Newcastle University/15 May 2008

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  [[Team:Newcastle University/Notebook|Back to Calendar]]
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  [[Team:Newcastle University/Meetings|Back to Calendar]]
'''Minutes'''
'''Minutes'''
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Action Plan for next week
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Minute Taker = Nina Nielson
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'''Action Plan for next week'''
Group
Group
• Register individually with Newcastle Team for iGEM 2008. Reference code for our team: ff53e1.
• Register individually with Newcastle Team for iGEM 2008. Reference code for our team: ff53e1.
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• Find unique quorum sensing peptides so the parts can de defined.
• Find unique quorum sensing peptides so the parts can de defined.
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• Set up a “Unique Peptides” section on the Wiki, describing the research carried out.
• Set up a “Unique Peptides” section on the Wiki, describing the research carried out.
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• Set up individual project lab work books on Wiki.
• Set up individual project lab work books on Wiki.
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• Design poster/web page for marketing.
• Design poster/web page for marketing.
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• Make sure all of the weeks work and the papers used are up on the Wiki
• Make sure all of the weeks work and the papers used are up on the Wiki
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Megan
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'''Megan'''
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• Produce individual models for the types of parts
• Produce individual models for the types of parts
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• CellML research
• CellML research
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• Investigate parts for the chosen peptide
• Investigate parts for the chosen peptide
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Nina
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'''Nina'''
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• RDF research, try to implement
• RDF research, try to implement
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• Make an ERD to contribute to design documentation.
• Make an ERD to contribute to design documentation.
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• CellML research
• CellML research
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• Finish compatibility matrix  
• Finish compatibility matrix  
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Mark
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'''Mark'''
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• Look further into neural network simulators
• Look further into neural network simulators
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• Generate noisy data
• Generate noisy data
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• Watch out for over training the network
• Watch out for over training the network
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• Source forge, look at codes.
• Source forge, look at codes.
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• Start planning the programme code.
• Start planning the programme code.
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Attended by:
Attended by:
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Neil Wipat – Supervisor
Neil Wipat – Supervisor
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Jen Hallinan – Supervisor
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Jen Hallinan – Supervisor
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Morgan Taschuk – Project 5
Morgan Taschuk – Project 5
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Mark Wappett – Project 3
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Mark Wappett – Project 3
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Megan Aylward – Project 1
Megan Aylward – Project 1
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                        Nina Nielsen – Project 2
 
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Nina Nielsen – Project 2
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Meeting Content
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'''Meeting Content'''
Agenda 1: Unique peptides in a range of species.
Agenda 1: Unique peptides in a range of species.
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Megan (S.  pneumoniae)  
Megan (S.  pneumoniae)  
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(Suntharalingam et al., 2005)
(Suntharalingam et al., 2005)
• The ComD (HK) and ComE (RR) two component system.
• The ComD (HK) and ComE (RR) two component system.
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• Quorum sensing peptide CSP (encoded by ComC) could be a potential peptide
• Quorum sensing peptide CSP (encoded by ComC) could be a potential peptide
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• An alternative sigma factor, ComX, controls the induction of the late competence genes after the early competence genes.
• An alternative sigma factor, ComX, controls the induction of the late competence genes after the early competence genes.
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Mark (Bacillus anthracis)
Mark (Bacillus anthracis)
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(Mark drew a schematic of this on the board.)
(Mark drew a schematic of this on the board.)
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• The ComP (HK) and ComA (RR) two component system
• The ComP (HK) and ComA (RR) two component system
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• Quorum sensing peptides (yes, two!) in question are ComX and CSF
• Quorum sensing peptides (yes, two!) in question are ComX and CSF
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• ComX is the main competence stimulating pheromone
• ComX is the main competence stimulating pheromone
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• Activation and secretion of ComX requires ComQ.
• Activation and secretion of ComX requires ComQ.
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• Both genes encoding the above proteins lie in the operon together with the genes encoding the TCS.
• Both genes encoding the above proteins lie in the operon together with the genes encoding the TCS.
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Nina (Staphylococcus epidermidis)
Nina (Staphylococcus epidermidis)
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• A single quorum sensing system exists (agr).
• A single quorum sensing system exists (agr).
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• The same as that characterized earlier in Staphylococcus aureus (I now know this not to be true as I found a more recent paper that has identified the presence of the LuxS quorum sensing system too!!)
• The same as that characterized earlier in Staphylococcus aureus (I now know this not to be true as I found a more recent paper that has identified the presence of the LuxS quorum sensing system too!!)
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Demo of his simulated neural network.  
Demo of his simulated neural network.  
Jen explains that the architecture should remain fixed and only the weights (not really the order of the parts) should be swapped/changed. There are two ways to train the simulation to reach a threshold value.  
Jen explains that the architecture should remain fixed and only the weights (not really the order of the parts) should be swapped/changed. There are two ways to train the simulation to reach a threshold value.  
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• Initially set random numbers and then look at the parameters to see which ones fit those numbers.
• Initially set random numbers and then look at the parameters to see which ones fit those numbers.
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• Build a real network working with the constraints all along. This takes longer.
• Build a real network working with the constraints all along. This takes longer.
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Morgan (5)
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'''Morgan (5)'''
Demo of the work bench so far. Showed how the projects will be communicating and how she would put the parts together. Different colours indicated the type, behaviour and constraints of the parts.  
Demo of the work bench so far. Showed how the projects will be communicating and how she would put the parts together. Different colours indicated the type, behaviour and constraints of the parts.  
Also showed her lab work book.
Also showed her lab work book.
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• Italicising bacterial species on the internal and external Wiki.
• Italicising bacterial species on the internal and external Wiki.
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• Getting rid of Staphylococcus Epidermidis.
• Getting rid of Staphylococcus Epidermidis.
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• Adding that a neural network in vivo will be implemented.
• Adding that a neural network in vivo will be implemented.
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• Editing sentence structure.
• Editing sentence structure.
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Agenda 4: Timeline
 
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This highlights the urgency of identifying unique peptides so we can finally define the parts.
 
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Month May June July August
 
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Week 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
 
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Task Parts defined,
 
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Design docs.  finished Programme
 
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design (pseudocode) Basic
 
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programme
 
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finished
 
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(CHAMPAGNE) Coding final
 
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programme Finish
 
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Coding Integration DNA sequence
 
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synthesis WRITE UP
 
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(possibly half hour labs too)
 
At least a week is needed for DNA synthesis.
At least a week is needed for DNA synthesis.
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• Jen suggests the students attend the writing group meetings on Thursday mornings. The meetings could be useful for writing up the projects in August.
• Jen suggests the students attend the writing group meetings on Thursday mornings. The meetings could be useful for writing up the projects in August.
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• Morgan creates a shorter and hopefully more memorable URL for the internal Wiki. http://beam.to/ncl_igem_private.
• Morgan creates a shorter and hopefully more memorable URL for the internal Wiki. http://beam.to/ncl_igem_private.
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• Mark explains his friend and potential addition to the team is in the process of finding out whether he can commit to iGem over the summer. When he finds out, he will email Neil.
• Mark explains his friend and potential addition to the team is in the process of finding out whether he can commit to iGem over the summer. When he finds out, he will email Neil.
 +
• The DNA sequences have arrived at Newcastle University. They are stored on paper… cooooool!!!
• The DNA sequences have arrived at Newcastle University. They are stored on paper… cooooool!!!
.
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Latest revision as of 19:34, 27 August 2008

Back to Calendar


Minutes

Minute Taker = Nina Nielson

Action Plan for next week

Group • Register individually with Newcastle Team for iGEM 2008. Reference code for our team: ff53e1.

• Find unique quorum sensing peptides so the parts can de defined.

• Set up a “Unique Peptides” section on the Wiki, describing the research carried out.

• Set up individual project lab work books on Wiki.

• Design poster/web page for marketing.

• Make sure all of the weeks work and the papers used are up on the Wiki

Megan

• Produce individual models for the types of parts

• CellML research

• Investigate parts for the chosen peptide

Nina

• RDF research, try to implement

• Make an ERD to contribute to design documentation.

• CellML research

• Finish compatibility matrix

Mark

• Look further into neural network simulators

• Generate noisy data

• Watch out for over training the network

• Source forge, look at codes.

• Start planning the programme code.


The meeting

Time: 14:30 – 17:20

Attended by:

Neil Wipat – Supervisor

Jen Hallinan – Supervisor

Morgan Taschuk – Project 5

Mark Wappett – Project 3

Megan Aylward – Project 1

Nina Nielsen – Project 2



Meeting Content

Agenda 1: Unique peptides in a range of species.

Each of the students have researched unique quorum sensing peptides to detect the presence for Streptococcus pneumoniae (Megan), Bacillus anthracis (Mark) and Staphylococcus epidermidis (Nina).

Megan (S. pneumoniae)

(Suntharalingam et al., 2005)

• The ComD (HK) and ComE (RR) two component system.

• Quorum sensing peptide CSP (encoded by ComC) could be a potential peptide

• An alternative sigma factor, ComX, controls the induction of the late competence genes after the early competence genes.

Neil Asks whether this system and the peptide are unique to S. pneumoniae? It is suggested to Blast the ComC gene to identify homologues.

Mark (Bacillus anthracis)

(Mark drew a schematic of this on the board.) http://dissertations.ub.rug.nl/FILES/faculties/science/2005/k.a.susanna/c1.pdf


• The ComP (HK) and ComA (RR) two component system

• Quorum sensing peptides (yes, two!) in question are ComX and CSF

• ComX is the main competence stimulating pheromone

• Activation and secretion of ComX requires ComQ.

• Both genes encoding the above proteins lie in the operon together with the genes encoding the TCS.

Neil Queries the possibility of having two biosensors. Suggests that one could use it to identify different species with different FP’s.

Group Begins discussion about what are primary colours.

Nina (Staphylococcus epidermidis)

• A single quorum sensing system exists (agr).

• The same as that characterized earlier in Staphylococcus aureus (I now know this not to be true as I found a more recent paper that has identified the presence of the LuxS quorum sensing system too!!)

Neil and Group Decide that since S. epidermidis predominantly causes infections associated with indwelling medical devices, rather than disease, it is not worth looking further into. The problem is not as severe as anthrax or pneumonia.

Neil and Jen Advise it might be easier to search for species specific quorum sensing peptides by initially identifying a peptide and working backwards towards the species. However, we need to keep in mind that the species must be pathogenic.


Agenda 2: Individual Project Progress

Megan (1) Showed an ERD she produced of the parts and the parameters to consider. Also showed the associated table format.

Mark (3) Demo of his simulated neural network. Jen explains that the architecture should remain fixed and only the weights (not really the order of the parts) should be swapped/changed. There are two ways to train the simulation to reach a threshold value.

• Initially set random numbers and then look at the parameters to see which ones fit those numbers.

• Build a real network working with the constraints all along. This takes longer.

Nina (2) Explains methods of defining which parts are compatible with others, rather than guesswork. These included finding structural homologues known to interact of the part(s) in question and using the search box on the parts repository database. She showed a matrix of her results so far, using the parts defined last week.


Morgan (5) Demo of the work bench so far. Showed how the projects will be communicating and how she would put the parts together. Different colours indicated the type, behaviour and constraints of the parts. Also showed her lab work book.


Agenda 3: The theme is edited on the Wiki

• Italicising bacterial species on the internal and external Wiki.

• Getting rid of Staphylococcus Epidermidis.

• Adding that a neural network in vivo will be implemented.

• Editing sentence structure.

At least a week is needed for DNA synthesis.


AOB

• Jen suggests the students attend the writing group meetings on Thursday mornings. The meetings could be useful for writing up the projects in August.

• Morgan creates a shorter and hopefully more memorable URL for the internal Wiki. http://beam.to/ncl_igem_private.

• Mark explains his friend and potential addition to the team is in the process of finding out whether he can commit to iGem over the summer. When he finds out, he will email Neil.

• The DNA sequences have arrived at Newcastle University. They are stored on paper… cooooool!!!


.

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