Organisms & Cultures

A Culture tracks living organisms as well as chemicals. An Organism is a species and strain identity with the fields genus, species, and strain. Each Organism in a Culture carries a Biomass quantity.

Registering an organism

CHESS already includes several lab strains. The @organism macro defines a new one:

julia> @organism BSU_168 "Bacillus" "subtilis" "168"
Bacillus subtilis 168

julia> genus(BSU_168)
"Bacillus"

julia> species(BSU_168)
"subtilis"

julia> strain(BSU_168)
"168"

julia> name(BSU_168)
"Bacillus subtilis 168"

name(x) joins all three fields. show(x) prints the binding name (BSU_168), as it does for Reagent and Species.

Recalling with @org_str

@org_str looks up organisms registered by CHESS or a lab module, like @loc_str, @attr_str, @rgt_str, and @spc_str:

julia> org"SMU_UA159"
SMU_UA159

Biomass

Organisms cannot be counted directly. The available measurement is optical density (OD), which is a concentration. Biomass is the quantity CHESS tracks for an organism: an absolute, conserved amount with dimensions of optical density times volume, so dividing biomass by volume gives an OD reading with no calibration factor. Like a solid's Mass or a liquid's Volume, Biomass is not tied to the stock's liquid volume, so a Culture can have organisms and no liquid (see Stocks).

The unit OD is one of the units that CHESS adds to Unitful. JensenLabUnits defines OD, the relative fluorescence unit RFU, X for an unspecified concentration such as 2X media, and xg for relative centrifugal force. It is loaded with CHESSCore.

Multiplying a Biomass quantity by an Organism writes an inoculum, as multiplying a quantity by a Reagent builds a Mixture or Solution:

julia> inoculum = 1u"OD*mL" * org"SMU_UA159"
0 mL Culture (0 reagent(s))
 Organisms  Name                        Biomass     OD
───────────────────────────────────────────────────────────
 SMU_UA159  Streptococcus mutans UA159  1.00 mL OD  Inf OD

The inoculum has no liquid, so its total quantity is 0 mL and its OD, biomass divided by liquid volume, shows as infinite until it is mixed into a liquid.

Promoting a Stock to a Culture

Adding a quantified Organism to any Stock promotes it to a Culture. The example uses the saline from Stocks. Biomass is conserved under mixing, subtraction, and scaling, like solids and liquids, so diluting or mixing a culture dilutes or combines its organisms:

julia> saline = 1u"mL" * rgt"water" + 5u"g" * rgt"sodium_chloride";

julia> culture = saline + inoculum
1.00 mL Culture (2 reagent(s))
 Organisms  Name                        Biomass     OD
────────────────────────────────────────────────────────────
 SMU_UA159  Streptococcus mutans UA159  1.00 mL OD  1.00 OD

 Solids           Name             Amount  Concentration
─────────────────────────────────────────────────────────
 sodium_chloride  Sodium Chloride  5.00 g    5.00 g mL⁻¹

 Liquids  Name   Amount   Concentration
────────────────────────────────────────
 water    water  1.00 mL          100 %

julia> diluted = 10u"mL" * culture # dilute to 10 mL total; biomass scales with it
10.0 mL Culture (2 reagent(s))
 Organisms  Name                        Biomass     OD
────────────────────────────────────────────────────────────
 SMU_UA159  Streptococcus mutans UA159  10.0 mL OD  1.00 OD

 Solids           Name             Amount  Concentration
─────────────────────────────────────────────────────────
 sodium_chloride  Sodium Chloride  50.0 g    5.00 g mL⁻¹

 Liquids  Name   Amount   Concentration
────────────────────────────────────────
 water    water  10.0 mL          100 %

The OD column above is the culture's current optical density, Biomass / quantity(culture), where quantity(::Stock) is the total liquid volume. It is derived on demand and never stored on the Organism.

Removing organisms

Subtraction removes organism biomass as it does solids and liquids (see The non-negativity constraint). Centrifuging off a supernatant or autoclaving a stock is subtraction of an explicitly constructed Stock:

julia> sterilized = culture - inoculum # remove exactly this much biomass; no organisms left
1.00 mL Solution (2 reagent(s))
 Solids           Name             Amount  Concentration
─────────────────────────────────────────────────────────
 sodium_chloride  Sodium Chloride  5.00 g    5.00 g mL⁻¹

 Liquids  Name   Amount   Concentration
────────────────────────────────────────
 water    water  1.00 mL          100 %