SOPs
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A model to describe the effect of K+ uptake by KdpFABC on the two-component system KdpD/KdpE, which enables the identification of control principles of the Kdp system
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The reverse transcriptase synthesizes DNA, which complements the mRNA template (complementary DNA, cDNA). Cy3/Cy5-dCTP are incorporated into cDNA during Reverse transcription. The obtained Cy3/Cy5 cDNA are then competitively hybridised onto Agilent microarray slide and subsequently scanned.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Cells were harvested from culture keeping the cells cold to quench the physiological condition of RNA and the cells were mechanically disrupted. RNA was isolated from the cells by conventional acid-phenol method and the quality was checked by Agilent bioanalyser.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
This SOP describes the SUMO procedure for determining B-galactosidase activities.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
A kinetic model that describess the activation of a dimeric efflux system that could bind either GSH or SLG
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
This SOP defines the format of SOPs used in the SUMO consortium.
Creator: Michael Ederer
Submitter: Michael Ederer
A model for translation elongation, which allows the prediction of how different conditions and parameters affect the rate and throughput of translation.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A model to describe aggregation of homomeric protein complexes in mechanosensitive channels in E.coli.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Measurement of the transmembrane pH gradient and thus pHi, when the external pH is known.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A procedure to analyse the genomic interaction of E.coli RNA polymerase (RNAP) upon methylglyoxal (MG) stress, a toxic keto-aldehyde by-product of metabolism.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
SOP used for detecting non influential parameters and interactions in non linear dynamical models. These parameters can be estabilished which allows the prioritization of parameters that can be subsequently estimated using robust global optimizations methods.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The model describes the series of chemical reactions in MG detoxification pathway, allowing one to predict the flux of all compounds produced during detoxification.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Mathematical model of pH buffering, which allows the prediction of how the buffering capacity depends on the cytoplasm's composition, for any number of buffers.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Method of how to perform the purification of glyoxalase II as well as kinetics assays.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A method of how to measure methylglyoxal present in the growth medium.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Measurements of K+ retained in the cytoplasm using flame photometry.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The fluorescent DNA-binding dye used in qRT-PCR binds to all kinds of double stranded DNA. To prevent false-positive results, the RNA is treated with DNase to remove remaining DNA.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Quantitative real-time PRC is used to compare kdpFABC expression between the E. coli strains MG1655 (wildtype)and MG1655 (kdpA4, a kdpFABC-inactive mutant after a shift to K+ limitation.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A method to compare kdpFABC expression between MG1655 (wildtype) and MG1655 (kdpA4) after a shift to K+ limitation, the RNA was extracted from samples taken at different points in time.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Pulsed-FRAP measure the diffusion constants in confined volumes in small cells like E. coli and other bacteria or cellular organelles.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A procedure to measure the levels of GSH and SLG before and after exposure to MG using formic acid. A similar expreimental set up as for potassium efflux experiments is used to which a silicon oil centrifugation step is incorporated. Samples are analysed by LC-MS-MS in order to quantify intracellular GSH and SLG levels.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The reverse transcriptase synthesizes DNA, which complements the mRNA template.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
To induce kdpFABC expression, cells are cultivated in K10 minimal medium (10mM K+) were shifted into K+ limiting growth medium (K0), containing 20 μM K+ by filtration.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
FRAP experiments are used for studying cytoplasmic diffusion in cells and cells membrane.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Growing Escherichia coli to express KefF by adding IPTG for purification and kinetics experiments.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Generating gene knock-ins using MJF618 expressing the defective lambdoid prophage recombination system λ red.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Generating gene knock-outs using DY330 expressing the defective lambdoid prophage recombination system λ red.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Experimental system that is designed to observe the in vivo stability and aggregation of a protein of interest.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg