https://actinobase.org/api.php?action=feedcontributions&user=Damien+Gayrard&feedformat=atomActinoBase - User contributions [en-gb]2024-03-29T07:12:43ZUser contributionsMediaWiki 1.39.3https://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1986Growing Marchantia from gemma spores2021-11-12T11:15:08Z<p>Damien Gayrard: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemmae}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemmae, haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Micropore tape<br />
*Plant growth chamber<br />
*If you want to remove the plant from the agar without destroying its rhizoids: sterile nylon mesh (cut to the shape of petri dish)<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma with the tip of a pipette tip and transfer over to the plate (coverd by nylon mesh if needed).<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.<br />
<br />
<h2><strong>References</h2></strong><br />
<br />
*Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato, Takayuki Kohchi, Molecular Genetic Tools and Techniques for Marchantia polymorpha Research , Plant and Cell Physiology, Volume 57, Issue 2, February 2016, Pages 262–270, https://doi.org/10.1093/pcp/pcv097<br />
*Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., ... & Schmutz, J. (2017). Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell, 171(2), 287-304, https://doi.org/10.1016/j.cell.2017.09.030</div>Damien Gayrardhttps://actinobase.org/index.php?title=Protocols&diff=1985Protocols2021-11-02T15:33:53Z<p>Damien Gayrard: /* Plant-microbe interactions */</p>
<hr />
<div>[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]] <br />
<br />
=Protocols organised by category=<br />
<br />
==[[Bacteriophage]]==<br />
<br />
*[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
*[[High titre preparation of phage]]<br />
<br />
*[[Isolation of phages from single plaques]]<br />
<br />
*[[Isolation of phages from environmental samples]]<br />
<br />
==[[Biochemistry]]==<br />
<br />
*[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
==Microbiology==<br />
<br />
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]<br />
<br />
*[[Conjugation using ET12567/pUZ8002]]<br />
<br />
*[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
*[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
*[[Isolating Actinomycetes from the environment]]<br />
<br />
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. <br />
<br />
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria]<br />
<br />
==[[Plant-microbe interactions]]==<br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Growing Marchantia from gemma spores]]<br />
<br />
==[[Microscopy]]==<br />
<br />
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
*[[Cultivating Actinobacteria for Microscopic Analysis]]<br />
<br />
==[[Mutagenesis]]==<br />
<br />
*[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
*[[Chemical mutagenesis]]<br />
<br />
*[[Depletion strains]]<br />
<br />
*[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
*[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
*[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
*[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
*[["Quikchange" site-directed mutagenesis]]<br />
<br />
*[[Random mutagenesis using a mutator strain]]<br />
<br />
*[[Random mutagenesis using error-prone PCR]]<br />
<br />
*[[Suicide vectors]]<br />
<br />
*[[Transposons]]<br />
<br />
*[[UV mutagenesis]]<br />
<br />
==[[Natural Products]]== <br />
<br />
*[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
*[[Metabolite extractions]]<br />
<br />
*[[Production of microbial volatile organic compounds]]<br />
<br />
==[[Next Generation Sequencing]]==<br />
<br />
*[[ChIP Sequencing]]<br />
*[[ChIP-exo sequencing]]<br />
https://www.nature.com/articles/s41467-018-05265-7/<br />
*[[RNA Sequencing]]<br />
*[[Differential RNA sequencing]]<br />
<br />
==[[Nucleic Acid Methods]]==<br />
<br />
*[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
*[[High GC PCR]]<br />
<br />
*[[RNA extraction from Actinobacteria]]<br />
<br />
*[[RNA interference]]<br />
<br />
*[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
*[[Southern Blotting]]<br />
<br />
==[[Protein Methods]]==<br />
<br />
*[[Isolating extracellular protein from Streptomyces]]<br />
<br />
=Alphabetical list of protocols=<br />
<br />
[[Characterisation of Actinomycetes]]<br />
<br />
[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
[[Chemical mutagenesis]]<br />
<br />
[[ChIP Seq]]<br />
<br />
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
[[Conjugation using ET12567/pUZ8002]]<br />
<br />
[[Depletion strains]]<br />
<br />
[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
[[High GC PCR]]<br />
<br />
[[High titre preparation of phage]]<br />
<br />
[[Isolating Actinomycetes from the environment]]<br />
<br />
[[Isolating extracellular protein from Streptomyces]]<br />
<br />
[[Isolating Streptomyces from plant roots]]<br />
<br />
[[Isolation of phages from environmental samples]]<br />
<br />
[[Isolation of phages from single plaques]]<br />
<br />
[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
[[Metabolite extractions]]<br />
<br />
[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
[["Quikchange" site-directed mutagenesis]]<br />
<br />
[[Random mutagenesis using a mutator strain]]<br />
<br />
[[Random mutagenesis using error-prone PCR]]<br />
<br />
[[RNA extraction from Actinobacteria]]<br />
<br />
[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
[[Southern Blotting]]<br />
<br />
[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
[[Suicide vectors]]<br />
<br />
[[Transposons]]<br />
<br />
[[UV mutagenesis]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Protocols&diff=1984Protocols2021-11-02T15:32:08Z<p>Damien Gayrard: /* Plant-microbe interactions */</p>
<hr />
<div>[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]] <br />
<br />
=Protocols organised by category=<br />
<br />
==[[Bacteriophage]]==<br />
<br />
*[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
*[[High titre preparation of phage]]<br />
<br />
*[[Isolation of phages from single plaques]]<br />
<br />
*[[Isolation of phages from environmental samples]]<br />
<br />
==[[Biochemistry]]==<br />
<br />
*[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
==Microbiology==<br />
<br />
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]<br />
<br />
*[[Conjugation using ET12567/pUZ8002]]<br />
<br />
*[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
*[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
*[[Isolating Actinomycetes from the environment]]<br />
<br />
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. <br />
<br />
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria]<br />
<br />
==[[Plant-microbe interactions]]==<br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Growing Marchantia from gemmae]]<br />
<br />
==[[Microscopy]]==<br />
<br />
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
*[[Cultivating Actinobacteria for Microscopic Analysis]]<br />
<br />
==[[Mutagenesis]]==<br />
<br />
*[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
*[[Chemical mutagenesis]]<br />
<br />
*[[Depletion strains]]<br />
<br />
*[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
*[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
*[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
*[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
*[["Quikchange" site-directed mutagenesis]]<br />
<br />
*[[Random mutagenesis using a mutator strain]]<br />
<br />
*[[Random mutagenesis using error-prone PCR]]<br />
<br />
*[[Suicide vectors]]<br />
<br />
*[[Transposons]]<br />
<br />
*[[UV mutagenesis]]<br />
<br />
==[[Natural Products]]== <br />
<br />
*[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
*[[Metabolite extractions]]<br />
<br />
*[[Production of microbial volatile organic compounds]]<br />
<br />
==[[Next Generation Sequencing]]==<br />
<br />
*[[ChIP Sequencing]]<br />
*[[ChIP-exo sequencing]]<br />
https://www.nature.com/articles/s41467-018-05265-7/<br />
*[[RNA Sequencing]]<br />
*[[Differential RNA sequencing]]<br />
<br />
==[[Nucleic Acid Methods]]==<br />
<br />
*[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
*[[High GC PCR]]<br />
<br />
*[[RNA extraction from Actinobacteria]]<br />
<br />
*[[RNA interference]]<br />
<br />
*[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
*[[Southern Blotting]]<br />
<br />
==[[Protein Methods]]==<br />
<br />
*[[Isolating extracellular protein from Streptomyces]]<br />
<br />
=Alphabetical list of protocols=<br />
<br />
[[Characterisation of Actinomycetes]]<br />
<br />
[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
[[Chemical mutagenesis]]<br />
<br />
[[ChIP Seq]]<br />
<br />
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
[[Conjugation using ET12567/pUZ8002]]<br />
<br />
[[Depletion strains]]<br />
<br />
[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
[[High GC PCR]]<br />
<br />
[[High titre preparation of phage]]<br />
<br />
[[Isolating Actinomycetes from the environment]]<br />
<br />
[[Isolating extracellular protein from Streptomyces]]<br />
<br />
[[Isolating Streptomyces from plant roots]]<br />
<br />
[[Isolation of phages from environmental samples]]<br />
<br />
[[Isolation of phages from single plaques]]<br />
<br />
[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
[[Metabolite extractions]]<br />
<br />
[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
[["Quikchange" site-directed mutagenesis]]<br />
<br />
[[Random mutagenesis using a mutator strain]]<br />
<br />
[[Random mutagenesis using error-prone PCR]]<br />
<br />
[[RNA extraction from Actinobacteria]]<br />
<br />
[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
[[Southern Blotting]]<br />
<br />
[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
[[Suicide vectors]]<br />
<br />
[[Transposons]]<br />
<br />
[[UV mutagenesis]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Protocols&diff=1983Protocols2021-11-02T15:31:24Z<p>Damien Gayrard: /* Plant-microbe interactions */</p>
<hr />
<div>[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]] <br />
<br />
=Protocols organised by category=<br />
<br />
==[[Bacteriophage]]==<br />
<br />
*[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
*[[High titre preparation of phage]]<br />
<br />
*[[Isolation of phages from single plaques]]<br />
<br />
*[[Isolation of phages from environmental samples]]<br />
<br />
==[[Biochemistry]]==<br />
<br />
*[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
==Microbiology==<br />
<br />
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]<br />
<br />
*[[Conjugation using ET12567/pUZ8002]]<br />
<br />
*[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
*[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
*[[Isolating Actinomycetes from the environment]]<br />
<br />
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. <br />
<br />
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria]<br />
<br />
==[[Plant-microbe interactions]]==<br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Growing Marchantia from gemma spores]]<br />
<br />
==[[Microscopy]]==<br />
<br />
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
*[[Cultivating Actinobacteria for Microscopic Analysis]]<br />
<br />
==[[Mutagenesis]]==<br />
<br />
*[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
*[[Chemical mutagenesis]]<br />
<br />
*[[Depletion strains]]<br />
<br />
*[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
*[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
*[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
*[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
*[["Quikchange" site-directed mutagenesis]]<br />
<br />
*[[Random mutagenesis using a mutator strain]]<br />
<br />
*[[Random mutagenesis using error-prone PCR]]<br />
<br />
*[[Suicide vectors]]<br />
<br />
*[[Transposons]]<br />
<br />
*[[UV mutagenesis]]<br />
<br />
==[[Natural Products]]== <br />
<br />
*[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
*[[Metabolite extractions]]<br />
<br />
*[[Production of microbial volatile organic compounds]]<br />
<br />
==[[Next Generation Sequencing]]==<br />
<br />
*[[ChIP Sequencing]]<br />
*[[ChIP-exo sequencing]]<br />
https://www.nature.com/articles/s41467-018-05265-7/<br />
*[[RNA Sequencing]]<br />
*[[Differential RNA sequencing]]<br />
<br />
==[[Nucleic Acid Methods]]==<br />
<br />
*[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
*[[High GC PCR]]<br />
<br />
*[[RNA extraction from Actinobacteria]]<br />
<br />
*[[RNA interference]]<br />
<br />
*[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
*[[Southern Blotting]]<br />
<br />
==[[Protein Methods]]==<br />
<br />
*[[Isolating extracellular protein from Streptomyces]]<br />
<br />
=Alphabetical list of protocols=<br />
<br />
[[Characterisation of Actinomycetes]]<br />
<br />
[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
[[Chemical mutagenesis]]<br />
<br />
[[ChIP Seq]]<br />
<br />
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
[[Conjugation using ET12567/pUZ8002]]<br />
<br />
[[Depletion strains]]<br />
<br />
[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
[[High GC PCR]]<br />
<br />
[[High titre preparation of phage]]<br />
<br />
[[Isolating Actinomycetes from the environment]]<br />
<br />
[[Isolating extracellular protein from Streptomyces]]<br />
<br />
[[Isolating Streptomyces from plant roots]]<br />
<br />
[[Isolation of phages from environmental samples]]<br />
<br />
[[Isolation of phages from single plaques]]<br />
<br />
[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
[[Metabolite extractions]]<br />
<br />
[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
[["Quikchange" site-directed mutagenesis]]<br />
<br />
[[Random mutagenesis using a mutator strain]]<br />
<br />
[[Random mutagenesis using error-prone PCR]]<br />
<br />
[[RNA extraction from Actinobacteria]]<br />
<br />
[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
[[Southern Blotting]]<br />
<br />
[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
[[Suicide vectors]]<br />
<br />
[[Transposons]]<br />
<br />
[[UV mutagenesis]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1982Growing Marchantia from gemma spores2021-11-02T15:30:44Z<p>Damien Gayrard: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemmae}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Micropore tape<br />
*Plant growth chamber<br />
*If you want to remove the plant from the agar without destroying its rhizoids: sterile nylon mesh (cut to the shape of petri dish)<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma with the tip of a pipette tip and transfer over to the plate (coverd by nylon mesh if needed).<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.<br />
<br />
<h2><strong>References</h2></strong><br />
<br />
*Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato, Takayuki Kohchi, Molecular Genetic Tools and Techniques for Marchantia polymorpha Research , Plant and Cell Physiology, Volume 57, Issue 2, February 2016, Pages 262–270, https://doi.org/10.1093/pcp/pcv097<br />
*Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., ... & Schmutz, J. (2017). Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell, 171(2), 287-304, https://doi.org/10.1016/j.cell.2017.09.030</div>Damien Gayrardhttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1981Plant-Microbe interactions2021-11-02T15:29:41Z<p>Damien Gayrard: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemma spores | Growing ''Marchantia'' from gemmae]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Wheat root exudate harvesting| Harvesting root exudates]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Damien Gayrardhttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1980Plant-Microbe interactions2021-11-02T15:27:58Z<p>Damien Gayrard: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemmae | Growing ''Marchantia'' from gemmae]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Wheat root exudate harvesting| Harvesting root exudates]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Damien Gayrardhttps://actinobase.org/index.php?title=Plant-Microbe_interactions&diff=1979Plant-Microbe interactions2021-11-02T15:27:24Z<p>Damien Gayrard: </p>
<hr />
<div><h2><strong>Studying the interactions between <em>Streptomyces</em> bacteria and plant roots</strong></h2><br />
<br />
In recent years it has become clear that actinomycete bacteria like <em>Streptomyces</em> species are not simply free-living soil bacteria. They also interact with plant roots and can colonise the rhizosphere and endosphere (inside the roots). For example, they are highly enriched inside the roots of bread wheat plants, which are a staple crop for humans ([https://pubmed.ncbi.nlm.nih.gov/34154664/ Prudence et al, 2021]). This is fascinating because it helps us understand the natural ecology of these bacteria and their natural products - i.e. why they evolved, how they are regulated - and also because they may have uses as plant beneficial bacteria, e.g., by incorporating <em>Streptomyces</em> spores into seed coatings. <br />
<br />
<h2><strong>Protocols</strong></h2><br />
<br />
<h3><strong>''Marchantia'' protocols</strong></h3><br />
<br />
*[[Growing Marchantia from gemmae | Growing ''Marchantia'' from gemmae ]]<br />
<br />
<h3><strong>Wheat protocols</h3></strong><br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Wheat seed sterilisation]]<br />
*[[Wheat root exudate harvesting| Harvesting root exudates]]<br />
<br />
<h2><strong>Further Reading</strong></h2><br />
<br />
Worsley SF et al (2021). Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana microbiome. Frontiers in Molecular Bioscience, 8:686110. https://pubmed.ncbi.nlm.nih.gov/34222338/<br />
<br />
Prudence, Newitt et al (2021). Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome. Environmental Microbiome 16:12. https://pubmed.ncbi.nlm.nih.gov/34154664/<br />
<br />
Worsley et al (2020). Streptomyces Endophytes Promote Host Health and Enhance Growth across Plant Species. Appl Env Microbiol. 86:e01053-20. https://pubmed.ncbi.nlm.nih.gov/32561579/<br />
<br />
Newitt et al (2019). Biocontrol of cereal crop diseases using streptomycetes. Pathogens. 8:78. https://pubmed.ncbi.nlm.nih.gov/31200493/<br />
<br />
Kim et al (2019). A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nature Comms. 22:4802 https://pubmed.ncbi.nlm.nih.gov/31641114/<br />
<br />
Rey and Dumas (2017). Plenty Is No Plague: Streptomyces Symbiosis with Crops. Trends Plant Sci. 22:30-37. https://pubmed.ncbi.nlm.nih.gov/27916552/<br />
<br />
van der Meij, Worsley et al (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev. 41: 392-416. https://pubmed.ncbi.nlm.nih.gov/28521336/<br />
<br />
Seipke et al (2011). Streptomyces as symbionts; a new and emerging theme? FEMS Microbiol Rev. 36:867-76. https://pubmed.ncbi.nlm.nih.gov/22091965/</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1978Growing Marchantia from gemma spores2021-11-02T15:26:59Z<p>Damien Gayrard: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemmae}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Micropore tape<br />
*Plant growth chamber<br />
*If you want to remove the plant from the agar without destroying its rhizoids: sterile nylon mesh (cut to the shape of petri dish)<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the plate (coverd by nylon mesh if needed).<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.<br />
<br />
<h2><strong>References</h2></strong><br />
<br />
*Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato, Takayuki Kohchi, Molecular Genetic Tools and Techniques for Marchantia polymorpha Research , Plant and Cell Physiology, Volume 57, Issue 2, February 2016, Pages 262–270, https://doi.org/10.1093/pcp/pcv097<br />
*Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., ... & Schmutz, J. (2017). Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell, 171(2), 287-304, https://doi.org/10.1016/j.cell.2017.09.030</div>Damien Gayrardhttps://actinobase.org/index.php?title=Protocols&diff=1977Protocols2021-11-02T15:26:43Z<p>Damien Gayrard: /* Plant-microbe interactions */</p>
<hr />
<div>[[File:Actinobase-icons-trans_Protocols.png|150px|Protocols|link=Protocols]] <br />
<br />
=Protocols organised by category=<br />
<br />
==[[Bacteriophage]]==<br />
<br />
*[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
*[[High titre preparation of phage]]<br />
<br />
*[[Isolation of phages from single plaques]]<br />
<br />
*[[Isolation of phages from environmental samples]]<br />
<br />
==[[Biochemistry]]==<br />
<br />
*[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
==Microbiology==<br />
<br />
*[[Characterisation of Actinomycetes | General Characterisaton of Actinomycetes]]<br />
<br />
*[[Conjugation using ET12567/pUZ8002]]<br />
<br />
*[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
*[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
*[[Isolating Actinomycetes from the environment]]<br />
<br />
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. <br />
<br />
[https://actinobase.org/downloads/DSMZ.pdf DSMZ Compendium of Actinobacteria]<br />
<br />
==[[Plant-microbe interactions]]==<br />
<br />
*[[Isolating Streptomyces from plant roots| Isolating ''Streptomyces'' from plant roots]]<br />
*[[Growing Marchantia from gemmae]]<br />
<br />
==[[Microscopy]]==<br />
<br />
*[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
*[[Cultivating Actinobacteria for Microscopic Analysis]]<br />
<br />
==[[Mutagenesis]]==<br />
<br />
*[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
*[[Chemical mutagenesis]]<br />
<br />
*[[Depletion strains]]<br />
<br />
*[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
*[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
*[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
*[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
*[["Quikchange" site-directed mutagenesis]]<br />
<br />
*[[Random mutagenesis using a mutator strain]]<br />
<br />
*[[Random mutagenesis using error-prone PCR]]<br />
<br />
*[[Suicide vectors]]<br />
<br />
*[[Transposons]]<br />
<br />
*[[UV mutagenesis]]<br />
<br />
==[[Natural Products]]== <br />
<br />
*[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
*[[Metabolite extractions]]<br />
<br />
*[[Production of microbial volatile organic compounds]]<br />
<br />
==[[Next Generation Sequencing]]==<br />
<br />
*[[ChIP Sequencing]]<br />
*[[ChIP-exo sequencing]]<br />
https://www.nature.com/articles/s41467-018-05265-7/<br />
*[[RNA Sequencing]]<br />
*[[Differential RNA sequencing]]<br />
<br />
==[[Nucleic Acid Methods]]==<br />
<br />
*[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
*[[High GC PCR]]<br />
<br />
*[[RNA extraction from Actinobacteria]]<br />
<br />
*[[RNA interference]]<br />
<br />
*[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
*[[Southern Blotting]]<br />
<br />
==[[Protein Methods]]==<br />
<br />
*[[Isolating extracellular protein from Streptomyces]]<br />
<br />
=Alphabetical list of protocols=<br />
<br />
[[Characterisation of Actinomycetes]]<br />
<br />
[[Cloning, Transformation and Expression of Gene Clusters]]<br />
<br />
[[CRISPR/Cas9-mediated genome editing]]<br />
<br />
[[Chemical mutagenesis]]<br />
<br />
[[ChIP Seq]]<br />
<br />
[[Codon Optimising Sequences for Heterologous Expression in Streptomyces]]<br />
<br />
[[Conjugation using ET12567/pUZ8002]]<br />
<br />
[[Depletion strains]]<br />
<br />
[[Exploration | ''Streptomyces'' Exploration]]<br />
<br />
[[General Growth and Maintenance of Streptomyces sp.]]<br />
<br />
[[GUS assay]] (β-Glucuronidase assay)<br />
<br />
[[High GC PCR]]<br />
<br />
[[High titre preparation of phage]]<br />
<br />
[[Isolating Actinomycetes from the environment]]<br />
<br />
[[Isolating extracellular protein from Streptomyces]]<br />
<br />
[[Isolating Streptomyces from plant roots]]<br />
<br />
[[Isolation of phages from environmental samples]]<br />
<br />
[[Isolation of phages from single plaques]]<br />
<br />
[[Lambda-red mediated recombination (PCR-targeting system a.k.a. "Redirect")]]<br />
<br />
[[Lambda-red mediated recombination using ssDNA]]<br />
<br />
[[Meganuclease I-SceI based system for gene deletions]]<br />
<br />
[[Metabolite extractions]]<br />
<br />
[[Protoplasts Formation, Regeneration and Transformation]]<br />
<br />
[["Quikchange" site-directed mutagenesis]]<br />
<br />
[[Random mutagenesis using a mutator strain]]<br />
<br />
[[Random mutagenesis using error-prone PCR]]<br />
<br />
[[RNA extraction from Actinobacteria]]<br />
<br />
[[Salting Out Genomic DNA Extraction Method]]<br />
<br />
[[Southern Blotting]]<br />
<br />
[[Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids| Staining of ''Streptomyces'' spp. Cell Wall and Nucleic Acids]]<br />
<br />
[[Streptomyces Bacteriophage plaque assay]]<br />
<br />
[[Suicide vectors]]<br />
<br />
[[Transposons]]<br />
<br />
[[UV mutagenesis]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1976Growing Marchantia from gemma spores2021-11-02T14:58:41Z<p>Damien Gayrard: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Micropore tape<br />
*Plant growth chamber<br />
*If you want to remove the plant from the agar without destroying its rhizoids: sterile nylon mesh (cut to the shape of petri dish)<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the plate (coverd by nylon mesh if needed).<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.<br />
<br />
<h2><strong>References</h2></strong><br />
<br />
*Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato, Takayuki Kohchi, Molecular Genetic Tools and Techniques for Marchantia polymorpha Research , Plant and Cell Physiology, Volume 57, Issue 2, February 2016, Pages 262–270, https://doi.org/10.1093/pcp/pcv097<br />
*Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., ... & Schmutz, J. (2017). Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell, 171(2), 287-304, https://doi.org/10.1016/j.cell.2017.09.030</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1975Growing Marchantia from gemma spores2021-11-02T14:45:55Z<p>Damien Gayrard: </p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Micropore tape<br />
*Plant growth chamber<br />
*If you want to remove the plant from the agar without destroying its rhizoids: sterile nylon mesh (cut to the shape of petri dish)<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the plate (coverd by nylon mesh if needed).<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.<br />
<br />
<h2><strong>References</h2></strong><br />
<br />
*Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato, Takayuki Kohchi, Molecular Genetic Tools and Techniques for Marchantia polymorpha Research , Plant and Cell Physiology, Volume 57, Issue 2, February 2016, Pages 262–270, https://doi.org/10.1093/pcp/pcv097</div>Damien Gayrardhttps://actinobase.org/index.php?title=1/2_MS%2BB5&diff=19741/2 MS+B52021-11-02T14:18:58Z<p>Damien Gayrard: </p>
<hr />
<div>==Preparation==<br />
Per Litre:<br />
*2.205 MS Salts and Gamborg B5 Vitamins (Duchefa M0231)<br />
*1 L ddH2O<br />
*5M KOH<br />
*Bacto Agar<br />
<br />
<br />
'''Instructions'''<br />
#Dissolve 2.2g MS Salts + Gamborg B5 Vitamin mix in 950ml ddH2O<br />
#Adjust pH to 6.7 with 5M KOH <br />
#Make up to final volume with water (for 1L, add the remaining ≈50ml ddH2O)<br />
#Divide into batches (in bottles containing Bacto Agar if required)<br />
#Autoclave until golden brown<br />
<br />
For solid media:<br />
Add 12 g Bacto Agar<br />
<br />
==Uses==<br />
*[[Growing Marchantia from gemma spores]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=1/2_MS%2BB5&diff=19731/2 MS+B52021-11-02T14:18:40Z<p>Damien Gayrard: Created page with "==Preparation== Per Litre: *2.205 MS Salts and Gamborg B5 Vitamins (Duchefa M0231) *1 L ddH2O *5M KOH *Bacto Agar '''Instructions''' #Dissolve 2.2g MS Salts + Gamborg B5 Vit..."</p>
<hr />
<div>==Preparation==<br />
Per Litre:<br />
*2.205 MS Salts and Gamborg B5 Vitamins (Duchefa M0231)<br />
*1 L ddH2O<br />
*5M KOH<br />
*Bacto Agar<br />
<br />
<br />
'''Instructions'''<br />
#Dissolve 2.2g MS Salts + Gamborg B5 Vitamin mix in 950ml ddH2O<br />
#Adjust pH to 6.7 with 5M KOH <br />
#Make up to final volume with water (for 1L, add the remaining ≈50ml ddH2O)<br />
#Divide into batches (in bottles containing Bacto Agar if required)<br />
#Autoclave until golden brown<br />
<br />
For solid media:<br />
#Add 12 g Bacto Agar<br />
<br />
==Uses==<br />
*[[Growing Marchantia from gemma spores]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1972Growing Marchantia from gemma spores2021-11-02T13:24:23Z<p>Damien Gayrard: /* Protocol */</p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your 1/2 MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Damien Gayrardhttps://actinobase.org/index.php?title=Media_recipes&diff=1971Media recipes2021-11-02T13:21:46Z<p>Damien Gayrard: /* Media Recipes */</p>
<hr />
<div>{{DISPLAYTITLE:Media Recipes}}<br />
<br />
[[File:Actinobase-icons-trans_Media-recipes.png|150px|Media Recipes|link=Media_recipes]]<br />
<br />
=Media Recipes=<br />
<br />
[[A1]]<br />
<br />
[[CM]] (Complete medium)<br />
<br />
[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth) | [[SNA]] (Soft Nutrient Agar)<br />
<br />
[[Emerson medium]]<br />
<br />
[[Gause's No. 1]]<br />
<br />
[[GYM]] (Glucose + Yeast Extract + Malt Extract) <br />
<br />
[[HT]] (Hickey-Tresner)<br />
<br />
[[HV]]<br />
<br />
[[IMA]] (Smash)<br />
<br />
[[LB]] (Lysogeny Broth) | [[Lennox]] (Lennox agar) | [[Luria]] (Luria agar)<br />
<br />
[[MC agar]] (Milk Casein Agar)<br />
<br />
[[MM]] (Minimal medium)<br />
<br />
[[SFM | MS]] (Mannitol Soya agar - a.k.a. Soya Flour Mannitol (SFM))<br />
<br />
[[1/2 MS0 | 1/2 MS-S]]<br />
<br />
[[1/2 MS+B5]]<br />
<br />
[[MYM]] (Maltose + Yeast Extract + Malt Extract) <br />
<br />
[[NMMP]] (minimal liquid medium)<br />
<br />
[[OT]] (oligotrophic agar)<br />
<br />
[[PDA]] (Potato Dextrose Agar)<br />
<br />
[[R2]] | [[R2YE]] | [[R5]]<br />
<br />
[[SC]] (Starch Casein agar)<br />
<br />
[[SFM]] (Soya Flour Mannitol - a.k.a. Mannitol Soya agar)<br />
<br />
[[SMM]] (supplemented liquid minimal medium) | [[SMMS]] (supplemented minimal medium, solid)<br />
<br />
[[SPY]] (Salt Peptone Yeast)<br />
<br />
[[TSB]] (Tryptone Soy Broth)<br />
<br />
[[YEME]] (Yeast Extract + Malt Extract)<br />
<br />
[[YMPD]] (Yeast Meat Peptone Dextrose)<br />
<br />
[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose) <br />
<br />
[[2X YT]]<br />
<br />
====<u>International ''Streptomyces'' Project Media (ISP's)</u>====<br />
<br />
[[ISP2]] <br />
<br />
[[ISP3]]<br />
<br />
[[ISP4]]<br />
<br />
[[ISP5]]<br />
<br />
[[ISP6]]<br />
<br />
[[ISP7]]<br />
<br />
==Media Supplements==<br />
<br />
[[Antibiotic stocks and working concentrations]]<br />
<br />
[[Indicator compounds]]<br />
<br />
[[Media supplements for activating cryptic biosynthetic gene clusters]]<br />
<br />
[[Media supplements for induction gene expression from inducible promoters]]<br />
<br />
[[Trace element solution]]</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1970Growing Marchantia from gemma spores2021-11-02T13:21:20Z<p>Damien Gayrard: /* You will need: */</p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[1/2 MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Damien Gayrardhttps://actinobase.org/index.php?title=Growing_Marchantia_from_gemma_spores&diff=1969Growing Marchantia from gemma spores2021-11-02T13:18:06Z<p>Damien Gayrard: /* You will need: */</p>
<hr />
<div>{{DISPLAYTITLE: Growing '''Marchantia'' from gemma spores}}<br />
<br />
==''Marchantia'' and their lifecycle==<br />
''Marchantia'' (or liverworts) are a genus of plant in the bryophyte taxonomic division along with mosses and hornworts which are thought to be the oldest extant plants on earth. ''Marchantia'' have two ways of reproducing - sexually (during their sporophytic phase) and asexually (during their gametophytic phase). In their gametophytic phase, the plant produces gemma cups which contain gemma haploid spores which, when dispersed by wind or rain, has the ability to create a clone of its parent.<br />
<br /><br />
''Marchantia polymorpha'' (the ‘Common liverwort’) is used as a model organism in biological studies.<br />
<br />
==You will need:==<br />
*Healthy ''Marchantia polymorpha'' plant with developed gemma cups and gemma<br />
*dH<sub>2</sub>O<br />
*Sterile pipette tips of any size<br />
*Sterile tweezers<br />
*[[Half MS+B5]] agar plates<br />
*Sterile nylon mesh (cut to the shape of petri dish)<br />
*Micropore tape<br />
*Plant growth chamber<br />
<br />
==Protocol==<br />
#In a sterile environment, place a nylon mesh sheet onto your MS+B5 agar plates.<br />
#Submerge the ''Marchantia'' plant in water and agitate gemma cups with a pipette tip so that the gemma float to the surface of the water.<br />
#Pick up a single gemma spore with the tip of a pipette tip and transfer over to the nylon mesh plate.<br />
#Close the lid of the plate and seal with micropore tape.<br />
#Grow in a growth chamber at 25°C and long daylight hours.</div>Damien Gayrard