Protocols: Difference between revisions
Jordanmurray (talk | contribs) |
|||
| (19 intermediate revisions by 5 users not shown) | |||
| Line 2: | Line 2: | ||
=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]]== | ||
| Line 10: | Line 20: | ||
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]] | *[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]] | ||
*[[Conjugation using ET12567/pUZ8002]] | |||
*[[Exploration | ''Streptomyces'' Exploration]] | *[[Exploration | ''Streptomyces'' Exploration]] | ||
| Line 20: | Line 32: | ||
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria] | [https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria] | ||
==[[Plant-Microbe interactions]]== | |||
* See [[Plant-Microbe interactions|main section]] for full list of protocols | |||
==[[Microscopy]]== | ==[[Microscopy]]== | ||
| Line 32: | Line 48: | ||
*[[Chemical mutagenesis]] | *[[Chemical mutagenesis]] | ||
*[[CUBIC]] | |||
*[[Depletion strains]] | *[[Depletion strains]] | ||
| Line 40: | Line 58: | ||
*[[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]] | ||
| Line 67: | Line 87: | ||
https://www.nature.com/articles/s41467-018-05265-7/ | https://www.nature.com/articles/s41467-018-05265-7/ | ||
*[[RNA Sequencing]] | *[[RNA Sequencing]] | ||
*[[rRNA depletion with Streptomyces coelicolor A3(2) specific probes]] | |||
*[[Differential RNA sequencing]] | *[[Differential RNA sequencing]] | ||
| Line 100: | Line 121: | ||
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]] | [[Codon Optimising Sequences for Heterologous Expression in Streptomyces]] | ||
[[Conjugation using ET12567/pUZ8002]] | |||
[[Depletion strains]] | [[Depletion strains]] | ||
| Line 110: | Line 133: | ||
[[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]] | ||
[[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 (PCR-targeting system a.k.a. "Redirect")]] | ||
| Line 122: | Line 153: | ||
[[Metabolite extractions]] | [[Metabolite extractions]] | ||
[[Protoplasts Formation, Regeneration and Transformation]] | |||
[["Quikchange" site-directed mutagenesis]] | [["Quikchange" site-directed mutagenesis]] | ||
| Line 136: | Line 169: | ||
[[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]] | ||
Latest revision as of 21:01, 22 January 2024
Protocols organised by category
Bacteriophage
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
Plant-Microbe interactions
- See main section for full list of protocols
Microscopy
Mutagenesis
Natural Products
Next Generation Sequencing
https://www.nature.com/articles/s41467-018-05265-7/
- RNA Sequencing
- rRNA depletion with Streptomyces coelicolor A3(2) specific probes
- Differential RNA sequencing
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
Conjugation using ET12567/pUZ8002
General Growth and Maintenance of Streptomyces sp.
GUS assay (β-Glucuronidase assay)
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
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
Staining of Streptomyces spp. Cell Wall and Nucleic Acids
