Brown:Journal club:Synthetic biology journal club

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[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.
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Minutes
 
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Below is a list of the team members and what each of them is responsible for doing.  Those in bold are new additions from the old to-do list.
 
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Victoria – faculty liaison, '''faculty mentoring group (when to meet), alumni database
 
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(biotech), contact entrepreneurship program'''
 
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Kara – MCB, Navartis, Industry funding
 
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Meghan – Pres. Funding, website, future planning
 
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Angela – funding, minutes
 
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John – lead, wiki, funding, department fundraising, future planning
 
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Jesse – funding, equipment
 
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Brendan – PR, CS, MCB, Sorin (contact), goldman sachs?
 
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Peter G – wiki, CS, redo to-do list
 
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Annie – research, courses and workshops (modeling, PCR, cloning, bio bricks, etc.)
 
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Jamie G – magnetic bacteria
 
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Hiyato – free radical reporter
 
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Ana – magnetic bacteria, contact Sheldon about alumni mag.
 
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Azeem – research, cell counter, monthly planning
 
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Jason – free radical reporter,  equipment needed
 
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Jamie L – alumni data base (biotech), contact entrepreneurship program
 
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- we will have a meeting the weekend after this one
 
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CS funding update:
 
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- they wanted to know if we had contacted MCB
 
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- go and meet (John and Peter)
 
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Sri presents on BacteriophageT7
 
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- phage goes into a cell, copied and the exits
 
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- T7 RNA polymerase encoded by gene 1
 
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- 19 mapped essential genes, new ones named under existing structure, about 50 total
 
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- self contained during infection
 
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- host’s RNA polymerase is the motor which brings in the phage’s DNA
 
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- process takes 10-15 min, infection completion takes 15-20 mins
 
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- investigate if there is reason for genome’s layout
 
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- T7 gene expression
 
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- create model for gene expression
 
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- measure mRNA levels
 
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- track polymerases as they transcribe DNA
 
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- take 100’s to get population data
 
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- data collected by real time PCR
 
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- can see when PCR products come up
 
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- results: model is completely wrong
 
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- early mRNA is degraded
 
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- adjust model, rates fit better
 
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- try to encode model onto DNA
 
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- see paper from last week
 
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- problems with physical rearrangement
 
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- overlaps – how important are they?
 
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- cloned as much as could with ecoli, then used PCR fusion techniques
 
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- produce a phage that can survive
 
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- then clone within the phage
 
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- alternative cloning vehicles?
 
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- Thinking of yeast
 
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- only weak promoters see point mutations
 
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- open reading frames: some known, unknown/unimportant
 
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- T7.1
 
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- Better control, inference about data easier
 
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- Eukaryotes have fewer overlaps b/c of larger genome
 
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- Being done with yeast
 
==[[Brown:Journal club/4.25.06|25th April]]==
==[[Brown:Journal club/4.25.06|25th April]]==

Revision as of 01:13, 6 May 2006

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Contents

Tuesday 2nd May, 6-7pm, Journal Club is in Walter Hall, 80 Waterman

Tuesday nights, 6-7pm

Location: | Technology House Lounge, Brown campus, please call 401-5238190 if you are unable to enter the building.


2nd May

[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.

25th April

John to present, + overview of Biobricks

[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7] Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2

18th April

Kara and Jesse

http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html

Programmable ligand-controlled riboregulators of eukaryotic gene expression.

Bayer TS, Smolke CD.

11th April

Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".

The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299

Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).


4th April

Brendan and Peter will be presenting the article entitled "Engineering a mevalonate pathway in Escherichia coli for production of terpenoids".

Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).

It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html

21st March

Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli"

Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]

Archive

14th March

John to give overview of last year's competition and to hand out readings [http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]


please add future weeks

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