on 31-May-2022 (Tue)

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The term “fermentation” is derived from the Latin verb fervere, to boil, thus describ- ing the appearance of the action of yeast on the extracts of fruit or malted grain. The boiling appearance is due to the production of carbon dioxide bubbles caused by the anaerobic catabolism of the sugar present in the extract.

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However, growth results in the consumption of nu- trients and the excretion of microbial products; events which influence the growth of the organism. Thus, after a certain time the growth rate of the culture decreases until growth ceases. The cessation of growth may be due to the depletion of some essential nutrient in the medium (substrate limitation), the accumulation of some autotoxic product of the organism in the medium (toxin limitation) or a combination of the two. The nature of the limitation of growth may be explored by growing the organ- ism in the presence of a range of substrate concentrations and plotting the biomass concentration at stationary phase against the initial substrate concentration, as shown in Fig. 2.3. From Fig. 2.3 it may be seen that over the zone A to B an increase in initial substrate concentration gives a proportional increase in the biomass produced at stationary phase, indicating that the substrate is limiting. The situation may be described by the equation: =− xY Ss(

where x is the concentration of biomass produced, Y is the yield factor (g biomass produced g

–1 substrate consumed), S R is the initial substrate concentration, and s is the residual substrate concentration. Over the zone A to B in Fig. 2.3, s equals zero at the point of cessation of growth.

Thus, Eq. (2.4) may be used to predict the biomass that may be produced from a certain amount of substrate. Over the zone C to D an increase in the initial substrate concentration does not give a proportional increase in biomass. This may be due to

either the exhaustion of another substrate or the accumulation of toxic products. Over the zone B to C the utilization of the substrate is deleteriously affected by either the accumulating toxins or the availability of another substrate

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The yield factor (Y) is a measure of the efficiency of conversion of any one sub- strate into biomass and it can be used to predict the substrate concentration required to produce a certain biomass concentration. However, it is important to appreciate that Y is not a constant—it will vary according to growth rate, pH, temperature, the limiting substrate, and the concentration of the substrates in excess.

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The decrease in growth rate and the cessation of growth, due to the depletion of substrate, may be described by the relationship between µ and the residual growth- limiting substrate, represented in Eq. (2.5) and in Fig. 2.4 (Monod, 1942): µµ =+ sK s/( ) smax (2.5) Where, s is the substrate concentration in the presence of the organism, K s is the substrate utilization constant, numerically equal to substrate concentration, when µ is half µ max and is a measure of the affinity of the organism for its substrate. The zone A to B in Fig. 2.4 is equivalent to the exponential phase in batch cul- ture where substrate concentration is in excess and growth is at µ max . The zone C to A in Fig. 2.4 is equivalent to the deceleration phase of batch culture where the growth of the organism has resulted in the depletion of substrate to a growth-limiting concentration which will not support µ max . If the organism has a very high affinity for the limiting substrate (a low K s value), the growth rate will not be affected until the substrate concentration has declined to a very low level. Thus, the deceleration phase for such a culture would be short. However, if the organism has a low affin- ity for the substrate (a high K s value) the growth rate will be deleteriously affected at a relatively high substrate concentration. Thus, the deceleration phase for such a culture would be relatively long. Typical values of K s for a range of organisms and

substrates are shown in Table 2.2, from which it may be seen that such values are

usually very small and the affinity for substrate is high. It will be appreciated that

the biomass concentration at the end of the exponential phase is at its highest and,

thus, the decline in substrate concentration will be very rapid so that the time period

during which the substrate concentration is close to K

s

is very short. While the con-

cept of K

s

facilitates the quantitative description of the relationship between specific

growth rate and substrate concentration it should not be regarded as a true constant.

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Exponential growth in batch culture may be prolonged by the addition of fresh me- dium to the vessel. Provided that the medium has been designed such that growth is substrate limited (ie, by some component of the medium), and not toxin limited, exponential growth will proceed until the additional substrate is exhausted. This ex- ercise may be repeated until the vessel is full. However, if an overflow device was fitted to the fermenter such that the added medium displaced an equal volume of cul- ture from the vessel then continuous production of cells could be achieved (Fig. 2.5). If medium is fed continuously to such a culture at a suitable rate, a steady state is

achieved eventually, that is, formation of new biomass by the culture is balanced by

the loss of cells from the vessel. The flow of medium into the vessel is related to the

volume of the vessel by the term dilution rate, D, defined as:

=D

F

V

(2.9)

where F is the flow rate (dm

3

h

–1

) and V is the volume (dm

3

).

Thus, D is expressed in the unit h

–1

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The net change in cell concentration over a time period may be expressed as: =− dx dt growth output or µ =− dx dt xD x. (2.10) Under steady-state conditions the cell concentration remains constant, thus dx/dt = 0 and: µ =xD x (2.11) and µ = D. (2.12) Thus, under steady-state conditions the specific growth rate is controlled by the dilution rate, which is an experimental variable. It will be recalled that under batch culture conditions, an organism will grow at its maximum specific growth rate and, therefore, it is obvious that a continuous culture may be operated only at dilution rates below the maximum specific growth rate. Thus, within certain limits, the dilu- tion rate may be used to control the growth rate of the culture. The growth of the cells in a continuous culture of this type is controlled by the availability of the growth limiting chemical component of the medium and, thus, the system is described as a chemostat. The mechanism underlying the controlling effect of the dilution rate is essentially the relationship expressed in Eq. (2.5), demonstrated by Monod in 1942: µµ =+ sK s/( ) smax At steady state, µ = D, and, therefore, µ =+ Ds Ks /( ) smax where s is the steady-state concentration of substrate in the chemostat, and µ = − s KD D ()

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Eq. (2.13) predicts that the substrate concentration is determined by the dilution rate. In effect, this occurs by growth of the cells depleting the substrate to a concen- tration that supports the growth rate equal to the dilution rate. If substrate is depleted below the level that supports the growth rate dictated by the dilution rate, the follow- ing sequence of events takes place: 1. The growth rate of the cells will be less than the dilution rate and they will be washed out of the vessel at a rate greater than they are being produced, resulting in a decrease in biomass concentration. 2. The substrate concentration in the vessel will rise because fewer cells are left in the vessel to consume it. 3. The increased substrate concentration in the vessel will result in the cells growing at a rate greater than the dilution rate and biomass concentration will increase. 4. The steady state will be reestablished.

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The concentration of cells in the chemostat at steady state is described by the equation: =− xY Ss() R (2.14) Where, x is the steady-state cell concentration in the chemostat. By combining Eqs. (2.13) and (2.14), then: µ =− − xYS KD D () R s max (2.15) Thus, the biomass concentration at steady state is determined by the operational variables, S R and D. If S R is increased, x will increase but s , the residual substrate concentration in the chemostat at the new steady state, will remain the same. If D is increased, µ will increase (µ = D) and the residual substrate at the new steady state would have increased to support the elevated growth rate; thus, less substrate will be available to be converted into biomass, resulting in a lower biomass steady state value.

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the term fed-batch culture to describe batch cultures which are fed continuously, or sequentially, with medium, without the removal of culture fluid. A fed-batch culture is established initially in batch mode and is then fed according to one of the following feed strategies: 1. The same medium used to establish the batch culture is added, resulting in an increase in volume. 2. A solution of the limiting substrate at the same concentration as that in the initial medium is added, resulting in an increase in volume. 3. A concentrated solution of the limiting substrate is added at a rate less than in (1) and (2), resulting in an increase in volume. 4. A very concentrated solution of the limiting substrate is added at a rate less than in (1), (2), and (3), resulting in an insignificant increase in volume. Fed-batch systems employing strategies (1) and (2) are described as variable vol- ume, whereas a system employing strategy (4) is described as fixed volume. The use of strategy (3) gives a culture intermediate between the two extremes of variable and fixed volume

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All microorganisms require water, sources of energy, carbon, nitrogen, mineral elements, and possibly vitamins plus oxygen if aerobic. On a small scale it is relatively simple to devise a medium containing pure compounds, but the result- ing medium, although supporting satisfactory growth, may be unsuitable for use in a large scale process. On a large scale one must normally use sources of nutrients to create a medium which will meet as many as possible of the following criteria: 1. It will produce the maximum yield of product or biomass per gram of substrate used. 2. It will produce the maximum concentration of product or biomass. 3. It will permit the maximum rate of product formation. 4. There will be the minimum yield of undesired products. 5. It will be of a consistent quality and be readily available throughout the year. 6. It will cause minimal problems during media making and sterilization. 7. It will cause minimal problems in other aspects of the production process particularly aeration and agitation, extraction, purification, and waste treatment.

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Medium formulation is an essential stage in the design of successful laboratory ex- periments, pilot-scale development, and manufacturing processes. The constituents of a medium must satisfy the elemental requirements for cell biomass and metabolite production and there must be an adequate supply of energy for biosynthesis and cell

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Water is the major component of almost all fermentation media, and is needed in many of the ancillary services such as heating, cooling, cleaning, and rinsing. Clean water of consistent composition is therefore required in large quantities from reliable permanent sources. When assessing the suitability of a water supply it is important to consider pH, dissolved salts, and effluent contamination

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Energy for growth comes from either the oxidation of medium components or from light. Most industrial microorganisms are chemoorganotrophs, therefore the com- monest source of energy will be the carbon source such as carbohydrates, lipids, and proteins. Some microorganisms can also use hydrocarbons or methanol as carbon and energy sources

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manipulated

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directed

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whole

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post-intervention

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conditional

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The Positivity-Unconfoundedness Tradeoff

Although conditioning on more covariates could lead to a higher chance of satisfying unconfoundedness, it can lead to a higher chance of violating positivity. As we [...] the dimension of the covariates, we make the subgroups for any level 𝑥 of the covariates smaller.

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increase

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incoming

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factorization

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under the null

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We have seen that confounding is a [...] bias when we are conducting causal inference research.

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systematic