Imaging GFP streptomyces on arabidopsis roots

2022-03-28T09:16:24Z

Jake Newitt:

2021-10-26T12:24:07Z

Jake Newitt:

[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]]

=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]]==

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

==Microbiology==

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

*[[Conjugation using ET12567/pUZ8002]]

*[[Exploration | ''Streptomyces'' Exploration]]

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

*[[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]

==[[Plant-microbe interactions]]==

*[[Isolating Streptomyces from plant roots]]

==[[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]]

*[[Protoplasts Formation, Regeneration and Transformation]]

*[["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=

[[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]]

[[Exploration | ''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]]

[[Isolating Streptomyces from plant roots]]

[[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| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]

[[Streptomyces Bacteriophage plaque assay]]

[[Suicide vectors]]

[[Transposons]]

[[UV mutagenesis]]

Protocols

2021-10-26T12:19:26Z

Jake Newitt:

[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]]

=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]]==

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

==Microbiology==

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

*[[Conjugation using ET12567/pUZ8002]]

*[[Exploration | ''Streptomyces'' Exploration]]

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

*[[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]]

*[[Protoplasts Formation, Regeneration and Transformation]]

*[["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=

[[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]]

[[Exploration | ''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]]

[[Isolating Streptomyces from plant roots]]

[[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| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]

[[Streptomyces Bacteriophage plaque assay]]

[[Suicide vectors]]

[[Transposons]]

[[UV mutagenesis]]