Model of energy uncoupling for substrate-sufficient culture

The growth yields (Y(obs)) are greater under substrate-limited conditions than those under substrate-sufficient conditions in continuous cultures. This indicates that the excess substrate should cause uncoupling between anabolism and catabolism, which leads to energy spilling. Although the uncoupling between anabolism and catabolism has already been recognized in the microbiology literature, how to quantitatively describe such uncoupling remains unclear. Based on a balance on substrate reaction, a growth yield model was developed in relation to residual substrate concentration for substrate-sufficient continuous cultures. On the basis of that yield model, the concept of an uncoupling coefficient between anabolism and catabolism is defined in this work. A model describing the effect of the residual substrate concentration on the uncoupling coefficient of anabolism to catabolism is proposed. This model agrees very well with literature data. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 571-576, 1997.     

Calculation of the heat of growth of Escherichia coli K-12 on succinic acid

Using data from the literature, a method is adopted for determining the empirical composition and the unit carbon formula for dried Escherichia coli K-12 cells by summing the quantities of C, H, O, N, P, and S in each of the major classes of macromolecular substances comprising the cellular biomass. With these data and the molar growth yield of cells on succinic acid, equations are written representing the anabolism and catabolism of E. coli K-12 on this quantity of substrate. The enthalpy change accompanying catabolism can be calculated directly using standard enthalpies of formation because there is no term representing cellular substance. The enthalpy change accompanying anabolism is calculated to be very small or zero using microcalorimetric and other data from which the enthalpy of formation of a unit quantity of living cellular substance can be obtained. This indicates that the net enthalpy change accompanying the growth process (anabolism plus catabolism) is the same as that calculated for catabolism alone, in agreement with the same conclusion by several investigators using direct microcalorimetry. The method described here of determining the unit carbon formula and the quantity of ash remaining after cellular combustion is compared to that conventionally used in which cellular P and S is considered either to be negligible or to be a part of the ash. It is concluded that equations representing anabolism and the growth process can be written more accurately using the presently described method, leading to more accurate thermodynamic calculations.     

Oxidation-reduction potentials in the cecal contents of rats and mice.

The oxidation-reduction potential (ORP) in the cecal contents of conventional rats, germ-free mice, and mice with a Colonization Resistance Factor flora (CRF-mice) was investigated. By using animals that were anaesthetized for a longer period of time, we attempted to eliminate the disturbing influence of oxygen. In addition, measurements were made under anaerobic conditions. For the rats, the ORP values reached a more or less constant level after about 30 min following the insertion of the electrodes. The mean ORP at that time was -458 mV (SD = 45 mV). The mean ORP values for the mice showed a more gradual reduction than was found in the rats. The curves leveled off at about 100 min following the insertion of the electrodes. The mean ORP values 100 min after electrode insertion were: germ-free mice, + 3 mV (SD = 39 mV); CRF-mice, -554 mV (SD = 29 mV). In rats, the ORP value decreased after death; no decrease was observed in mice. No difference was found in the values obtained when measuring under anaerobic or aerobic conditions after death.     

Metabolic Changes in Klebsiella oxytoca in Response to Low Oxidoreduction Potential,as Revealed by Comparative Proteomic Profiling Integrated with Flux Balance Analysis

Oxidoreduction potential (ORP) is an important physiological parameter for biochemical production in anaerobic or microaerobic processes. However, the effect of ORP on cellular physiology remains largely unknown, which hampers the design of engineering strategies targeting proteins associated with ORP response. Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis. Decreasing the extracellular ORP from −150 to −240 mV retarded cell growth and enhanced 1,3-propanediol production. Comparative proteomic analysis identified 61 differentially expressed proteins, mainly involved in carbohydrate catabolism, cellular constituent biosynthesis, and reductive stress response. A hypothetical oxidoreductase (HOR) that catalyzes 1,3-propanediol production was markedly upregulated, while proteins involved in biomass precursor synthesis were downregulated. As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. From the integrated protein expression profiles and flux distributions, we can construct a rational analytic framework that elucidates how (facultative) anaerobes respond to extracellular ORP changes.     

Interaction between catabolism and anabolism in the oxidative assimilation of dissolved organic carbon

Catabolism is tightly coupled to anabolism in substrate-limited cultures. However, the dissolved organic carbon (DOC) distribution between catabolism and anabolism has been hardly studied. Based on a balanced DOC reaction, the DOC distribution between catabolism and anabolism was defined using a ratio of the DOC channeled into CO₂ ( ) to that DOC converted to biomass (S _g). A /S _g-dependent growth yield model was proposed for substrate-limited cultures and was verified using the literature data obtained in the oxidative assimilation processes of different types of organic substrates. The model showed that the growth yield (Y _s) was proportional to anabolic activity, but was inversely related to catabolic activity. Results indicated that both Y _s and /S _g varied markedly with the free energy of oxidation of the organic substrate. Further, the observed phenomena were closely associated with maintenance metabolism under substrate-limited conditions.     

Model of dissolved organic carbon distribution for substrate-sufficient continuous culture.

The growth yields (Yobs) are greater under substrate-limited conditions than those under substrate-sufficient conditions in continuous cultures. This indicates that the excess substrate should cause uncoupling between anabolism and catabolism. It appears that the excess substrate could determine metabolic pathways of microorganisms, which further control dissolved organic carbon (DOC) distribution under substrate-sufficient conditions. However, how to quantitatively describe the DOC distribution remains unclear in substrate-sufficient continuous culture. Based on a balanced DOC reaction, a DOC distribution model was developed in relation to residual substrate concentration for substrate-sufficient continuous cultures. Results showed that a considerable portion of the DOC consumed was directly oxidized to carbon dioxide through energy spilling under substrate-sufficient conditions. The proposed model for the first time quantified the DOC distribution between nongrowth-associated and growth-associated metabolisms of cells. The proposed model was verified with literature data very well.     

Charges of nicotinamide adenine nucleotides and adenylate energy charge as regulatory parameters of the metabolism in Escherichia coli.

Methods for measurements of catabolic reduction charge (defined as NADH/(NADH+NAD+)) and anabolic reduction charge (defined as NADPH/(NADPH + NADP+)) are described using [14C]nicotinamide labeling of Escherichia coli cultures. Together with these parameters the adenylate energy charge (ATP + 1/2ADP)/(ATP + ADP + AMP) was measured using labeling with [2-3H]adenine. These three charges were found under different exponential growth conditions to have values independent of the growth conditions: catabolic reduction charge, 0.05; anabolic reduction charge, 0.45; and adenylate energy charge, 0.9. The charges were examined during interruption of growth primarily affecting catabolism, respiration, or anabolism, leading to changes of the charges. The changes of charges are evaluated as a possible regulation of the metabolic rates utilizing or producing the nucleotides by their respective charges.     

The coupling between catabolism and anabolism of Methanobacterium thermoautotrophicum in H2- and iron-limited continuous cultures

The aim of the present work was to investigate whether uncoupling of catabolism from anabolism, which was often observed in heterotrophic microorganisms under energy-sufficient growth conditions, also occurs in the autotrophic bacterium Methanobacterium thermoautotrophicum. For this purpose, M. thermoautotrophicum was cultivated in continuous cultures that were limited by the trace element iron. The influences of both dilution rate and iron supply rate on the coupling between anabolism and catabolism were investigated. As compared to continuous cultures of M. thermoautotrophicum limited by the energy substrate H₂, a 5-fold decrease in the biomass concentration and a 3-fold decrease in H₂, CO₂, and CH₄ conversion rates were observed in iron-limited cultures. However, the specific substrate and product conversion rates increased as compared to the values determined in energy-limited cultures. Thus, iron limitation provoked an uncoupling of catabolism from anabolism. At a dilution rate of 0.096 h⁻¹ and at an iron concentration of 17 μM in the feed, the specific H₂ consumption rate was 100% higher than the rate determined under H₂-limiting conditions, whereas at a dilution rate of 0.168 h⁻¹, the values differed only by 5%. Uncoupling of catabolism from anabolism also increased dramatically when the iron supply rate was lowered but the dilution rate was kept constant. Thus, the extent of uncoupling is a function of both the dilution rate and the iron supply rate. It was found that the specific consumption rate of H₂ increased in parallel with the partial pressure of H₂ in the culture medium. This suggested that the catabolic activity of M. thermoautotrophicum was not stringently controlled at the enzymatic level and can be considerably stimulated by the excess of H₂ in the medium. Hypotheses as to the fate of the excess energy derived from uncoupled catabolism are discussed, but the physiological reason for the partial uncoupling between catabolism and anabolism remains yet to be clarified.     

A cometabolic kinetics model incoroporating enzyme inhibition, inactivation, and recovery: II. Trichloroethylene degradaation experiments

A Cometabolism enzyme kinetics model has been presented which takes into account changes in bacterial activity associated with enzyme inhibitiion, inactivation, inactivation of enzyme resulting from product toxicty, and respondent synthesis of new enzyme. Although this process is inherently unsteady-state, the model assumes that cometabolic degradation of a compound exhibiting product toxicity can be modeled as pseudo-steady-staate under certain conditions. In its simplified from, the model also assumes that enzyme inactivation is directly propoertional to nongrawth substrate oxidation, and that recovery is directly proportionla to growth substrate oxidation. In part 1, model drivation, simplification, and analyses were described. In this articles, model assuptiions are tested by analyzing data from experiments exmining trichloroethylene (TCE) degradation by the ammoniaoxidizing baceterium Nitrosomonas europaea in a quasisteady-state bioreactor. Model solution results showed steady-state bioreactor. Model solution results showed TCE to be a competitive inhibitoer of ammonia oxidation, with TCE affinity for ammonia monooxygenase (AMO) being about four times greater than that of ammonia for the enzyme. Inhibition was independent fo TCE oxidation and occurred essentially instantly upon exposure to TCE. In contrast, inactivation of AMO occurred more gradually and was proportional to the rate and amount of TCE oxidized. Evaluation of other O(2)-dependent enzymes and electron transport proteins suggested that TCE-related damage was predominantly confined to AMO. In response to inhibition and/or inactivation, bacterial recovery was initiated, even in the presence of TCE, implying that membranes adn protein synthesis systems were functioning. Analysis of data and comparison of model results showed the inhibition/inactivation/recovery concept to provide a reasonable basis for understandign the effects fo TCE on AMO function and bacterial response. The model assumptions were verified except tht questions remain regarding the factores controlling recovery and its role in the long term. (c) 1995 John Wiley & Sons, Inc.     

Potential strategies for process control and monitoring of stabilization of dairy wastewaters in batch aerobic treatment systems

This research was conducted to study the relationships between pH, dissolved oxygen (DO), and oxidation–reduction potential (ORP) during low-intensity aeration of dairy wastewaters and to determine potential strategies for monitoring and/or control of this treatment process. The results of this study ascertained that, close to the detection limit of commercially available DO probes (0.1 mg/l), DO is a poor indicator of the oxidation–reduction status of the dairy wastewater during this treatment processes. All the three parameters (ORP, DO, and pH) displayed features defining stabilization of the wastewater and hence all three can be used singly or in combination to monitor and/or to control this treatment process. The study also established strong linear relations between ORP and the log of DO; manifest in the high-correlation coefficients of 0.98 and 0.95 at the aeration rates of 0.067 and 0.034-l [air] l⁻¹ [manure] min⁻¹, respectively. The latter observation confirms the higher sensitivity of ORP over DO at very low-oxygen levels; a fact which indicates the superiority of ORP in the monitoring and control of oxidation–reduction status of the wastewater close to DO detection limit. Finally, both total volatile solids (TVS) and chemical oxygen demand (COD), which are common measures of wastewater stabilization; correlated well with pH, DO, and ORP during the entire treatment process. However, because the measurements of DO are erratic close to the DO detection limit, and because ORP and pH measurements are much more consistent than the DO in the entire range of treatment, these two parameters will be more suitable for monitoring and control especially of extended aeration treatments.     

Analysis of growth curve of stem volume in some woody species using theu-w diagram

Growth curves of stem volume without bark were analyzed on the basis of theu-w diagram and the growth model equivalent to the Bertalanffy model. Some trees experienced several growth phases, in which characteristic values of growth changed. Presumable factors to cause the shifting of growth phase were discussed. In a 130-year-old sugi at Kaneyama in Yamagata Prefecture, estimated rates of anabolism and catabolism were related by a linear relationship with time delay of about 30 years.     

Anabolism versus catabolism of [5-3H]uridine and its relationship to ribonucleic acid labelling in mouse liver after partial hepatectomy

The balance between anabolism and catabolism of [5-(3)H]uridine was studied in the mouse after partial hepatectomy. Labelling of RNA and UDP-glucose was determined and evaluated in relation to changes in the specific radioactivity of UTP. The amounts of labelled catabolic products of uridine were increased several-fold in liver and blood after partial hepatectomy. The specific radioactivity of RNA decreased to about 60% of the control value at 6h and was in the same range as that of control liver at 24h after operation. Decreased labelling of RNA and UDP-glucose was attributable to decreased specific radioactivity of UTP. No changes in the size of the UTP pool or in the balance between uridine anabolism and catabolism were found that could explain the decreased specific radioactivity of UTP. Rather, the alterations in the labelling of this metabolite induced by the partial hepatectomy may be related to decreased phosphorylating capacity in the liver cells and/or dilution of the labelled precursor in an expanded uridine pool. The enhanced amounts of uridine catabolic products in liver and blood were probably a consequence of accumulation and altered incorporation of the metabolites from the blood into the liver cells. Despite the increased amounts of labelled catabolic products and the decreased labelling of RNA, the results reported here actually suggest decreased uridine catabolism and slightly increased RNA synthesis in mouse liver after partial hepatectomy. The results stress the importance of proper controls in determination of nucleic acid synthesis and in metabolic studies by use of labelled precursors.     

Real-time treatment of dairy manure: implications of oxidation reduction potential regimes to nutrient management strategies

A pilot-scale sequencing batch reactor (SBR) was operated at a dairy farm to test real-time based control in winter operation conditions. A combination of high loading and low oxidation reduction potential (ORP) conditions in the aerobic stage of SBR treatment (an end value of -50 to -150 mV) inhibited nitrification while maintaining carbon removal. After a period of over-aeration over several cycles, the ORP at the end of the aerobic stage increased to values of 50-75 mV. Subsequently, nitrification was observed, accompanied by higher total cycle times. Significant increase in removal efficiencies of ammonical nitrogen (alpha<0.0001) and chemical oxygen demand (alpha<0.001) were observed for the high ORP phase. It is postulated that higher ORP regimes are needed for nitrification. In low ORP regimes, nitrification is absent or occurs at an extremely low rate. It is also noted that nitrifying systems treating high strength animal manure can possibly lead to unacceptably high levels of effluent nitrate+nitrite nitrogen (NO(x)-N). Two manure management schemes are proposed that give the farmer an option to either retain the nutrients, or remove them from the wastewater. Some advantages and disadvantages of the schemes are also discussed.     

Oxysterol binding proteins: in more than one place at one time?

Oxysterols are potent signalling lipids that directly bind liver X receptors (LXRs) and a subset of oxysterol binding protein (OSBP) related proteins (ORPs). It is relatively well established that the oxysterol-regulated function of LXRs is to control the expression of genes involved in reverse cholesterol transport, catabolism of cholesterol, and lipogenesis. In contrast, the mechanisms by which oxysterols and ORPs affect cellular lipid metabolism have remained poorly understood. In this review, we summarize the information available on function of the ORPs and compare the two families of proteins binding oxysterol to demonstrate the different responses that similar lipids can elicit within cells. The other focus is on the membrane targeting determinants and the protein interaction partners of ORPs, which provide interesting clues to the mode(s) of ORP action. Specifically, we suggest a model in which a general property of ORPs is to function at membrane contact sites, specialized zones of communication between two different organelles.     

Nonequilibrium freezing of one-cell mouse embryos. Membrane integrity and developmental potential.

A thermodynamic model was used to evaluate and optimize a rapid three-step nonequilibrium freezing protocol for one-cell mouse embryos in the absence of cryoprotectants (CPAs) that avoided lethal intracellular ice formation (IIF). Biophysical parameters of one-cell mouse embryos were determined at subzero temperatures using cryomicroscopic investigations (i.e., the water permeability of the plasma membrane, its temperature dependence, and the parameters for heterogeneous IIF). The parameters were then incorporated into the thermodynamic model, which predicted the likelihood of IIF. Model predictions showed that IIF could be prevented at a cooling rate of 120 degrees C/min when a 5-min holding period was inserted at -10 degrees C to assure cellular dehydration. This predicted freezing protocol, which avoided IIF in the absence of CPAs, was two orders of magnitude faster than conventional embryo cryopreservation cooling rates of between 0.5 and 1 degree C/min. At slow cooling rates, embryos predominantly follow the equilibrium phase diagram and do not undergo IIF, but mechanisms other than IIF (e.g., high electrolyte concentrations, mechanical effects, and others) cause cellular damage. We tested the predictions of our thermodynamic model using a programmable freezer and confirmed the theoretical predictions. The membrane integrity of one-cell mouse embryos, as assessed by fluorescein diacetate retention, was approximately 80% after freezing down to -45 degrees C by the rapid nonequilibrium protocol derived from our model. The fact that embryos could be rapidly frozen in the absence of CPAs without damage to the plasma membrane as assessed by fluorescein diacetate retention is a new and exciting finding. Further refinements of this protocol is necessary to retain the developmental competence of the embryos.     

Relating a calcium indicator signal to the unperturbed calcium concentration time-course

Carbohydrate restriction as a strategy for control of obesity is based on two effects: a behavioral effect, spontaneous reduction in caloric intake and a metabolic effect, an apparent reduction in energy efficiency, greater weight loss per calorie consumed. Variable energy efficiency is established in many contexts (hormonal imbalance, weight regain and knock-out experiments in animal models), but in the area of the effect of macronutrient composition on weight loss, controversy remains. Resistance to the idea comes from a perception that variable weight loss on isocaloric diets would somehow violate the laws of thermodynamics, that is, only caloric intake is important ("a calorie is a calorie"). Previous explanations of how the phenomenon occurs, based on equilibrium thermodynamics, emphasized the inefficiencies introduced by substrate cycling and requirements for increased gluconeogenesis. Living systems, however, are maintained far from equilibrium, and metabolism is controlled by the regulation of the rates of enzymatic reactions. The principles of nonequilibrium thermodynamics which emphasize kinetic fluxes as well as thermodynamic forces should therefore also be considered. Here we review the principles of nonequilibrium thermodynamics and provide an approach to the problem of maintenance and change in body mass by recasting the problem of TAG accumulation and breakdown in the adipocyte in the language of nonequilibrium thermodynamics. We describe adipocyte physiology in terms of cycling between an efficient storage mode and a dissipative mode. Experimentally, this is measured in the rate of fatty acid flux and fatty acid oxidation. Hormonal levels controlled by changes in dietary carbohydrate regulate the relative contributions of the efficient and dissipative parts of the cycle. While no experiment exists that measures all relevant variables, the model is supported by evidence in the literature that 1) dietary carbohydrate, via its effect on hormone levels controls fatty acid flux and oxidation, 2) the rate of lipolysis is a primary target of insulin, postprandial, and 3) chronic carbohydrate-restricted diets reduce the levels of plasma TAG in response to a single meal. In summary, we propose that, in isocaloric diets of different macronutrient composition, there is variable flux of stored TAG controlled by the kinetic effects of insulin and other hormones. Because the fatty acid-TAG cycle never comes to equilibrium, net gain or loss is possible. The greater weight loss on carbohydrate restricted diets, popularly referred to as metabolic advantage can thus be understood in terms of the principles of nonequilibrium thermodynamics and is a consequence of the dynamic nature of bioenergetics where it is important to consider kinetic as well as thermodynamic variables.