SOPs

This protocol describes the procedure of conjugation of pK18mobSacB suicide plasmid containing fragments UP and DOWN that delimit the recombination region from E. coli S17λpir to P. putida cells.

Creators: Felipe de Salas, Laura de Eugenio, Beatriz Galán

Submitter: Felipe de Salas

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 4th Aug 2021 at 16:29, Last updated: 4th Aug 2021 at 16:30

Cultivation of P. putida (and E. coli) in rich-, minimal-, and selective medium

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:18

Design of spacers and cloning of them in pSEVA231-CRISPR

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:06

Determination of cell dry weight

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:15

DNA and RNA concentration measurement

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:07

Enzymatic actyl-CoA determination

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:08

Genomic DNA isolation

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:15

Golden gate cloning

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:09

Gram staining of bacteria

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:10

In vitro enrichments of microbial environmental sample from high-temperature environments

SULFOCEL

No description specified

Creator: Beatrice Cobucci-Ponzano

Submitter: Beatrice Cobucci-Ponzano

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 13th Apr 2022 at 12:33

Infiltration of N. benthamiana leaves with Agrobacterium tumefaciens

PlanOvac

Leaf agroinfiltration is a method used in plant biology and biotechnology to induce transient expression of genes in leaf tissue, in order to produce a desired protein. In the method, a suspension of Agrobacterium tumefaciens, which contains a plasmid with the gene of interest, is introduced into a plant leaf by direct injection, whereafter the bacteria transfer the desired gene into the plant cells via transfer of T-DNA. The main benefit of agroinfiltration, when compared to the more traditional ...

Creators: Emanuela Pedrazzini, Emanuela Pedrazzini

Submitter: Emanuela Pedrazzini

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 2nd Feb 2021 at 15:24

Inoculating and sampling anaerobic cultures and CFU determination

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:14

Lignocellulosic biomass pretreatment protocol

SULFOCEL

No description specified

Creator: Beatrice Cobucci-Ponzano

Submitter: Beatrice Cobucci-Ponzano

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 13th Apr 2022 at 12:36

Live/dead staining of bacteria

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:16

Making a growth curve of a bacterial or yeast strain

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 31st Oct 2018 at 14:40

Making electro-competent E. coli cells and transformation of them

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 31st Oct 2018 at 14:45

Marker-less multiple gene deletions in P. putida KT2440

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:11

MASC-PCR

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:17

Metagenomic and culturomic DNA and RNA extractions

SULFOCEL

No description specified

Creator: Beatrice Cobucci-Ponzano

Submitter: Beatrice Cobucci-Ponzano

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 13th Apr 2022 at 12:39

Mix&Go competent cells and transformation of E. coli

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 14:12, Last updated: 28th Mar 2019 at 14:12

Optimal Synthesis of Pathways – I

DBTL-P

(Show All)

GEM preparation

Creators: Konstantinos Pyrgakis, Ioannis Ntekas, ANTONIS KOKOSSIS

Submitter: Konstantinos Pyrgakis

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 16th Dec 2020 at 15:56

Optimal Synthesis of Pathways – II

DBTL-P

(Show All)

Pathways elimination

Creators: Konstantinos Pyrgakis, Ioannis Ntekas, ANTONIS KOKOSSIS

Submitter: Konstantinos Pyrgakis

Investigations: Computational strain design

Studies: Computational strain optimization

Assays: Pathway improvement by mutations

Created: 16th Dec 2020 at 16:00

Optimal Synthesis of Pathways – III

DBTL-P

(Show All)

Scale-up

Creators: Konstantinos Pyrgakis, Ioannis Ntekas, ANTONIS KOKOSSIS

Submitter: Konstantinos Pyrgakis

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 16th Dec 2020 at 16:01

Plasmid isolation from E. coli and P. putida using the Thermo Scientific GeneJET Plasmid Miniprep Kit

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: 1 hidden item

Studies: 1 hidden item

Assays: 1 hidden item

Created: 31st Oct 2018 at 14:44

Restriction / digestion of DNA

Uncurated Protocols Library

No description specified

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 31st Oct 2018 at 14:41

TEMPLATE FOR LEARN

DBTL-P

Template to collect input data for execution of LEARN step

Creator: Konstantinos Pyrgakis

Submitter: Konstantinos Pyrgakis

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 16th Dec 2020 at 16:06

Transformation of Pseudomonas putida by electroporation

Uncurated Protocols Library

This is a Protocol for transforming plasmid DNA into P. putida cells by electroporation. This is a fast and easy-to-use method of introducing plasmid DNA in P. putida cells with high transformation efficiency. This Protocol is adapted from [1] and encompasses the steps for the preparation of competent cells and transformation of plasmid DNA by electroporation.

All Inputs of the Protocol, listed in the section 4.1., can be acquired either from other IBISBA Protocols or purchased from commercial ...

Creator: Rita Volkers

Submitter: Rita Volkers

Investigations: 2 hidden items

Studies: Transformation of production host and 1 hidden item

Assays: 2 hidden items

Created: 28th Mar 2019 at 14:19, Last updated: 13th Jan 2021 at 13:43

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