Protocols: Difference between revisions

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=Protocols organised by category=
=Protocols organised by category=


[[Microbiology]]
==[[Biochemistry]]==


[[Microscopy]]
*[[GUS assay]] (β-Glucuronidase assay)


[[Mutagenesis]]
==Microbiology==


[[Natural Products]]  
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]


[[Nucleic Acid Methods]]
*[[Exploration | ''Streptomyces'' Exploration]]


[[Protein Methods]]
*[[General Growth and Maintenance of Streptomyces sp.]]


[[Reporter Gene Assays]]
*[[Isolating Actinomycetes from the environment]]
 
For a comprehensive guide to actinomycete characterisation see the [https://www.dsmz.de/collection/catalogue/microorganisms/special-groups-of-organisms/compendium-of-actinobacteria Compendium of Actinobacteria] from [https://www.helmholtz-hzi.de/en/research/research-topics/anti-infectives/microbial-strain-collection/our-research/#anchorsection Prof. Joachim Wink] at the German Collection of Microorganisms & Cell Cultures ([https://www.dsmz.de/ DSMZ]). This resouce provides protocols for characterising a wide range of features for new isolates, but may also be applicable more broadly for example for phenotyping experiments. The tests include colony morphology, melanin production, salt tolerance, carbon utlilisation and much more. To download the guide please see the link below.
 
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria]
 
==[[Microscopy]]==
 
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]
 
*[[Cultivating Actinobacteria for Microscopic Analysis]]
 
==[[Mutagenesis]]==
 
*[[CRISPR/Cas9-mediated genome editing]]
 
*[[Chemical mutagenesis]]
 
*[[Depletion strains]]
 
*[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]
 
*[[Lambda-red mediated recombination using ssDNA]]
 
*[[Meganuclease I-SceI based system for gene deletions]]
 
*[["Quikchange" site-directed mutagenesis]]
 
*[[Random mutagenesis using a mutator strain]]
 
*[[Random mutagenesis using error-prone PCR]]
 
*[[Suicide vectors]]
 
*[[Transposons]]
 
*[[UV mutagenesis]]
 
==[[Natural Products]]==
 
*[[Cloning, Transformation and Expression of Gene Clusters]]
 
*[[Metabolite extractions]]
 
*[[Production of microbial volatile organic compounds]]
 
==[[Next Generation Sequencing]]==
 
*[[ChIP Sequencing]]
*[[ChIP-exo sequencing]]
https://www.nature.com/articles/s41467-018-05265-7/
*[[RNA Sequencing]]
*[[Differential RNA sequencing]]
 
==[[Nucleic Acid Methods]]==
 
*[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]
 
*[[High GC PCR]]
 
*[[RNA extraction from Actinobacteria]]
 
*[[RNA interference]]
 
*[[Salting Out Genomic DNA Extraction Method]]
 
*[[Southern Blotting]]
 
==[[Protein Methods]]==
 
*[[Isolating extracellular protein from Streptomyces]]


=Alphabetical list of protocols=
=Alphabetical list of protocols=
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[[Depletion strains]]
[[Depletion strains]]
[[Exploration | ''Streptomyces'' Exploration]]


[[General Growth and Maintenance of Streptomyces sp.]]
[[General Growth and Maintenance of Streptomyces sp.]]

Revision as of 14:31, 31 January 2020

Protocols

Protocols organised by category

Biochemistry

Microbiology

For a comprehensive guide to actinomycete characterisation see the Compendium of Actinobacteria from Prof. Joachim Wink at the German Collection of Microorganisms & Cell Cultures (DSMZ). This resouce provides protocols for characterising a wide range of features for new isolates, but may also be applicable more broadly for example for phenotyping experiments. The tests include colony morphology, melanin production, salt tolerance, carbon utlilisation and much more. To download the guide please see the link below.

DSMZ Compendium of Actinobacteria

Microscopy

Mutagenesis

Natural Products

Next Generation Sequencing

https://www.nature.com/articles/s41467-018-05265-7/

Nucleic Acid Methods

Protein Methods

Alphabetical list of protocols

Characterisation of Actinomycetes

Cloning, Transformation and Expression of Gene Clusters

CRISPR/Cas9-mediated genome editing

Chemical mutagenesis

ChIP Seq

Codon Optimising Sequences for Heterologous Expression in Streptomyces

Depletion strains

Streptomyces Exploration

General Growth and Maintenance of Streptomyces sp.

GUS assay (β-Glucuronidase assay)

High GC PCR

Isolating Actinomycetes from the environment

Isolating extracellular protein from Streptomyces

Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")

Lambda-red mediated recombination using ssDNA

Meganuclease I-SceI based system for gene deletions

Metabolite extractions

"Quikchange" site-directed mutagenesis

Random mutagenesis using a mutator strain

Random mutagenesis using error-prone PCR

RNA extraction from Actinobacteria

Salting Out Genomic DNA Extraction Method

Southern Blotting

Staining of Streptomyces spp. Cell Wall and Nucleic Acids

Suicide vectors

Transposons

UV mutagenesis