Biochemical Reaction Rates Research Articles

Life rhythm as a symphony of oscillatory patterns: electromagnetic energy and sound vibration modulates gene expression for biological signaling and healing.

All life exists within a sea of vibration, and rhythm is fundamental to all of life. Diurnal, seasonal, lunar, and solar cycles, and the resonant electromagnetic field (EMF) oscillations of our planet make up the symphony of rhythms in which life on Earth exists. As life evolved amidst these natural rhythms, they were integrated into many basic human biological responses, which coincide with diurnal and seasonal cycles1 and the many aspects of human and animal behavior and physiology that are correlated with the phases of the moon.2 From the basic activities of daily life to our relationship with the animals on Earth,3 human society is structured around the moon's rhythm, and deeply rooted monthly circadian rhythms govern human sleep patterns, persisting even in isolation from our conscious awareness of the lunar phase.4 Our lives contain a seeming infinity of rhythms, with vibrations at the atomic and molecular levels and within biochemical reaction rates. The physiological correlates of the rhythms of t...

¹³C-based metabolic flux analysis in yeast: the Pichia pastoris case.

Metabolic flux analysis based on tracing patterns of stable isotopes, particularly (13)C, comprises a set of methodologies to experimentally quantify intracellular biochemical reaction rates, i.e., to measure carbon flux distributions through a metabolic network. This allows quantifying the response of a metabolic network to an environmental or genetic perturbation (i.e., the metabolic phenotype). Here, we describe a protocol based on growing yeast on a (13)C-labelled substrate and subsequent NMR detection of (13)C-patterns in proteinogenic amino acids. To calculate metabolic fluxes, we describe two complementary mathematical approaches using available software; namely, an approach based on the estimation of local ratios in network nodes, and a method based on a global iterative fitting approach. Furthermore, we consider specificities of these protocols for their application to the yeast Pichia pastoris growing on multicarbon substrates other than glucose (glycerol), as well as the case when methanol is used as co-substrate in combination with glucose or glycerol.

Global streamflow and thermal habitats of freshwater fishes under climate change

Climate change will affect future flow and thermal regimes of rivers. This will directly affect freshwater habitats and ecosystem health. In particular fish species, which are strongly adapted to a certain level of flow variability will be sensitive to future changes in flow regime. In addition, all freshwater fish species are exotherms, and increasing water temperatures will therefore directly affect fishes’ biochemical reaction rates and physiology. To assess climate change impacts on large-scale freshwater fish habitats we used a physically-based hydrological and water temperature modelling framework forced with an ensemble of climate model output. Future projections on global river flow and water temperature were used in combination with current spatial distributions of several fish species and their maximum thermal tolerances to explore impacts on fish habitats in different regions around the world. Results indicate that climate change will affect seasonal flow amplitudes, magnitude and timing of high and low flow events for large fractions of the global land surface area. Also, significant increases in both the frequency and magnitude of exceeding maximum temperature tolerances for selected fish species are found. Although the adaptive capacity of fish species to changing hydrologic regimes and rising water temperatures could be variable, our global results show that fish habitats are likely to change in the near future, and this is expected to affect species distributions.

Psychrophily and Catalysis

Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.

Study of oxygen mass transfer coefficient and oxygen uptake rate in a stirred tank reactor for uranium ore bioleaching

In this work, the volumetric oxygen mass transfer coefficient and the oxygen uptake rate (OUR) were studied for uranium ore bioleaching process by Acidthiobacillus ferrooxidans in a stirred tank reactor. The Box-Bohnken design method was used to study the effect of operating parameters on the oxygen mass transfer coefficient. The investigated factors were agitation speed (rpm), aeration rate (vvm) and pulp density (% weight/volume) of the stirred tank reactor. Analysis of experimental results showed that the oxygen mass transfer coefficient had low dependence on biomass concentration but had higher dependence on the agitation speed, aeration rate and pulp density.The obtained biological enhancement factors were equal to ones in experiments. On the other hand, the obtained values for Damkohler number (Da<0.468) indicated that the process was limited by the biochemical reaction rate. Experimental results obtained for oxygen mass transfer coefficient were correlated with the empirical relations proposed by Garcia-Ochoa and Gomez (2009) and Neale and Pinches (1994). Due to the high relative error in the correlation of Neale and Pinches, that correlation was corrected and the coefficient of determination was calculated to be 89%. The modified correlation has been obtained based on a wide range of operating conditions, which can be used to determine the mass transfer coefficient in a bioreactor.

Polar and alpine microbiology

Scientists, politicians and the general public alike now share the conviction that understanding (micro)biology of polar and alpine systems is of paramount importance to many urgent questions related to global climate, shrinking of polar areas and disappearing of glaciers and other habitats, with the concomitant threat of species extinctions, such as that of the polar bear. Most of the Earth's biosphere is characterized by low temperatures (below 5 °C) and cold-adapted microorganisms are now known to be widespread in nature. Low temperatures and freezing conditions influence microbial life in multiple ways, e.g. reduced biochemical reaction rates, changes in membrane fluidity and protein conformation, ability to reproduce successfully, and the need for protection against freezing. There is thus considerable interest in understanding the adaptations, activities and survival of microorganisms in cold environments, as well as the ecological interactions of communities active in these environments. However, these …

Bioluminescence as a tool for studying detoxification processes in metal salt solutions involving humic substances

The paper considers effects of humic substances (HS), as natural attenuators of toxicity, on solutions of model inorganic pollutants, metal salts – Pb(NO3)2, СоСl2, CuSO4, Eu(NO3)3, СrСl3, and K3[Fe(СN)6]. Luminous bacteria Photobacterium phosphoreum and bioluminescent system of coupled enzymatic reactions were used as bioassays to monitor toxicity of salt solutions. The ability of HS to decrease or increase toxicity was demonstrated. Detoxifying concentrations of HS were determined; detoxification coefficients were calculated at different times of exposure of salt solutions to HS. To study the combined effects of HS and salts on bioluminescent assay systems, the rates of biochemical reactions and bacterial ultrastructure were analyzed. The detoxifying effects were explained by: (1) decrease of free metal content in water solutions under metal–HS binding; (2) increase of biochemical reaction rates in a bioluminescent assay system under HS effect; (3) enhancement of mucous layers on cell surface as a response to unfavorable impact of toxicants. Detoxifying mechanisms (2) and (3) reveal the active role of bioassay systems in detoxification processes.

On Models of the Temperature Effect on the Rate of Chemical Reactions and Biological Processes in Foods

The most popular model of the temperature effect on the rate of chemical and biochemical reactions and biological processes in foods is the Arrhenius equation. Reactions and processes that have an optimal or threshold temperature, or whose rate constant versus the absolute temperature reciprocal plot is curvilinear, clearly do not follow the original Arrhenius model. Their kinetics has been described by expanded versions of the Arrhenius equation, the WLF model or log-logistic model and more recently by the Eyring–Polanyi equation. Computer simulations and re-analysis of published experimental rate–temperature relationships show that over a wide range of temperatures, the fit of the Arrhenius equation can be matched by a simpler exponential model, akin to the log-linear model used in food microbiology. This indicates that the temperature-independent energy of activation’s existence cannot be inferred from the Arrhenius plot’s linearity alone and needs independent verification. The same can be said about the Eyring–Polanyi model’s fit and the inference of a temperature-independent free energy of activation. These two models’ good fit might be primarily due to their mathematical structure and not the validity of their underlying statistical mechanistic assumptions. Similarly, the WLF model’s fit can be matched by other two-parameter empirical models that do not imply any analogy between the response of food systems to heat and the rheology of plasticized synthetic rubbery polymers. Therefore, parameters of temperature dependence models obtained by curve fitting should not be considered as having physical meaning unless verified experimentally by an independent test.

Temperature-fastened sodium inactivation accounts for energy efficient cortical action potentials in mammalian brains

Recent experimental evidencs showed that action potential (AP) generation in mammalian, versus invertebrate, axons is remarkably energy efficient [1]. Here we perform both computational (based on both traditional Hodgkin-Huxley model [2] and a cortical axon model [3] whose parameters are modified from experimental data) and experimental studies. Each supports that temperature is a major factor which directly modulates the level of energy cost of APs. Temperature increase results in a remarkable decrease in time constant of sodium channel closing and an increase in inactivation level of Na+ channel due to the Q10 effect (which quantifies the temperature dependent rate of biochemical reactions). This results in a marked reduction in overlap of the inward Na+, and outward K+ currents. As a consequence, the Na+ entry ratio gradually reaches to 1 (the theoretical optimal level, which requires only minimal Na+ charge for generating an AP) as temperature rises. Moreover, we also notice a remarkable exponential increase in firing rate and an exponential decrease in spike duration by both experimental and model studies. The total energy charge in response to a signal reaches a global minimum when temperature is around 37-42 oC. This suggests that warm body temperatures may help the mammalian brain to operate with minimal energy cost. In addition, classic investigations by Hodgkin of squid giant axon revealed an excess entry of approximately 4 times as much Na+ as minimally required to generate an AP [4]. This value of 4 times excess Na+ entry has figured prominently in estimates of the distribution of the sources of energy consumption in the mammalian brain. Here we have to point out that this calculation is based on original Hodgkin-Huxley model with a temperature at 18 oC. It should not be used for calculation of mammalian brain energy budget since mammalian animals have a warm body temperature around 37 oC, around which the sodium entry ratio is close to 1.3. Figure 1 Energy efficiency of AP increases as temperature increases. A. Sodium entry ratio (SER, defined as ∫INa(t)dt/(Cm∆V), where INa(t) is Na+ current, Cm is capacitance, ∆V is the change in voltage during an AP) vs temperature. For ...

Direct Response Analysis in cellular signalling networks

Direct Response Analysis is a general computational tool for quantifying direct functional interactions between components in cellular signalling systems from experimental perturbations and measurements alone. This paper aims to reveal the biological meaning of the direct response coefficients obtained upon applying DRA to simple Michaelis–Menten type proteomic and gene regulatory systems. These systems describe dimer formation and dissociation, protein preduction and decay, and transcription. We derive explicit formulae for the direct response coefficients in terms of biochemical reaction rates, and clarify the potential and limitations of the DRA method. We find that response coefficients are strongly asymmetric, and that they balance persistent characteristics of reactions (e.g. the ratios of on- and off rates) against the time-scales over which these reactions act; fast reactions give stronger response coefficients. The direct interactions between protein species, caused by dimer formation, are effectively negative. We illustrate our results with numerical simulations.

Development of an in situ dissolved oxygen measurement system and calculation of its effective diffusion coefficient in a biofilm

Dissolved oxygen (DO) plays an important role in biological wastewater treatment. The DO concentration in a biofilm interior, which is controlled by its effective diffusion coefficient, determines the biochemical reaction rate. In the current study, a measurement system for the in situ determination of DO levels in a biofilm was developed. A piece of biofilm from a sequencing batch biofilm reactor was used as the experimental example. The DO distribution in the biofilm was measured and the effective diffusion coefficients in water film and in biofilm were calculated as 6.9 × 10−5 m2 d−1 and 1.7 × 10−5 m2 d−1. No anaerobic area in the biofilm was found.

Textural and biochemical properties of cobia (Rachycentron canadum) sashimi tenderised with the ultrasonic water bath

The present study investigated the tenderisation effects ultrasound processing (UT) on farmed cobia sashimi. Age-treated cobia trunk muscles (AT) were used as the control. The pH, total volatile base nitrogen, trimethylamine nitrogen, thiobarbituric acid reactive substances, ATP catabolism components, K1 value, and texture were evaluated. The texture of AT sashimi reached the optimal firmness range with 8.53N at day 7. However, AT samples could not be served raw after day 7 because of their poor freshness indexes, including a TVBN value of 18.53g/100g, a TMAN value of 3.25mg/100g, and a TBARS value 0.983MDAmg/100g. Moreover, the K1 value of AT sashimi was 20.21% at day 5. UT was employed to efficiently tenderise cobia sashimi with an initial firmness of 9.70–7.82N after 90min of treatment. The results of this study indicate that UT accelerates the biochemical reaction rate, as evidenced by the increases in the TVBN, TMAN, and TBARS contents; however, these values were very low. The results of this study could provide basic information for the development of a novel ultrasonic tenderisation technique in raw seafood designed for restaurants and consumers.

Physical limits of cells and proteomes

What are the physical limits to cell behavior? Often, the physical limitations can be dominated by the proteome, the cell’s complement of proteins. We combine known protein sizes, stabilities, and rates of folding and diffusion, with the known protein-length distributions P ( N ) of proteomes ( Escherichia coli , yeast, and worm), to formulate distributions and scaling relationships in order to address questions of cell physics. Why do mesophilic cells die around 50 °C? How can the maximal growth-rate temperature (around 37 °C) occur so close to the cell-death temperature? The model shows that the cell’s death temperature coincides with a denaturation catastrophe of its proteome. The reason cells can function so well just a few degrees below their death temperature is because proteome denaturation is so cooperative. Why are cells so dense-packed with protein molecules (about 20% by volume)? Cells are packed at a density that maximizes biochemical reaction rates. At lower densities, proteins collide too rarely. At higher densities, proteins diffuse too slowly through the crowded cell. What limits cell sizes and growth rates? Cell growth is limited by rates of protein synthesis, by the folding rates of its slowest proteins, and—for large cells—by the rates of its protein diffusion. Useful insights into cell physics may be obtainable from scaling laws that encapsulate information from protein knowledge bases.

Regulation of biochemical reaction rates by flexible tethers

We explore how ligand-receptor binding kinetics can be controlled by tethering the receptor to the end of a flexible polymer. The tether confines the diffusive motion of the receptor thus influencing the rate at which it captures ligands that are free in solution. We compute steady-state collision rates between ligand and receptor for this "tethered-capture" mechanism using a combination of analytic and numerical techniques. In doing so, we uncover a dimensionless control parameter, the "opacity," that determines under what conditions and to what extent a tether regulates the ligand-receptor collision rate. We compute the opacity for a number of different tethering scenarios that appear in biology and use these results to predict the affect of changing the length and flexibility of the tether on the rate at which ligands are captured from solution.

A new type of poly(vinyl alcohol)/nitrocellulose/granular activated carbon/KNO3 composite bead used as a biofilter material

A new type of poly(vinyl alcohol)/nitrocellulose/granular activated carbon/KNO3 composite bead was prepared and shown to be suitable for use as a filter material in the biofiltration process. This composite bead was a porous spherical particle with a diameter of 2.4–6.0 mm and a density of 1.125 g/cm3. The amount of water-soluble nitrogen dissolved out of this composite bead was 145.5 mg N/g dry composite bead. The biochemical kinetic behaviors of n-butyl acetate in a spherical poly(vinyl alcohol) (PVA)/nitrocellulose (NC)/granular activated carbon (GAC)/KNO3 composite bead biofilter (NC biofilter) and a spherical PVA/peat/GAC/KNO3 composite bead biofilter (peat biofilter) were investigated. The values of the half-saturation constant K s for the NC biofilter and the peat biofilter were 33.55 and 35.54 ppm, respectively. The values of the maximum reaction rate V m for the NC biofilter and the peat biofilter were 23.83 and 22.46 ppm/s, respectively. Diffusion-limited zero-order kinetics were regarded as the most adequate biochemical reaction model for the two biofilters. The microbial growth rates and biochemical reaction rates for the two biofilters were inhibited at higher inlet concentrations. The biochemical kinetic behaviors of the two biofilters were similar. The maximum elimination capacities of the NC biofilter and the peat biofilter were 170.72 and 174.51 g C/h m3 bed volume, respectively. The PVA/nitrocellulose/GAC/KNO3 composite bead made it easier for the microbes to adjust to their new environment and secrete exocellular enzymes to break down the substrate.

Synthesis of a new type poly(vinyl alcohol)/peat/bamboo charcoal/KNO3 composite bead used as biofilter material

A new type poly(vinyl alcohol) (PVA)/peat/bamboo charcoal (BC)/KNO3 composite bead was prepared, which has a diameter of 2.4–6.0 mm and a density of 1.133 g/cm3 and is a porous spherical particle. The biochemical kinetic behaviors of n-butyl acetate in PVA/peat/BC/KNO3 spherical composite bead biofilter (BC biofilter) and PVA/peat/granular activated carbon (GAC)/KNO3 spherical composite bead biofilter (GAC biofilter) were investigated. The values of half-saturation constant Ks for BC biofilter and GAC biofilter were 27.89 and 27.95 ppm, respectively. The values of maximum reaction rate Vm for BC biofilter and GAC biofilter were 13.49 and 13.65 ppm/s, respectively. Zero-order kinetic with the diffusion limitation was regarded as the most adequate biochemical reaction model for the two biofilters. The microbial growth rate and biochemical reaction rate for two biofilters were inhibited at higher inlet concentration, and the degree of inhibitive effect was more pronounced in the inlet concentration range of 100–800 ppm. The biochemical kinetic behaviors of the two biofilters were similar. The maximum elimination capacity of BC biofilter and GAC biofilter were 111.65 and 122.67 g C/h m3 bed volume, respectively. The PVA/peat/BC/KNO3 composite bead was suitable as a biofilter material. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011

The influence of nonionic surfactant Brij 30 on biodegradation of toluene in a biofilter

-1 . Zero-order kinetics with diffusion limitation was regarded as the most adequate biochemical reaction kinetic model. The microbial growth rate and biochemical reaction rate were inhibited at higher surfactant content and toluene inlet concentration. The degree of inhibitive effect was more pronounced at lower toluene inlet concentration. The maximum elimination capacity decreased with increasing surfactant content. The addition of nonionic surfactant Brij 30 into filter material was unfavorable for toluene degraded by the microbial.

Comparison of the Effects of Possible Mechanical Stimuli on the Rate of Biochemical Reactions

The aim of this work is to address the question of what constitutes a mechanical stimulation of biochemical reactions in general and further to compare the importance of the two possible mechanical stimulations: shear rate and the rate of volume variation. Using linear nonequilibrium thermodynamics, the Curie principle (the relation for coupling phenomena) is retrieved for a phenomenological relation for a scalar flux in an isotropic system. From these phenomenological relations for the rate of chemical reaction, it is established that the only scalar quantity related to the rate of deformation tensor D that cannot be neglected is the rate of volume variation D((1)). This leads us to the conclusion that, although tissues are exposed to all variety of mechanical factors: straining, shear, pressure, and even dynamic electric fields, the volume variation rate D((1)) is the most important mechanical stimulus driving the processes in them.

Biofiltration kinetics of ethylacetate and xylene using sugarcane bagasse based biofilter

Biodegradation kinetic behaviors of ethyl acetate and xylene in a sugarcane bagasse biofilter were investigated. Microbial growth rate, biochemical reaction rate and kinetic analysis were inhibited at higher inlet concentration. For the microbial growth process, the microbial growth rate of ethyl acetate was greater than that of xylene in the inlet concentration range of 0.2 - 1.2 g.m-3. The degree of inhibitive effect was almost the same for ethyl acetate and xylene in this concentration range. The half-saturation constant Ks values of ethyl acetate and xylene were 1.8489 and 1.784 g.m-3, respectively. The maximum reaction rate Vm values of ethyl acetate and xylene were 0.8073and 0.8438 g C h-1 kg-1 packed material, respectively at a concentration of 0.2 g.m-3. For the biochemical reaction process, the biochemical reaction rate of ethyl acetate was greater than that of xylene in the inlet concentration range of 0.2 - 1.2 g.m-3. The inhibitive effect for ethyl acetate was more pronounced than that for 0.2 - 1.2 g.m-3 in this concentration range. The EAX concentration profiles along the depth were also determined by using diffusion reaction model. It was observed that at low concentration and low flow rate, the model is in good agreement with the experimental values for ethylacetate and xylene.Keywords: Xylene, ethyl acetate, sugarcane bagasse, biofilter, biochemical reactionDOI = 10.3329/cerb.v14i1.4683 Chemical Engineering Research Bulletin 14 (2010) 51-57

Mathematical Modeling for Studying Microbial Processes – Some Examples

Mathematical modeling may have different purposes in chemical and biochemical engineering sciences. One of them is to confirm or to reject kinetic models for certain processes, or to evaluate the importance of some transport phenomena on the net chemical or biochemical reaction rate. In the present paper different microbial processes are considered and modeled for evaluation of kinetic constants for batch and continuous processes accomplished by free and immobilized microbial cells. The practical examples are from the field of wastewater treatment and biosynthesis of products, like enzymes, lactic acid, gluconic acid, etc. By the aid of mathematical modeling the kinetics and the type of inhibition are specified for microbial wastewater denitrification and biodegradation of halogenated hydrocarbons. The importance of free and immobilized cells and their separate contribution to the overall microbial process is also evaluated for some fermentation processes: gluconic acid production, dichloroethane biodegradation, lactic acid fermentation and monochloroacetic acid biodegradation.