Brown:Journal club:Synthetic biology journal club
From 2006.igem.org
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]