Difference between revisions of "Methods"
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== Antibodies == | == Antibodies == | ||
− | * [[ | + | * List of available [[Antibodies]] |
== Protein expression == | == Protein expression == |
Revision as of 11:15, 2 April 2015
Here you can find a list of methods for working with Bacillus subtilis:
Contents
- 1 Media
- 2 Analysis of protein-protein interactions
- 3 Analysis of membrane proteins
- 4 Antibodies
- 5 Protein expression
- 6 Strain construction
- 7 RNA analysis
- 8 Genetic work with non-standard strains
- 9 General procedures
- 10 Microscopic techniques
- 11 Transposon mutagenesis
- 12 Protein-DNA interactions
- 13 Genome engineering
- 14 Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation
- 15 Key references
Media
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
Analysis of membrane proteins
- application of a split green fluorescent protein reporter PubMed
Antibodies
- List of available Antibodies
Protein expression
- the LIKE system PubMed
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
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
- 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