Overview
- External ontology
- TOGO:M2041 — M9-Phenanthrene
- Applications
-
- Microbial cultivation
- Notes
- TOGO M2041 imports NBRC Medium 1339 M9-Phenanthrene. NBRC 1339 lists 900 ml agar solution, 100 ml 10xM9 solution, 2.1 ml 1 M MgSO4, 1 ml 0.1 M CaCl2, and 10 ml 250 mM phenanthrene in DMSO per liter. Agar, 10xM9, MgSO4, and CaCl2 are autoclaved; the phenanthrene stock is filter-sterilized, added after cooling to 65 C, sonicated for about 30 seconds, and poured into plates.
Composition
flowchart LR
CultureMech_008631["m9_phenanthrene"]
ing0_Agar_solution["Agar solution"]
CultureMech_008631 --> ing0_Agar_solution
ing1_10xM9_solution["10xM9 solution"]
CultureMech_008631 --> ing1_10xM9_solution
ing2_MgSO4_solution["MgSO4 solution"]
CultureMech_008631 --> ing2_MgSO4_solution
ing3_CaCl2_solution["CaCl2 solution"]
CultureMech_008631 --> ing3_CaCl2_solution
ing4_Phenanthrene_solution["Phenanthrene solution"]
CultureMech_008631 --> ing4_Phenanthrene_solution
Ingredients (5)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | Agar solution | 900 ML_PER_L | TOGO M2041 / NBRC Medium 1339 adds 900 ml/L autoclaved agar solution. | |
| 2 | 10xM9 solution | 100 ML_PER_L | TOGO M2041 / NBRC Medium 1339 adds 100 ml/L separately autoclaved 10xM9 solution. | |
| 3 | MgSO4 solution | 2.1 ML_PER_L | TOGO M2041 / NBRC Medium 1339 adds 2.1 ml/L 1 M MgSO4 stock. | |
| 4 | CaCl2 solution | 1 ML_PER_L | TOGO M2041 / NBRC Medium 1339 adds 1 ml/L 0.1 M CaCl2 stock. | |
| 5 | Phenanthrene solution | 10 ML_PER_L | TOGO M2041 / NBRC Medium 1339 adds 10 ml/L 250 mM phenanthrene solution in DMSO. |
Preparation
- Dissolve 15 g agar in 900 ml distilled water.
- Autoclave the agar solution.
- Sterilize the 10xM9 solution separately by autoclaving.
- Dissolve MgSO4 and CaCl2 stocks in distilled water and sterilize by autoclaving.
- Filter-sterilize the 250 mM phenanthrene solution in DMSO using DMSO-safe filters.
- Aseptically mix autoclaved agar, 10xM9, MgSO4, and CaCl2 solutions.
- After cooling to 65 C, aseptically add phenanthrene solution, sonicate for approximately 30 seconds, and pour into plates.
Solutions
Agar solution
Dose: 900 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Agar | 15 G_PER_L | NBRC Medium 1339 dissolves 15 g agar in 900 ml distilled water. |
| Distilled water | 900 ML_PER_L | NBRC Medium 1339 prepares the agar solution in 900 ml water. |
10xM9 solution
Dose: 100 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| KH2PO4 | 30 G_PER_L | NBRC Medium 1339 lists 30 G_PER_L KH2PO4 in 10xM9 solution. |
| Na2HPO4 | 60 G_PER_L | NBRC Medium 1339 lists 60 G_PER_L Na2HPO4 in 10xM9 solution. |
| NH4Cl | 10 G_PER_L | NBRC Medium 1339 lists 10 G_PER_L NH4Cl in 10xM9 solution. |
| NaCl | 5 G_PER_L | NBRC Medium 1339 lists 5 G_PER_L NaCl in 10xM9 solution. |
| Distilled water | 1 L | NBRC Medium 1339 lists 1 L Distilled water in 10xM9 solution. |
MgSO4 solution
Dose: 2.1 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| MgSO4 | 1 MOLAR | NBRC Medium 1339 adds 2.1 ml/L of 1 M MgSO4 solution. |
CaCl2 solution
Dose: 1 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| CaCl2 | 0.1 MOLAR | NBRC Medium 1339 adds 1 ml/L of 0.1 M CaCl2 solution. |
Phenanthrene solution
Dose: 10 ML_PER_L
| Ingredient | Concentration | Notes |
|---|---|---|
| Phenanthrene | 250 MILLIMOLAR | NBRC Medium 1339 adds 10 ml/L of 250 mM phenanthrene solution. |
| Dimethyl sulfoxide (DMSO) | variable VARIABLE | NBRC Medium 1339 uses DMSO as the phenanthrene stock solvent. |
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:58.940796Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M2041 |
| 2026-01-28T19:48:22.219404Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: Phenanthrene solution; Added default concentration for ingredient: dimethyl sulfoxide (DMSO) |
| 2026-03-09T08:04:37.094194+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 6 solution(s) from ingredients |
| 2026-03-13T03:09:06.616427Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:58.870104Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008631 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:30:12.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:17.492986+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "M9-Phenanthrene" to "m9_phenanthrene" for consistent matching |
| 2026-05-16T09:03:39.656246+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:12.082682+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 6 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:47:00.723721+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 2 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-09-12T00:00:00-07:00 | repair_togo_m2041_m9_phenanthrene_score15.py | RESOLVED_TOGO_M2041_M9_PHENANTHRENE_SCORE15 | TOGO M2041 imports NBRC Medium 1339 M9-Phenanthrene. NBRC 1339 lists 900 ml agar solution, 100 ml 10xM9 solution, 2.1 ml 1 M MgSO4, 1 ml 0.1 M CaCl2, and 10 ml 250 mM phenanthrene in DMSO per liter. Agar, 10xM9, MgSO4, and CaCl2 are autoclaved; the phenanthrene stock is filter-sterilized, added after cooling to 65 C, sonicated for about 30 seconds, and poured into plates. Removed the flattening artifact that merged agar water with 10xM9 water, restored five stock additions in ml/L, and expanded their nested compositions. |