Protocols: Difference between revisions
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[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]] | |||
=Protocols organised by category= | |||
==[[Biochemistry]]== | |||
*[[GUS assay]] (β-Glucuronidase assay) | |||
==Microbiology== | |||
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]] | |||
*[[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]] | |||
*[["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]] | |||
[[Depletion strains]] | |||
[[Exploration | ''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| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]] | |||
[[Suicide vectors]] | |||
[[Transposons]] | |||
[[UV mutagenesis]] |
Revision as of 14:31, 31 January 2020
Protocols organised by category
Biochemistry
- GUS assay (β-Glucuronidase assay)
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
Codon Optimising Sequences for Heterologous Expression in Streptomyces
General Growth and Maintenance of Streptomyces sp.
GUS assay (β-Glucuronidase assay)
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
"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