Experimental adaptive on-line optimization of cellular productivity of a continuous bakers' yeast culture

An adaptive on-line optimization method that utilizes dynamic model identification has been applied to maximize the cellular productivity of a continuous bakers' yeast culture. Experiments were conducted on a sophisticated computerized fermentation system. Experimental results show that the adaptive on-line optimization method requires very little a priori information, is easy to implement, converges quickly, adapts to changes in the process, and is stable even when operational difficulties are encountered.     

Experimental multivariable adaptive optimization of the steady-state cellular productivity of a continuous baker's yeast culture

A multivariable adaptive optimization algorithm that uses transient data to improve the optimization speed was successfully implemented on-line to maximize the steady-state cellular productivity of a continuous culture of baker's yeast. The algorithm was shown to be stable even during periods of oscillatory growth and was able to reoptimize the culture when planned disturbances were introduced. Although adaptive tuning of the forgetting factor improved the performance, further refinements in the adaptive forgetting factor algorithm are necessary for completely satisfactory results.     

A sensitive method for continuous measurement of the carbon dioxide evolution rate of soil samples

Summary A differential infrared CO₂ analyser combined with a 12 channel gas handling system have been used for the measurement of CO₂ evolution rates of soil samples. A constant flow of air over the soil was maintained during the incubation period. Automatic sequential measurement and recording of the increase of the CO₂ content of the flushed air of the 12 channels lasted 24 min with a dwell time of 2 min per channel. This technique has proven to be very useful for accurate and rapid measurement of the biological activities in untreated and treated soil.     

Effect of carbon dioxide on growth of Zymomonas mobilis in continuous culture

Summary Biomass production of Zymomonas mobilis in continuous cultivation on synthetic or complex glucose media was increased up to 100% when CO₂ partial pressure was reduced from 1,460 to 95 mbar at high dilution rates. Biomass yield increased and specific glucose uptake and ethanol production rates decreased approximately 6% when pCO₂ was lowered from 1,160 to 95 mbar. Product yield was not affected by pCO₂. Long time adaptation superimposing these effects was considered.     

Effect of chromium on the rate of carbon dioxide evolution fromSaccharomyces cerevisiae

The rate of carbon dioxide evolution by whole yeast cells was measured under conditions of both chromium starvation and availability. Preincubation experiments show that there is no evidence for the view thatSaccharomyces cerevisiae can synthesize a biologically important form of chromium from simple chromium(III) salts. Chromium enters the yeast cell, possibly by way of the glucose transport system, and exerts a slight inhibitory effect on the fermentation rate but does not affect the rate of cell growth. Glucose tolerance factor fractions show a stimulatory effect in the yeast fermentation assay irrespective of whether the yeast is chromium depleted. The evidence shows that chromium is not an essential trace element for normal yeast metabolism and hence the activity of glucose tolerance factor preparations is unlikely to be due to a chromium complex as is commonly assumed. Some other as yet unidentified compound or compounds must be responsible for the observed increase in the rate of carbon dioxide evolution.     

Periodic operation of a continuous culture of Baker's yeast

The possibility of enhancing the biomass productivity of a continuous culture of Saccharomyces cerevisiae growing on a glucose-limited medium is addressed. An unstructured Monod-type model is first identified using steady-state data. The culture is subjected to step changes in dilution rate, and it is seen that the Monod model is unable to predict even qualitatively the dynamic response of the culture. Incorporation of a time delay allows significant improvement in the transient fit. It is found that the culture has a time lag of about 3 h in adapting its growth rate. Cycling the dilution rate with a period of 3 h leads to substantial improvement in the average biomass productivity.     

Effect of carbon dioxide on yeast growth and fermentation

Inhibition of yeast function by ethanol and by high substrate concentrations is well recognized and, to a limited extent, quantified. The role of carbon dioxide in affecting yeast metabolism (particularly growth processes) is not clear although inhibition is generally found at moderate to high concentrations of the dissolved gas. A similar situation exists with other microorganisms and with other fermentation systems. An understanding of the role of carbon dioxide, and particularly of its inhibitory effects on enzyme action and membrane function, is required if the observed global inhibition of yeasts and other fermentation systems is to be partitioned to its appropriate causes.     

Regulation of methanol oxidation and carbon dioxide fixation in Xanthobacter strain 25a grown in continuous culture

The regulation of C₁-metabolism in Xanthobacter strain 25a was studied during growth of the organism on acetate, formate and methanol in chemostat cultures. No activity of methanol dehydrogenase (MDH), formate dehydrogenase (FDS) or ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisC/O) could be detected in cells grown on acetate alone over a range of dilution rates tested. Addition of methanol or formate to the feed resulted in the immediate induction of MDH and FDH and complete utilization (D=0.10 h^-1) of acetate and the C ₁-substrates. The activities of these enzymes rapidly dropped at the higher growth rates, which suggests that their synthesis is further controlled via repression by heterotrophic substrates such as acetate. Synthesis of RuBisC/O already occurred at low methanol concentrations in the feed, resulting in additive growth yields on acetate/methanol mixtures. The energy generated in the oxidation of formate initially allowed an increased assimilation of acetate (and a decreased dissimilation), resulting in enhanced growth yields on the mixture. RuBisC/O activity could only be detected at the higher formate/acetate ratios in the feed. The data suggest that synthesis of RuBisC/O and CO₂ fixation via the Calvin cycle in Xanthobacter strain 25 a is controlled via a (de)repression mechanism, as is the case in other facultatively autotrophic bacteria. Autotrophic CO₂ fixation only occurs under conditions with a diminished supply of heterotrophic carbon sources and a sufficiently high availability of suitable energy sources. The latter point is further supported by the clearly more pronounced derepressing effect exerted by methanol compared to formate.Abbreviations FDH formate dehydrogenase - FBPase fructose-1,6-bisphosphatase - ICDH isocitrate dehydrogenase - MDH methanol dehydrogenase - PQQ pyrrolo quinoline quinone - PRK phosphoribulokinase - RuBisC/O ribulose-1,5-bisphosphate carboxylase/oxygenase - RuMP ribulose monophosphate - TCA tricarboxylic acid cycle     

The genomic rate of adaptive evolution

The role of positive darwinian selection in evolution at the molecular level has been keenly debated for many years, with little resolution. However, a recent increase in DNA sequence data and the development of new methods of analysis have finally made this question tractable. Here, I review the current state-of-play of the field. Initial estimates in Drosophila suggest that approximately 50% of all amino acid substitutions, and a substantial fraction of substitutions in non-coding DNA, have been fixed as a consequence of adaptive evolution. Estimates in microorganisms are even higher. By contrast, there is little evidence of widespread adaptive evolution in our own species.     

The influence of cyclic glucose feeding on a continuous bakers' yeast culture

Conclusions Except for the pronounced adaptation-hysteresis effect, the pulse experiments exhibited the expected trend: deviation from the steady feed reference curve was greatest at lowest dilution rates. Under conditions of lowest glucose level the effect of pulsing would be expected to cause the largest fluctuations in glucose, causing a certain fraction of the cells to ferment. Generally over the entire dilution rate range the biomass production was decreased and the ethanol was increased by pulsing the feed stream. There is, however, some evidence that pulse feeding can trigger quite unexpected results. Point (6) at D=0.3 h^–1 in Fig. 1 exhibit a biomass productivity which was about 20% greater than the continuous feeding reference value (DX=3.6 kg m^–3 h^–1 as compared with 3.0 kg m^–3 h^–1). Such performance would be of significant commercial value, but the poor reproducibility due to adaptation, as seen here, certainly would preclude its application.The results obtained should also be applicable to fed batch operation at the corresponding glucose level. Further experiments including the variation of the glucose feeding period would be necessary to obtain a conclusive picture. The observed phenomena are likely to occur in other fermentations and could eventually explain some of the problems existing with scale up of fermentation processes.Symbols D dilution rate h^–1 - P product (ethanol) concentration kg m^–3 - Q_O2 specific oxygen uptake rate mol kg^–1 s^–1 - Q_CO2 specific CO₂ production rate mol kg^–1 s^–1 - S substrate (glucose) concentration kg m^–3 - X biomass concentration kg m^–3 - Y_P/S yield of ethanol from glucose kg kg^–1 - Y_X/S yield of biomass from glucose kg kg^–1     

Invertase and phosphatase of yeast in a phosphate-limited continuous culture

Summary Deficiency of inorganic phosphate caused the hyper production of invertase and the derepression of acid phosphatase in a continuous culture ofSaccharomyces carlsbergensis. The specific invertase activity was 40,000 enzyme units per g dry cell weight at a dilution rate lower than 0.05 h^–1 with a synthetic glucose medium of which the molecular ratio of KH₂PO₄ to glucose was less than 0.006. This activity is eight fold higher than in a batch growth and 1.5 fold as much as the highest enzyme activity observed so far in a glucose-limited continuous culture.For the hyper production of invertase, it is necessary to culture the yeast continuously by keeping the Nyholm's conservative inorganic phosphate concentration at less than 0.2 m mole per g dry weight cell. The derepression of acid phosphatase brought about by phosphate deficiency, was similar in both batch and continuous cultures.Nomenclature D dilution rate of continuous culture (h^–1) - E_i invertase concentration in culture (enzyme unit l^–1) - E_p acid phosphatase concentration in culture (enzyme unit l^–1) - P inorganic phosphate concentration in culture (mM) - S glucose concentration in culture (mM) - X cell concentration in culture (g dry weight cell l^–1) Greek Letter specific rate of growth (h^–1) Suffix f feed - 0 initial value     

Determination of carbon dioxide evolution rate using on-line gas analysis during dynamic biodegradation experiments

Respirometry is a precious tool for determining the activity of microbial populations. The measurement of oxygen uptake rate is commonly used but cannot be applied in anoxic or anaerobic conditions or for insoluble substrate. Carbon dioxide production can be measured accurately by gas balance techniques, especially with an on-line infrared analyzer. Unfortunately, in dynamic systems, and hence in the case of short-term batch experiments, chemical and physical transfer limitations for carbon dioxide can be sufficient to make the observed carbon dioxide evolution rate (OCER) deduced from direct gas analysis very different from the biological carbon dioxide evolution rate (CER).To take these transfer phenomena into account and calculate the real CER, a mathematical model based on mass balance equations is proposed. In this work, the chemical equilibrium involving carbon dioxide and the measured pH evolution of the liquid medium are considered. The mass transfer from the liquid to the gas phase is described, and the response time of the analysis system is evaluated.Global mass transfer coefficients (K(L)a) for carbon dioxide and oxygen are determined and compared to one another, improving the choice of hydrodynamic hypotheses. The equations presented are found to give good predictions of the disturbance of gaseous responses during pH changes.Finally, the mathematical model developed associated with a laboratory-scale reactor, is used successfully to determine the CER in nonstationary conditions, during batch experiments performed with microorganisms coming from an activated sludge system. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 243-252, 1997.     

Effect of growth rate on the glucose metabolism of yeast grown in continuous culture. Radiorespirometric studies

Specifically labelled¹⁴C-d-glucose was used to estimate the percentage participation of glycolysis and pentose phosphate cycle in the glucose catabolism ofCandida utilis andSaccharomyces cerevisiae. The two yeasts were cultivated at various growth rates (0.1 to 0.5 h^?1) in a chemostat on synthetic medium limited with glucose under aerobic conditions. The results show a considerable increase in the percentage participation of pentose phosphate cycle in the glucose catabolized bySaccharomyces cerevisiae with the increase in specific growth rate. However, inCandida utilis, the specific growth rate does not influence significantly the part of glucose catabolized via pentose phosphate cycle, but its absolute values are relatively higher than inSaccharomyces cerevisiae. A rough quantitative estimate indicates that a maximum of 60 to 72% of the assimilated glucose is catabolized through the pentose phosphate cycle while inSaccharomyces cerevisiae the percentage participation of the pentose phosphate cycle varies from 24 to 60% (maximum) and 9 to 34% (minimum).     

Accelerated and adaptive evolution of yeast sexual adhesins

There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337-341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by analyses using the PAML pairwise model, a modified McDonald-Kreitman test, and the PAML branch model. Moreover, using a combination of a new statistic of neutrality, an information theory-based measure of evolutionary variability, and functional characterization of amino acid changes, we found that a higher proportion of amino acid changes are fixed in the sexual adhesins than in other proteins and a greater proportion of the fixed amino acid changes either between the two species or the two subgroups of S. paradoxus are functionally dissimilar or radically different. These results suggest that the accelerated evolution of sexual adhesin genes may facilitate speciation, or incipient speciation, and promote sexual selection in general.     

Multilayer adaptive control of continuous bioprocesses using optimising control technique. Case study: Bakers' yeast culture

High costs associated with many fermentation processes in an increasingly competitive industry make any prompt application of modern control techniques to industrial bioprocesses very desirable. However, this is often hampered by the lack of adequate mathematical models, on the one hand, and by the absence of continuous, on-line measurement of the most relevant process variables, on the other hand. This paper addresses these problems and offers a new strategy to control continuous bioprocesses using a hierarchical structure such that neither structured process models nor continuous measurement of all relevant variables have to be available. The control system consists of two layers. The lower layer represents a dynamic adaptive follow-up control of a continuously measured output — in our case dissolved oxygen concentration. This variable is supposed to be strongly correlated with the key output variable — in our case cellular concentration which is not continuously available for measurement. The higher layer is then designed to maintain a desired profile of the process key output using a set-point optimising control technique. The Integrated System Optimisation and Parameter Estimation method used operates on an appropriately chosen steady-state performance criterion. A prerequisite for successful application of the proposed approach is an approximate steady-state model, describing the relationship between the measured output and the process key output variable. Furthermore, occasional in situ, off-line or laboratory measurement values of the key output variable are needed. Promising simulation results of the biomass concentration control, by manipulating the air flow-rate in the continuous bakers' yeast culture are presented.     

Assessment of human operator functional state using a novel differential evolution optimization based adaptive fuzzy model

With the development of human–machine systems, there has been a growing concern about the consequences of operator performance breakdown under excessive level of workload, especially in safety-critical situations. Assessment and detection of the operator functional state (OFS) enable us to predict the high operational risks of operator. This paper adopts the psychophysiological signals and task performance measures to evaluate OFS under different levels of mental workload. Four indices extracted from electrocardiogram and electroencephalogram, including heart rate (HR), ratio of the standard deviation to the average of HR segment, task load indices (TLI1 and TLI2), are chosen as the inputs of the proposed model. A technique of differential evolution with ant colony search (DEACS) is developed to optimize the parameters of Adaptive-Network-based Fuzzy Inference System (ANFIS). The optimized ANFIS model is employed to estimate the OFS under a series of process control tasks on a simulated software platform of AUTOmation-enhanced Cabin Air Management System. The results showed that the proposed adaptive fuzzy model based on ANFIS and DEACS algorithm is applicable for the operator functional state assessment.