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

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

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) Download the paper here

Archive

14th March

John to give overview of last year's competition and to hand out readings Download paper here


please add future weeks

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