ActinoBase - User contributions [en-gb]

Metabolite extractions

2019-07-26T15:43:40Z

ActinoCommittee: Protocols to extract metabolites from Actinobacteria

Actinobacteria isolation from marine environments

2019-07-26T15:29:21Z

ActinoCommittee:

=Pre-treatment methods of marine samples=
Pre-treatment methods for the isolation of marine actinobacteria have been applied to eliminate the growth of terrestrial actinobacteria, gram-negative bacteria and fungi (1). These methods include drying the samples using laminar air flow hood, mixing the samples with seawater, applying UV irradiation, applying high frequency radiation and the use of certain antibiotics to kill gram negative bacteria.

==Drying marine samples with laminar air flow hood==
Several drying pre-treatment methods can be used to enhance the isolation of Actinobacteria from marine environments (2):

1- Drying sediment overnight in a laminar flow hood until clumping occurs. Press a sterile foam plug against the sediment sample and onto the surface of an agar plate making a serial dilution (2).

2- Drying sediment overnight in a laminar flow hood until clumping occurs. Dilute dried sediment with 5 ml of sterile seawater and mix well. Add 50 µl of the solution onto an agar plate and spread with an spreader (2).

==Mixing the samples with seawater==
Media can be enriched with 2% of seawater or samples can be added directly grown in sterile (autoclaved) seawater (3).

==Applying UV irradiation==
Directly apply UV‐irradiation to the sediment suspension (5 ml) for 30 s. Use a wavelength of 254 nm and leave a distance of 20 cm (4).

==Applying high frequency radiation==
Apply superhigh frequency radiation directly to sediment samples by placing the sediment solution in a Eppendorf tube and microwave it for 45 seonds at 2460 MHz and 80 W (4).

==Media selection==

==References==
1- Subramani, R. and Sipkema, D. (2019) ‘Marine rare actinomycetes: A promising source of structurally diverse and unique novel natural products’, Marine Drugs. doi: 10.3390/md17050249.

2- Jensen, P. R. et al. (2005) ‘Culturable marine actinomycete diversity from tropical Pacific Ocean sediments’, Environmental Microbiology. doi: 10.1111/j.1462-2920.2005.00785.x.

3- Mincer, T. J., Fenical, W. and Jensen, P. R. (2005) ‘Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora’, Applied and Environmental Microbiology. doi: 10.1128/AEM.71.11.7019-7028.2005.

4- Bredholt, H. et al. (2008) ‘Actinomycetes from sediments in the Trondheim fjord, Norway: Diversity and biological activity’, Marine Drugs. doi: 10.3390/md6010012.

Actinobacteria isolation from marine environments

2019-07-26T15:28:48Z

ActinoCommittee:

Actinobacteria isolation from marine environments

2019-07-26T15:28:02Z

ActinoCommittee:

=Pre-treatment methods of marine samples=
Pre-treatment methods for the isolation of marine actinobacteria have been applied to eliminate the growth of terrestrial actinobacteria, gram-negative bacteria and fungi (1). These methods include drying the samples using laminar air flow hood, mixing the samples with seawater, applying UV irradiation, applying high frequency radiation and the use of certain antibiotics to kill gram negative bacteria.

==Drying marine samples with laminar air flow hood==
Several drying pre-treatment methods can be used to enhance the isolation of Actinobacteria from marine environments (2):
1- Drying sediment overnight in a laminar flow hood until clumping occurs. Press a sterile foam plug against the sediment sample and onto the surface of an agar plate making a serial dilution (2).

2- Drying sediment overnight in a laminar flow hood until clumping occurs. Dilute dried sediment with 5 ml of sterile seawater and mix well. Add 50 µl of the solution onto an agar plate and spread with an spreader (2).

==Mixing the samples with seawater==
Media can be enriched with 2% of seawater or samples can be added directly grown in sterile (autoclaved) seawater (3).

==Applying UV irradiation==
Directly apply UV‐irradiation to the sediment suspension (5 ml) for 30 s. Use a wavelength of 254 nm and leave a distance of 20 cm (4).

==Applying high frequency radiation==
Apply superhigh frequency radiation directly to sediment samples by placing the sediment solution in a Eppendorf tube and microwave it for 45 seonds at 2460 MHz and 80 W (4).

==Media selection==

==References==
1- Subramani, R. and Sipkema, D. (2019) ‘Marine rare actinomycetes: A promising source of structurally diverse and unique novel natural products’, Marine Drugs. doi: 10.3390/md17050249.
2- Jensen, P. R. et al. (2005) ‘Culturable marine actinomycete diversity from tropical Pacific Ocean sediments’, Environmental Microbiology. doi: 10.1111/j.1462-2920.2005.00785.x.
3- Mincer, T. J., Fenical, W. and Jensen, P. R. (2005) ‘Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora’, Applied and Environmental Microbiology. doi: 10.1128/AEM.71.11.7019-7028.2005.
4- Bredholt, H. et al. (2008) ‘Actinomycetes from sediments in the Trondheim fjord, Norway: Diversity and biological activity’, Marine Drugs. doi: 10.3390/md6010012.

Emerson medium

2019-07-26T14:08:24Z

ActinoCommittee: Created page with "=Emerson medium= Emerson medium is a rich medium formulated by Emerson et al (1) to isolate mould and Actinobacteria. It is composed of beef extract, yeast extract, peptic di..."

=Emerson medium=

Emerson medium is a rich medium formulated by Emerson et al (1) to isolate mould and Actinobacteria. It is composed of beef extract, yeast extract, peptic digest of animal tissue, dextrose and sodium chloride.
This medium is also used for the maintenance of mould and actinobacteria pure cultures.

==Preparation==
Per litre of distilled water:
Beef extract 4.0 g
Yeast extract 1.0 g
Peptic digest of animal tissue 4.0 g
Dextrose 10.0 g
Sodium chloride 2.5 g
Agar 20.0 g
Final pH (at 25°C) 7.0

'''Instructions'''
Mix well all the components in 1000 mL of distilled water. Sterilize by autoclaving at 15 lbs pressure (121°C) for 15 minutes. Mix well and pour into sterile Petri dishes.

==Uses==
*[[Actinobacteria maintenance]]
*[[Mould maintenance]]
*[[Fungi maintenance]]
*[[Isolation experiments]]
*[[Induce antibiotic production of antibiotic producing organisms]]

==Notes==
For growth in liquid culture, Emerson Agar can be made without the agar.

==References==
EMERSON, R. L. and WHIFFEN, A. J. (1946) ‘Studies on the production of antibiotics by actinomycetes and molds.’, Journal of bacteriology.

Environmental isolation

2019-07-26T13:36:19Z

ActinoCommittee: ActinoCommittee moved page Environmental isolation to Actinobacteria isolation from marine environments

#REDIRECT [[Actinobacteria isolation from marine environments]]

Actinobacteria isolation from marine environments

2019-07-26T13:36:18Z

ActinoCommittee: ActinoCommittee moved page Environmental isolation to Actinobacteria isolation from marine environments

Actinobacteria isolation from marine environments

2019-07-26T13:21:59Z

ActinoCommittee: Protocols to isolate Actinobacteria from different environments

MM

2019-06-26T13:23:09Z

ActinoCommittee:

=MM (Minimal Medium)=
MM is a minimal medium suitable for growth of many Streptomyces sp (S. coelicolor and S. venezuelae both grow well on it). It is often made up with glucose or mannitol, but other carbon sources can be used. It can be further supplemented with additional growth factors as described below.

==Preparation==
Per litre:
*0.5g L-asparagine
*0.5g K2HPO4
*0.2g MgSO4*7H2O
*0.01g FeSO4*7H2O
*10g glucose (added after autoclaving)
*10g agar
*1L dH2O

'''Instructions'''
#Dissolve all of the ingredients except the agar and the glucose in the distilled water
#Adjust the pH to 7.0-7.2
#Dispense 200ml into flasks each containing 2g agar
#Autoclave
#After autoclaving, add 4 ml sterile 50% glucose solution (autoclaved separately or filter-sterilized) to each flask
#Add any other growth factors required for auxotrophic mutants

==Uses==
*studies of auxotrophic mutants and carbon source utilization

==Notes==
The glucose can be replaced by alternative carbon sources such as glycerol, arabinose, or mannitol (each at 5g/L). Mannitol is often preferable to glucose for optimal growth and development.

To study carbon source utilization, the L-asparagine should be replaced by ammonium sulfate (5 g/L(NH4)2SO4) - to avoid confusion due to utilization of asparagine as a carbon source.

Additional supplements can be added as follows (amount/L): amino acids except histidine, 50 mg; histidine, 70 mg; adenine and uracil, 10 mg; vitamins, 1 mg; dihydrostreptomycin sulfate, 50 mg; acriflavine, 15 mg. (Hopwood 1967)

==References==
Hopwood DA. Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol Rev. 1967;31(4):373–403.

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics: John Innes Foundation, Norwich Research Park, Colney, Norwich NR4 7UH, UK

MM

2019-06-26T13:21:11Z

ActinoCommittee:

=MM (Minimal Medium)=
MM is a minimal medium suitable for growth of many Streptomyces sp. It is often made up with glucose or mannitol, but other carbon sources can be used. It can be further supplemented with additional growth factors as described below.

==Preparation==
Per litre:
*0.5g L-asparagine
*0.5g K2HPO4
*0.2g MgSO4*7H2O
*0.01g FeSO4*7H2O
*10g glucose (added after autoclaving)
*10g agar
*=1L dH2O

'''Instructions'''
#Dissolve all of the ingredients except the agar and the glucose in the distilled water
#Adjust the pH to 7.0-7.2
#Dispense 200ml into flasks each containing 2g agar
#Autoclave
#After autoclaving, add 4 ml sterile 50% glucose solution to each flask
#Add any other growth factors required for auxotrophic mutants

==Uses==
*studies of auxotrophic mutants and carbon source utilization

==Notes==
The glucose can be replaced by alternative carbon sources such as glycerol, arabinose, or mannitol (each at 5g/L). Mannitol is often preferable to glucose for optimal growth and development.

To study carbon source utilization, the L-asparagine should be replaced by ammonium sulfate (5 g/L(NH4)2SO4) - to avoid confusion due to utilization of asparagine as a carbon source.

Additional supplements can be added as follows (amount/L): amino acids except histidine, 50 mg; histidine, 70 mg; adenine and uracil, 10 mg; vitamins, 1 mg; dihydrostreptomycin sulfate, 50 mg; acriflavine, 15 mg. (Hopwood 1967)

==References==
Hopwood DA. Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol Rev. 1967;31(4):373–403.

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics: John Innes Foundation, Norwich Research Park, Colney, Norwich NR4 7UH, UK

MM

2019-06-26T11:50:42Z

ActinoCommittee: Created page with "=MM Medium= ==Preparation== Per litre: *0.5g L-asparagine *0.5g K2HPO4 *0.2g MgSO4*7H2O *0.01g FeSO4*7H2O *10g glucose (added after autoclaving) *10g agar *=1L dH2O '''Instr..."

=MM Medium=

==Preparation==
Per litre:
*0.5g L-asparagine
*0.5g K2HPO4
*0.2g MgSO4*7H2O
*0.01g FeSO4*7H2O
*10g glucose (added after autoclaving)
*10g agar
*=1L dH2O

'''Instructions'''
#Dissolve all of the ingredients except the agar and the glucose in the distilled water
#Adjust the pH to 7.0-7.2
#Dispense 200ml into flasks each containing 2g agar
#Autoclave
#After autoclaving, add 4 ml sterile 50% glucose solution to each flask
#Add any other growth factors required for auxotrophic mutants

==Uses==

==Notes==

==References==
Hopwood DA. Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol Rev. 1967;31(4):373–403.

LB

2019-06-26T09:57:56Z

ActinoCommittee:

=LB=
Known as Lysogeny Broth (or sometimes, mistakenly, as Luria-Bertani medium), this rich medium is used routinely for growth of Escherichia coli. There are several variants on this medium, with differing amounts of NaCl; glucose may also be added, as in the original recipe (Bertani 1951).

==Preparation==
Per litre:
*5g Yeast Extract
*10g NaCl
*10g Tryptone
*Up to 1L dH2O

'''Instructions'''
#Add 5g Yeast Extract, 10g NaCl and 10g Tryptone to a beaker
#Add 800ml dH2O and stir until all solids are fully suspended
#Make up to 1L with dH2O
#For solid media, add 4g agar per 200ml LB
#Autoclave

===-NaCl LB===
Per litre:
*5g Yeast Extract
*10g Tryptone
*Up to 1L dH2O

==Uses==
*Routine growth of Escherichia coli
*Checking for contamination in Streptomyces spore stocks or cultures

==Notes==
This is the Miller formulation, with 10g/L NaCl. Alternatively, 5g/L NaCl can be used (Lennox formulation) or no salt (-NaCl).
The -NaCl (no salt) version of LB should be used when using salt sensitive antibiotics like [[hygromycin]]: for example, when cloning into [[pSS170]]. (Alternatively, [[DNA]] or [[DNB]] can be used for hygromycin selection.)

To make liquid LB medium, omit the agar and autoclave as above.

==References==
Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951;62(3):293–300.

Protocols

2019-06-26T09:57:04Z

ActinoCommittee:

[[General Growth and Maintenance of Streptomyces sp.]]

[[Mutagenesis]]

[[Nucleic Acid Methods]]

[[Protein Methods]]

[[PCR]]

LB

2019-06-26T09:56:38Z

ActinoCommittee:

=LB=
Known as Lysogeny Broth (or sometimes, mistakenly, as Luria-Bertani medium), this rich medium is used routinely for growth of Escherichia coli. There are several variants on this medium, with differing amounts of NaCl; glucose may also be added, as in the original recipe (Bertani 1951).

==Preparation==
Per litre:
*5g Yeast Extract
*10g NaCl
*10g Tryptone
*Up to 1L dH2O

'''Instructions'''
#Add 5g Yeast Extract, 10g NaCl and 10g Tryptone to a beaker
#Add 800ml dH2O and stir until all solids are fully suspended
#Make up to 1L with dH2O
#For solid media, add 4g agar per 200ml LB
#Autoclave

===-NaCl LB===
Per litre:
*5g Yeast Extract
*10g Tryptone
*Up to 1L dH2O

==Uses==
*Routine growth of Escherichia coli
*Checking for contamination in Streptomyces spore stocks or cultures

==Notes==
This is the Miller formulation, with 10g/L NaCl. Alternatively, 5g/L NaCl can be used (Lennox formulation) or no salt (see below).
The -NaCl (no salt) version of LB should be used when using salt sensitive antibiotics like [[hygromycin]]: for example, when cloning into [[pSS170]]. (Alternatively, [[DNA]] or [[DNB]] can be used for hygromycin selection.)

To make liquid LB medium, omit the agar and autoclave as above.

==References==
Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951;62(3):293–300.

Media recipes

2019-06-26T09:49:23Z

ActinoCommittee:

[[A1]]

[[CM]] (Complete medium)

[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth) | [[SNA]] (soft nutrient agar)

[[Emerson medium]]

[[GYM]] (Glucose + Yeast Extract + Malt Extract)

[[HT]] (Hickey-Tresner)

[[IMA]] (Smash)

[[ISP2]]

[[ISP3]]

[[ISP4]]

[[ISP5]]

[[ISP6]]

[[ISP7]]

[[LB]] (Lysogeny Broth) | [[L]] (L agar)

[[MM]] (Minimal medium)

[[MYM]] (Maltose + Yeast Extract + Malt Extract)

[[NMMP]] (minimal liquid medium)

[[PGA]] (Potato Glucose)

[[R2]] | [[R2YE]] | [[R5]]

[[SFM]] (Soy Flour Mannitol)

[[SMM]] (supplemented liquid minimal medium) | [[SMMS]] (supplemented minimal medium, solid)

[[SPY]] (Salt Peptone Yeast)

[[TSB]] (Tryptone Soy Broth)

[[YEME]] (Yeast Extract + Malt Extract)

[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose)

[[2X YT]]

Media recipes

2019-06-25T16:11:43Z

ActinoCommittee:

[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth) | [[SNA]] (soft nutrient agar)

[[LB]] (Lysogeny Broth - sometimes also called Luria Bertani) | [[L]] (L agar)

[[MYM]] (Maltose + Yeast Extract + Malt Extract)

[[GYM]] (Glucose + Yeast Extract + Malt Extract)

[[SFM]] (Soy Flour Mannitol)

[[TSB]] (Tryptone Soy Broth)

[[YEME]] (Yeast Extract + Malt Extract)

[[MM]] (Minimal medium)

[[ISP2]]

[[ISP3]]

[[A1]]

[[Emerson medium]]

[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose)

[[SPY]] (Salt Peptone Yeast)

[[PGA]] (Potato Glucose)

[[IMA]] (Smash)

[[CM]] (Complete medium)

[[HT]] (Hickey-Tresner)

[[R2]] | [[R2YE]] | [[R5]]

[[SMM]] (supplemented liquid minimal medium) | [[SMMS]] (supplemented minimal medium, solid)

[[NMMP]] (minimal liquid medium)

[[2X YT]]

SFM

2019-06-25T16:05:00Z

ActinoCommittee:

=Soy Flour Mannitol Medium=

Soy Flour Mannitol (SFM) medium, also called Mannitol Soy Flour (MS) medium, is a complex medium used for the routine cultivation of Streptomyces sp. Most will sporulate well on this medium.

==Preparation==
Per Litre:
*20g Mannitol
*20g Soy Flour
*20g Agar
*1L with tap water

'''Instructions'''
#Dissolve 20g mannitol in 1L tap water
#Add 2g soy flour and 2g agar to each 250mL flask
#Add 100mL mannitol solution to each flask
#Autoclave

==Uses==
*Routine growth of Streptomyces sp.
*[[Conjugations]]
*[[Preparing spore stocks]]

==Notes==
Soya flour is available from many health food shops and supermarkets (it is not necessary to purchase the more expensive material from a laboratory supplier).

Liquid SFM medium may be made by omitting the agar.

Kieser et al (2000) recommend autoclaving SFM twice. Though this is not strictly necessary, the second autoclave cycle can help to break down some of the complex carbohydrates present in the soy flour, making them more readily available to the Streptomyces. Thus, you may observe improved growth and/or development when growing your strains on 2x autoclaved SFM.

[[Streptomyces venezuelae]] does not sporulate well on SFM medium.

SFM may also be used for bioassays, especially if supplemented with e.g. [[N-acetylglucosamine]] or [[sodium butyrate]] to elicit antibiotic production.

==References==

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics: John Innes Foundation, Norwich Research Park, Colney, Norwich NR4 7UH, UK

Hobbs, G, Frazer, CM, Gardner, DCJ, Cullum, JA & Oliver, SG 1989, 'Dispersed growth of Streptomyces in liquid culture', Applied microbiology and biotechnology, vol. 31, no. 3, pp. 272-277. https://doi.org/10.1007/BF00258408

Media recipes

2019-06-25T16:03:16Z

ActinoCommittee:

[[DNA]] (Difco Nutrient Agar) | [[DNB]] (Difco Nutrient Broth)

[[LB]] (Lysogeny Broth - sometimes also called Luria Bertani)

[[MYM]] (Maltose + Yeast Extract + Malt Extract)

[[GYM]] (Glucose + Yeast Extract + Malt Extract)

[[SFM]] (Soy Flour Mannitol)

[[TSB]] (Tryptic Soy Broth)

[[YEME]] (Yeast Extract + Malt Extract)

[[MM]] (Minimal medium)

[[ISP2]]

[[ISP3]]

[[A1]]

[[Emerson medium]]

[[YP]] (Yeast Peptone) | [[YPD]] (Yeast Peptone Dextrose)

[[SPY]] (Salt Peptone Yeast)

[[PGA]] (Potato Glucose)

[[IMA]] (Smash)

YEME

2019-06-25T15:48:39Z

ActinoCommittee:

=YEME Medium=

==Preparation==
Per litre:
*3g Yeast Extract
*3g Malt Extract (Oxoid)
*5g Peptone
*10g Glucose
*340 g sucrose (34% final concentration)
*Up to 1L dH2O

'''Instructions'''
#Add 3g Yeast Extract, 3g Malt Extract, 5g Peptone and 10g Glucose to a beaker
#Add 800ml dH2O and stir until all solids are fully suspended
#Make up to 1L with dH2O
#Autoclave
#After autoclaving, add 2mL MgCl2*6H2O (2.5M) - (5mM final concentration)
#For preparing protoplasts, also add 25mL 20% glycine (0.5% final concentration)

==Uses==

==Notes==

==References==
Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics: John Innes Foundation, Norwich Research Park, Colney, Norwich NR4 7UH, UK

TSB

2019-06-25T15:41:10Z

ActinoCommittee:

=Tryptic Soy Broth (TSB)=

==Preparation==
Per litre:
*17g Tryptone
*3g Soy peptone
*5g NaCl
*2.5g dipotassium phosphate (K2HPO4)
*2.5g glucose
*1L with distilled water

'''Instructions'''
#Dissolve ingredients in water under gentle heat
#Autoclave

==Uses==

==Notes==

==References==

MYM

2019-06-25T15:39:23Z

ActinoCommittee:

=MYM Medium=

Maltose-Yeast Extract-Malt Extract (MYM) medium is a rich medium used especially for the growth of ''[[Streptomyces venezuelae]]'', as it sporulates to >90% completion in liquid MYM (Bibb et al 2012). Other Streptomyces sp. may also grow well on this medium.

==Preparation==
Per litre:
*4g Maltose
*4g Yeast Extract Oxoid
*10g Malt Extract
*500ml Tap Water
*500ml dH2O

'''Instructions'''

#Dissolve all ingredients in 500ml tap water & 250ml dH2O
#pH to 7.2-7.3 with NaOH
#add dH2O up to 1L
#For solid medium add add 2g agar & 100mL liquid MYM to each flask
#Autoclave, expect a precipitate to form afterward.
#For optimal ''[[Streptomyces venezuelae]]'' sporulation, add [[trace elements]] at a 1:500 dilution.

==Uses==
*routine growth of ''[[Streptomyces venezuelae]]''
*developmental studies on ''[[Streptomyces venezuelae]]''

==Notes==
If using for growth measurements in liquid medium, it is best to allow the precipitate to settle overnight before pipetting the medium into growth vessels - take from the top to avoid the precipitate.

==References==
Stuttard C. 1982. Temperate phages of Streptomyces venezuelae: lysogeny and host specificity shown by phages SV1 and SV2. Microbiology 128:115–121.

Bibb MJ, Domonkos A, Chandra G, Buttner MJ. 2012. Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σBldN and a cognate anti-sigma factor, RsbN. Mol. Microbiol. 84:1033–1049

DNB

2019-06-25T15:18:20Z

ActinoCommittee:

=Difco Nutrient Broth (DNB)=

Difco Nutrient Broth is a rich medium commercially available from BD and routinely used for cultivating many non-fastidious organisms. It contains beef extract and peptones; exact composition will vary between batches.

==Preparation==
Per Litre:
*4g Difco Nutrient Broth Powder
*1L dH2O

'''Instructions'''
#Add DNB powder to dH2O and mix to dissolve
#Autoclave

==Uses==
*Selection for resistance to salt-sensitive antibiotics

==Notes==
According to the recipe in Practical Streptomyces Genetics, it should be 8 g DNB per litre (can someone check this please and edit the recipe with the correct amount if necessary)

==References==

LB

2019-06-25T15:17:14Z

ActinoCommittee:

=LB=
Known as Lysogeny Broth (or sometimes, mistakenly, as Luria-Bertani medium), this rich medium is used routinely for growth of Escherichia coli. There are several variants on this medium, with differing NaCl recipes; glucose may also be added, as in the original recipe (Bertani 1951).

==Preparation==
Per litre:
*5g Yeast Extract
*10g NaCl
*10g Tryptone
*Up to 1L dH2O

'''Instructions'''
#Add 5g Yeast Extract, 10g NaCl and 10g Tryptone to a beaker
#Add 800ml dH2O and stir until all solids are fully suspended
#Make up to 1L with dH2O
#For solid media, add 4g agar per 200ml LB
#Autoclave

===-NaCl LB===
Per litre:
*5g Yeast Extract
*10g Tryptone
*Up to 1L dH2O

==Uses==
*Routine growth of Escherichia coli
*Checking for contamination in Streptomyces spore stocks or cultures

==Notes==
This is the Miller formulation, with 10g/L NaCl. Alternatively, 5g/L NaCl can be used (Lennox formulation) or no salt (see below).
The -NaCl (no salt) version of LB should be used when using salt sensitive antibiotics like [[hygromycin]]: for example, when cloning into [[pSS170]]. (Alternatively, [[DNA]] or [[DNB]] can be used for hygromycin selection.)

To make liquid LB medium, omit the agar and autoclave as above.

==References==
Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951;62(3):293–300.

DNB

2019-06-25T15:04:49Z

ActinoCommittee:

=Difco Nutrient Broth (DNB)=

Difco Nutrient Broth is a rich medium commercially available from BD and routinely used for cultivating many non-fastidious organisms. It contains beef extract and peptones; exact composition will vary between batches.

==Preparation==
Per Litre:
*4g Difco Nutrient Broth Powder
*1L dH2O

'''Instructions'''
#Add DNB powder to dH2O and mix to dissolve
#Autoclave

==Uses==
*[[Selection for resistance to salt-sensitive antibiotics]]

==Notes==
According to the recipe in Practical Streptomyces Genetics, it should be 8 g DNB per litre (can someone check this please and edit the recipe with the correct amount if necessary)

==References==

DNB

2019-06-25T15:02:04Z

ActinoCommittee:

=Difco Nutrient Broth (DNB)=

Difco Nutrient Broth is a rich medium commercially available from BD and routinely used for cultivating many non-fastidious organisms. It contains beef extract and peptones; exact composition will vary between batches.

==Preparation==
Per Litre:
*4g Difco Nutrient Broth Powder
*1L dH2O

'''Instructions'''
#Add DNB powder to dH2O and mix to dissolve
#Autoclave

==Uses==
*[[Streptomyces Colony PCR]]
*[[Spore titres]]
*[[Re-isolation experiments]]
*[[Selection for resistance to salt-sensitive antibiotics]]

==Notes==
According to the recipe in Practical Streptomyces Genetics, it should be 8 g DNB per litre.

==References==

DNA

2019-06-25T14:58:51Z

ActinoCommittee:

=Difco Nutrient Agar (DNA)=

Difco Nutrient Agar is a rich medium commercially available from BD and routinely used for cultivating many non-fastidious organisms. It contains beef extract and peptones; exact composition will vary between batches.

Many Streptomyces sp. grow well on DNA, but developmental and/or antibiotic production phenotypes may differ compared to growth on other media (e.g. [[SFM]]).

==Preparation==
Per Litre:
*4g Difco Nutrient Broth Powder
*10g Agar
*1L dH2O

'''Instructions'''
#For solid medium, add 0.8g of DNB powder into each 250ml conical flask
#Add 2g of Agar
#Add 200ml dH2O
#Autoclave

==Uses==
*[[Streptomyces Colony PCR]]
*[[Spore titres]]
*[[Re-isolation experiments]]
*[[Selection for resistance to salt-sensitive antibiotics]]

==Notes==
For growth in liquid culture, [[DNB]] can be made without the agar.

==References==

DNA

2019-06-25T14:58:31Z

ActinoCommittee: Created page with "=Difco Nutrient Agar (DNA)= Difco Nutrient Agar is a rich medium commercially available from BD and routinely used for cultivating many non-fastidious organisms. It contains..."

Media recipes

2019-06-25T14:57:51Z

ActinoCommittee:

[[DNA]] (Difco Nutrient Agar) and [[DNB]] (Difco Nutrient Broth)

[[LB]] (Lysogeny Broth - sometimes also called Luria Bertani)

[[MYM]] (Maltose + Yeast Extract + Malt Extract)

[[SFM]] (Soya Flour + Mannitol agar)

[[TSB]] (Tryptic Soy Broth)

[[YEME]] (Yeast Extract + Malt Extract)

SFM

2019-06-25T14:55:59Z

ActinoCommittee:

=Soy Flour Mannitol Medium=

Soy Flour Mannitol (SFM) medium, also called Mannitol Soy Flour (MS) medium, is a complex medium used for the routine cultivation of Streptomyces sp. Most will sporulate well on this medium.

==Preparation==
Per Litre:
*20g Mannitol
*20g Soy Flour
*20g Agar
*1L with tap water

'''Instructions'''
#Dissolve 20g mannitol in 1L tap water
#Add 2g soy flour and 2g agar to each 250mL flask
#Add 100mL mannitol solution to each flask
#Autoclave

==Uses==
*Routine growth of Streptomyces sp.
*[[Conjugations]]
*[[Preparing spore stocks]]

==Notes==
Soya flour is available from many health food shops and supermarkets (it is not necessary to purchase the more expensive material from a laboratory supplier).

Liquid SFM medium may be made by omitting the agar.

Kieser et al (2000) recommend autoclaving SFM twice. Though this is not strictly necessary, the second autoclave cycle can help to break down some of the complex carbohydrates present in the soy flour, making them more readily available to the Streptomyces. Thus, you may observe improved growth and/or development when growing your strains on 2x autoclaved SFM.

[[Streptomyces venezuelae]] does not sporulate well on SFM medium.

==References==

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F. and Hopwood, D.A. (2000) Practical Streptomyces Genetics: John Innes Foundation, Norwich Research Park, Colney, Norwich NR4 7UH, UK

Hobbs, G, Frazer, CM, Gardner, DCJ, Cullum, JA & Oliver, SG 1989, 'Dispersed growth of Streptomyces in liquid culture', Applied microbiology and biotechnology, vol. 31, no. 3, pp. 272-277. https://doi.org/10.1007/BF00258408

DNB

2019-06-25T14:28:48Z

ActinoCommittee:

DNB

2019-06-25T14:11:32Z

ActinoCommittee:

=Difco Nutrient Agar (DNA)=

==Preparation==
For 1 Litre:
*4g Difco Nutrient Broth Powder
*10g Agar
*1L dH2O

'''Instructions'''
#For solid medium, add 0.8g of DNB powder into each 250ml conical flask
#Add 2g of Agar
#Add 200ml dH2O
#Autoclave

==Uses==
*[[Streptomyces Colony PCR]]
*[[Spore titres]]
*[[Re-isolation experiments]]

==Notes==

==References==

DNB

2019-06-25T14:03:25Z

ActinoCommittee: /* Difco Nutrient Agar (DNA) */

=Difco Nutrient Agar (DNA)=

==For 1 Litre:==
*4g Difco Nutrient Broth Powder
*10g Agar
*1L dH2O

'''Instructions'''
#For solid medium, add 0.8g of DNB powder into each 250ml conical flask
#Add 2g of Agar
#Add 200ml dH2O
#Autoclave

==Uses==
*[[Streptomyces Colony PCR]]
*[[Spore titres]]
*[[Re-isolation experiments]]

LB

2019-06-25T12:49:05Z

ActinoCommittee: /* LB */

=LB=
Known as Lysogeny Broth

==For 1 Litre:==
*5g Yeast Extract
*10g NaCl
*10g Tryptone
*Up to 1L dH2O

'''Instructions'''
#Add 5g Yeast Extract, 10g NaCl and 10g Tryptone to a beaker
#Add 800ml dH2O and stir until all solids are fully suspended
#Make up to 1L with dH2O
#For solid media, add 4g agar per 200ml LB
#Autoclave

Notes:
This is the Miller formulation, with 10g/L NaCl. Alternatively, 5g/L NaCl can be used (Lennox formulation) or no salt (see below).
The -NaCl (no salt) version of LB should be used when using salt sensitive antibiotics like [[hygromycin]]: for example, when cloning into [[pSS170]]. (Alternatively, [[Difco Nutrient Agar]] can be used for hygromycin selection.)

To make liquid LB medium, omit the agar and autoclave as above.

==-NaCl LB==
===For 1 Litre:===
*5g Yeast Extract
*10g Tryptone
*Up to 1L dH2O

Media recipes

2019-06-25T12:33:47Z

ActinoCommittee:

[[DNB]] (Difco Nutrient Broth)

[[LB]] (Lysogeny Broth - sometimes also called Luria Bertani)

[[MYM]] (Maltose + Yeast Extract + Malt Extract)

[[SFM]] (Soya Flour + Mannitol agar)

[[TSB]] (Tryptic Soy Broth)

[[YEME]] (Yeast Extract + Malt Extract)

Genome mining tools

2019-06-10T10:02:18Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7 https://doi.org/10.1016/j.jbiotec.2009.01.007

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al, Cell 2014, 158:412-21 https://doi.org/10.1016/j.cell.2014.06.034

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43 https://doi.org/10.1093/bioinformatics/btv713.

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-10T09:59:21Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7 https://doi.org/10.1016/j.jbiotec.2009.01.007

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43 https://doi.org/10.1093/bioinformatics/btv713.

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-10T09:57:49Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43 https://doi.org/10.1093/bioinformatics/btv713.

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-10T09:55:10Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217 https://doi.org/10.1016/S0076-6879(09)04808-3

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-10T09:50:26Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H., et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A., et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J., et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al, J. Biotechnol. 2009, 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al, Bioinformatics 2015, 32:1138-43

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O., and Ravel, J., Methods Enzymol. 2009 458:181-217

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim, J., Yi, G.S., BMC Microbiol. 2012 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand, S., et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal, P., Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz, J. I., Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Streptomyces

2019-06-08T21:31:41Z

ActinoCommittee:

[[Streptomyces albus]]

[[Streptomyces coelicolor]]

Protein & peptide analysis

2019-06-08T21:30:37Z

ActinoCommittee:

Useful resources for analysing protein and peptide features, structures and families:

STRING: https://string-db.org/
*Protein-Protein Interaction Networks

pFam: https://pfam.xfam.org/
*Database of protein families

Phobius: http://phobius.cbr.su.se/
*Combined transmembrane topology and signal peptide predictor

SignalP: http://www.cbs.dtu.dk/services/SignalP/
*Signal peptide predictor

PDB: https://www.rcsb.org/
*Protein data bank

Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
*Protein fold recognition

ExPASy: https://expasy.org/proteomics
*Collection of proteomics resources

MEME suite: http://meme-suite.org/tools/meme
*Motif-based sequence analysis

Protein & peptide analysis

2019-06-08T21:23:06Z

ActinoCommittee: Created page with "Useful resources for analysing protein and peptide features, structures and families: STRING: https://string-db.org/ pFam: https://pfam.xfa..."

Useful resources for analysing protein and peptide features, structures and families:

STRING: https://string-db.org/

pFam: https://pfam.xfam.org/

Phobius: http://phobius.cbr.su.se/

SignalP: http://www.cbs.dtu.dk/services/SignalP/

PDB: https://www.rcsb.org/

Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

ExPASy: https://www.expasy.org/

MEME suite: http://meme-suite.org/tools/meme

Main Page

2019-06-08T21:16:43Z

ActinoCommittee:

<h2>ActinoBase: a Streptomyces Community Wiki</h2>

===Message from the developers- Site currently under construction!===
----
ActinoBase is a community resource, available to anyone interested studying Actinobacteria! This wiki is being created by the community and for the community to share knowledge and resources pertaining to the study of filamentous actinomycetes such as Streptomyces.

When complete, ActinoBase will provide media recipes, experimental protocols, plasmid maps and links to other useful resources. This database will be curated by the Streptomyces scientific community to ensure this resource is accurate and up to date. We hope ActinoBase will not only mediate the sharing of scientific resources amongst the existing Streptomyces community, but make accessible invaluable resources for those looking to begin studying the biology of Actinobacteria. Streptomyces bacteria have the potential to contribute solutions to global issues such as antibiotic resistance & food security through their prolific production of antibiotics and relationships with plant roots. This makes Streptomyces biology an important system to study as we seek to address these issues.

Over the coming months we will be redesigning the site layout and adding useful content, please follow us on twitter [https://twitter.com/ActinoBase @ActinoBase] or join the discussion via [https://twitter.com/hashtag/ActinoBase?src=hash #ActinoBase] to keep up to date with the our progresses! If you have any questions or requests you can email the ActinoBase committee overseeing the construction of this website at teamwikimyces@gmail.com

Updated- 30.05.2019
----

 Useful external links.

* [https://twitter.com/ActinoBase Twitter @ActinoBase]
* [http://streptomyces.org.uk Additional Streptomyces resources including the StrepDB genome database]

Recipes for buffers and growth media:

[[Media recipes]]

Protocols for purifying nucleic acids:

[[RNA preps]]

[[DNA preps]]

Organism profiles:

[[Streptomyces]]

Protocols for cloning:

Bioinformatic resources:

[[Genome mining tools]]

[[Protein & peptide analysis]]

Main Page

2019-06-08T21:13:36Z

ActinoCommittee:

Genome mining tools

2019-06-08T21:03:00Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H. et al, Nucleic Acids Res. 2011 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A. et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J. et al, Nucleic Acids Res. 2018 2;46 https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T. et al, J. Biotechnol. 2009, 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P. et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T. et al, Bioinformatics 2015, 32:1138-43

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M. et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O. and Ravel, J., Methods Enzymol. 2009 458:181-217

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim J, Yi GS BMC Microbiol. 2012 Aug 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand S et al. Nucleic Acids Res. 2010 ;38(Web Server issue):W487-96. https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal P. Nucleic Acids Res. 2017 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz J. I, Nat Chem Biol. 2017;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637 https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-08T21:01:03Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H. et al, Nucleic Acids Res. 2011 Jul 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A. et al, Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel, A.J. et al, Nucleic Acids Res. 2018 Jul 2;46
*https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T. et al, J. Biotechnol. 2009, 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P. et al, Cell 2014, 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T. et al, Bioinformatics 2015, 32:1138-43

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M. et al. Nucleic Acids Res. 2017 https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O. and Ravel, J., Methods Enzymol. 2009 458:181-217

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim J, Yi GS BMC Microbiol. 2012 Aug 8;12:169. https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand S et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96.
*https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal P. Nucleic Acids Res. 2017 Jul 3;45 https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz J. I, Nat Chem Biol. 2017 May;13(5):470-478 https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Res., 2019, 47;(9):4624–4637
*https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-08T20:50:07Z

ActinoCommittee:

Actinobacteria are talented producers of secondary metabolites, many of which have useful biological activities. Thanks to the development of many targeted genome mining tools for bacteria, we can now identify previously uncharacterised biosynthetic gene clusters (BGCs) for natural products.

Some useful genome mining resources are listed below:

antiSMASH: https://antismash.secondarymetabolites.org/#!/start
*Reference: Medema, M.H. et al Nucleic Acids Res. 2011 Jul 1; 39
*Twitter: https://twitter.com/antiSMASH_dev

PRISM: http://grid.adapsyn.com/prism/#!/prism
*Reference: Skinnider, M.A. et al, Nucleic Acids Research 2017
*https://doi.org/10.1093/nar/gkx320

BAGEL: http://bagel4.molgenrug.nl/
*Reference: Van Heel AJ Nucleic Acids Res. 2018 Jul 2;46(W1):W278-W281.
*https://doi.org/10.1093/nar/gky383.

CLUSEAN: https://omictools.com/clusean-tool
*Reference: Weber, T., et al., 2009, J. Biotechnol. 140:13-7

ClusterFinder: https://github.com/petercim/ClusterFinder
*Reference: Cimermancic, P., et al., 2014, Cell 158:412-21

CASSIS: https://sbi.hki-jena.de/cassis/
*Reference: Wolf, T., et al., 2015, Bioinformatics 32:1138-43

ARTS: https://arts3.ziemertlab.com/
*Reference: Alanjary, M., et al., 2017, Nucleic Acids Res.
*https://doi.org/10.1093/nar/gkx360

2metDB: https://sourceforge.net/projects/secmetdb/
*Reference: Bachmann, B. O. and Ravel, J., 2009, Methods Enzymol. 458:181-217

PKMiner: http://pks.kaist.ac.kr/pkminer/
*Reference: Kim J, Yi GS BMC Microbiol. 2012 Aug 8;12:169.
*https://doi.org/10.1186/1471-2180-12-169.

SBSPKS: http://www.nii.ac.in/sbspks2.html
*Reference: Anand S et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96.
*https://doi.org/10.1093/nar/gkq340.

RiPPMINER: http://www.nii.ac.in/~priyesh/lantipepDB/new_predictions/index.php
*Reference: Agrawal P Nucleic Acids Res. 2017 Jul 3;45(W1):W80-W88.
*https://doi.org/10.1093/nar/gkx408.

RODEO: http://www.ripprodeo.org/manual.html
*Reference: Tietz J INat Chem Biol. 2017 May;13(5):470-478.
*https://doi.org/10.1038/nchembio.2319.

RiPPER: https://github.com/streptomyces/ripper
*Reference: Santos-Aberturas, J. et al Nucleic Acids Research, Volume 47, Issue 9, 21 May 2019, Pages 4624–4637
*https://doi.org/10.1093/nar/gkz192

BiG-SCAPE: https://omictools.com/big-scape-tool

EvoMining: https://github.com/nselem/EvoMining/wiki

Genome mining tools

2019-06-08T19:34:23Z

ActinoCommittee:

Genome mining tools

2019-06-08T19:33:23Z

ActinoCommittee:

Genome mining tools

2019-06-08T19:33:08Z

ActinoCommittee: