Brown:March142006

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[[Brown:iGEM portal 2006 |Home]]
 +
==Meeting Minutes for June 30, 2006==
 +
Agenda:<br>
 +
1. Update on project: split into three projects<br>
 +
2. Magnetotactic bacteria<br>
 +
3. everyone happy?<br>
 +
4. Actions <br>
 +
 +
'''Meeting Notes:'''<br>
 +
1. Update on project:<br>
 +
- Freeze machine: transformed all parts<br>
 +
- Sender: parts grown up, will start minipreps, restriction digests<br>
 +
- Unfreeze machine: parts grew<br>
 +
- Receiver: grew up parts for miniprep<br>
 +
2. Magnetotactic Bacteria<br>
 +
- they are growing<br>
 +
- wait five to seven days.<br>
 +
- plasmid: Peter: hasn’t found information. Needs help<br>
 +
- Hayato sent Tayhas an email and she has sent it regarding plasmid.<br>
 +
3. Money update<br>
 +
- we have 8000 in account<br>
 +
- Brenden will go and ask Carol<br>
 +
4. Device<br>
 +
- Azeem will talk to Professor Tripathi about building microfluidics chamber<br>
 +
- Guest speaker?<br>
 +
5. Modeling<br>
 +
- installing software<br>
 +
- Peter’s been using it. Has produced model of Azeem’s paper<br>
 +
6. Guest speakers<br>
 +
- reason is to have communications with other people in synthetic biology<br>
 +
- Somebody organizes the guest speaker and that organizer looks after the guest speaker. This job is shared around the department. Would this work for iGEM?<br>
 +
- People talk about project with guest speaker. Sign up for 45 minutes or so.<br>
 +
- Send out an email about signing up to talking with guest lecturer<br>
 +
7. Weekly meetings<br>
 +
- email people when you can’t come<br>
 +
8. Sequencing:<br>
 +
- To avoid sequencing, restriction digest and check with around right size with DNA ladder. <br>
 +
- Limit: 800 base pairs<br>
 +
- If longer than 800 base pairs, can order an oligo.<br>
 +
- Gene Wiz- someone on the third floor<br>
 +
- Prep the samples and send out. See Jamie for help. <br>
 +
9. Pfizer<br>
 +
- Send a thank you note and the wish list- Victoria<br>
 +
10. Project<br>
 +
- Brenden will draw pictures in photoshop<br>
 +
- Have a few to explain each part. <br>
 +
- Somebody put the idea onto the wiki<br>
 +
- Put everything on the public wiki<br>
 +
- Peter will move everything from private wiki to the public wiki<br>
 +
- Brenden to organize group picture<br>
 +
==Meeting Minutes for March 14, 2006==
==Meeting Minutes for March 14, 2006==
-
Assignment of roles:
+
===Assignment of roles===
-
Community Maker - Nick, Megan
+
'''Community Maker''' - Nick, Megan
-
Notetaker/Organizer (Secretary) - Angela
+
'''Notetaker/Organizer (Secretary)''' - Angela
-
Journal Club Coordinator - Elena
+
'''Journal Club Coordinator''' - Elena
-
Fundraising/PR
+
'''Fundraising/PR'''
-
Julie: Fundraising
+
* Julie: Fundraising, Sheldon
-
Brendan: PR
+
* Brendan: PR
-
Elaine: helping both
+
* Elaine: helping both
-
Faculty Liaison - Victoria
+
'''Faculty Liaison''' - Victoria
-
Wiki Development - Peter
+
'''Wiki Development''' - Peter
-
Research - Annie
+
'''Research''' - Annie, Sheldon
-
"Benevolent Dictator" =) - John
+
'''"Benevolent Dictator"''' =) - John
 +
'''Commercialization Potential''' (patents, etc)
 +
 +
'''Industry Laison'''
We have lab space in JWW!!!
We have lab space in JWW!!!
 +
==Meeting Minutes for March 21, 2006==
 +
 +
Present: John, Kara, Angela, Annie, Jessie, Peter, Brendan, Katherine, Victoria, Megan
 +
 +
===Journal Club Presentation===
 +
 +
====Construction of a Genetic Toggle Switch in E. Coli====
 +
 +
by Victoria and Megan
 +
 +
*purpose: to integrate theory and experiment by constructing and testing a synthetic, bistable gene circuit (Toggle switch) based on the predictions of a simple mathematical model
 +
*integrate (mathetic) theory and (biology) experiment
 +
*mathematical models supposed to predict how much transcribed, testing expected outcomes
 +
*took a switch that self-regulates and has inducer (heat, chemical) that starts
 +
*prediction was wrong due to gene variability
 +
*simplest, as few reagents as possible better
 +
*specialized promoters
 +
*ribozyme binding sites, harnessed in plasmid; ensure that they are turned into proteins individually
 +
*genetic engineering (memory device) insert into something that you would want to be turned on for a long time
 +
*registry of biological parts at MIT; biological switch, wire linked together (electronic diagramà biological diagram
 +
 +
===2005 iGEM project summaries:===
 +
 +
UCSF: Kara; genetic circuit of bacteria to respond to temperature gradient, analog vs. digital
 +
 +
Toronto: Angela; Cell See-Us Thermometer and Bacterial Etch-a-Sketch; used mRFP and GFP didn’t have a result
 +
 +
Berkeley: John; cell-cell communicator, send out genomes to other bacteria via a specific pore (channel) and the other bacteria would send something back when it received that message
 +
 +
Harvard: Peter; bio-sketch; use UV pen to write on bacteria, use GFP mutation as reporter; not so much a toggle switch as a one way switch; used heat to “erase”; didn’t work
 +
 +
Caltech: Annie; detect caffeine in solution; YFP and GFP high concentration of caffeine would repress GFP and YFP would glow; if decaf, YFP would be repressed and GFP would grow; if medium, then both would be present.
 +
 +
==Meeting Minutes for April 4, 2006==
 +
 +
Present: Jamie, Azime, John, Angela, Bo, Brendan, Peter, Jason, Jamie, Victoria Elena
 +
 +
===Journal Club Presentation===
 +
 +
====Engineering a pathway in E. Coli for turpenoids====
 +
 +
by Brendan and Peter
 +
 +
*turponoids - organic compound for making steroids
 +
*antimalarial medicine, etc. (anticancer, antihallucenogenic)
 +
*purified from plants, extracted from plants and then synthesized – limits
 +
*pathway from yeast and put into E. Coli
 +
*PCR created 3 mutant pathways, point mutations which inserted into E. Coli
 +
*2 of the sequences worked; combined the two (beginning of one and end of another)
 +
*isoprene 5C structure; double, single, double building blocks
 +
*IPP is inhibitor that halts cell growth (for MAP)
 +
*amorphodyein synthase consumes IPP, increases levels of mevalonate acid without halting cell growth
 +
*pathway doesn’t exist in nature; this pathway 10-300 fold increase in production
 +
*head of synthetic bio department of Berkeley (Gates Foundation gave lots of funding)
 +
*Melavonatic → MevP → MevPP → IPP &→ DMAPP
 +
::genes:  -ERG12  -ERG8    -MVD    -1d1              = these genes are in plants but not in E. Coli, so codon optimization corrects for differences in codons between bacteria and plants
 +
*then stepped back to beginning: melavonatic not a good precursor, so XYZ converts acetyl CoA (naturally occurring in cell and a lot *cheaper) into Melavonatic Acid (which is hard to get)
 +
concerned about product yield and amounts of cells, so another step was making sure that [IPP] kept low  à keeping cells alive as we put in genes, etc.
 +
 +
===Notes:===
 +
 +
*forward papers the week before to John so that he can make copies of diagrams, etc.
 +
*there will be workshops at beginning of summer about PCR, etc.
 +
*Ideas: get some more detail (make a concise description of) and let the faculty know about them and get their opinions on whether they are viable, linked to current faculty research:
 +
*#John: cell division counter – when (yeast) cells aging, different colors emitted from fluorochrome (like binary signal, red=1, blue =2, green = 3, etc. counts up to 32) if besides bacteria, takes longer to take up; bacteria, e.coli overnight; Harvard last year tried doing this; first round fine, but second on, harder; link color to cdk when transcribed, produced fluorochrome, activator and binds to promoter region of next and then repressor on next represses color from first one while another activator produces another color
 +
*#Julie: bacteria producing alkanes – products poisoning cells (alcohols, alkanes that act as detergents on membrane); talk to Dept of Energy? (speaker) – Prof Moulton
 +
*#analog devices: transistors scalable super computing; the more the cells grow, the more computational power you have; producing something useful is impractical; quorum sensing? like Minesweeper - Jamie
 +
*#bio sensors and actuators – live inside body and transmit info out; bio sensors sense the signals and actuators would amplify getting info of cell out (more complex than on/off); possibly like tumors
 +
*#free radical reporter - Victoria
 +
*#chemical detector – assembly line from input to receiver (like Berkeley team) Annie
 +
*#artificial organelle
 +
*#microbes that maintain/fix environment
 +
*#bacterial eye/radar – emit light (through reporter) and if reflects back, send out signal
 +
 +
==ACTIONS==
 +
 +
===March 14, 2006===
 +
* Victoria will go to SAO to get info about table for ADOCH
 +
* possibly also a web page/link to Brown iGEM
 +
* have a site for prospective students to see who we are, as well as our contact info
 +
* also, for everyone: think of ways to gain more attention
 +
 +
* Everyone: create a section on the wiki for the category you are overseeing
 +
 +
* Create a community portal:
 +
** serve as a site that can be linked possibly from admissions page
 +
** emphasizing that we are cross-disciplinary undergraduates performing research at Brown University, even several freshmen involved
 +
** have our slightly more colorful biolographical infos attached
 +
 +
* Possible ideas for our project?
 +
 +
* Victoria/Megan doing the Journal Club presentation next week.
 +
 +
===March 21, 2006===
 +
 +
Come up with an idea by first meeting after Spring Break
 +
 +
Journal Club Presenters: (in order of presentation): talk to faculty about them (we have 19!!!) send out papers to faculty early just to make sure.
 +
 +
*Peter and Brendan 4/4
 +
 +
*Angela and Annie 4/11
-
ACTIONS:
+
*Kara and Jessie 4/18
-
-Victoria will go to SAO to get info about table for ADOCH
+
-
-possibly also a web page/link to Brown iGEM
+
-
-have a site for prospective students to see who we are, as well as our contact info
+
-
-also, for everyone: think of ways to gain more attention
+
-
-Everyone: create a section on the wiki for the category you are overseeing
+
*Katherine and John 4/25
-
-Create a community portal by tomorrow
+
===April 4, 2006===
-
-serve as a site that can be linked possibly from admissions page
+
Journal projects for future:
-
-emphasizing that we are cross-disciplinary undergraduates performing research at Brown University, even several freshmen involved
+
*Angela and Annie 4/11
-
-have our slightly more colorful biolographical infos attached
+
*Kara and Jessie 4/18
 +
*Katherine and John 4/25
 +
*Jason and Azime 5/2
 +
*Elena and Jamie 5/9
-
-Possible ideas for our project?
+
Remember to decide a week ahead of time so that faculty can be contacted and help with your paper.
 +
Also remember that you can email John diagrams, etc. so that he can make copies for everyone at the Journal Club meeting.
-
-Victoria/Megan doing the Journal Club presentation next week.
 
-
-Jamie can't make this time, how should we accomodate?
+
Make concise descriptions of our ideas to send to faculty

Latest revision as of 14:13, 7 July 2006

Home

Contents

Meeting Minutes for June 30, 2006

Agenda:
1. Update on project: split into three projects
2. Magnetotactic bacteria
3. everyone happy?
4. Actions

Meeting Notes:
1. Update on project:
- Freeze machine: transformed all parts
- Sender: parts grown up, will start minipreps, restriction digests
- Unfreeze machine: parts grew
- Receiver: grew up parts for miniprep
2. Magnetotactic Bacteria
- they are growing
- wait five to seven days.
- plasmid: Peter: hasn’t found information. Needs help
- Hayato sent Tayhas an email and she has sent it regarding plasmid.
3. Money update
- we have 8000 in account
- Brenden will go and ask Carol
4. Device
- Azeem will talk to Professor Tripathi about building microfluidics chamber
- Guest speaker?
5. Modeling
- installing software
- Peter’s been using it. Has produced model of Azeem’s paper
6. Guest speakers
- reason is to have communications with other people in synthetic biology
- Somebody organizes the guest speaker and that organizer looks after the guest speaker. This job is shared around the department. Would this work for iGEM?
- People talk about project with guest speaker. Sign up for 45 minutes or so.
- Send out an email about signing up to talking with guest lecturer
7. Weekly meetings
- email people when you can’t come
8. Sequencing:
- To avoid sequencing, restriction digest and check with around right size with DNA ladder.
- Limit: 800 base pairs
- If longer than 800 base pairs, can order an oligo.
- Gene Wiz- someone on the third floor
- Prep the samples and send out. See Jamie for help.
9. Pfizer
- Send a thank you note and the wish list- Victoria
10. Project
- Brenden will draw pictures in photoshop
- Have a few to explain each part.
- Somebody put the idea onto the wiki
- Put everything on the public wiki
- Peter will move everything from private wiki to the public wiki
- Brenden to organize group picture

Meeting Minutes for March 14, 2006

Assignment of roles

Community Maker - Nick, Megan

Notetaker/Organizer (Secretary) - Angela

Journal Club Coordinator - Elena

Fundraising/PR

  • Julie: Fundraising, Sheldon
  • Brendan: PR
  • Elaine: helping both

Faculty Liaison - Victoria

Wiki Development - Peter

Research - Annie, Sheldon

"Benevolent Dictator" =) - John

Commercialization Potential (patents, etc)

Industry Laison

We have lab space in JWW!!!

Meeting Minutes for March 21, 2006

Present: John, Kara, Angela, Annie, Jessie, Peter, Brendan, Katherine, Victoria, Megan

Journal Club Presentation

Construction of a Genetic Toggle Switch in E. Coli

by Victoria and Megan

  • purpose: to integrate theory and experiment by constructing and testing a synthetic, bistable gene circuit (Toggle switch) based on the predictions of a simple mathematical model
  • integrate (mathetic) theory and (biology) experiment
  • mathematical models supposed to predict how much transcribed, testing expected outcomes
  • took a switch that self-regulates and has inducer (heat, chemical) that starts
  • prediction was wrong due to gene variability
  • simplest, as few reagents as possible better
  • specialized promoters
  • ribozyme binding sites, harnessed in plasmid; ensure that they are turned into proteins individually
  • genetic engineering (memory device) insert into something that you would want to be turned on for a long time
  • registry of biological parts at MIT; biological switch, wire linked together (electronic diagramà biological diagram

2005 iGEM project summaries:

UCSF: Kara; genetic circuit of bacteria to respond to temperature gradient, analog vs. digital

Toronto: Angela; Cell See-Us Thermometer and Bacterial Etch-a-Sketch; used mRFP and GFP didn’t have a result

Berkeley: John; cell-cell communicator, send out genomes to other bacteria via a specific pore (channel) and the other bacteria would send something back when it received that message

Harvard: Peter; bio-sketch; use UV pen to write on bacteria, use GFP mutation as reporter; not so much a toggle switch as a one way switch; used heat to “erase”; didn’t work

Caltech: Annie; detect caffeine in solution; YFP and GFP high concentration of caffeine would repress GFP and YFP would glow; if decaf, YFP would be repressed and GFP would grow; if medium, then both would be present.

Meeting Minutes for April 4, 2006

Present: Jamie, Azime, John, Angela, Bo, Brendan, Peter, Jason, Jamie, Victoria Elena

Journal Club Presentation

Engineering a pathway in E. Coli for turpenoids

by Brendan and Peter

  • turponoids - organic compound for making steroids
  • antimalarial medicine, etc. (anticancer, antihallucenogenic)
  • purified from plants, extracted from plants and then synthesized – limits
  • pathway from yeast and put into E. Coli
  • PCR created 3 mutant pathways, point mutations which inserted into E. Coli
  • 2 of the sequences worked; combined the two (beginning of one and end of another)
  • isoprene 5C structure; double, single, double building blocks
  • IPP is inhibitor that halts cell growth (for MAP)
  • amorphodyein synthase consumes IPP, increases levels of mevalonate acid without halting cell growth
  • pathway doesn’t exist in nature; this pathway 10-300 fold increase in production
  • head of synthetic bio department of Berkeley (Gates Foundation gave lots of funding)
  • Melavonatic → MevP → MevPP → IPP &→ DMAPP
genes: -ERG12 -ERG8 -MVD -1d1 = these genes are in plants but not in E. Coli, so codon optimization corrects for differences in codons between bacteria and plants
  • then stepped back to beginning: melavonatic not a good precursor, so XYZ converts acetyl CoA (naturally occurring in cell and a lot *cheaper) into Melavonatic Acid (which is hard to get)

concerned about product yield and amounts of cells, so another step was making sure that [IPP] kept low à keeping cells alive as we put in genes, etc.

Notes:

  • forward papers the week before to John so that he can make copies of diagrams, etc.
  • there will be workshops at beginning of summer about PCR, etc.
  • Ideas: get some more detail (make a concise description of) and let the faculty know about them and get their opinions on whether they are viable, linked to current faculty research:
    1. John: cell division counter – when (yeast) cells aging, different colors emitted from fluorochrome (like binary signal, red=1, blue =2, green = 3, etc. counts up to 32) if besides bacteria, takes longer to take up; bacteria, e.coli overnight; Harvard last year tried doing this; first round fine, but second on, harder; link color to cdk when transcribed, produced fluorochrome, activator and binds to promoter region of next and then repressor on next represses color from first one while another activator produces another color
    2. Julie: bacteria producing alkanes – products poisoning cells (alcohols, alkanes that act as detergents on membrane); talk to Dept of Energy? (speaker) – Prof Moulton
    3. analog devices: transistors scalable super computing; the more the cells grow, the more computational power you have; producing something useful is impractical; quorum sensing? like Minesweeper - Jamie
    4. bio sensors and actuators – live inside body and transmit info out; bio sensors sense the signals and actuators would amplify getting info of cell out (more complex than on/off); possibly like tumors
    5. free radical reporter - Victoria
    6. chemical detector – assembly line from input to receiver (like Berkeley team) Annie
    7. artificial organelle
    8. microbes that maintain/fix environment
    9. bacterial eye/radar – emit light (through reporter) and if reflects back, send out signal

ACTIONS

March 14, 2006

  • Victoria will go to SAO to get info about table for ADOCH
  • possibly also a web page/link to Brown iGEM
  • have a site for prospective students to see who we are, as well as our contact info
  • also, for everyone: think of ways to gain more attention
  • Everyone: create a section on the wiki for the category you are overseeing
  • Create a community portal:
    • serve as a site that can be linked possibly from admissions page
    • emphasizing that we are cross-disciplinary undergraduates performing research at Brown University, even several freshmen involved
    • have our slightly more colorful biolographical infos attached
  • Possible ideas for our project?
  • Victoria/Megan doing the Journal Club presentation next week.

March 21, 2006

Come up with an idea by first meeting after Spring Break

Journal Club Presenters: (in order of presentation): talk to faculty about them (we have 19!!!) send out papers to faculty early just to make sure.

  • Peter and Brendan 4/4
  • Angela and Annie 4/11
  • Kara and Jessie 4/18
  • Katherine and John 4/25

April 4, 2006

Journal projects for future:

  • Angela and Annie 4/11
  • Kara and Jessie 4/18
  • Katherine and John 4/25
  • Jason and Azime 5/2
  • Elena and Jamie 5/9

Remember to decide a week ahead of time so that faculty can be contacted and help with your paper. Also remember that you can email John diagrams, etc. so that he can make copies for everyone at the Journal Club meeting.


Make concise descriptions of our ideas to send to faculty

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