Meeting Minutes for July 7, 2006

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Minutes for Weekly meeting (7/7)
Minutes for Weekly meeting (7/7)
-
Indiv. Member Responsibilities: still underway
+
'''Indiv. Member Responsibilities: still underway'''
-
Project Progress
+
'''Freeze tag:'''<br>
 +
-MotB flagellar machinery is intact, not structurally changing bacteria, just the motor (good)<br>
 +
- it bridges into to the cell, shouldn’t cause a quantum increase <br>
-
Freeze tag:
+
'''Sender cell:''' all parts grown up, minipreps on all parts. Colonies didn’t grow run another gel, digest it, get it sequenced and ligate the 3 parts together. <br>
-
Problems:
+
-will sequence after first digestion (Brendan)<br>
-
-MotB flagellar machinery is intact, not structurally changing bacteria, just the motor (good)
+
-designing the primers: Annie and Prof. Wessel<br>
-
- it bridges into to the cell, shouldn’t cause a quantum increase
+
'''Receiver cell:''' need to run digest of the two parts (Victoria and Megan)<br>
-
-LVA: is it made individually? Cell recognizes it as mRNA
+
'''“Freeze Machine”:''' need to incubate cells, do minipreps (Jamie and Annie) <br>
 +
'''Unfreeze:''' do miniprep tonight (Jason and Azeem)<br>
-
Sender cell: all parts grown up, minipreps on all parts. Colonies didn’t grow
+
'''Modeling Mechanism'''<br>
-
run another gel, digest it, get it sequenced and ligate the 3 parts together
+
-put a gene then a protein with a line connecting it, RBS and primer is an effector of that pathway <br>
-
-will sequence after first digestion (Brendan)
+
-
-designing the primers: Annie and Prof. Wessel
+
-
Receiver cell: need to run digest of the two parts (Victoria and Megan)
+
-
“Freeze Machine”: need to incubate cells, do minipreps
+
-
Unfreeze: do miniprep tonight (Jason and Azeem)
+
-
Modeling Mechanism
+
Problems: can’t inhibit the rate the promoter outputs<br>
-
-put a gene then a protein with a line connecting it, RBS and primer is an effector of that pathway
+
-talks about having a metabox<br>
 +
-website: bio tapestry<br>
-
Problems: can’t inhibit the rate the promoter outputs
+
'''What are hopes of model?''' <br>
-
-talks about having a metabox
+
-10 internal signaling pathways, worth running time courses seeing how stable system is <br>
-
-website: bio tapestry
+
-does system break down if we vary concentrations?<br>
 +
-is there a way to do positive control, repressalator<br>
 +
-To check that logical sensible<br>
 +
-want to see if signaling cell will actually stop the receiver cell, if not, can we figure out the strength of the RBS necessary to get the job done<br>
 +
-focus of small steps: once we get the sensor and sender of AHL working we can then test it out to define rate laws (do so by putting GFP at end of sequences-to test the POPs)<br>
-
What are hopes of model?
+
'''Magnetotacticbacteria'''<br>
-
-10 internal signaling pathways, worth running time courses seeing how stable system is
+
-
-does system break down if we vary concentrations?
+
-
-is there a way to do positive control, repressalator
+
-
-To check that logical sensible
+
-
-want to see if signaling cell will actually stop the receiver cell, if not, can we figure out the strength of the RBS necessary to get the job done
+
-
-focus of small steps: once we get the sensor and sender of AHL working we can then test it out to define rate laws (do so by putting GFP at end of sequences-to test the POPs)
+
-
How do we test AHL concentration (it is a lactose analog-a simple carbohydrate)?
+
-still alive<br>
 +
-looked at most concentrated vile, 3 cells in each visual field 200microliters, 50 microliters of food<br>
 +
-divided to some extent<br>
 +
-mixed up another vile to grow in anerobic bacterial incubator<br>
 +
-Hyato requested 4 types of plasmid, that Luciferase expresses much better, email has been sent out
 +
-Plamids modified in D5Halpha cells<br>
 +
-can electroborate into bacterial cells and the other to conjugate them<br>
 +
- before we can do anything we need to get a stable stock of the bacteria<br>
 +
-will try plating the bacteria now that we have access to anerobic chamber<br>
-
Right now we are using TetR promoter, will that be strong enough? Not that well characterisized.
 
-
-Brendan suggesting making a biobrick with T4 promoter (wouldn’t be that hard)
 
-
-Think we need 0.2 nanomoles of AHL to activate the AHL receiver
 
-
-look into buying AHL
+
'''Tasks that members have taken on:'''<br>
-
Magnetotacticbacteria
+
-Megan will look at options to synthesize avadin from scratch. Costs ? Practicality ?<br>
 +
-end goal to make a standard shuttle vector that can be used. <br>
-
-still alive
+
-take origin of replication from plasmids that we are looking for and insert them into the shuttle vector as a contribution to the biobricks registry. Important to make it compatible with most bacteria used in the project (Jason)<br>
-
-looked at most concentrated vile, 3 cells in each visual field 200microliters, 50 microliters of food
+
 
-
-divided to some extent
+
'''-wiki has been updated by Annie and Jamie'''
-
-mixed up another vile to grow in anerobic bacterial incubator
+
'''NB: you can update the particular parts for “the Freeze Tag”'''
-
-Hyato requested 4 types of plasmid, that Luciferase expresses much better, email has been sent out
+
-
-Plamids modified in D5Halpha cells
+
-
-can electroborate into bacterial cells and the other to conjugate them
+
-
- before we can do anything we need to get a stable stock of the bacteria
+
-
-will try plating the bacteria now that we have access to anerobic chamber
+
-
-can a biobick could be created for the plasmids?
+
'''General overview of Project (Azeem)'''
-
-we should get a hold of avadin part, then optimize codon usage, find restriction sites
+
'''Outreach Coordinator:  Megan'''
-
-look at article with Mag A,
+
-
Tasks that members have taken on:
+
'''Industry Liaison: Victoria'''
-
-Megan will look at options to synthesize avadin from scratch. Costs ? Practicality ?
+
'''Future Planning: Jason, Brendan, John Cumbers'''
-
-end goal to make a standard shuttle vector that can be used
+
-
-take origin of replication from plasmids that we are looking for and insert them into the shuttle vector as a contribution to the biobricks registry. Important to make it compatible with most bacteria used in the project (Jason)
+
'''Questions, Thoughts, Concerns?'''
-
-wiki has been updated by Annie and Jamie
+
(1.)can a biobick could be created for the plasmids?
-
you can update the particular parts for “the Freeze Tag”
+
-
-General overview of Project (Azeem)
+
-we should get a hold of avadin part, then optimize codon usage, find restriction sites <br>
 +
-look at article with Mag A <br>
-
Outreach Coordinator:  Megan
+
(2.)look into buying AHL<br>
-
Industry Liaison: Victoria
+
(3.)How do we test AHL concentration (it is a lactose analog-a simple carbohydrate)? <br>
 +
-Right now we are using TetR promoter, will that be strong enough? Not that well      characterisized.<br>
 +
-Brendan suggesting making a biobrick with T4 promoter (wouldn’t be that hard)<br>
 +
-Think we need 0.2 nanomoles of AHL to activate the AHL receiver<br>
-
Future Planning: Jason, Brendan, John Cumbers
+
(4.)LVA: is it made individually? Cell recognizes it as mRNA<br>

Latest revision as of 19:20, 13 July 2006

Minutes for Weekly meeting (7/7)

Indiv. Member Responsibilities: still underway

Freeze tag:
-MotB flagellar machinery is intact, not structurally changing bacteria, just the motor (good)
- it bridges into to the cell, shouldn’t cause a quantum increase

Sender cell: all parts grown up, minipreps on all parts. Colonies didn’t grow run another gel, digest it, get it sequenced and ligate the 3 parts together.
-will sequence after first digestion (Brendan)
-designing the primers: Annie and Prof. Wessel
Receiver cell: need to run digest of the two parts (Victoria and Megan)
“Freeze Machine”: need to incubate cells, do minipreps (Jamie and Annie)
Unfreeze: do miniprep tonight (Jason and Azeem)

Modeling Mechanism
-put a gene then a protein with a line connecting it, RBS and primer is an effector of that pathway

Problems: can’t inhibit the rate the promoter outputs
-talks about having a metabox
-website: bio tapestry

What are hopes of model?
-10 internal signaling pathways, worth running time courses seeing how stable system is
-does system break down if we vary concentrations?
-is there a way to do positive control, repressalator
-To check that logical sensible
-want to see if signaling cell will actually stop the receiver cell, if not, can we figure out the strength of the RBS necessary to get the job done
-focus of small steps: once we get the sensor and sender of AHL working we can then test it out to define rate laws (do so by putting GFP at end of sequences-to test the POPs)

Magnetotacticbacteria

-still alive
-looked at most concentrated vile, 3 cells in each visual field 200microliters, 50 microliters of food
-divided to some extent
-mixed up another vile to grow in anerobic bacterial incubator
-Hyato requested 4 types of plasmid, that Luciferase expresses much better, email has been sent out -Plamids modified in D5Halpha cells
-can electroborate into bacterial cells and the other to conjugate them
- before we can do anything we need to get a stable stock of the bacteria
-will try plating the bacteria now that we have access to anerobic chamber


Tasks that members have taken on:

-Megan will look at options to synthesize avadin from scratch. Costs ? Practicality ?
-end goal to make a standard shuttle vector that can be used.

-take origin of replication from plasmids that we are looking for and insert them into the shuttle vector as a contribution to the biobricks registry. Important to make it compatible with most bacteria used in the project (Jason)

-wiki has been updated by Annie and Jamie NB: you can update the particular parts for “the Freeze Tag”

General overview of Project (Azeem)

Outreach Coordinator: Megan

Industry Liaison: Victoria

Future Planning: Jason, Brendan, John Cumbers

Questions, Thoughts, Concerns?

(1.)can a biobick could be created for the plasmids?

-we should get a hold of avadin part, then optimize codon usage, find restriction sites
-look at article with Mag A

(2.)look into buying AHL

(3.)How do we test AHL concentration (it is a lactose analog-a simple carbohydrate)?
-Right now we are using TetR promoter, will that be strong enough? Not that well characterisized.
-Brendan suggesting making a biobrick with T4 promoter (wouldn’t be that hard)
-Think we need 0.2 nanomoles of AHL to activate the AHL receiver

(4.)LVA: is it made individually? Cell recognizes it as mRNA

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