Protocols: Difference between revisions

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=Protocols organised by category=
=Protocols organised by category=
==[[Bacteriophage]]==
*[[Streptomyces Bacteriophage plaque assay]]
*[[High titre preparation of phage]]
*[[Isolation of phages from single plaques]]
*[[Isolation of phages from environmental samples]]


==[[Biochemistry]]==
==[[Biochemistry]]==
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*[[GUS assay]] (β-Glucuronidase assay)
*[[GUS assay]] (β-Glucuronidase assay)


==[[Microbiology]]==
==Microbiology==
 
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]


*[[Characterisation of Actinomycetes]]
*[[Conjugation using ET12567/pUZ8002]]


*[[Exploration | ''Streptomyces'' Exploration]]
*[[Exploration | ''Streptomyces'' Exploration]]
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*[[Isolating Actinomycetes from the environment]]
*[[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]]==
==[[Microscopy]]==


*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]
*[[Cultivating Actinobacteria for Microscopic Analysis]]


==[[Mutagenesis]]==
==[[Mutagenesis]]==
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*[[Meganuclease I-SceI based system for gene deletions]]
*[[Meganuclease I-SceI based system for gene deletions]]
*[[Protoplasts Formation, Regeneration and Transformation]]


*[["Quikchange" site-directed mutagenesis]]
*[["Quikchange" site-directed mutagenesis]]
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==[[Next Generation Sequencing]]==
==[[Next Generation Sequencing]]==


*[[ChIP Sequencing|ChIP Seq]]
*[[ChIP Sequencing]]
*[[ChIP-exo sequencing]]
*[[ChIP-exo sequencing]]
https://www.nature.com/articles/s41467-018-05265-7/
https://www.nature.com/articles/s41467-018-05265-7/
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*[[RNA extraction from Actinobacteria]]
*[[RNA extraction from Actinobacteria]]
*[[RNA interference]]


*[[Salting Out Genomic DNA Extraction Method]]
*[[Salting Out Genomic DNA Extraction Method]]
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*[[Isolating extracellular protein from Streptomyces]]
*[[Isolating extracellular protein from Streptomyces]]


=Alphabetical list of protocols=
=Alphabetical list of protocols=
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[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]
[[Conjugation using ET12567/pUZ8002]]


[[Depletion strains]]
[[Depletion strains]]
[[Exploration | ''Streptomyces'' Exploration]]


[[General Growth and Maintenance of Streptomyces sp.]]
[[General Growth and Maintenance of Streptomyces sp.]]
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[[High GC PCR]]
[[High GC PCR]]
[[High titre preparation of phage]]


[[Isolating Actinomycetes from the environment]]
[[Isolating Actinomycetes from the environment]]


[[Isolating extracellular protein from Streptomyces]]
[[Isolating extracellular protein from Streptomyces]]
[[Isolation of phages from environmental samples]]
[[Isolation of phages from single plaques]]


[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]
[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]
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[[Metabolite extractions]]
[[Metabolite extractions]]
[[Protoplasts Formation, Regeneration and Transformation]]


[["Quikchange" site-directed mutagenesis]]
[["Quikchange" site-directed mutagenesis]]
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[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]
[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]
[[Streptomyces Bacteriophage plaque assay]]


[[Suicide vectors]]
[[Suicide vectors]]

Revision as of 14:11, 21 May 2020

Protocols

Protocols organised by category

Bacteriophage

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

Conjugation using ET12567/pUZ8002

Depletion strains

Streptomyces Exploration

General Growth and Maintenance of Streptomyces sp.

GUS assay (β-Glucuronidase assay)

High GC PCR

High titre preparation of phage

Isolating Actinomycetes from the environment

Isolating extracellular protein from Streptomyces

Isolation of phages from environmental samples

Isolation of phages from single plaques

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

Protoplasts Formation, Regeneration and Transformation

"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

Streptomyces Bacteriophage plaque assay

Suicide vectors

Transposons

UV mutagenesis