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

Revision as of 23:24, 3 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.

Minutes

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.

Victoria – faculty liaison, faculty mentoring group (when to meet), alumni database (biotech), contact entrepreneurship program Kara – MCB, Navartis, Industry funding

Meghan – Pres. Funding, website, future planning

Angela – funding, minutes

John – lead, wiki, funding, department fundraising, future planning

Jesse – funding, equipment

Brendan – PR, CS, MCB, Sorin (contact), goldman sachs?

Peter G – wiki, CS, redo to-do list

Annie – research, courses and workshops (modeling, PCR, cloning, bio bricks, etc.)

Jamie G – magnetic bacteria

Hiyato – free radical reporter

Ana – magnetic bacteria, contact Sheldon about alumni mag.

Azeem – research, cell counter, monthly planning

Jason – free radical reporter, equipment needed

Jamie L – alumni data base (biotech), contact entrepreneurship program


- we will have a meeting the weekend after this one


CS funding update:

- they wanted to know if we had contacted MCB

- go and meet (John and Peter)


Sri presents on BacteriophageT7

- phage goes into a cell, copied and the exits

- T7 RNA polymerase encoded by gene 1

- 19 mapped essential genes, new ones named under existing structure, about 50 total

- self contained during infection

- host’s RNA polymerase is the motor which brings in the phage’s DNA

- process takes 10-15 min, infection completion takes 15-20 mins

- investigate if there is reason for genome’s layout

- T7 gene expression

- create model for gene expression

- measure mRNA levels

- track polymerases as they transcribe DNA

- take 100’s to get population data

- data collected by real time PCR

- can see when PCR products come up

- results: model is completely wrong

- early mRNA is degraded

- adjust model, rates fit better

- try to encode model onto DNA

- see paper from last week

- problems with physical rearrangement

- overlaps – how important are they?

- cloned as much as could with ecoli, then used PCR fusion techniques

- produce a phage that can survive

- then clone within the phage

- alternative cloning vehicles?

- Thinking of yeast

- only weak promoters see point mutations

- open reading frames: some known, unknown/unimportant

- T7.1

- Better control, inference about data easier

- Eukaryotes have fewer overlaps b/c of larger genome

- Being done with yeast

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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