SOPs

Metabolomics perturbation sample preparation and description of how the exact details of the perturbations.
Perturbations:
-Glucose starvation
-Amino acid starvation
-Fe2+ depletion
-Oxidative stress via H2O2
-Glycerol addition to the medium

Explains the different steps involved in building the core dynamic model of glycolysis, pyruvate metabolism and ATPase in M. pneumoniae
-Construction of the model
-Parameter estimation, selection of best parameter set

Standard Operating Procedure describing the process and software used in generating a Genome Scale Metabolic model of M. hyopneumoniae.
Used software:
Pathway tools
PathLogic
Cobrapy
the Cobra Toolbox
libSBML

We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:

Programme = Overarching research theme (The Digital Salmon)
Project = Research grant (DigiSal, GenoSysFat)
Investigation = a particular biological process, phenomenon or thing
(typically corresponds to [plans for] one or more closely related papers)
Study = experiment whose design reflects a specific biological research question
Assay = standardized measurement or diagnostic experiment using a
...

SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.
Current draft.

Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples.
So far succesfully used for pelleted cells from planktonic cultures.

steps conducted to pellet cells for RNA and protein extraction

Initial configuration and parameters of the Bioleaching

This README file describes how the s-core / s-core+ analysis perl script is to be executed together with data files.

Metabolic networks with gene expression are researched under very different banners with different techniques. For example, there are the dynamic enzyme-cost Flux Balance Analysis (deFBA) [1], conditional Flux Balance Analysis [2], Metabolism and Expression models (ME models) [3], Resource Balance Analysis [4], etc. At their core, these methods can all understood as Resource Allocation Models (RAM) and while investigating their potential and their results, we encountered the problem of sharing
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Method extraction of intracellular metabolites in Lactococcus lactis

Method extraction of intracellular metabolites in Lactococcus lactis

Method for transformation of plasmids into Lactococcus lactis

Method for synthesis of LAB-medium sued for the SYSMO-LAB project

Method for analysis of various organic acids in the medium

Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis

A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.

Protocol for applying a glucose perturbation in Streptococcus pyogenes.

Perturbation of starved cells with glucose. Concentrations of intra- and extracellular metabolites are followed in time.

This HPLC method uses a isocratic method and a RI detector to identify and quantify almost all excreted catabolic metabolites.

This protocol for applying glucose perturbations works for Lactococcus lactis and Enterococcus faecalis

A protocol for acidic quenching of lactic acid bacteria used for analyses of intracellular metabolites.