Overview
- External ontology
- nbrc.medium:1339 (source link unavailable) — NBRC Medium 1339
- Notes
- Source: NBRC Medium 1339 | Link: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=1339 NBRC lists M9-Phenanthrene as an agar medium prepared from autoclaved agar, 10xM9, 1 M MgSO4, and 0.1 M CaCl2 solutions plus filter-sterilized 250 mM phenanthrene in dimethyl sulfoxide. Phenanthrene is added after cooling to 65 C, mixed by sonication, and poured into plates.
Composition
flowchart LR
CultureMech_007473["M9-Phenanthrene"]
ing0_Agar_solution_["Agar solution*"]
CultureMech_007473 --> ing0_Agar_solution_
ing1_10xM9_solution__["10xM9 solution**"]
CultureMech_007473 --> ing1_10xM9_solution__
ing2_MgSO4_solution__1_M____["MgSO4 solution (1 M)***"]
CultureMech_007473 --> ing2_MgSO4_solution__1_M____
ing3_CaCl2_solution__0_1_M____["CaCl2 solution (0.1 M)***"]
CultureMech_007473 --> ing3_CaCl2_solution__0_1_M____
ing4_Phenanthrene_solution__250_mM__in_dimethyl_sulfoxide__DMSO_____["Phenanthrene solution (250 mM) in dimethyl sulfoxide (DMSO)****"]
CultureMech_007473 --> ing4_Phenanthrene_solution__250_mM__in_dimethyl_sulfoxide__DMSO_____
Ingredients (5)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | Agar solution* | 900 ML_PER_L | ||
| 2 | 10xM9 solution** | 100 ML_PER_L | ||
| 3 | MgSO4 solution (1 M)*** | 2.1 ML_PER_L | ||
| 4 | CaCl2 solution (0.1 M)*** | 1 ML_PER_L | ||
| 5 | Phenanthrene solution (250 mM) in dimethyl sulfoxide (DMSO)**** | 10 ML_PER_L |
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
| Ingredient | Concentration | Notes |
|---|---|---|
| Agar | 15 G_PER_L | NBRC Medium 1339 dissolves 15 g agar in the 900 ml agar solution. |
| Distilled water | 900 ML_PER_L | NBRC Medium 1339 prepares the agar solution in 900 ml distilled water. |
10xM9 solution
| 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
| Ingredient | Concentration | Notes |
|---|---|---|
| MgSO4 | 1 MOLAR | NBRC Medium 1339 adds 2.1 ml/L of 1 M MgSO4 solution. |
CaCl2 solution
| Ingredient | Concentration | Notes |
|---|---|---|
| CaCl2 | 0.1 MOLAR | NBRC Medium 1339 adds 1 ml/L of 0.1 M CaCl2 solution. |
Phenanthrene solution
| Ingredient | Concentration | Notes |
|---|---|---|
| Phenanthrene | 250 MILLIMOLAR | NBRC Medium 1339 adds 10 ml/L of 250 mM phenanthrene solution in DMSO. |
| Dimethyl sulfoxide (DMSO) | variable VARIABLE | NBRC Medium 1339 uses dimethyl sulfoxide as the solvent for the 250 mM phenanthrene stock. |
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-02-20T00:22:36.064419Z | nbrc-import | Imported from NBRC | Source: NBRC, Media No. 1339, URL: http://www.nbrc.nite.go.jp/NBRC2/NBRCMediumDetailServlet?NO=1339. Imported via ethical web scraping. |
| 2026-03-09T08:04:48.373313+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 1 solution(s) from ingredients |
| 2026-03-13T03:09:19.393797Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 20 duplicate ingredient(s) |
| 2026-03-13T06:19:49.193469Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007473 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name |
| 2026-05-16T09:03:06.644571+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=1 |
| 2026-08-19T21:54:22.774228+00:00 | recover_nbrc_composition.py | Recovered composition from source HTML | Re-parsed the NBRC medium 1339 composition table from the preserved scrape; 5 ingredient(s) restored, 1 stock solution(s) nested rather than flattened, 1 unparsed solution blob(s) removed (#299). |
| 2026-08-20T19:01:15.904473+00:00 | apply_mim_groundings.py | Adopted MIM published grounding | Grounded 5 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308). |
| 2026-09-11T00:00:00-07:00 | repair_nbrc_1340_score15.py | RESOLVED_NBRC_1340_SCORE15 | Added the NBRC Medium 1339 source term and official title, expanded missing agar, MgSO4, CaCl2, and phenanthrene stock solutions, and converted M9-Phenanthrene sterilization instructions into structured steps. |