Difference between revisions of "Wet Lab Pages"

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Our part numbers will be in this range only: '''BBa_K091000 to BBa_K091999'''.  
 
Our part numbers will be in this range only: '''BBa_K091000 to BBa_K091999'''.  
  
−
# [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Wet Lab Protocols]
+
# [[Davidson Protocols]]
−
#[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Wet Lab Protocols]
+
# [[MWSU_protocols]]
 +
# [http://spreadsheets.google.com/pub?key=pw-NamR_FPJOfhl6mDrkZcw Davidson -80 Stocks]
 +
# [[Status Of Building Parts]]
 +
# [[Divide and Conquer Biological Challenges]]
 +
#[[Designing XOR Gates - two campus approach]]
 +
#[[Davidson Projects with Updates]]
 +
# [http://en.wikipedia.org/wiki/Logic_gates#Symbols Logic Gates in Wikipedia]
 +
# [http://www.bio.davidson.edu/Courses/Synthetic/papers/LuxR.pdf Build a LuxR Repressor '''PDF Reprint''']
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html Plasmid Compatability]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html Plasmid Compatability]
−
# [http://spreadsheets.google.com/pub?key=pw-NamR_FPJOfhl6mDrkZcw Davidson -80 Stocks]
+
# [[Using Amp and Amp^R as communication]]
−
#[http://tools.wikimedia.de/~tangotango/nubio/ FAQs for Wikis]
+
# [http://tools.wikimedia.de/~tangotango/nubio/ FAQs for Wikis]
 +
# [[Oligos to Build]]
 +
# [[Parts to send to Davidson on Thursday, 6/26/08]]
 +
 
 
<br>
 
<br>
 
----
 
----
 
== Registry parts to clone ==
 
== Registry parts to clone ==
 +
'''Things to Do'''
 +
 +
#  Experiment with making lines of media in petri dishes.
 +
# Determine concentration of HSL needed to turn on our receiver + reporter. Compare with [http://partsregistry.org/wiki/index.php?title=Part:BBa_T9002 BBa_T9002]
 +
# Determine what percent of a colony need to be sender cells in order for an entire colony to become switched on by HSL.
 +
# We need to make sender and receiver cells (using existing sub-parts such as [http://partsregistry.org/wiki/index.php?title=Part:BBa_F1610 F1610]), and/or take from registry (''e.g.'', [http://partsregistry.org/wiki/index.php?title=Part:BBa_T9002 BBa_T9002])
 +
# Design experiments to test the distance HSL and beta lactamase can diffuse in agar and over what time spans.
 +
# Make a derived pLac promoter that will permit LuxR+HSL to be a repressor to be used in combination with Lux pR promoter. [http://www.bio.davidson.edu/Courses/Synthetic/papers/LuxR.pdf See this paper.]Andrew Gordon, Robert Cool
 +
# Make an Amp<sup>R</sup> sender device. Look for Amp<sup>R</sup> basic part in Registry.
 +
 +
  
 
'''Composite Parts''':
 
'''Composite Parts''':
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!width="30"|Resistance
 
!width="30"|Resistance
 
!width="30"|Results from 5/22/08
 
!width="30"|Results from 5/22/08
 +
!width="30"|miniprep
 +
|-
 +
|BBa_F2621|| AHL receiver with lux pR and codes for LuxR || Karlesha Roland (DC) || 1001 12B pSB1A2 || amp || growth MW  ||no
 
|-
 
|-
−
|BBa_F2621|| AHL receiver with lux pR and codes for LuxR || Karlesha Roland (DC) || 1001 12B pSB1A2 || amp || growth MW
+
|BBa_I15030 || Lux-sender(Autoinducing)Codes for LuxI and LuxR || Kelly Davis (DC) will this send to part BBa_I13263 || 1015 8F pSB3K3 || kan || growth MW || no
 
|-
 
|-
−
|BBa_I15030 || Lux-sender(Autoinducing)Codes for LuxI and LuxR || Kelly Davis (DC) will this send to part BBa_I13263 || 1015 8F pSB3K3 || kan || growth MW
+
|BBa_I13263 || Lux Receiver (HSL & R0063 driven)produces YFP || Pallavi Penumetcha (DC)|| 1002 8E pSB1A2 || amp || growth MW & DC || yes 210ng/ml
 
|-
 
|-
−
|BBa_I13263 || Lux Receiver (HSL & R0063 driven)produces YFP || Pallavi Penumetcha (DC)|| 1002 8E pSB1A2 || amp || growth MW & DC
+
|BBa_f2622 || 3OC6HSL receiver that outputs PoPS || James Barron (DC) || 1001 12E pSB1A2 || amp || no growth || no
 
|-
 
|-
−
|BBa_f2622 || 3OC6HSL receiver that outputs PoPS || James Barron (DC) || 1001 12E pSB1A2 || amp || no growth
+
|BBa_F1610 || Device that receives PoPS and outputs LuxI || Malcolm Campbell (DC) || 1016 10D pSB1AK3 || amp & kan || growth MW || no  
 
|-
 
|-
−
|BBa_F1610 || Device that receives PoPS and outputs LuxI || Malcolm Campbell (DC) || 1016 10D pSB1AK3 || amp & kan || growth MW
+
|BBa_I0426 || Las-reciver(EYFP) || Kristi Muscalino (DC) || 1008 5B pSB1A2 || amp || growth MW & DC || yes 210ng/ml
 
|-
 
|-
−
|BBa_I0426 || Las-reciver(EYFP) || Kristi Muscalino (DC) || 1008 5B pSB1A2 || amp || growth MW & DC
+
|BBa_I0407 || LasI test || Erin Feeney (DC) || 1008 4F pSB1A2 || amp || growth MW & DC || yes 76.37ng/ml
 
|-
 
|-
−
|BBa_I0407 || LasI test || Erin Feeney (DC) || 1008 4F pSB1A2 || amp || growth MW & DC
+
|BBa_I0466|| RhlR Protein Generator without LVA || Laurie Heyer (DC) || 1001 5C pSB1A2 || amp || growth MW || yes 129.7ng/ml
 
|-
 
|-
−
|BBa_I0466|| RhlR Protein Generator without LVA || Laurie Heyer (DC) || 1001 5C pSB1A2 || amp || growth MW
+
|BBa_F2620|| Device receives 3OC6HSL outputs PoPS || Robert Cool (MW) || 1001 12D pSB1A2 || amp || growth MW || yes 83ng/ml
 
|-
 
|-
 
|}
 
|}
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!width="30"|Resistance
 
!width="30"|Resistance
 
!width="30"|Results from 5/22/08
 
!width="30"|Results from 5/22/08
 +
!width="30"|miniprep
 
|-
 
|-
−
|BBa_C0061 || LuxI gene with LVA || Madeline Parra (DC) || 1000 3E pSB1A2 || amp || growth MW
+
|BBa_C0061 || LuxI gene with LVA || Madeline Parra (DC) || 1000 3E pSB1A2 || amp || growth MW || yes 143ng/ml
 
|-
 
|-
−
|BBa_C0161 || LuxI gene without LVA || Xiao Zhu (MW) || 1001 8B pSB1A2 || amp ||
+
|BBa_C0161 || LuxI gene without LVA || Xiao Zhu (MW) || 1001 8B pSB1A2 || amp || ||no
 
|-
 
|-
−
|BBa_C0062 || LuxR gene without LVA || John Igo (MW) || 1000 3F pSB1A2 || amp ||
+
|BBa_C0062 || LuxR gene without LVA || John Igo (MW) || 1000 3F pSB1A2 || amp || ||no
 
|-
 
|-
−
|BBa_R0063 || lux pL|| Aaron Lewis (MW) || 1000 4H pSB1A2 || amp ||  
+
|BBa_R0063 || lux pL|| Aaron Lewis (MW) || 1000 4H pSB1A2 || amp || ||yes 8.86 ng/ml
 
|-
 
|-
−
|BBa_R0062|| lux pR|| Andrew Gordon(MW) || 1000 4G pSB1A2 || amp ||
+
|BBa_R0062|| lux pR|| Andrew Gordon(MW) || 1000 4G pSB1A2 || amp || ||yes 62.4ng/ml
 
|-
 
|-
−
|BBa_C0070||  rhlI gene  ||  Jeff Poet (MW) || 1013 3E pSB2K3 || kan ||  
+
|BBa_C0070||  rhlI gene  ||  Jeff Poet (MW) || 1013 3E pSB2K3 || kan || ||no
 
|-
 
|-
−
|BBa_C0071|| rhlR gene with LVA|| Max Win (DC) || 1013 3F pSB2K3 || kan || no growth
+
|BBa_C0071|| rhlR gene with LVA|| Max Win (DC) || 1013 3F pSB2K3 || kan || no growth ||no
 
|-
 
|-
−
|BBa_C0171|| rhlR gene without LVA || MWSU || 1001 6F pSB1A2 || amp ||  
+
|BBa_C0171|| rhlR gene without LVA || MWSU || 1001 6F pSB1A2 || amp || ||no
 
|-
 
|-
−
|BBa_R0079 || las pR || Todd Eckdahl (MW) || 1001 10F pSB1A2 || amp ||  
+
|BBa_R0079 || las pR || Todd Eckdahl (MW) || 1001 10F pSB1A2 || amp || ||yes 117.2ng/ml
 
|-
 
|-
−
|BBa_C0079 || lasR gene || Robert Cool (MW) || 1013 4F pSB2K3 || kan ||  
+
|BBa_C0079 || lasR gene || Robert Cool (MW) || 1013 4F pSB2K3 || kan || ||no
 
|-
 
|-
−
|BBa_C0078 || LasI gene || Alicia Allen (MW) || 1013 4E pSB2K3 || kan ||  
+
|BBa_C0078 || LasI gene || Alicia Allen (MW) || 1013 4E pSB2K3 || kan ||   ||no
 
|-
 
|-
 
|BBa_J07019 || fecA promoter with Fur box || Not in Registry|| || ||  
 
|BBa_J07019 || fecA promoter with Fur box || Not in Registry|| || ||  
 
|-
 
|-
−
|BBa_#### || Description || Sven(MW) || || ||  
+
|}
 +
 
 +
'''Fluorescent Protein Gradient Testers''':
 +
 
 +
{| border="1" cellpadding="2"
 +
!width="50"|Part
 +
!width="225"|Description
 +
!width="225"|Student Responsible (DC or MW)
 +
!width="30"|Location and Vector
 +
!width="30"|Resistance
 +
!width="30"|Results
 +
!width="30"|miniprep
 +
|-
 +
|BBa_J04450 || [http://partsregistry.org/Part:BBa_J04450 Lac-RBS-RFP-T] || Robert Cool (MW) ||1004 4f pSB1A2 || amp ||  ||yes 183ng/ml
 +
|-
 +
|BBa_J04451 || [http://partsregistry.org/Part:BBa_J04451 pLac-RBS-RFP w/ LVA tag-T-T] || Erin Feeney  and Kelly Davis (DC) ||1016 9F pSB1AK3 || amp and kan ||  ||no
 +
|-
 +
|BBa_I13520 || [http://partsregistry.org/Part:BBa_I13520 pBAD-RBS-mRFP-T-T] || Erin Feeney and Kelly Davis (DC) || 1009 7B pSB1A2 || amp || ||no
 
|-
 
|-
−
|BBa_#### || Description || Sven(MW) || || ||  
+
|BBa_J5528 || [http://partsregistry.org/Part:BBa_J5528 pBAD-RBS-GFP-T-T] || Erin Feeney and Kelly Davis (DC) || 1015 7A pSB2K3 || kan || ||no
 
|-
 
|-
−
|BBa_#### || Description || Sven(MW) || || ||  
+
|BBa_J04430 || [http://partsregistry.org/Part:BBa_J04430 pLac-RBS-GFP-T-T] || Erin Feeney and Kelly Davis (DC) || 1004 4H pSB1A2 || amp || ||yes 143ng/ml
 
|}
 
|}
  
−
'''Fluorescent Protein Gradient Testers''':
+
 
 +
'''Parts for Sending and Receiving Signals''':
  
 
{| border="1" cellpadding="2"
 
{| border="1" cellpadding="2"
Line 89: Line 132:
 
!width="30"|Resistance
 
!width="30"|Resistance
 
!width="30"|Results
 
!width="30"|Results
 +
!width="30"|miniprep
 +
|-
 +
|BBa_J07019 || [http://partsregistry.org/Part:BBa_J07019 fec A promoter with fur box]|| James Barron (DC) || Not in Registry-Needs to be amplified || ||
 
|-
 
|-
−
|BBa_J04450 || Lac-RBS-RFP-T || Robert Cool (MW) ||1004 4f pSB1A2 ||amp ||  
+
|BBa_F2622 || [http://partsregistry.org/Part:BBa_F2622 3OC6HSL Receiver Device]|| Pallavi Penumetcha (DC) ||1001 12e pSB1A2 || amp || ||no
 
|-
 
|-
−
|BBa_#### || Description || Surfer dude (DC) || || ||  
+
|BBa_I14032 || [http://partsregistry.org/Part:BBa_I14032 pLac promoter]|| Pallavi Penumetcha (DC) || 1013 8e pSB2K3 || kan || ||no
 
|-
 
|-
−
|BBa_#### || Description || Surfer dude (DC) || || ||  
+
|BBa_S03632 || [http://partsregistry.org/Part:BBa_S03632 lacI promoter and luxI gene]|| Pallavi Penumetcha (DC) || 1016 7f pSB1AK3 || amp and kan || ||no
 
|-
 
|-
−
|BBa_#### || Description || Surfer dude (DC) || || ||  
+
|BBa_E0240 || [http://partsregistry.org/Part:BBa_E0240 RBS and GFP]|| Pallavi Penumetcha (DC) || 1001 4B pSB1A2 || amp || ||yes 130ng/ml
 
|}
 
|}

Latest revision as of 16:40, 30 March 2011

This is the space for MWSU and DC wet lab students to create content. Our part numbers will be in this range only: BBa_K091000 to BBa_K091999.

  1. Davidson Protocols
  2. MWSU_protocols
  3. Davidson -80 Stocks
  4. Status Of Building Parts
  5. Divide and Conquer Biological Challenges
  6. Designing XOR Gates - two campus approach
  7. Davidson Projects with Updates
  8. Logic Gates in Wikipedia
  9. Build a LuxR Repressor PDF Reprint
  10. Plasmid Compatability
  11. Using Amp and Amp^R as communication
  12. FAQs for Wikis
  13. Oligos to Build
  14. Parts to send to Davidson on Thursday, 6/26/08


Registry parts to clone

Things to Do

  1. Experiment with making lines of media in petri dishes.
  2. Determine concentration of HSL needed to turn on our receiver + reporter. Compare with BBa_T9002
  3. Determine what percent of a colony need to be sender cells in order for an entire colony to become switched on by HSL.
  4. We need to make sender and receiver cells (using existing sub-parts such as F1610), and/or take from registry (e.g., BBa_T9002)
  5. Design experiments to test the distance HSL and beta lactamase can diffuse in agar and over what time spans.
  6. Make a derived pLac promoter that will permit LuxR+HSL to be a repressor to be used in combination with Lux pR promoter. See this paper.Andrew Gordon, Robert Cool
  7. Make an AmpR sender device. Look for AmpR basic part in Registry.


Composite Parts:

Part Description Student Responsible (DC or MW) Location and Vector Resistance Results from 5/22/08 miniprep
BBa_F2621 AHL receiver with lux pR and codes for LuxR Karlesha Roland (DC) 1001 12B pSB1A2 amp growth MW no
BBa_I15030 Lux-sender(Autoinducing)Codes for LuxI and LuxR Kelly Davis (DC) will this send to part BBa_I13263 1015 8F pSB3K3 kan growth MW no
BBa_I13263 Lux Receiver (HSL & R0063 driven)produces YFP Pallavi Penumetcha (DC) 1002 8E pSB1A2 amp growth MW & DC yes 210ng/ml
BBa_f2622 3OC6HSL receiver that outputs PoPS James Barron (DC) 1001 12E pSB1A2 amp no growth no
BBa_F1610 Device that receives PoPS and outputs LuxI Malcolm Campbell (DC) 1016 10D pSB1AK3 amp & kan growth MW no
BBa_I0426 Las-reciver(EYFP) Kristi Muscalino (DC) 1008 5B pSB1A2 amp growth MW & DC yes 210ng/ml
BBa_I0407 LasI test Erin Feeney (DC) 1008 4F pSB1A2 amp growth MW & DC yes 76.37ng/ml
BBa_I0466 RhlR Protein Generator without LVA Laurie Heyer (DC) 1001 5C pSB1A2 amp growth MW yes 129.7ng/ml
BBa_F2620 Device receives 3OC6HSL outputs PoPS Robert Cool (MW) 1001 12D pSB1A2 amp growth MW yes 83ng/ml

Basic Parts:

Part Description Student Responsible (DC or MW) Location and Vector Resistance Results from 5/22/08 miniprep
BBa_C0061 LuxI gene with LVA Madeline Parra (DC) 1000 3E pSB1A2 amp growth MW yes 143ng/ml
BBa_C0161 LuxI gene without LVA Xiao Zhu (MW) 1001 8B pSB1A2 amp no
BBa_C0062 LuxR gene without LVA John Igo (MW) 1000 3F pSB1A2 amp no
BBa_R0063 lux pL Aaron Lewis (MW) 1000 4H pSB1A2 amp yes 8.86 ng/ml
BBa_R0062 lux pR Andrew Gordon(MW) 1000 4G pSB1A2 amp yes 62.4ng/ml
BBa_C0070 rhlI gene Jeff Poet (MW) 1013 3E pSB2K3 kan no
BBa_C0071 rhlR gene with LVA Max Win (DC) 1013 3F pSB2K3 kan no growth no
BBa_C0171 rhlR gene without LVA MWSU 1001 6F pSB1A2 amp no
BBa_R0079 las pR Todd Eckdahl (MW) 1001 10F pSB1A2 amp yes 117.2ng/ml
BBa_C0079 lasR gene Robert Cool (MW) 1013 4F pSB2K3 kan no
BBa_C0078 LasI gene Alicia Allen (MW) 1013 4E pSB2K3 kan no
BBa_J07019 fecA promoter with Fur box Not in Registry

Fluorescent Protein Gradient Testers:

Part Description Student Responsible (DC or MW) Location and Vector Resistance Results miniprep
BBa_J04450 Lac-RBS-RFP-T Robert Cool (MW) 1004 4f pSB1A2 amp yes 183ng/ml
BBa_J04451 pLac-RBS-RFP w/ LVA tag-T-T Erin Feeney and Kelly Davis (DC) 1016 9F pSB1AK3 amp and kan no
BBa_I13520 pBAD-RBS-mRFP-T-T Erin Feeney and Kelly Davis (DC) 1009 7B pSB1A2 amp no
BBa_J5528 pBAD-RBS-GFP-T-T Erin Feeney and Kelly Davis (DC) 1015 7A pSB2K3 kan no
BBa_J04430 pLac-RBS-GFP-T-T Erin Feeney and Kelly Davis (DC) 1004 4H pSB1A2 amp yes 143ng/ml


Parts for Sending and Receiving Signals:

Part Description Student Responsible (DC or MW) Location and Vector Resistance Results miniprep
BBa_J07019 fec A promoter with fur box James Barron (DC) Not in Registry-Needs to be amplified
BBa_F2622 3OC6HSL Receiver Device Pallavi Penumetcha (DC) 1001 12e pSB1A2 amp no
BBa_I14032 pLac promoter Pallavi Penumetcha (DC) 1013 8e pSB2K3 kan no
BBa_S03632 lacI promoter and luxI gene Pallavi Penumetcha (DC) 1016 7f pSB1AK3 amp and kan no
BBa_E0240 RBS and GFP Pallavi Penumetcha (DC) 1001 4B pSB1A2 amp yes 130ng/ml
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