Difference between revisions of "Methods"

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Here you can find a list of methods for working with ''Bacillus subtilis'':
 
Here you can find a list of methods for working with ''Bacillus subtilis'':
  
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*Bacterial Two Hybrid: [[BACTH]]
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== Media ==
 +
* [[C minimal medium]]
 +
* [[M9 minimal medium]]
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* [[Spizizen minimal medium]]
  
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*[[SPINE]]: A method to detect ''in vivo'' protein-protein interactions
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== A collection of mutant strains ==
 +
* the complete mutant strain collection from the [http://www.sciencedirect.com/science/article/pii/S2405471216304471?via%3Dihub Koo et al.] paper is now available: get access [https://www.addgene.org/kits/grosslab-bsubtilis-collections/ here]
  
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* introduction of markerfree deletions: {{PubMed|20057169}}
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== Toolboxes for the work with ''B. subtilis'' ==
 +
* the biobrick box {{PubMed|24295448}}
 +
* the biobrick box 2.0 {{PubMed|29118374}}
 +
* a part toolbox to tune genetic expression {{PubMed|27402159}}
  
−
* generation of markerfree mutations: {{PubMed|20134232}}
+
==Analysis of protein-protein interactions==
 +
* Bacterial Two Hybrid: [[BACTH]]
  
 +
* [[SPINE]]: A method to detect ''in vivo'' [[protein-protein interactions]]
 +
 +
* ''in vivo'' detection of [[protein-protein interactions]] using [[DivIVA]] and GFP {{PubMed|19698693}}
 +
 +
==Analysis of membrane proteins==
 +
* application of a split green fluorescent protein reporter  {{PubMed|22285978}}
 +
 +
== Antibodies ==
 +
* List of available [[Antibodies]]
 +
 +
== Protein expression ==
 +
* the LIKE system {{PubMed|23110498}}
 +
 +
==Strain construction==
 +
* introduction of markerfree deletions: {{PubMed|26238998,24140578,23916947,23911571,22422839,20057169}}
 +
* generation of markerfree mutations: {{PubMed|20134232,21542786,24282588}}
 +
* an improved method for transformation: {{PubMed|24838881}}
 +
 +
==RNA analysis==
 
* Mechanical cell disruption and extraction of RNA from ''B. subtilis'': [[Media:SOP-RNA.pdf]]
 
* Mechanical cell disruption and extraction of RNA from ''B. subtilis'': [[Media:SOP-RNA.pdf]]
  
 +
==Genetic work with non-standard strains==
 
* transformation of wild-type ''B. subtilis'' strains incl. NCIB3610: {{PubMed|20300532}}
 
* transformation of wild-type ''B. subtilis'' strains incl. NCIB3610: {{PubMed|20300532}}
 +
* efficient electroporation of ''B. subtilis'' {{PubMed|22387342}}
 +
* a novel transformation protocol for ''B. subtilis'' DB104 {{PubMed|22395911}}
  
 +
==General procedures==
 
* Standard operation procedures ([[SOP]]s) of the SYSMO-BACELL consortium
 
* Standard operation procedures ([[SOP]]s) of the SYSMO-BACELL consortium
 +
 +
==Microscopic techniques==
 +
* Live cell imaging of ''B. subtilis'' cells using automated time-lapse microscopy {{PubMed|21841760}}
 +
* Assay of gene expression dynamics using live cell imaging {{PubMed|22179594}}
 +
* Visualization and quantification of gene expression heterogeneity in growing microbial cells {{PubMed|23874729}}
 +
* GFP variants specifically optimizd for use in ''B. subtilis'' {{PubMed|23956387}}
 +
* Quantitative analysis of cell types by comparing microscoy images {{PubMed|25448819}}
 +
* Semi-automated single cell analysis using membrane or DNA staining {{PubMed|27008090}}
 +
 +
==Transposon mutagenesis==
 +
* mariner transposon mutagenesis for random inducible-expression insertions and transcriptional reporter fusion insertions  {{PubMed|22113911}}
 +
 +
==Protein-DNA interactions==
 +
* ChAP-chip: A modified ChIP-chip protocol for the ''in vivo'' identification of binding sites of DNA-binding proteins {{PubMed|17932079}}
 +
 +
==Genome engineering==
 +
* generalized bacterial genome editing using mobile group II introns and Cre-lox {{PubMed|24002656}}
 +
* genome engineering using a synthetic gene circuit {{PubMed|25552415}}
 +
* Ordered Gene Assembly in Bacillus subtilis (OGAB) {{PubMed|25990947}}
 +
* construction of a super-competent strain {{PubMed|26732353}}   
 +
* use of the CRISPR-Cas system {{PubMed|27260361,27255973,27238023,27342565}}   
 +
 +
* A review on genome engineering:
 +
<pubmed>23340847 </pubmed>
 +
 +
== Visual descriptions of methods for ''B. subtilis'' in the ''Journal of Visual Experimentation'' ==
 +
<pubmed> 24473333 24457605 24300024 24300445 22371091 20142799 21841760 </pubmed>
 +
 +
==Key references==
 +
<pubmed>22179594 20057169 20134232 21542786 20300532 19698693 17932079 21841760 17994626 23956387 22285978,22113911 24002656 24282588 26238998 25990947 26732353</pubmed>

Latest revision as of 10:31, 10 November 2017

Here you can find a list of methods for working with Bacillus subtilis:

Media

A collection of mutant strains

  • the complete mutant strain collection from the Koo et al. paper is now available: get access here

Toolboxes for the work with B. subtilis

  • the biobrick box PubMed
  • the biobrick box 2.0 PubMed
  • a part toolbox to tune genetic expression PubMed

Analysis of protein-protein interactions

  • Bacterial Two Hybrid: BACTH

Analysis of membrane proteins

  • application of a split green fluorescent protein reporter PubMed

Antibodies

Protein expression

Strain construction

  • introduction of markerfree deletions: PubMed
  • generation of markerfree mutations: PubMed
  • an improved method for transformation: PubMed

RNA analysis

  • Mechanical cell disruption and extraction of RNA from B. subtilis: Media:SOP-RNA.pdf

Genetic work with non-standard strains

  • transformation of wild-type B. subtilis strains incl. NCIB3610: PubMed
  • efficient electroporation of B. subtilis PubMed
  • a novel transformation protocol for B. subtilis DB104 PubMed

General procedures

  • Standard operation procedures (SOPs) of the SYSMO-BACELL consortium

Microscopic techniques

  • Live cell imaging of B. subtilis cells using automated time-lapse microscopy PubMed
  • Assay of gene expression dynamics using live cell imaging PubMed
  • Visualization and quantification of gene expression heterogeneity in growing microbial cells PubMed
  • GFP variants specifically optimizd for use in B. subtilis PubMed
  • Quantitative analysis of cell types by comparing microscoy images PubMed
  • Semi-automated single cell analysis using membrane or DNA staining PubMed

Transposon mutagenesis

  • mariner transposon mutagenesis for random inducible-expression insertions and transcriptional reporter fusion insertions PubMed

Protein-DNA interactions

  • ChAP-chip: A modified ChIP-chip protocol for the in vivo identification of binding sites of DNA-binding proteins PubMed

Genome engineering

  • generalized bacterial genome editing using mobile group II introns and Cre-lox PubMed
  • genome engineering using a synthetic gene circuit PubMed
  • Ordered Gene Assembly in Bacillus subtilis (OGAB) PubMed
  • construction of a super-competent strain PubMed
  • use of the CRISPR-Cas system PubMed
  • A review on genome engineering:


Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation

Lorena Stannek, Richard Egelkamp, Katrin Gunka, Fabian M Commichau
Monitoring intraspecies competition in a bacterial cell population by cocultivation of fluorescently labelled strains.
J Vis Exp: 2014, (83);e51196
[PubMed:24473333] [WorldCat.org] [DOI] (I e)

Samantha M Desmarais, Felipe Cava, Miguel A de Pedro, Kerwyn Casey Huang
Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography.
J Vis Exp: 2014, (83);e51183
[PubMed:24457605] [WorldCat.org] [DOI] (I e)

Ewa Król, Dirk-Jan Scheffers
FtsZ polymerization assays: simple protocols and considerations.
J Vis Exp: 2013, (81);e50844
[PubMed:24300445] [WorldCat.org] [DOI] (I e)

Elizabeth Anne Shank
Using coculture to detect chemically mediated interspecies interactions.
J Vis Exp: 2013, (80);e50863
[PubMed:24300024] [WorldCat.org] [DOI] (I e)

Juan C Garcia-Betancur, Ana Yepes, Johannes Schneider, Daniel Lopez
Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry.
J Vis Exp: 2012, (60);
[PubMed:22371091] [WorldCat.org] [DOI] (I e)

Imke G de Jong, Katrin Beilharz, Oscar P Kuipers, Jan-Willem Veening
Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy.
J Vis Exp: 2011, (53);
[PubMed:21841760] [WorldCat.org] [DOI] (I e)

Andrew D Klocko, Kaleena M Crafton, Brian W Walsh, Justin S Lenhart, Lyle A Simmons
Imaging mismatch repair and cellular responses to DNA damage in Bacillus subtilis.
J Vis Exp: 2010, (36);
[PubMed:20142799] [WorldCat.org] [DOI] (I e)


Key references

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