BIOL388/S19:Class Journal Week 11

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Ava's Journal Reflection

  1. Discuss amongst yourselves whether or not the Tai et al (2007) journal club paper gives you enough information to perform such a simulation.
    • I do not feel that enough information was given to perform a simulation through matlab as they did not provide r, E, or K and these are parameters required for the model to run so I think it would be impossible to try and recreate their chemostat experiment.
  2. What parameters are explicitly given?
    • Specific growth rate: 0.03 h−1
    • Dilution rate (D) of 0.03 h−1
    • Working volume of 1.0 L
    • pH: Kept constant at 5.0
    • Stirrer speed: 600 rpm
  3. Can you back any others out from the data tables?
    • Table 2 shows the nutrient biomass for each condition.
  4. To what in the model do the quantities in Table 1 correspond?
    • Table 1 provides the growth rate and dilution rates for each of the various environmental configurations.

Avalekander Avalekander (talk) 19:43, 10 April 2019 (PDT)

Brianna's Reflection

  1. We both agreed that it didn't provide enough information to perform a simulation. We felt that they left out important parameters like the initial concentrations and biomass to compare to.
  2. They give us the specific growth rate, dilution rate, and volume
  3. Nutrient biomass and concentration, pH, speed of stirring
  4. It displays the growth and dilution rates during the steady state growth period

Briannansamuels (talk) 15:31, 10 April 2019 (PDT)

Desiree's Reflection

  1. Discuss amongst yourselves whether or not the Tai et al (2007) journal club paper gives you enough information to perform such a simulation.
    • Both myself and my individual assignment partner believed that not enough information was given by Tai and the researchers in their scientific paper to perform the chemostat simulation. Especially since the parameters of u, K, ep, or r were not given.
  2. What parameters are explicitly given?
    • The parameters that were explicitly given by the researchers in the scientific article, included the dilution rate (0.03 h^-1), the working volume of the chemostat (1L), the pH (5), and the temperatures (12 degrees C and 30 degrees C).
  3. Can you back any others out from the data tables?
    • Data Table 1 shows the dilution rates at steady state, while Data Table 2 shows the nutrient and cell biomass (as dry weight).
  4. To what in the model do the quantities in Table 1 correspond?
    • The quantities in Table 1 in the scientific paper, correspond to the dilution rates (depicted by q) for steady state experimental conditions.

Desireegonzalez (talk) 22:27, 10 April 2019 (PDT)

Austin Dias Reflection

1. Discuss amongst yourselves whether or not the Tai et al (2007) journal club paper gives you enough information to perform such a simulation.

The Tai et al (2007) paper does not provide enough information to perform an accurate simulation of steady state because we are unaware of the initial cell population and initial yeast concentration.

2. What parameters are explicitly given?

The researchers only explicitly provide the dilution rate and the volume in the container. Searching back through their previous paper is necessary to find nutrient concentrations. The parameters that were explicitly stated are listed below:

  • dilution rate = 0.03 h^-1
  • volume in container = 1 L
  • provide nutrient concentrations by referencing methods from previous study (Tai et al., 2005)
    • glucose limited culture
      • 5.0 g liter^1 (NH4)2SO4
      • 3.0 g liter^1 KH2PO4
      • 0.5 g liter^1 MgSO47H2O
      • 25 g liter^1 glucose
    • ammonia limited culture
      • 0.65 g liter^1(NH4)2SO4
      • 5.75 g liter^1 K2SO4
      • 3.0 g liter^1 KH2PO4
      • 0.5 g liter^1 MgSO47H2O
      • 46 g liter^1 glucose

3. Can you back any others out from the data tables?

Table 1 provides dilution rates for each experimental set up. While Table 2 provides cell biomass and nutrient mass values.

4. To what in the model do the quantities in Table 1 correspond?

Table 1 corresponds to dilution rates and the parameter 'q' in the simulation model. The values in Table 1 reflect the equilibrium between cell biomass and nutrient mass. Since we know the nutrient dilution rate, we also know the growth rate at steady state, since these two values are equal at equilibrium.

Austindias (talk) 15:24, 10 April 2019 (PDT)

Edward's Journal Reflection

  1. I have to agree with the others that there is not enough information in the paper to perform the same simulations as they do not provide all of the parameters for the equation.
  2. Parameters given:
    • Growth rate: 0.03h^−1
    • Dilution rate: 0.03h^−1
    • Volume: 1.0 L
    • pH: 5.0
    • Stirrer speed: 600 rpm
  3. Table 1 shows the dilution rates for each experimental set up, and table 2 shows the cell biomass and nutrient mass.
  4. Again, table 1 shows the dilution rates for the various environmental conditions.

Sahil's Reflection

  • The Tai et al (2007) paper was discussed and was concluded to have insufficient information to conduct a chemostat experiment because the paper left out important information (parameters).
  • Parameters given:
    • dilution rate: 0.03h^-1
    • Temperature: 12C or 30C
    • System Volume: 1L
    • pH: 5.0
    • nutrient concentrations: another paper was referenced for the information needed
  • The cell biomass and nutrient mass can be taken from Table 2.
  • The quantities in Table 1 correspond to the dilution rate used in the model.

Sahil Patel (talk) 18:47, 10 April 2019 (PDT)

Leanne's Reflection

  1. The Tai et al. paper does not provide parameters E, r, and K, which are required to run the model. Additionally, the paper does not provide the initial nutrient and cell concentrations. Therefore, there would not be enough information to simulate a model.
  2. Parameters given:
    • dilution rate = specific growth rate: 0.03h-1
    • Temperatures: 12C or 30C
    • working volume: 1.0L
    • nutrient concentrations: referenced another paper
    • pH: 5.0
  3. Table 2 provides cell biomass for each condition.
  4. Table 1 corresponds to the dilution rate (q in our model) for each condition at equilibrium.

Fatimah's Reflection

  1. I don't think Tai et al (2007) journal club paper gave enough information to perform such a simulation.
  2. parameters that were given were: dilution rate, pH, Temp, and volume.
  3. growth rate.
  4. q which is dilution rate.

Falghane (talk) 16:54, 10 April 2019 (PDT)

Alison's Reflection

  1. The Tai et al. paper gives us parameters q and V, but I don't think we know u, K, E, or r.
  2. They gave the following parameters: specific growth rate (0.03 h−1), dilution rate (0.03 h−1), volume (1.0 L), pH (5.0).
  3. Table 1 gives us dilution rates when at steady-state for each experiment. Table 2 gives us biomass dry weights for each experiment.
  4. Table 1 gives us dilution rates (our variable q) at steady-state.

Alison S King (talk) 18:38, 10 April 2019 (PDT)

Angela's Reflection

  1. The Tai et al (2007) paper does not provide the sufficient parameters needed to run a MATLAB simulation. Specifically the E, r, and k parameters are unknown.
  2. The following parameters are given: dilution rate/specific growth rate = 0.03h-1; pH: 5.0; temperature = 12C or 30C, volume = 1L
  3. The dilution rates and cell biomass and nutrient mass can be seen in Tables 1 and 2, respectively.
  4. The quantities in Table 1 correspond to the dilution rates, q, in our model.

Angela C Abarquez (talk) 20:46, 10 April 2019 (PDT)

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