Difference between revisions of "Methods"
(→Strain construction) |
(→Toolboxes for the work with B. subtilis) |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 4: | Line 4: | ||
* [[C minimal medium]] | * [[C minimal medium]] | ||
* [[M9 minimal medium]] | * [[M9 minimal medium]] | ||
| + | * [[Spizizen minimal medium]] | ||
| + | |||
| + | == 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] | ||
| + | |||
| + | == 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}} | ||
==Analysis of protein-protein interactions== | ==Analysis of protein-protein interactions== | ||
| Line 43: | Line 52: | ||
* GFP variants specifically optimizd for use in ''B. subtilis'' {{PubMed|23956387}} | * GFP variants specifically optimizd for use in ''B. subtilis'' {{PubMed|23956387}} | ||
* Quantitative analysis of cell types by comparing microscoy images {{PubMed|25448819}} | * 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== | ==Transposon mutagenesis== | ||
| Line 54: | Line 64: | ||
* genome engineering using a synthetic gene circuit {{PubMed|25552415}} | * genome engineering using a synthetic gene circuit {{PubMed|25552415}} | ||
* Ordered Gene Assembly in Bacillus subtilis (OGAB) {{PubMed|25990947}} | * 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: | * A review on genome engineering: | ||
<pubmed>23340847 </pubmed> | <pubmed>23340847 </pubmed> | ||
| Line 61: | Line 74: | ||
==Key references== | ==Key references== | ||
| − | <pubmed>22179594 20057169 20134232 21542786 20300532 19698693 17932079 21841760 17994626 23956387 22285978,22113911 24002656 24282588 25990947</pubmed> | + | <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:
Contents
- 1 Media
- 2 A collection of mutant strains
- 3 Toolboxes for the work with B. subtilis
- 4 Analysis of protein-protein interactions
- 5 Analysis of membrane proteins
- 6 Antibodies
- 7 Protein expression
- 8 Strain construction
- 9 RNA analysis
- 10 Genetic work with non-standard strains
- 11 General procedures
- 12 Microscopic techniques
- 13 Transposon mutagenesis
- 14 Protein-DNA interactions
- 15 Genome engineering
- 16 Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation
- 17 Key references
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
- 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
- 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:
Kevin M Esvelt, Harris H Wang
Genome-scale engineering for systems and synthetic biology.
Mol Syst Biol: 2013, 9;641
[PubMed:23340847]
[WorldCat.org]
[DOI]
(I p)
Visual descriptions of methods for B. subtilis in the Journal of Visual Experimentation
Key references
