Kinetics Of Biochemical Reactions Research Articles

Surface plasmon resonance demodulation by optical ring-down cavity technology

The field of plasmonics has experience a renaissance in recent years by providing a large variety of new physical effects and applications. Surface plasmon polaritons, i.e. the collective electron oscillations at the interface of a metal/dielectric, may bridge the gap between electronic and photonic devices, provided a fast switching mechanism is identified. Here, we presents a cavity ring-down technique called SPR sensor for conducting demodulated applications. Theoretical derivation indicates the conditions in which the laser frequency and linewidth remain unchanged, the optical field strength that mainly depends on the cavity mirror reflectivity, and the PZT scanning speed. Simulated experiments show that higher ring-down cavity precision, smaller anti-cross linewidth, and less time for increases and ring-downs are observed when the reflection coefficient is large. As a photon leaves the ring-down cavity, the photon quantities decrease again. The relative light intensity in the ring-down cavity is large when the PZT scanning speed is small. The application of a demodulation system shows that the ring-down cavity technology can largely improve the sensitivity of SPR sensors. The demodulation speed can also reach the ms level. A demodulation system is important for biochemical reaction kinetics and remote monitoring applications.

Synchrotron Radiation Sheds Fresh Light on Plant Research: The Use of Powerful Techniques to Probe Structure and Composition of Plants.

While synchrotron radiation is a powerful tool in material and biomedical sciences, it is still underutilized in plant research. This mini review attempts to introduce the potential of synchrotron-based spectroscopic and imaging methods and their applications to plant sciences. Synchrotron-based Fourier transform infrared spectroscopy, X-ray absorption and fluorescence techniques, and two- and three-dimensional imaging techniques are examined. We also discuss the limitations of synchrotron-based research in plant sciences, specifically the types of plant samples that can be used. Despite limitations, the unique features of synchrotron radiation such as high brightness, polarization and pulse properties offer great advantages over conventional spectroscopic and imaging tools and enable the correlation of the structure and chemical composition of plants with biochemical function. Modern detector technologies and experimental methodologies are thus enabling plant scientists to investigate aspects of plant sciences such as ultrafast kinetics of biochemical reactions, mineral uptake, transport and accumulation, and dynamics of cell wall structure and composition during environmental stress in unprecedented ways using synchrotron beamlines. The potential for the automation of some of these synchrotron technologies and their application to plant phenotyping is also discussed.

The middle Eocene climatic optimum (MECO): A multiproxy record of paleoceanographic changes in the southeast Atlantic (ODP Site 1263, Walvis Ridge)

AbstractThe middle Eocene climatic optimum (MECO, ~40 Ma) was a transient period of global warming that interrupted the secular Cenozoic cooling trend. We investigated the paleoceanographic, paleoenvironmental, and paleoecological repercussions of the MECO in the southeast Atlantic subtropical gyre (Ocean Drilling Program Site 1263). TEX86and δ18O records support an ~4°C increase in surface and deepwater temperatures during the MECO. There is no long‐term negative carbon isotope excursion (CIE) associated with the early warming, consistent with other sites, and there is no short‐term negative CIE (~50 kyr) during the peak of the MECO, in contrast to what has been observed at some sites. This lack of a CIE during the peak of the MECO at Site 1263 could be due to poor sediment recovery or geographic heterogeneity of the δ13C signal. Benthic and planktic foraminiferal mass accumulation rates markedly declined during MECO, indicating a reduction of planktic foraminiferal production and export productivity. Vertical δ13C gradients do not indicate major changes in water column stratification, and there is no biomarker or micropaleontological evidence that hypoxia developed. We suggest that temperature dependency of metabolic rates could explain the observed decrease in foraminiferal productivity during warming. The kinetics of biochemical reactions increase with temperature, more so for heterotrophs than for autotrophs. Steady warming during MECO may have enhanced heterotroph (i.e., foraminiferal) metabolic rates, so that they required more nutrients. These additional nutrients were not available because of the oligotrophic conditions in the region and the lesser response of primary producers to warming. The combination of warming and heterotroph starvation altered pelagic food webs, increased water column recycling of organic carbon, and decreased the amount of organic carbon available to the benthos.

Analysis of a Chemostat Model with Variable Yield Coefficient and Substrate Inhibition: Contois Growth Kinetics

We analyze the steady-state operation of a generalized reactor model that encompasses a continuous flow bioreactor and an idealized continuous flow membrane reactor as limiting cases. The biochemical reaction kinetics is governed by a Contois growth model subject to noncompetitive substrate inhibition with a variable substrate yield coefficient. The steady-state performance of the reactor is predicted and stability of the steady-state solutions as a function of dimensionless residence time reported. Our results identified two cases of practical interest. The first feature corresponds to the case where solutions to both no-washout and washout conditions are bistable. The second feature identifies the parameter region in which periodic solutions can occur when the yield coefficient is not constant. Both these features are often undesirable in practical applications and must be avoided. Scaling of the model equations reveals that both the second-bifurcation parameters are functions of the influent concentration. Our results predict how the reactor behavior varies as a function of influent concentration and identify the range of influent concentrations where the reactor displays neither periodic nor bistable behavior.

Relaxationskinetik in lebenden Zellen

Fast kinetics of biochemical reactions can be measured in vitro using relaxation experiments. Recently, temperature jump techniques have been developed that can also be applied for in-cell studies. The high spatio-temporal resolution of such experiments leads to new insights of how the cellular environment modifies reaction kinetics.

In Memoriam

Robert A. Alberty, professor emeritus in the Department of Chemistry and former dean of MIT’s School of Science—whose seminal contributions to the thermodynamics and kinetics of biochemical reactions are still at the forefront of chemistry—passed away on 18 January 2014, at the age of 92.

Challenges for an enzymatic reaction kinetics database

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.

In Vivo Probing of the Temperature Responses of Intracellular Biomolecules in Yeast Cells by Label‐Free Raman Microspectroscopy

Environmental temperature is an essential physical quantity that substantially influences cell physiology by changing the equilibria and kinetics of biochemical reactions occurring in cells. Although it has been extensively used as a readily controllable parameter in genetic and biochemical research, much remains to be explored about the temperature responses of intracellular biomolecules in vivo and at the molecular level. Here we report in vivo probing, achieved with label-free Raman microspectroscopy, of the temperature responses of major intracellular components such as lipids and proteins in living fission yeast cells. The characteristic Raman band at 1602 cm(-1), which has been attributed mainly to ergosterol, showed a significant decrease (≈47 %) in intensity at elevated temperatures above 35 °C. In contrast to this high temperature sensitivity of the ergosterol Raman band, the phospholipid and protein Raman bands did not vary much with increasing culture temperature in the 26-38 °C range. This finding agrees with a previous biochemical study that showed that the initial stages of ergosterol biosynthesis in yeast are hindered by temperature elevation. Moreover, our result demonstrates that Raman microspectroscopy holds promise for elucidation of temperature-dependent cellular activities in living cells, with a high molecular specificity that the commonly used fluorescence microscopy cannot offer.

Invariance and optimality in the regulation of an enzyme

BackgroundThe Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cellular metabolism, often including time-dependent enzyme levels. However, even for a single reaction, there remains a fundamental disconnect between our understanding of the reaction kinetics, and the regulation of that reaction through changes in the abundance of active enzyme.ResultsWe revisit the Michaelis-Menten equation under the assumption of a time-dependent enzyme concentration. We show that all temporal enzyme profiles with the same average enzyme level yield identical substrate degradation– a simple analytical conclusion that can be thought of as an invariance principle, and which we validate experimentally using a β-galactosidase assay. The ensemble of all time-dependent enzyme trajectories with the same average concentration constitutes a space of functions. We develop a simple model of biological fitness which assigns a cost to each of these trajectories (in the form of a function of functions, i.e. a functional). We then show how one can use variational calculus to analytically infer temporal enzyme profiles that minimize the overall enzyme cost. In particular, by separately treating the static costs of amino acid sequestration and the dynamic costs of protein production, we identify a fundamental cellular tradeoff.ConclusionsThe overall metabolic outcome of a reaction described by Michaelis-Menten kinetics is ultimately determined by the average concentration of the enzyme during a given time interval. This invariance in analogy to path-independent phenomena in physics, suggests a new way in which variational calculus can be employed to address biological questions. Together, our results point to possible avenues for a unified approach to studying metabolism and its regulation.ReviewersThis article was reviewed by Sergei Maslov, William Hlavacek and Daniel Kahn.

Severe osmotic compression triggers a slowdown of intracellular signaling, which can be explained by molecular crowding

Regulation of the cellular volume is fundamental for cell survival and function. Deviations from equilibrium trigger dedicated signaling and transcriptional responses that mediate water homeostasis and volume recovery. Cells are densely packed with proteins, and molecular crowding may play an important role in cellular processes. Indeed, increasing molecular crowding has been shown to modify the kinetics of biochemical reactions in vitro; however, the effects of molecular crowding in living cells are mostly unexplored. Here, we report that, in yeast, a sudden reduction in cellular volume, induced by severe osmotic stress, slows down the dynamics of several signaling cascades, including the stress-response pathways required for osmotic adaptation. We show that increasing osmotic compression decreases protein mobility and can eventually lead to a dramatic stalling of several unrelated signaling and cellular processes. The rate of these cellular processes decreased exponentially with protein density when approaching stalling osmotic compression. This suggests that, under compression, the cytoplasm behaves as a soft colloid undergoing a glass transition. Our results shed light on the physical mechanisms that force cells to cope with volume fluctuations to maintain an optimal protein density compatible with cellular functions.

Almost sure convergence of numerical approximations for Piecewise Deterministic Markov Processes

Hybrid systems, and Piecewise Deterministic Markov Processes in particular, are widely used to model and numerically study systems exhibiting multiple time scales in biochemical reaction kinetics and related areas. In this paper an almost sure convergence analysis for numerical simulation algorithms for Piecewise Deterministic Markov Processes is presented. The discussed numerical methods arise through discretising a constructive method defining these processes. The stochastic problem of simulating the random, path-dependent jump times of such processes is reformulated as a hitting time problem for a system of ordinary differential equations with random threshold. Then deterministic continuous methods (methods with dense output) are serially employed to solve these problems numerically. We show that the almost sure convergence rate of the stochastic algorithm is identical to the order of the embedded deterministic method. We illustrate our theoretical findings by numerical examples from mathematical neuroscience, Piecewise Deterministic Markov Processes are used as biophysically accurate stochastic models of neuronal membranes.

Integration of mixing, heat transfer, and biochemical reaction kinetics in anaerobic methane fermentation

An extensive investigation of anaerobic methane fermentation requires identifying the relationship between the physical environment and biological process. In this study, a computational fluid dynamics (CFD) technique was used to characterize bacterial fermentation mechanisms intertwined with mixing and heat transfer in anaerobic digesters. The results demonstrate that the methane yield remains almost unchanged while the energy efficiency decreases with increasing mixing power in a complete-mix digester, and that the energy output increases nonlinearly with the increase in heating energy in a plug-flow digester. The CFD method can be applied to other bioreactors to gain valuable insights into their behavior as well. Integrating flow and temperature with kinetic behavior for anaerobic digestion not only solves the controversy about how mixing influences the digestive process, but also assists in optimizing the digester design and increasing the efficiency of energy conversion, and additionally, provides a reference for improving the mixing guidelines recommended by the U.S. Environmental Protection Agency.

A review of models of fluctuating protrusion and retraction patterns at the leading edge of motile cells

A characteristic feature of motile cells as they undergo a change in motile behavior is the development of fluctuating exploratory motions of the leading edge, driven by actin polymerization. We review quantitative models of these protrusion and retraction phenomena. Theoretical studies have been motivated by advances in experimental and computational methods that allow controlled perturbations, single molecule imaging, and analysis of spatiotemporal correlations in microscopic images. To explain oscillations and waves of the leading edge, most theoretical models propose nonlinear interactions and feedback mechanisms among different components of the actin cytoskeleton system. These mechanisms include curvature-sensing membrane proteins, myosin contraction, and autocatalytic biochemical reaction kinetics. We discuss how the combination of experimental studies with modeling promises to quantify the relative importance of these biochemical and biophysical processes at the leading edge and to evaluate their generality across cell types and extracellular environments.

Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation

The chemical master equation (CME) is the fundamental evolution equation of the stochastic description of biochemical reaction kinetics. In most applications it is impossible to solve the CME directly due to its high dimensionality. Instead, indirect approaches based on realizations of the underlying Markov jump process are used, such as the stochastic simulation algorithm (SSA). In the SSA, however, every reaction event has to be resolved explicitly such that it becomes numerically inefficient when the system's dynamics include fast reaction processes or species with high population levels. In many hybrid approaches, such fast reactions are approximated as continuous processes or replaced by quasi-stationary distributions in either a stochastic or a deterministic context. Current hybrid approaches, however, almost exclusively rely on the computation of ensembles of stochastic realizations. We present a novel hybrid stochastic--deterministic approach to solve the CME directly. Our starting point is a part...

SABIO-RK: Access to Biochemical Reaction Kinetics Data

AbstractSABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. New RESTful web services, as well as a new browser interface both offer extended functionality, such as hierarchical search for data based on organism taxonomy or tissue and cell type ontology.SABIO-RK facilitates the exchange of kinetic data between experimentalists and modelers, and thereby supports the setup of quantitative computer models. The web services and the degree of data integration make it well suited for its integration into applications using or requiring kinetic data, such as systems biology modeling platforms.

Metabolic theory and elevational diversity of vertebrate ectotherms

The Metabolic Theory of Ecology (MTE) posits that the temperature-dependent kinetics of metabolism shape broad-scale patterns of biodiversity. Here we test whether the MTE accounts for patterns of diversity using 102 elevational diversity gradients of reptiles and amphibians. In particular, we examined the support for the two key predictions of the MTE: that the reciprocal of absolute temperature (1/kT) and diversity are linearly related and that the slope of that relationship is -0.65. We also tested two underlying assumptions of the MTE in cases with appropriate data, namely, that abundance is invariant among samples, and that behavioral thermoregulation influences the MTE predictions. We found that few studies supported the predictions of the MTE for the relationship between environmental temperature and elevational diversity using previous methods on individual gradients and using meta-analysis. The predominant relationship was curvilinear, and the slopes were steeper than predicted. In analyses of individual gradients, only 6% followed the MTE predictions in the strictest application, and 25% in the broadest. We found violations of the assumption of invariant abundances in all five test cases. All four herpetofaunal groups, regardless of behavioral thermoregulatory abilities, demonstrated poor fits to the MTE predictions. Even when arid gradients are removed, ameliorating the potential effects of water limitation, the MTE did not account for herpetofaunal elevational diversity. We conclude that an interplay of factors shapes elevational diversity gradients rather than the simple kinetics of biochemical reactions.

On-demand generation of monodisperse femtolitre droplets by shape-induced shear

We describe a method for creating discrete femtolitre-scale water-in-oil droplets on demand, based solely on a geometrically induced reduction in oil/water interfacial area at microfabricated junction orifices. This on-demand generation method is driven by self-shear of droplets due to interfacial tension induced forces resulting from a localized transition in microchannel height. The magnitudes of shear stresses involved appear to be significantly less than the shearing instabilities used to split off daughter droplets from aqueous mother plugs at microfabricated junctions in continuous water-in-oil segmented flows, which implies that this method may be better suited for studying biochemical reactions and reaction kinetics in droplets of decreased volume without loss of chemical reactivity due to redistribution of surfactant density used to passivate the oil/water interface. Predictable droplet generation rates under constant pressure conditions or the gated formation of one, two or more droplets at a time with fixed pressure pulses have been demonstrated in a similar manner to active on-demand droplet generation strategies, but with a simpler system not needing actuation and sensing equipment beyond a pressure regulator.

Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics

Studies of the kinetics of biochemical reactions, especially of folding of proteins and RNA, are important for understanding the function of biomolecules and processes in live cells. Many biochemical reactions occur rapidly and thus need to be triggered on very short time scales for their kinetics to be studied, which is often accomplished by mixing in a turbulent flow. More rapid and sample-efficient mixing is achieved in laminar flow in a microfluidic device, in which the sample is two-dimensionally (2D) focused to a thin sheet. Here we describe the design and operation of an ultrafast microfluidic mixer with three-dimensional (3D) flow focusing. The confinement of a 3D-focused sample to a narrow stream near the middle of a microchannel renders its velocity nearly uniform and makes it possible to monitor the reaction kinetics without exclusion of any parts of the sample. Hence, the sample consumption is substantially reduced and the fluorescence of the sample can be monitored without a confocal setup. Moreover, the 3D-focusing allows facile measurements of velocity of the sample with a high spatial resolution using a specially developed technique based on epi-fluorescence imaging. The data on the velocity vs. position are used to precisely calibrate the conversion between position and the reaction time, which is essential for accurate kinetic measurements. The device performs mixing on a 10 micros scale, which is comparable to that of the laminar mixers with 2D focusing. Unlike previous ultrafast laminar mixers, which were machined in hard materials, the present microfluidic device is made of a single cast of poly(dimethylsiloxane), PDMS, and is thus simpler and less expensive to manufacture.

1P311 非線形生化学反応動力学の統一とNMRメタボロミクス(非平衡・生体リズム,第48回日本生物物理学会年会)

1P311 非線形生化学反応動力学の統一とNMRメタボロミクス(非平衡・生体リズム,第48回日本生物物理学会年会)

EFFECT OF INTERNAL DIFFUSION ON BIOETHANOL PRODUCTION IN A BIOREACTOR WITH YEAST CELLS IMMOBILIZED ON MOBILE BEDS

This paper develops the previous studies on the transfer processes and biochemical reaction kinetics involved in the bioethanol production by immobilized S. cerevisiae cells using a bioreactor with mobile beds of biocatalysts. Although the immobilization of cells or enzymes offers a lot of advantages compared to the free ones, it induces the appearance of the internal diffusion of substrate or product, with negative effect on the overall biochemical process. In the investigated case, the influences of the substrate internal diffusion on physical and biochemical processes have been quantified by means of the Biot number, Thiele modulus and reduction factor λ. The biocatalyst particles size and volumetric fraction exhibit significant and different influences on these three parameters. The increase of particle diameter led to the increase of Bi number, to the decrease of Thiele modulus and to the decrease of factor λ, but the influence of biocatalysts concentration is favorable for all discussed parameters.