module 1 Data summary, figures will be important in how you report your results for the Mod 2 Research article. For this homework, use the skills you developed throughout Mod 1 to craft a data figure from the sequencing results. In addition to the figure include the text that will accompany your figure in the Results section of Research article.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Did you include an appropriately sized and labeled data figure? <br><br />
<font color=red>'''&#9744;'''</font color> Do you have a concise conclusive title (one with a take-home message)? <br><br />
<font color=red>'''&#9744;'''</font color> Does your figure caption begin with a topic sentence and have the information necessary to interpret the figure? <br><br />
<font color=red>'''&#9744;'''</font color> Does the results section begin with a conclusive title? (This title should be different from the figure title.) <br><br />
<font color=red>'''&#9744;'''</font color> Do you begin the results by providing the overall goal of the experiment(s)? <br><br />
<font color=red>'''&#9744;'''</font color> Do you indicate your expected result? <br><br />
<font color=red>'''&#9744;'''</font color> Do you explain why your result would be correct or incorrect? (i.e. experimental controls) <br><br />
<font color=red>'''&#9744;'''</font color> Do you describe all of the data you show when indicating the result of your experiment? (i.e. all populations on a scatterplot, or all lanes on a gel) <br><br />
<font color=red>'''&#9744;'''</font color> Do you describe the data quantitatively? <br><br />
<font color=red>'''&#9744;'''</font color> Do you state the results objectively while omitting interpretation? <br><br />
<font color=red>'''&#9744;'''</font color> Do you use your last sentence to transition to the next experiment? <br><br />
<font color=red>'''&#9744;'''</font color> Hint: review the information concerning how to write text for the Results section provided on the [[20.109(S24):Research_article#Results | Research article]] page for help! <br><br />
<br />
</p style><br />
<br />
===Due M2D6===<br />
<br />
*The major written assignment in Mod2 is the Research article. In Mod 1 you practiced writing a methods section with your laboratory partner. Now you will use this practice to write a methods section that will be included in the Research article. For this homework, you will begin working on the methods section of your Research article. Write a methods section that details the procedures that you completed on M2D2-M2D4. <br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Do you have descriptive subsection headers in a logical order? <br><br />
<font color=red>'''&#9744;'''</font color> Do each of your experimental sections begin with a topic sentence to introduce the purpose of the technique? <br><br />
<font color=red>'''&#9744;'''</font color> Do you write full sentences in passive voice and past tense? (i.e. His-tagged recombinant protein was purified using nickel resin.) <br><br />
<font color=red>'''&#9744;'''</font color> Do all reagents include manufacturer information in parentheses? <br><br />
<font color=red>'''&#9744;'''</font color> Are all abbreviations and acronyms written in full? (if this is the first use of the acronym) <br><br />
<font color=red>'''&#9744;'''</font color> Are all 20.109-specific details omitted? (i.e. do not include "Row A and Row B" or "the experiment was completed by the teaching faculty") <br><br />
<font color=red>'''&#9744;'''</font color> Are all mentions of tubes and water omitted? <br><br />
<font color=red>'''&#9744;'''</font color> Are the most flexible units used? (i.e. concentrations rather than volumes) <br><br />
<font color=red>'''&#9744;'''</font color> Is only information necessary to repeat the experiment included? <br><br />
<font color=red>'''&#9744;'''</font color> Are all descriptions concise and clear? <br><br />
<font color=red>'''&#9744;'''</font color> Hint: you should review the M1 methods homework and corresponding feedback for help! <br><br />
<br />
</p style><br />
<br />
===Due M2D7===<br />
<br />
*Figures serve many functions in scientific communication. In previous homeworks you crafted data figures and experiment schematics. Another type of figure is the research overview schematic, or visual abstract. In this type of figure only the important experiments / methods are represented to illustrate the workflow at a high-level. <br />
<br />
<p style="margin-left:100px;"> Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Is your schematic correctly sized (legible, but no more than 1/2 of a 8.5x11" page)? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include a title below the images that concisely states the figure purpose? <br><br />
<font color=red>'''&#9744;'''</font color> Does your caption concisely define all symbols, jargon, abbreviations, and other relevant information for the schematic? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include only the details needed to understand the main purpose/goal of the study? <br><br />
<font color=red>'''&#9744;'''</font color> Does your schematic include appropriate images that are not plagiarized from class materials or the wiki? <br><br />
<font color=red>'''&#9744;'''</font color> Is any text in the schematic concise and legible? <br><br />
<br />
</p style><br />
<br />
*In the Discussion section of the Research article you will convey how the results of your experiments provide an answer to your research question, consider how the sequencing and future metal uptake data relate to the broader goal of your research project, and how well the data support conclusions related to your research question.<br />
<br />
<p style="margin-left:100px;"> <br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> Were there any unexpected results? Is there a technical reason (i.e. an error in the setup or data collection)? <br><br />
<font color=red>'''&#9744;'''</font color> What follow-up experiment might you perform to clarify any unexpected results? <br><br />
<font color=red>'''&#9744;'''</font color> What are the limitations of your experimental approach? Is there another method that might better answer your research question? Is there another variable that should be tested to better answer your research question? <br><br />
<font color=red>'''&#9744;'''</font color> What next step experiment might you perform to further confirm your results?<br />
<br><br />
<font color=red>'''&#9744;'''</font color> Hint: review the information concerning how to write a Discussion provided on the [[20.109(S24):Research_article#Discussion | Research article]] page for help! <br><br />
<br />
</p style><br />
<br />
===Due M2D8===<br />
<br />
As the final section of your Research article, you will write a formal Discussion that summarizes the key findings and states the implications of your research. For this homework you will draft an outline of the Discussion.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Do you begin by reiterating the major findings of your work and the specific purpose of your study? <br><br />
<font color=red>'''&#9744;'''</font color> Do you discuss the data in the same order they were presented in the "Results" section? <br><br />
<font color=red>'''&#9744;'''</font color> Do you explain what the data presented in the "Results" section indicates? <br><br />
<font color=red>'''&#9744;'''</font color> Do you indicate whether or not the results support your hypothesis and why you have arrived at that conclusion? <br><br />
<font color=red>'''&#9744;'''</font color> For each result, do you provide information to explain why your result was expected or unexpected? (i.e. Were there any technical issues? How do the controls support your conclusions?) <br><br />
<font color=red>'''&#9744;'''</font color> Do you explain any limitations in the study and how they should be addressed to further clarify your results? <br><br />
<font color=red>'''&#9744;'''</font color> If you encountered unexpected results, do you indicate a potential clarifying experiment that would help elucidate your findings? <br><br />
<font color=red>'''&#9744;'''</font color> Do you propose at least two follow-up experiments that would help confirm your results and build on your findings? <br><br />
<font color=red>'''&#9744;'''</font color> Does your final paragraph explain how your study advances what is known in the field? <br><br />
<font color=red>'''&#9744;'''</font color> Does your final sentence tie back in to your impact statement from the "Introduction"? <br><br />
<font color=red>'''&#9744;'''</font color> Does your discussion follow a pyramid structure where you begin with specific information from your study and continually broaden until you indicate the impact on the field? <br><br />
<font color=red>'''&#9744;'''</font color> Does each topic/paragraph make a logical transition to the next topic? <br><br />
<font color=red>'''&#9744;'''</font color> Do you include references for relevant follow-up experiments and information on the overall field?<br><br />
<br />
<font color=red>'''&#9744;'''</font color> Hint: review the information concerning how to write a Discussion provided on the [[20.109(S24):Research_article#Discussion | Research article]] page for help! <br><br />
<br />
</p style><br />
<br />
==Module 3: Research design==<br />
<br />
===Due M3D1===<br />
<br />
*The culminating major assignment in 20.109 is the Research proposal presentation. As part of this assignment you will present a novel research idea to the class. For this homework, consider what topics you might find interesting or what problems you might want to solve.<br />
<br />
<p style="margin-left:100px;"> <br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> What personal interests do you have that are related to the field of Biological engineering? <br><br />
<font color=red>'''&#9744;'''</font color> What core classes have you found to be the most interesting? <br><br />
<font color=red>'''&#9744;'''</font color> What concepts are of interest to you? <br><br />
<font color=red>'''&#9744;'''</font color> What techniques are of interest to you? <br><br />
<font color=red>'''&#9744;'''</font color> What types of problems (health-related, environment-related, technology-related, etc.) are of interest to you? <br />
<br />
</p style><br />
<br />
===Due M3D3===<br />
<br />
*For this homework, '''work with your co-investigator''' to develop your research question and to refine your Research proposal idea.<br />
<br />
<p style="margin-left:100px;"> <br />
To get you started, answer the questions below: <br><br />
<font color=red>'''&#9744;'''</font color> What is your research question? <br><br />
<font color=red>'''&#9744;'''</font color> What is already known and how will your project advance what is already known? <br><br />
<font color=red>'''&#9744;'''</font color> What is the novel aspect of your project? Are you identifying something? Making something? <br> <br />
<font color=red>'''&#9744;'''</font color> What types of techniques / experiments might you use to answer your research question? <br><br />
<font color=red>'''&#9744;'''</font color> How is your research proposal related to the field of Biological engineering? <br><br />
<br />
</p style><br />
<br />
===Due M3D4===<br />
<br />
*During your laboratory session, you will practice presenting your Research proposal idea to your classmates. The goal of this exercise is to give you a chance to relay your idea verbally to a new audience and also to provide an opportunity for you to receive feedback on your idea. For this homework, prepare a write-up of your proposal idea to get you ready for the in-class discussion exercise.<br />
<br />
<p style="margin-left:100px;"> <br />
Use the checklist below to assist you as you complete this assignment: <br><br />
<font color=red>'''&#9744;'''</font color> Write a brief project overview that identifies the problem / idea you are addressing and your research question. <br><br />
<font color=red>'''&#9744;'''</font color> Clearly state your research question that will address this problem you've identified. <br><br />
<font color=red>'''&#9744;'''</font color> Describe what is currently known and how your project advances what is already known. Be clear on how your project is novel. <br><br />
<font color=red>'''&#9744;'''</font color> Include your project aims and the proposed methods / approaches that can be used to accomplish the proposed experiments. <br><br />
<font color=red>'''&#9744;'''</font color> Be sure your sources are appropriately cited! <br><br />
<br />
</p style></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T21:16:32Z<p>Noreen Lyell: /* Part 1: Image EMSA experiment */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add X mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add X &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix XX mL of Substrate A with XX mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your mebrane, then use a pipet to transfer all of the XX mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes at room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**10X Detection wash buffer<br />
**10X Blocking buffer<br />
**Streptavidin-HRP conjugate<br />
**Substrate A<br />
**Substrate B<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T21:15:48Z<p>Noreen Lyell: /* Reagent list */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add X mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add X &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix XX mL of Substrate A with XX mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your mebrane, then use a pipet to transfer all of the XX mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes and room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**10X Detection wash buffer<br />
**10X Blocking buffer<br />
**Streptavidin-HRP conjugate<br />
**Substrate A<br />
**Substrate B<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T21:13:49Z<p>Noreen Lyell: /* Part 1: Image EMSA experiment */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
#Obtain the membrane with your EMSA experiment from the front laboratory bench.<br />
#Decant the 0.5X TBE buffer from the container.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer.<br />
#*To wash the membrane, rock the container 3-5 times, then decant the buffer.<br />
#Add X mL of Blocking Buffer, then incubate for 20 minutes at room temperature at 50 rpm.<br />
#Remove 1 mL of the Blocking Buffer from Step #4 and transfer to a microcentrifuge tube.<br />
#Add X &mu;L of Streptavidin-HRP Conjugate to the 1 mL aliquot of Blocking Buffer.<br />
#Transfer the 1 mL of Blocking Buffer + Streptavidin-HRP Conjugate into the container with your membrane.<br />
#Incubate the membrane for 45 minutes at room temperature at 50 rpm.<br />
#Decant the Blocking Buffer.<br />
#Wash the membrane with X mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.<br />
#*Complete a total of three washes.<br />
#In a microcentrifuge tube, mix XX mL of Substrate A with XX mL of Substrate B.<br />
#Carefully place your membrane between the flaps of the Detection Sheet.<br />
#Hold the top flap of the Detection Sheet away from your mebrane, then use a pipet to transfer all of the XX mL of the Substrate Solution onto your membrane.<br />
#*Pipet the Substrate Solution evenly across the surface of your membrane.<br />
#Gently lay the top flap down onto the membrane ensuring that the Substrate Solution covers the entire surface without trapping air bubbles.<br />
#Incubate for 5 minutes and room temperature.<br />
#Alert your Instructor when you are ready to image your membrane.<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T20:56:43Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
The goal for today is to give you time and space to get started on the Mod 1 major writing assignment, the Data summary. Be sure to take advantage of the 'work day' to discuss the assignment with your laboratory partner and to ask the Instructors any questions you may have about the material covered, data analyzed, or assignment details.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
<br />
<br />
===Part 2: Outline Data summary and divide workload accordingly===<br />
<br />
In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.<br />
<br />
'''Assess what needs to be done'''<br />
<br />
Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").<br />
<br />
'''Distribute what needs to be done between partners'''<br />
<br />
With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Review the submitted homework assignments and comments as this may help determine which partner should complete which components (hint: which homework is most easily revised based on the comments?).<br />
<br />
Note that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and are accountable to each other.<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your discussion with your laboratory partner, record the following:<br />
**What has been done?<br />
**What needs to be done?<br />
**Who will complete which components?<br />
**When will you meet to discuss progress and review the completed components?<br />
<br />
===Part 3: Prepare Data summary===<br />
<br />
Use the remaining class time to prepare your Data summary!!.<br />
<br />
==Reagent list==<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T20:53:45Z<p>Noreen Lyell: /* Introduction */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
The electromobility shift assay (EMSA) is used to study nucleic acid-protein interactions. Specifically, an EMSA can address if a protein binds to a DNA or RNA probe. Probes used for EMSA experiments consist of a given DNA or RNA sequence that is labeled with fluorophores. The probe is incubated with protein and then the product is electrophoresed using a polyacrylamide gel. If the probe sequence is bound to protein, it will migrate through the gel more slowly than free target sequence due to the increased size of the DNA complex (see the 'gel separation' panel of the image below).<br />
<br />
Following electrophoresis, the DNA complexes are transferred to a membrane for visualization (see 'probe detection' panel of the image below). The fluorophore attached to the nucleic acid probe enables visualization. Free probe will appear lower on the membrane than protein-bound probe. Binding of a specific DNA or RNA sequence to protein is confirmed when a shift is observed between a negative control sample (probe with no protein included) and the experimental sample (probe with protein included).<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume of nuclear extract you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D (I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T20:50:49Z<p>Noreen Lyell: /* Introduction */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
The electromobility shift assay (EMSA) is used to study nucleic acid-protein interactions. Specifically, an EMSA can address if a protein binds to a DNA or RNA probe. Probes used for EMSA experiments consist of a given DNA or RNA sequence that is labeled with fluorophores. The probe is incubated with protein and then the product is electrophoresed using a polyacrylamide gel. If the probe sequence is bound to protein, it will migrate through the gel more slowly than free target sequence due to the increased size of the DNA complex (see the 'gel separation' panel of the image below).<br />
<br />
Following electrophoresis, the DNA complexes are transferred to a membrane for visualization (see 'probe detection' panel of the image below). The fluorophore attached to the nucleic acid probe enables visualization. Free probe will appear lower on the membrane than protein-bound probe.<br />
<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume of nuclear extract you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D (I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T20:47:01Z<p>Noreen Lyell: /* Introduction */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
The electromobility shift assay (EMSA) is used to study nucleic acid-protein interactions. Specifically, an EMSA can address if a protein binds to a DNA or RNA probe. Probes used for EMSA experiments consist of a given DNA or RNA sequence that is labeled with fluorophores. The probe is incubated with protein and then the product is electrophoresed using a polyacrylamide gel. If the probe sequence is bound to protein, it will migrate through the gel more slowly than free target sequence due to the increased size of the DNA complex (see the 'gel separation' panel of the image below).<br />
<br />
Following electrophoresis, the DNA complexes are transferred to a membrane for visualization (see 'probe detection' panel of the image below.<br />
<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume of nuclear extract you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D (I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T19:00:20Z<p>Noreen Lyell: /* Part 2: Practice statistical analysis */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
Today is the final laboratory session for Module 1! You have completed all of the bench work for your research; however, there is still data analysis to complete for your experiments. In addition to plotting the data, you will complete statistical analysis to determine the significance of your results.<br />
<br />
Statistics are mathematical tools used to analyze, interpret, and organize data. The specific tools that you will use are confidence intervals (CI) and the Student's ''t''-test. To begin, review the following definitions:<br />
*Mean (or average) is defined as: <br />
<br />
<br />
<center><br />
<math> \overline{\chi } = \frac{\sum_{i}^{n}\chi _{i}}{n}</math>, ''where'' <math>\chi _{i}</math> = ''individual value and n = number of samples''<br />
</center><br />
<br />
<br />
*With infinite data, the mean (<math> \overline{\chi }</math>) approaches the true mean (&mu;).<br />
*Standard deviation measures the variation in the data and is defined as:<br />
<br />
<br />
<center><br />
<math> s = \sqrt{\frac{\sum_{i}^{n }(\chi _{_{i}}-\overline{\chi })}{n - 1}}</math>, ''where n - 1 = degrees of freedom''<br />
</center><br />
<br />
<br />
*With infinite data, the standard deviation (''s'') approaches the true standard deviation (&sigma;).<br />
<br />
An assumption is made when using standard deviation to report the variation in a data set. It is assumed that sufficient data have been collected to generate a normal curve.<br />
<br />
So, what does this all mean in regard to the data you will report? As an example, if the calculated <math> \overline{\chi }</math> of a data set equals 80 au there is a 95% chance the &mu; is between 50 au and 110 au, where au = arbitrary units. And how does this relate to ''s''? If you know the &mu;, the &sigma; represents a 68% confidence interval. <br />
<br />
When interpreting data, the error bars are representative of the noise in the data or how different the data points are for each of the replicates. Replicates come in two types: technical and biological. Technical replicates indicate that the same sample was tested multiple times and is measure of experimenter error (for example, pipetting errors between aliquots). Biological replicates indicate that different preparations of the same sample were tested and is a measure of the difference in a response to a variable (for example, response to a treatment between separate cultures of the same cell line). Though both types have value in data analysis, the interpretation of the error represented in each case is different. Because of this it is important to indicate if the replicates used in the data analysis are technical or biological. For your data, what type of replicates did you analyze for the &gamma;H2AX experiment? For the CometChip experiment?<br />
<br />
Lastly, you will use Student's ''t''-test to report if your data are statistically different between treatments. <br />
*Student's ''t''-test is defined as:<br />
<br />
<br />
<center><br />
<math>t = \frac{\left | \overline{\chi_{_{1}}} - \overline{\chi_{_{2}}} \right |}{s_{pooled}}\sqrt{\frac{n_{1} n_{2}}{n_{1}+n_{2}}}</math>, ''where'' <math>s_{pooled} = \sqrt{\frac{s_{1}^{2} (n_{1} -1) + {s_{2}^{2} (n_{2} - 1)}{}}{n_{1} + n_{2} - 2}}</math><br />
</center><br />
<br />
<br />
The value you calculate with the Student's ''t''-test equation is referred to as ''t''<sub>calculated</sub>. This ''t''<sub>calculated</sub> value is compared to the ''t''<sub>tabulated</sub> value in the the ''t'' table, according to the appropriate ''n'' - 1 using the p-value for the two-tailed distribution (which assumes that you do not know how the data will shift). If the ''t''<sub>calculated</sub> value is greater than the ''t''<sub>tabulated</sub>, then the data sets are significantly different at the specific p-value. So, what does this all mean in regard to the data you will report? As an example, if the ''t''<sub>calculated</sub> for a data set with ''n'' - 1 = 10 is 3 (given that the ''t''<sub>tabulated</sub> is 2.228), then the data sets are different with a ''p''-value &le; 0.05. Which means that there is less that a 5% chance that the data sets are the same.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
<br />
<br />
===Part 2: Practice statistical analysis===<br />
'''This exercise is optional. If you are confident in your ability to apply the statistics tests discussed in the prelab lecture, feel free to continue to Part 3. If you would like to practice the tests that were discussed, complete the exercise included here.''' <br />
<br />
Review data from an experiment where cells were exposed to increasing amounts of radiation (linked [[Media: CometAssay_M1D6stats_F14.xlsx |here]]). Your goal is to determine if a statistically significant amount of DNA damage was induced. For the purpose of this exercise, the values in the spreadsheet are in arbitrary units of 'DNA damage', where the higher numbers indicate more damage. <br />
<br />
When interpreting the statistics, consider how you may use the information to convince someone that the DNA damage was significant. You may find the spreadsheet originally created by Prof. Bevin Engelward and modified for the 20.109 laboratory, helpful for this exercise (linked [[Media: S09_20109_M2D5-Stats-4.xls‎ |here]]). <br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Attach the completed spreadsheet.<br />
**Include a bar graph of the data with standard deviations.<br />
**Indicate if there is a statistically significant difference (''i.e.'' provide a ''p''-value) between the conditions tested.<br />
<br />
===Part 3: Complete data analysis===<br />
<br />
==Reagent list==<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D820.109(S24):M1D82024-03-01T18:59:40Z<p>Noreen Lyell: /* Part 2: Practice statistical analysis */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
Today is the final laboratory session for Module 1! You have completed all of the bench work for your research; however, there is still data analysis to complete for your experiments. In addition to plotting the data, you will complete statistical analysis to determine the significance of your results.<br />
<br />
Statistics are mathematical tools used to analyze, interpret, and organize data. The specific tools that you will use are confidence intervals (CI) and the Student's ''t''-test. To begin, review the following definitions:<br />
*Mean (or average) is defined as: <br />
<br />
<br />
<center><br />
<math> \overline{\chi } = \frac{\sum_{i}^{n}\chi _{i}}{n}</math>, ''where'' <math>\chi _{i}</math> = ''individual value and n = number of samples''<br />
</center><br />
<br />
<br />
*With infinite data, the mean (<math> \overline{\chi }</math>) approaches the true mean (&mu;).<br />
*Standard deviation measures the variation in the data and is defined as:<br />
<br />
<br />
<center><br />
<math> s = \sqrt{\frac{\sum_{i}^{n }(\chi _{_{i}}-\overline{\chi })}{n - 1}}</math>, ''where n - 1 = degrees of freedom''<br />
</center><br />
<br />
<br />
*With infinite data, the standard deviation (''s'') approaches the true standard deviation (&sigma;).<br />
<br />
An assumption is made when using standard deviation to report the variation in a data set. It is assumed that sufficient data have been collected to generate a normal curve.<br />
<br />
So, what does this all mean in regard to the data you will report? As an example, if the calculated <math> \overline{\chi }</math> of a data set equals 80 au there is a 95% chance the &mu; is between 50 au and 110 au, where au = arbitrary units. And how does this relate to ''s''? If you know the &mu;, the &sigma; represents a 68% confidence interval. <br />
<br />
When interpreting data, the error bars are representative of the noise in the data or how different the data points are for each of the replicates. Replicates come in two types: technical and biological. Technical replicates indicate that the same sample was tested multiple times and is measure of experimenter error (for example, pipetting errors between aliquots). Biological replicates indicate that different preparations of the same sample were tested and is a measure of the difference in a response to a variable (for example, response to a treatment between separate cultures of the same cell line). Though both types have value in data analysis, the interpretation of the error represented in each case is different. Because of this it is important to indicate if the replicates used in the data analysis are technical or biological. For your data, what type of replicates did you analyze for the &gamma;H2AX experiment? For the CometChip experiment?<br />
<br />
Lastly, you will use Student's ''t''-test to report if your data are statistically different between treatments. <br />
*Student's ''t''-test is defined as:<br />
<br />
<br />
<center><br />
<math>t = \frac{\left | \overline{\chi_{_{1}}} - \overline{\chi_{_{2}}} \right |}{s_{pooled}}\sqrt{\frac{n_{1} n_{2}}{n_{1}+n_{2}}}</math>, ''where'' <math>s_{pooled} = \sqrt{\frac{s_{1}^{2} (n_{1} -1) + {s_{2}^{2} (n_{2} - 1)}{}}{n_{1} + n_{2} - 2}}</math><br />
</center><br />
<br />
<br />
The value you calculate with the Student's ''t''-test equation is referred to as ''t''<sub>calculated</sub>. This ''t''<sub>calculated</sub> value is compared to the ''t''<sub>tabulated</sub> value in the the ''t'' table, according to the appropriate ''n'' - 1 using the p-value for the two-tailed distribution (which assumes that you do not know how the data will shift). If the ''t''<sub>calculated</sub> value is greater than the ''t''<sub>tabulated</sub>, then the data sets are significantly different at the specific p-value. So, what does this all mean in regard to the data you will report? As an example, if the ''t''<sub>calculated</sub> for a data set with ''n'' - 1 = 10 is 3 (given that the ''t''<sub>tabulated</sub> is 2.228), then the data sets are different with a ''p''-value &le; 0.05. Which means that there is less that a 5% chance that the data sets are the same.<br />
<br />
==Protocols==<br />
<br />
===Part 1: Image EMSA experiment===<br />
<br />
<br />
===Part 2: Practice statistical analysis===<br />
'''This exercise is optional. If you are confident in your ability to apply the statistics tests discussed in prelab, feel free to continue to Part 3. If you would like to practice, complete the exercise included here.''' <br />
<br />
Review data from an experiment where cells were exposed to increasing amounts of radiation (linked [[Media: CometAssay_M1D6stats_F14.xlsx |here]]). Your goal is to determine if a statistically significant amount of DNA damage was induced. For the purpose of this exercise, the values in the spreadsheet are in arbitrary units of 'DNA damage', where the higher numbers indicate more damage. <br />
<br />
When interpreting the statistics, consider how you may use the information to convince someone that the DNA damage was significant. You may find the spreadsheet originally created by Prof. Bevin Engelward and modified for the 20.109 laboratory, helpful for this exercise (linked [[Media: S09_20109_M2D5-Stats-4.xls‎ |here]]). <br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Attach the completed spreadsheet.<br />
**Include a bar graph of the data with standard deviations.<br />
**Indicate if there is a statistically significant difference (''i.e.'' provide a ''p''-value) between the conditions tested.<br />
<br />
===Part 3: Complete data analysis===<br />
<br />
==Reagent list==<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M2D1 |Determine peptide design strategy ]] <br><br />
Previous day: [[20.109(S24):M1D7 |Complete EMSA experiment]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T18:24:34Z<p>Noreen Lyell: /* Reagent list */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume of nuclear extract you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D (I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T18:24:16Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume of nuclear extract you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Research_talk20.109(S24):Research talk2024-03-01T18:18:58Z<p>Noreen Lyell: /* Logistics */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
<br />
==Overview==<br />
In addition to the Data Summary, you will complete a short Research talk that focuses on training in oral communication. Specifically, you will verbally describe your research project and results from Module 1 in an "elevator pitch" or a "flash talk" format. <br />
<br />
The ability to present your research orally is important for networking and relaying your work in settings where you do not have access to visual aids. The term "elevator pitch" is used to describe a brief oral presentation of your work; it suggests that you have the time of an elevator ride to explain the importance and results of your research to someone unfamiliar with your project.<br />
<br />
The target audience for this Research talk is a scientifically literate listener who is unfamiliar with your specific field. Thus, you can assume rapid comprehension - but not ''a priori'' knowledge.<br />
<br />
==Logistics==<br />
<font color=#0404B4>'''You will complete this assignment individually.'''</font color><br />
<br />
Please review the 20.109 [http://engineerbiology.org/wiki/20.109(S24):Laboratory_tour#Statement_on_collaboration_and_integrity statement on collaboration and integrity] as you proceed.<br />
<br />
As you prepare your assignment be sure to review the resources provided on the [[20.109(S24):Communication| Communication tab]].<br />
<br />
Please submit your completed Research talk <font color=red>'''due by Monday, March 4th at 10 pm'''</font color> to bioeng20.109@gmail.com, with filename '''Name_LabSection_RT.extension''' (for example, ImaStudent_TR_RT.mov).<br />
<br />
==Formatting and length guidelines==<br />
<br />
*Your Research talk should be 3 minutes long and include the following:<br />
**introduction of your project<br />
**key results from your research (including a statement as to the method(s) used to generate data)<br />
**take-home message<br />
*Your submission should be a video of you talking about your research.<br />
**The purpose of this assignment is to develop skills in verbal communication '''without''' the use of visual aids. In this, you will not use slides or images to convey the results of your research. Instead focus on using clear and descriptive language to describe the data.<br />
**You may use any recording device to which you have access (iPhone, video recorder, etc) or use the record function in Zoom. If you do not have access to a recording device, alert the Instructors for alternate options.<br />
**The video you submit should not be edited together from multiple attempts. The goal is to describe your research as you would do with a live listener.<br />
<br />
==Content considerations==<br />
<br />
===Introduction===<br />
<br />
The introduction of your Research talk should both introduce your research project and convey the importance of your work in the context of the field. You want the listener to understand why your project is important and give them the information they need to understand your data.<br />
<br />
===Results===<br />
<br />
Your results should be summarized such that the key finding is clear to your listener. When discussing your results, include details that support your claims. For example, instead of simply stating "We identified hits..." include the actual numerical values, "We identified X positive hits with Z-scores of Y, which indicates that ..."<br />
<br />
In addition to stating your results, you should include your interpretations of the data you collected. <br />
<br />
If it is necessary, you can include details used to obtain your data (''e.g.'' "Using a His tag, we...").<br />
<br />
===Conclusions===<br />
<br />
The conclusion should put your project into the context of the larger field of research. How is it that your research advances the field?<br />
<br />
==Evaluation==<br />
<br />
{|border="1"<br />
!Category<br />
!Elements of a strong presentation<br />
!Weight<br />
|-<br />
|Introduction<br />
|<br />
* Introduce yourself and the research<br />
* Summarize the background information necessary to understand the research<br />
* State the research question<br />
|25%<br />
|-<br />
|Methods & Data<br />
|<br />
* Provide ONLY the method information necessary to understand the results<br />
* Give complete and concise explanations of the results<br />
* Relate the results to the central question<br />
|25%<br />
|-<br />
|Summary & Conclusions<br />
|<br />
* Highlight the key finding(s) relevant to the central question / hypothesis<br />
|25%<br />
|-<br />
|Organization<br />
|<br />
* Give a logical, easy-to-follow narrative<br />
* Include transition statements<br />
|15%<br />
|-<br />
|Delivery<br />
|<br />
* Show confidence / enthusiasm and speak clearly<br />
* Use appropriate language (technical or informal, as appropriate)<br />
* Be mindful of the time limit (3 minutes +/- 15 seconds!)<br />
|10%<br />
|-<br />
|}<br />
<br />
<br />
The Research talk will be graded by Dr. Becky Meyer with input from Dr. Noreen Lyell and Jamie Zhan.</div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):Spring_2024_schedule20.109(S24):Spring 2024 schedule2024-03-01T18:18:27Z<p>Noreen Lyell: </p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
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.<br />
<br />
<font color= #2f9b91 >'''SCHEDULE DETAILS:'''</font color><br><br />
<font color= #3bc2b6 >'''Lecture times:'''</font color> Tuesday (T) and Thursday (R) 11 - 12 pm in 4-237<br><br />
<font color= #3bc2b6 >'''Laboratory section times:'''</font color> Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322<br><br />
<br />
<font color= #2f9b91 >'''ABSENCE POLICY:'''</font color><br><br />
<font color= #3bc2b6 >'''Absences from lecture:'''</font color> Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture. <br><br />
<font color= #3bc2b6 >'''Absences from laboratory:'''</font color> Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).<br />
<br />
{| border=1px<br />
|'''MODULE'''<br />
|'''DATE'''<br />
|'''LECTURER'''<br />
|'''LABORATORY EXPERIMENTS'''<br />
|'''ASSIGNMENTS'''<br />
|--<br />
| <br />
| T/W Feb 6/7 <br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [[Media:Sp24 Orientation lecture student.pdf| Lecture slides]]<br />
| [[20.109(S24):Laboratory tour | Orientation and laboratory tour]]<br> [[Media:Sp24 EHS slides.pdf | EHS slides]]<br>[[Media:Sp24 M0 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M0_jz.pdf| WF prelab slides]]<br />
|<br />
|--<br />
| M1D1<br />
| R/F Feb 8/9<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L1 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D1 | Complete in-silico cloning of protein expression vector]]<br> [[Media:Sp24 M1D1 nll.pdf| TR prelab slides]]<br> [[Media:Sp24 M1D1 jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Orientation quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D1|Homework due]]<br />
|--<br />
| M1D2<br />
| T/W Feb 13/14 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D2 |Purify expressed protein]] <br> [[Media:Sp24 M1D2 nll.pdf| TR prelab slides]] & [https://www.dropbox.com/scl/fi/qq54ep8nhjhwk5xy80x5l/Protein-Purification-Demo.mp4?rlkey=h00htz57i5tt2y9hz8qpieily&dl=0| Protein purification video] <br>[[Media:Sp24 M1D2 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D2|Homework due]]<br />
|--<br />
| M1D3<br />
| R/F Feb 15/16 <br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L2 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D3 |Assess purity and concentration of expressed protein]] <br> [[Media:Sp24 M1D3 nll.pdf| TR prelab slides]] <br> [[Media:Sp24 M1D3 jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D3|Homework due]]<br />
|--<br />
| <br />
| T/W Feb 20/21<br />
| <br />
| <font color = #e1452f>'''President's Day holiday'''</font color><br />
| <br />
|--<br />
| M1D4<br />
| R/F Feb 22/23<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L3 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D4 |Review results of small molecule microarray (SMM) screen]] <br> [[Media:Sp24 M1D4 nll.pdf| TR prelab slides]] <br> [[Media:Sp24_M1D4_jz.pdf| WF prelab slides]]<br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D4|Homework due]]<br />
|--<br />
| M1D5<br />
| T/W Feb 27/28<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L4 2024.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D5 |Setup differential scanning flourimetry (DSF) experiment]] <br> [[Media:Sp24 M1D5v2 nll.pdf| TR prelab slides]]<br>[[Media:Sp24_M1D5_jz.pdf| WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D5|Homework due]] <br> <br />
|--<br />
| M1D6<br />
| R/F Feb/Mar 29/1<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> [[Media:20109 M1L6 2024 short.pdf| Lecture slides]]<br />
| [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br> [[Media:Sp24 M1D6 nll.pdf|TR prelab slides]] <br> [[Media:Sp24 M1D6 jz.pdf|WF prelab slides]]<br />
| [[20.109(S24):Homework#Due_M1D6|Homework due]] <br> [[20.109(S24):Research talk| <font color = #2f9b91>'''Research talk due'''</font color>]] Mon, Mar 4 at 10pm <br><br />
|--<br />
| M1D7<br />
| T/W Mar 5/6<br />
| [http://be.mit.edu/directory/angela-koehler AK] <br> <br />
| [[20.109(S24):M1D7 |Complete EMSA experiment]] <br> <br />
| [[20.109(S24):Homework#Due_M1D7|Homework due]] <br />
|--<br />
| M1D8<br />
| R/F Mar 7/8<br />
| BE Comm Lab <br> <br />
| [[20.109(S24):M1D8 |Evaluate experimental results]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M1D8|Homework due]] <br />
|--<br />
| M2D1<br />
| T/W Mar 12/13<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D1 |Determine peptide design strategy]] <br> <br />
| [[20.109(S24):Homework#Due_M2D1|Homework due]] <br />
|--<br />
| M2D2<br />
| R/F Mar 14/15<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D2 |Clone cell surface peptide display plasmid]] <br> <br />
| [[20.109(S24):Homework#Due_M2D2|Homework due]] <br> [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary draft due'''</font color>]] Sat, Mar 16 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Mon, Mar 18 at 10 pm<br />
|--<br />
| M2D3<br />
| T/W Mar 19/20<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D3 |Sequence clones and transform into yeast]] <br> <br />
| [[20.109(S24):Homework#Due_M2D3|Homework due]] <br> <br />
|--<br />
| M2D4<br />
| R/F Mar 21/22 <br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D4 |Align sequencing and prepare for Journal Article presentations]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D4|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Mar 26/27 - R/F Mar 28/29 </font color><br />
| <br />
| <font color = #e1452f>'''Spring Break'''</font color><br />
| [[20.109(S24):Data Summary| <font color = #2f9b91>'''Data Summary revision due'''</font color>]] Mon, Mar 25 at 10 pm <br> <br />
|--<br />
|<br />
| T/W Apr 2/3<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
|<br />
|--<br />
| <br />
| R/F Apr 4/5<br />
| <br />
| [[20.109(S24):Journal article presentation| <font color = #2f9b91>'''Journal article presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, Apr 6 at 10 pm<br />
|--<br />
| M2D5<br />
| T/W Apr 9/10<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D5 | Perform flow cytometry and harvest cells to test cadmium sequestration]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| M2D6<br />
| R/F Apr 11/12<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M2D6 | Quantify cadmium removal from media]] <br> <br />
| [[20.109(S24):Homework#Due_M2D5|Homework due]] <br />
|--<br />
| <br />
| <font color = 999999>T/W Apr 16/17 </font color><br />
| <br />
| <font color = #e1452f>'''Patriots' Day holiday'''</font color><br />
| <br />
|--<br />
| M2D7<br />
| R/F Apr 18/19<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br> <br />
| [[20.109(S24):M2D7 | Visualize cadmium sequestration and assess quality of cadmium sulfide production]] <br> <br />
| [[20.109(S24):Homework#Due_M2D7|Homework due]]<br />
|--<br />
| M2D8<br />
| T/W Apr 23/24<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M2D8 |Complete data analysis and organize Research Article figures]] <br> <br />
| <font color= #3bc2b6 >'''Laboratory quiz'''</font color> <br> [[20.109(S24):Homework#Due_M2D8|Homework due]]<br />
|--<br />
| M3D1<br />
| R/F Apr 25/26<br />
| [http://be.mit.edu/directory/angela-belcher AB] <br> <br />
| [[20.109(S24):M3D1 |Brainstorm ideas for Research proposal presentation]] <br> <br />
| [[20.109(S24):Homework#Due_M3D1|Homework due]] <br><br />
|--<br />
| M3D2<br />
| T/W Apr/May 30/1<br />
| BE Comm Lab<br />
| [[20.109(S24):M3D2 |Pitch research proposal presentation ideas ]] <br> <br />
| [[20.109(S24):Research article| <font color = #2f9b91>'''Research article due'''</font color>]] Mon, Apr 29 at 10 pm <br> [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Tue, Apr 30 at 10 pm<br />
|--<br />
| M3D3<br />
| R/F May 2/3<br />
| [http://be.mit.edu/directory/noreen-lyell NLL] <br> [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D3 |Develop ideas for Research proposal presentation ]] <br> <br />
| [[20.109(S24):Homework#Due_M3D3|Homework due]]<br><br />
|--<br />
| M3D4<br />
| T/W May 7/8<br />
| [http://be.mit.edu/directory/becky-meyer BCM] <br><br />
| [[20.109(S24):M3D4 |Participate in Research proposal peer reviews]] <br> <br />
| [[20.109(S24):Homework#Due_M3D4|Homework due]]<br />
|--<br />
| <br />
| R/F May 9/10<br />
| <br />
| [[20.109(S24):Research proposal presentation| <font color = #2f9b91>'''Research proposal presentations'''</font color>]]<br />
| [https://mit.enterprise.slack.com/archives/C06H3BYMX8E Blog post due] Sat, May 11 at 10 pm<br />
|--<br />
| <br />
| T May 14<br />
| <font color = #e1452f>'''Celebration lunch!'''</font color> <br><br />
| <br />
| <br />
|}<br />
</div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:54:12Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60 V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:53:32Z<p>Noreen Lyell: /* Reagent list */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% 0.5X TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:42:20Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:41:43Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image to right for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|450px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:41:33Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image to right for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|300px|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:41:22Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Use the following steps to build the transfer stack (see image to right for reference): [[Image:Sp24 M1D7 transfer stack.png|thumb|300ps|right]]<br />
#*Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#*Place 1 filter sponge on top of the black plastic side.<br />
#*Place 1 sheet of filter paper on the sponge.<br />
#*Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#*Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#**Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#*Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#*Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/File:Sp24_M1D7_transfer_stack.pngFile:Sp24 M1D7 transfer stack.png2024-03-01T17:39:28Z<p>Noreen Lyell: </p>
<hr />
<div></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:26:43Z<p>Noreen Lyell: /* Reagent list */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#Place 1 filter sponge on top of the black plastic side.<br />
#Place 1 sheet of filter paper on the sponge.<br />
#Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#*Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
*EMSA kit (from Signosis):<br />
**Poly D(I-C)<br />
**5X binding buffer<br />
**10X loading buffer<br />
*10X TBE (from BioRad)<br />
*5% TBE polyacrylamide gel (from BioRad)<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:21:57Z<p>Noreen Lyell: /* Part 2: Transfer DNA complexes onto membrane */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
Because the gels are shared between several teams, your Instructor will complete the following steps as a demonstration.<br />
#Add cold 0.5X TBE buffer to a dish.<br />
#Place the transfer cartridge in the dish such that the black plastic (negative) side is submerged in the buffer.<br />
#Place 1 filter sponge on top of the black plastic side.<br />
#Place 1 sheet of filter paper on the sponge.<br />
#Carefully remove the TBE polyacrylamide gel from the electrophoresis cartridge and place it on top of the filter paper.<br />
#Briefly submerge the NB membrane in cold 0.5X TBE buffer, then place it on top of the TBE polyacrylamide gel.<br />
#*Notch the top, right corner of the membrane to note the orientation and order of the samples.<br />
#Submerge 1 sheet of filter paper in cold 0.5X TBE buffer and place on top of the membrane.<br />
#Submerge 1 filter sponge in cold 0.5X TBE buffer and place on top of the filter paper.<br />
#Close the transfer cartridge.<br />
#Insert the transfer cartridge into the buffer chamber, then fill the chamber with cold 0.5X TBE buffer and attach lid.<br />
#Transfer the DNA complexes for 60 minutes at 60V at 4 &deg;C.<br />
#Remove the membrane from the transfer stack and place into a clean dish.<br />
#Immobolize the DNA complexes onto the membrane using the UV Cross-linker.<br />
#Store the membrane in cold 0.5X TBE buffer at 4 &deg;C.<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:06:26Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#Electrophorese the DNA complexes for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:03:07Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|750px|left]]<br />
#The DNA complexes will electrophorese for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:02:53Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|800px|left]]<br />
#The DNA complexes will electrophorese for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:02:35Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|700px|left]]<br />
#The DNA complexes will electrophorese for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyellhttp://measurebiology.org/wiki/20.109(S24):M1D720.109(S24):M1D72024-03-01T17:02:14Z<p>Noreen Lyell: /* Part 1: Prepare and electrophorese DNA complexes */</p>
<hr />
<div><div style="padding: 10px; width: 820px; border: 5px solid #434a43;"><br />
{{Template:20.109(S24)}}<br />
<br />
<br />
==Introduction==<br />
<br />
[[Image:Sp24 M1D6 EMSA schematic.png|thumb|500px|center|Image modified from Signosis, Inc.]]<br />
<br />
==Protocols==<br />
<br />
===Part 1: Prepare and electrophorese DNA complexes===<br />
#Obtain your nuclear extract from the front laboratory bench.<br />
#*Be sure to keep your extract on ice as you are working!<br />
#To calculate the volume of extract for the DNA complex reaction, you will use the NanoDrop to determine the concentration.<br />
#*Alert the teaching assistant when you are ready to use the NanoDrop and they will assist you.<br />
#Determine the volume of extract needed to add 2 &mu;g of protein to your reaction.<br />
#*If the volume calculated is more than 6 &mu;L alert your Instructor.<br />
#Add the following components to a 0.2 mL PCR tube in an ice bucket:<br />
#*X &mu;L nuclear extract (2 &mu;g)<br />
#** X = volume you calculated in Step #3.<br />
#*1 &mu;L Poly D (I-C)<br />
#*2 &mu;L 5X binding buffer<br />
#*1 &mu;L small molecule<br />
#*Y &mu;L nuclease-free water<br />
#**Y = volume of nuclease-free water needed to bring final volume up to 10 &mu;L.<br />
#Incubate the reaction on ice for 5 minutes.<br />
#Add 1 &mu;L of TF probe.<br />
#Incubate the reaction at 22 &deg;C for 30 minutes in the PCR machine.<br />
#Add 1 &mu;L of 10X loading buffer.<br />
#Load your sample into the TBE polyacrylamide gel according to the maps below:<br />
#*[[Image:Sp24 M1D7 gel load map.png|thumb|600px|left]]<br />
#The DNA complexes will electrophorese for 60 minutes at 100 V at 4 &deg;C.<br />
<br />
===Part 2: Transfer DNA complexes onto membrane===<br />
<br />
===Part 3: In-class paper discussion===<br />
<br />
To further help you in preparing your Data summary, we will discuss how similar data are presented in a publication from the Koehler laboratory.<br />
<br />
Chen ''et al.'' titled "[[Media:SMMAlzABPeptide Koehler2010.pdf |Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's A&beta; peptide]]" (2010) ''J Am Chem Soc'' 132:17015-17022.<br />
<br />
The initial experiment presented by Chen ''et. al.'' was an SMM that identified ligands binders of the amyloid-&beta; (A&beta;) petptide. This first step is very similar to what was done to identify the hits you are testing in this module! To further assess the results of the SMM, the authors completed several follow-up experiments to test the effect of the small molecule on functionality of the A&beta; petptide. <br />
<br />
In the context of your research, this article focuses on the next step experiments that can be performed after a drug candidate is discovered from a screen. Though you can use this article as guidance as you consider the experiments that could follow your screen, remember that the specific next step experiments should be related to the protein target and drug candidate(s) identified in your project. For this exercise, the focus in on how the data are organized and presented.<br />
<br />
'''From the Introduction'''<br />
<br />
Consider the key components of an introduction:<br />
*What is the big picture? <br />
*Is the importance of this research clear?<br />
*Are you provided with the information you need to understand the research?<br />
*Do the authors include a preview of the key results?<br />
<br />
'''From the Results'''<br />
<br />
Carefully examine the figures. First, read the captions and use the information to 'interpret' the data presented within the image. Second, read the text within the results section that describes the figure.<br />
*Do you agree with the conclusion(s) reached by the authors?<br />
*What controls were included and are they appropriate for the experiment performed?<br />
*Are you convinced that the data are accurate and/or representative?<br />
<br />
'''From the Discussion'''<br />
<br />
Consider the following components of a discussion:<br />
*Are the results summarized?<br />
*Did the authors 'tie' the data together into a cohesive and well-interpreted story?<br />
*Do the authors overreach when interpreting the data?<br />
*Are the data linked back to the big picture from the introduction?<br />
<br />
<font color = #4a9152 >'''In your laboratory notebook,'''</font color> complete the following:<br />
*Based on your reading and the group discussion of the article, answer the questions above.<br />
<br />
==Reagent list==<br />
<br />
<br />
<br />
==Navigation links==<br />
Next day: [[20.109(S24):M1D8 |Evaluate experimental results]] <br><br />
Previous day: [[20.109(S24):M1D6 |Prepare cells for electromobility shift assay (EMSA)]] <br></div>Noreen Lyell