Team:KULeuven/Modeling

= Modeling =


 * Numbers.xls


 * Synthetic biology: Engineering Escherichia coli to see light

Output




ETHZ list of parameters

 * ETHZ list of parameters

mRNA decay

 * Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

T7 RNAP

 * Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters
 * Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence
 * data T7 team Tsinghua 2007
 * Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase

LacI - LuxI

 * Coupled repressilators


 * A synthetic oscillatory network of transcriptional regulators

LuxI, LuxR, mRNALuxI, mRNALuxR decay

 * Noise-induced cooperative behavior in a multicell system


 * LuxI kinetics

HSL stuff

 * Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h


 * Kinetics of the AHL Regulatory System in a Model Biofilm System


 * HSL lactone synthesis kinetics by a LuxI-related enzyme


 * Lactonase mediated HSL degradation (hydrolysis)

OmpR, OmpF

 * A simulation model of Escherichia coli osmoregulatory switch using E-CELL system (Relevance: High), bekijk pg.11/13
 * Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR (Relevance: Medium)
 * Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ (Relevance:?), geen toegang tenzij account
 * DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity (Relevance: Low)
 * A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene (Relevance: ?), voor repressor regulatie van OmpF door OmpR
 * micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli (Relevance: Low), invloed 'Antisense RNA' op OmpF regulatie, hmm...

Psid met P2ogr promotor

 * Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter


 * Psid promotor with different activators

Constitutive promoters

 * Estimated transcription rate for J23105:
 * Scale other transcription rate with table in parts registry.


 * Estimate the rate of transcription from a constitutive promotor family member.

E. coli transcription rates
Paper about the calculated transcription rates for every E.coli ORF Tables with the calculated transcription rates for every E.coli ORF