Lenski's E coli experimental data sets

E coli evolution

http://myxo.css.msu.edu/ecoli/genomicsdat.html

E coli flow cytometer, PI staining

Hawley & Hawley
PI stain

E coli genomics resources

Strains

CGSC
Coli Genetic Stock Center

E. coli Genetic Resources at Yale
CGSC, The Coli Genetic Stock Center

http://cgsc.biology.yale.edu/KeioList.php



E coli PPI

M. Arifuzzaman, M. Maeda, A. Itoh, K. Nishikata, C. Takita,

R. Saito, T. Ara, K. Nakahigashi, H. C. Huang, A. Hirai,

K. Tsuzuki, S. Nakamura, M. Altaf-Ul-Amin, T. Oshima,

T. Baba, N. Yamamoto, T. Kawamura, T. Ioka-Nakamichi,

M. Kitagawa, M. Tomita, S. Kanaya, C. Wada and H. Mori,

Large-scale identification of protein–protein interaction of escherichia

coli k-12, Genome Res., 2006, 16(5), 686–91.

Essential gene interactions
https://www.jstage.jst.go.jp/article/ggs/88/4/88_233/_article



E coli essential genes
http://www.shigen.nig.ac.jp/ecoli/pec/   Profiles of Escherichia coli chromosomes (PEC)
302 essential genes, 4400 nonessential genes
Used in Jordan02GR paper

303 essential genes in E coli K12, Ecogene
http://www.ecogene.org/old/topic.php?topic_id=5

295 essential genes in Ecowiki
http://ecoliwiki.net/colipedia/index.php/Essential_genes

Gerdes03JB, essential genes in E coli MG1655
http://jb.asm.org/content/185/19/5673.short
620 essential gene, 3126 non-essential genes


http://www.genome.wisc.edu/resources/essential.htm


Essential genome of Caulobacter crescentus
http://onlinelibrary.wiley.com/doi/10.1038/msb.2011.58/full

Homologs of B subtilis essential genes?

EcoK12 Expression data, GO
http://www.porteco.org/downloads/dataAccess/

bio386 reading Stewart 2006 E coli aging paper

Stewart 2005 Plos E coli aging paper.

I asked the student to put red mark all over the paper.

Somehow, "susceptible to aging" was misinterpreted as "not able to aging" by the student.

E coli aging !!

Suckjoon Jun and Minsu Kim: 

CFU viability is exponential, but RLS is Gompertz. When SOS is knocked out, RLS become exponential.

RLS for E coli is measured in good growth condition, and CLS for E coli is measured in depleted nutrient condition. It is possible that CLS condition overwhelm network buffering and resulted in a network with too little redundancy.  On the other hand,  aging was able to manifest itself during growth, because the external 'insults' are below the 'critical' point for network robustness.

Craig Skinner and Su-ju Lin, 2010 AMB review on CR

CR on E coli aging
http://precedings.nature.com/documents/2071/version/1