Simulation of C1 fluxes in cyanobacteria: comparison between the carboxysome hypothesis and the equilibrium proposal

1997 ◽  
Vol 75 (12) ◽  
pp. 2117-2130 ◽  
Author(s):  
Christophe Salon ◽  
David Thomas Canvin
Keyword(s):  
Mathematical Model ◽  
Steady State ◽  
Kinetic Constants ◽  
Experimental Conditions ◽  
Extracellular Medium ◽  
Blue Green Algae ◽  
Permeability Coefficients ◽  
Inorganic Species ◽  
Wide Range ◽  
Entire Cell

Inorganic carbon fluxes were simulated by a mathematical model using an equilibrium hypothesis for a wide range of conditions in a closed system composed of air-grown cells of Synechococcus UTEX 625 in a reaction vessel connected to a mass spectrometer. The metabolic scheme took into account the input fluxes of CO2 and HCO3− transport into the cells, the output fluxes of CO2 and HCO3− efflux, the diversion of Q toward the formation of the internal C2 pool, and photosynthetic CO2 fixation. The equations expressed the variation in concentration of each inorganic species outside and inside the cell as a function of time. The input fluxes were previously characterized by their kinetic constants (K1/2 and Vm) both during initial uptake occurring upon illumination of the cells and under steady-state photosynthesis conditions. The efflux rates of the various Ci species from the cells were investigated under a wide variety of experimental conditions. Using these efflux rates, the permeability coefficients of the cell for CO2 and HCO3− were calculated previously. Using the kinetic constants for CO2 and HCO3− transport, the permeability coefficients of the cell for CO2 and HCO3− and the geometrical characteristics of the cells, the model simulated precisely the [HCO3−]/[CO2] ratio and the [CO2] and [O2] changes in the extracellular medium as well as the rate of filling of the internal Ci pool under various conditions. Accurate fitting of experimental data with calculated values were possible only when the intracellular Ci species were assumed to be in equilibrium throughout the entire cell volume. Results are discussed and compared with those given by previous hypotheses. Key words: Synechococcus UTEX 625, blue green algae, cyanobacteria, mathematical model, active CO2 transport, active HCO3− transport, steady state, photosynthesis, Ci concentrating mechanism.

Measurement of the amount and isotopic composition of the CO2 released from the cyanobacterium Synechococcus UTEX 625 after rapid quenching of the active CO2 transport system

1997 ◽  
Vol 75 (6) ◽  
pp. 981-997 ◽  
Author(s):  
Anthony G. Miller ◽  
Christophe Salon ◽  
David T. Canvin ◽  
George S. Espie
Keyword(s):  
Isotopic Composition ◽  
Cell Volume ◽  
Mass Spectrometer ◽  
Transport System ◽  
Time Course ◽  
Rapid Quenching ◽  
Experimental Conditions ◽  
Extracellular Medium ◽  
Fully Depleted ◽  
Entire Cell

Air-grown cells of the cyanobacterium Synechococcus UTEX 625 were suspended in a cuvette connected to a mass spectrometer and supplied with H13C18O3− to investigate the intracellular interconversion between CO2 and HCO3− as determined from the isotopic composition of CO2 appearing in the extracellular medium under a wide variety of experimental conditions. Upon injection of H13C18O3− to the cell suspension in the light, the extracellular [13C16O2] increased. As the CO2 species were 13C labelled, this demonstrated that the 18O-depleted CO2 was originating from the added H13C18O3−. A comparison of the rates of 13C16O16O appearance in the medium with the formation of 13C16O16O from spontaneous dehydration–hydration in the extracellular medium in the presence of cells demonstrated that most of it had to originate from a series of intracellular dehydration–hydration cycles of H13C18O3− that had been recently transported into the cells. During the time course of the experiments both the m/z (mass to charge) = 49 (i.e., 13C18O18O) and 47 (i.e., 13C18O16O) signals decreased constantly, whereas the m/z = 45 signal (i.e.,13C16O2) always increased. Inhibiting CO2 fixation enhanced the amount of CO2 arising in the medium but did not change its isotopic composition, and the CO2 was always fully depleted of 18O. When the CO2 transport system was inhibited by darkening the cells, adding inhibitors such as Na2S or COS, or quenching the uptake of inorganic 13C with an excess of inorganic 12C, the magnitude of the extracellular [13C16O2] was increased but the CO2 species were still always depleted of 18O. Various incubation times of the illuminated cells in the presence of H13C18O3− were used to obtain a variety of internal Ci pool sizes. When the inhibitor (COS) was added, the amount of 13C16O2 arising during the response time of the mass spectrometer was equivalent to the amount of CO2 that would have been present in the whole cell if CO2 and HCO3− were in equilibrium throughout the entire cell volume, but it was at least 40 times higher than the amount of CO2 that would have been present in the cell if the CO2 was confined to the carboxysomes. Experiments were also conducted at pH 9.0 where the spontaneous rate of 13C16O2 production from H13C1803− dehydration–hydration would be negligible, and again the same features were observed. Results show that intracellular HCO3− and CO2 are in rapid equilibrium throughout the entire cell volume. Key words: Synechococcus UTEX 625, cyanobacteria, CO2 leakage, 18O exchange, active CO2 transport, carboxysomes, inorganic C concentrating mechanism.

Spool Hydraulic Stiffness and Flow Force Effects in Electrohydraulic Servo-Valves

1987 ◽  
Vol 201 (3) ◽  
pp. 193-199 ◽  
Author(s):  
H A Arafa ◽  
M Rizk
Keyword(s):  
Mathematical Model ◽  
Steady State ◽  
Linear Feedback ◽  
Magnetic Saturation ◽  
Stable Operation ◽  
Experimental Assessment ◽  
Servo Valve ◽  
Supply Pressure ◽  
Wide Range ◽  
Good Agreement

This paper deals with an analytical and experimental assessment of the flow force effects on electrohydraulic servo-valve steady state characteristics. The system mathematical model is derived, and special consideration is given to non-linearity of the feedback wire stiffness and magnetic saturation of the armature. The ‘spool hydraulic stiffness’ is defined and expressed in terms of the servo-valve parameters and supply pressure to allow clear interpretation of the nature of flow force effects. Experimental results of spool displacement decrement due to flow force versus net displacement are in good agreement with the predicted performance in a wide range of input current up to almost full magnetic saturation. The results provide evidence, on an alternative basis, of the non-linear feedback behaviour. Correlation is also made between flow force and limits of stable operation, and an expression is derived for the maximum allowable supply pressure.

Studies of the growth and mineral nutrition of barley varieties. II. Potassium uptake and its regulation

1983 ◽  
Vol 61 (6) ◽  
pp. 1551-1558 ◽  
Author(s):  
M. Yaeesh Siddiqi ◽  
Anthony D. M. Glass
Keyword(s):  
Steady State ◽  
Kinetic Constants ◽  
Growth Responses ◽  
Short Term ◽  
Potential Growth ◽  
Wide Range ◽  
Rapid Loading ◽  
State Growth ◽  
Complete Nutrient Solution ◽  
Growth Experiments

Short-term K+ (86Rb) influx and its regulation by root K+ concentration was studied in barley varieties, using plants grown in complete nutrient solution at constant concentrations. The varieties employed in this study exhibited substantial differences not only in K+ influx but also in the intensity and the pattern of regulation of K+ influx. In the high-potential growth-rate varieties these K+ uptake characteristics were found to correlate well with their growth responses to K+ supply reported earlier by Siddiqi and Glass. Predictions of K+ influx, based upon kinetic constants and internal K+ concentrations derived from steady-state growth experiments, were found to correspond well with the observed fluxes for plants grown under these conditions over a wide range of root K+ concentrations. These predictions also provided good estimates of influx in CaSO4-grown plants for intermediate levels of root K+ concentration. However, at low root K+ concentration, predictions greatly overestimated observed fluxes, while at high root K+, influx was underestimated. Similarly, when kinetic constants derived from CaSO4-grown plants (whose root K+ concentrations were increased by rapid loading) were applied to steady-state plants, predicted influx values were close to observed in the intermediate range of root K+ concentration. However, at high root K+, influx was overestimated. These adjustments serve, in the steady state, to maintain tissue K+ concentration within rather narrow limits.

scholarly journals RNA-sequencing and Mathematical Modeling Identify Suite of Light-sensitive Circadian Genes in an Orb-web Weaving Spider

2021 ◽  
Author(s):  
Natalia Toporikova ◽  
Wenduo Cheng ◽  
Leyuan Qian ◽  
Andrew Mah ◽  
Thomas Clarke ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Circadian Clock ◽  
Rna Sequencing ◽  
Light Pulse ◽  
Genetic Model ◽  
Single Gene ◽  
Constant Darkness ◽  
Experimental Conditions ◽  
Circadian Genes ◽  
Wide Range

Abstract BackgroundMost organisms rely on a molecular circadian clock to orchestrate a wide range of physiological processes to match the 24-hour day. These molecular clocks are typically based on a negative feedback loop among a small set of proteins that govern the circadian output. Light or other environmental conditions can reset the circadian clock, but true circadian behaviors continue to cycle even in constant darkness, with an intrinsic period called the free-running period (FRP). Spiders have unusual FRPs, with some species having extremely short FRP (e.g. 18 hours for trashline orb weaver), and many having highly variable FRPs (intraspecific variation of up to 10 hours). In the absence of any genetic model of circadian rhythms in spiders, we developed a mathematical model to optimize experimental conditions for identifying circadian genes that also respond to light cues. ResultsOur mathematical model involved a single gene that encodes a protein that inhibits its own transcription. In our model, light degrades the circadian transcript, which allows a broad range of FRPs to be entrained to a 24-hour day. Our model predicted that exposing spiders to a pulse of light in the middle of the night would cause a pattern of expression between two later time points that was opposite the pattern exhibited by spiders who did not receive a pulse of light. RNA-sequencing of four groups of adult female orb weaving spiders, Metazygia wittfeldae, under these experimental conditions resulted in 528 significantly differentially expressed (DE) transcripts between the two collection times or between the light pulse and no light pulse. Consistent with our model, we found a cluster of transcripts with the flipped pattern of expression between the two collection times, dependent on the application of light.ConclusionsOur DE transcripts represent the first genetic evidence for circadian output in spiders. Furthermore, those transcripts with a flipped pattern of expression represent prime candidates for light-sensitive circadian genes, which may be involved in entraining the circadian clock to light. Functions of these genes varied from growth and development to reproduction to gene regulation, consistent with other circadian systems.

Glycolaldehyde inhibition of CO2transport in the cyanobacteriumSynechococcusUTEX 625

1998 ◽  
Vol 76 (1) ◽  
pp. 1-11
Author(s):  
Christophe Salon ◽  
Qinglin Li ◽  
David Thomas Canvin
Keyword(s):  
Steady State ◽  
Carbonic Anhydrase ◽  
Cell Suspension ◽  
Time Course ◽  
Initial Period ◽  
Cyanobacterial Cell ◽  
Extracellular Medium ◽  
Blue Green Algae ◽  
Carbon Dioxide Uptake ◽  
Concentrating Mechanism

In studies of the inorganic carbon (Ci) concentrating mechanism of cyanobacteria glycolaldehyde is often used to inhibit photosynthetic CO2fixation. As a partial inhibition of active CO2transport by glycolaldehyde under steady-state Ciflux conditions has been recently suggested, in this paper, using mass spectrometry, we investigate in detail the relationship between glycolaldehyde concentration ([GLY]) and CO2transport both during the initial period following illumination of a cyanobacterial cell suspension and during the so-called steady state when an internal Cipool has been allowed to develop. Carbon dioxide uptake following illumination of a cyanobacterial cell suspension was progressively reduced by increasing [GLY] in the medium, both in the absence or in the presence of carbonic anhydrase. The same features were found when either Ciin the form of bicarbonate was injected to a pre-illuminated cell suspension in the presence of carbonic anhydrase in the medium or a pulse of CO2was provided to the cells in the light without carbonic anhydrase in the extracellular medium. Although photosynthesis was completely abolished with 10 mM glycolaldehyde, CO2uptake was only inhibited 20% but was decreased further by higher [GLY]. Double reciprocal plots of CO2uptake versus initial [CO2] determined with a range of [GLY] showed the inhibition to be noncompetitive. To simultaneously study CO2uptake and CO2efflux, H13C18O3was used with cells in which CO2transport alone, or both CO2and HCO3-transport system were allowed to proceed. Cells were inhibited with either iodoacetamide or glycolaldehyde and the time course of the various CO2species in the medium demonstrated that CO2uptake was inhibited partially with glycolaldehyde resulting in a greater CO2efflux from the cells. When the cell suspension was again illuminated, in the presence of glycolaldehyde, initial CO2uptake was greatly reduced, and the extracellular [CO2] eventually rose to a level higher than that which would be expected to be in equilibrium with the amount of Cipresent in the medium. Results are discussed in terms of glycolaldehyde use in Citransport mechanism studies in cyanobacteria. Key words: Synechococcus UTEX 625, blue-green algae, cyanobacteria, CO2transport, HCO3-transport, CO2efflux, inhibitor, Ciconcentrating mechanism.

Development and Validation of a Steady-State Mathematical Model for the Physicochemical Processing of Biopolymers by Reactive Extrusion

2010 ◽  
Vol 8 (1) ◽  
Author(s):  
Marie-Amélie De Ville d'Avray ◽  
Arsène Isambert ◽  
Stéphane Brochot ◽  
Pierre Ferchaud
Keyword(s):  
Mathematical Model ◽  
Steady State ◽  
Chemical Reactions ◽  
Chemical Engineering ◽  
Research Work ◽  
Hybrid Approach ◽  
Reactive Extrusion ◽  
Modelling And Simulation ◽  
Wide Range ◽  
Twin Screw

In reactive extrusion, the extruder is used as a solvent-free continuous chemical reactor able to process highly viscous materials. The chemical transformation of biopolymers by reactive extrusion appears as a very promising technology. Although punctual applications in this field have already been achieved on a laboratory or pilot scale, the amount of work to carry out is still considerable. A wide range of reactions and raw materials may be explored, and the reactions achieved on a laboratory scale have to be optimized and transposed to an industrial scale. Process modelling and simulation constitute useful tools for process understanding, development, optimization and scale-up. Although reactive extrusion modelling has interested many authors, it still remains a challenge because of the complex geometry and the strong coupling between operating parameters, flow conditions, material rheological behavior and reaction kinetics. A steady-state mathematical model for a biopolymer oxidation process by reactive extrusion is here proposed. The model is based on a hybrid approach combining chemical engineering methods and simplified continuum mechanics laws. The combination of these two approaches enables to simplify the calculations related to chemical reactions while ensuring a predictive character. The flexible structure of the model enabled its implementation within a global process simulator. A method to minimize the amount of experimental data required for model parameter adjustment is also presented. The model was validated by experiments conducted on a semi-pilot corotating twin-screw extruder. Even if it may be refined, the model proposed already constitutes a useful tool for later research work dealing with the development, modelling and simulation of chemical reactions in corotating twin-screw extruders.

scholarly journals Adrenalin-Induced Na+/H+ Exchange in' Trout Erythrocytes and its Effects Upon Oxygen-Carrying Capacity

1985 ◽  
Vol 118 (1) ◽  
pp. 229-246 ◽  
Author(s):  
A. R. COSSINS ◽  
P. A. RICHARDSON
Keyword(s):  
Steady State ◽  
Intracellular Ph ◽  
Carrying Capacity ◽  
Extracellular Ph ◽  
Extracellular Medium ◽  
Root Effect ◽  
Fish Blood ◽  
Wide Range ◽  
Oxygen Carrying Capacity ◽  
Normal Relationship

Addition of adrenalin (10−4moll−1) to trout erythrocytes in an unbuffered saline resulted in a rapid acidification of the extracellular medium. This process was inhibited by amiloride (K½10−4moll−1) and by the removal of extracellular Na+. The rate of acidification was a saturable function of extracellular Na+ concentration. When extracellular pH was maintained constant by continual titration with KOH, adrenalin induced a transient burst of H+ efflux. During this period the loss of cellular H+ equivalents was approximately equal to the net gain of Na+, providing evidence for a Na+/H+ exchange with a stoichiometry of 1. The steady state following stimulation with adrenalin could be disturbed by changes in extracellular pH. After the addition of adrenalin, intracellular pH (pHi) was increased by 0.2-0.3 units but did not exceed extracellular pH, as required if the Na+ and H+ concentration ratios came into equilibrium. The increase in pHi in stimulated compared with control cells was maintained approximately constant over a wide range of pHo, suggesting that pH equilibration by the Jacob-Stewart cycle was operating normally and that the activation of Na+/H+ exchange provides an offset to the normal relationship between pHi and pHo. The steady state results from a balance of an increase Na+/H+ and CI−/HCO3− exchange with an increased rate of Na+ pumping and next KCl efflux. In a buffered saline, adrenalin caused a 22–46% increase in the oxygen-carrying capacity of trout erythrocytes. It is suggested that this was due to a Root effect of trout haemoglobin caused by cellular alkalinization when the Na+/H+ exchange mechanism was activiated. This observation suggests that many published values for oxygencarrying capacity of fish blood require re-evaluation.

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

2019 ◽  
Author(s):  
Christopher John ◽  
Greg M. Swain ◽  
Robert P. Hausinger ◽  
Denis A. Proshlyakov
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Heme Iron ◽  
Chemical Transformations ◽  
Experimental Conditions ◽  
Strongly Coupled ◽  
Non Heme Iron ◽  
Reversible Redox ◽  
Wide Range ◽  
Complex Structural

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semi-empirical computational methods, demonstrating that the Fe (III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and 171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

Spectroscopic Studies of Asparaginyl-tRNA Synthetase from Entamoeba histolytica

2019 ◽  
Vol 26 (6) ◽  
pp. 435-448
Author(s):  
Priyanka Biswas ◽  
Dillip K. Sahu ◽  
Kalyanasis Sahu ◽  
Rajat Banerjee
Keyword(s):  
Circular Dichroism ◽  
Steady State ◽  
Entamoeba Histolytica ◽  
Protein Concentration ◽  
Trna Synthetase ◽  
Solvent Exposure ◽  
Steady State Fluorescence ◽  
State Process ◽  
Wide Range ◽  
Circular Dichroïsm

Background: Aminoacyl-tRNA synthetases play an important role in catalyzing the first step in protein synthesis by attaching the appropriate amino acid to its cognate tRNA which then transported to the growing polypeptide chain. Asparaginyl-tRNA Synthetase (AsnRS) from Brugia malayi, Leishmania major, Thermus thermophilus, Trypanosoma brucei have been shown to play an important role in survival and pathogenesis. Entamoeba histolytica (Ehis) is an anaerobic eukaryotic pathogen that infects the large intestines of humans. It is a major cause of dysentery and has the potential to cause life-threatening abscesses in the liver and other organs making it the second leading cause of parasitic death after malaria. Ehis-AsnRS has not been studied in detail, except the crystal structure determined at 3 Å resolution showing that it is primarily α-helical and dimeric. It is a homodimer, with each 52 kDa monomer consisting of 451 amino acids. It has a relatively short N-terminal as compared to its human and yeast counterparts. Objective: Our study focusses to understand certain structural characteristics of Ehis-AsnRS using biophysical tools to decipher the thermodynamics of unfolding and its binding properties. Methods: Ehis-AsnRS was cloned and expressed in E. coli BL21DE3 cells. Protein purification was performed using Ni-NTA affinity chromatography, following which the protein was used for biophysical studies. Various techniques such as steady-state fluorescence, quenching, circular dichroism, differential scanning fluorimetry, isothermal calorimetry and fluorescence lifetime studies were employed for the conformational characterization of Ehis-AsnRS. Protein concentration for far-UV and near-UV circular dichroism experiments was 8 µM and 20 µM respectively, while 4 µM protein was used for the rest of the experiments. Results: The present study revealed that Ehis-AsnRS undergoes unfolding when subjected to increasing concentration of GdnHCl and the process is reversible. With increasing temperature, it retains its structural compactness up to 45ºC before it unfolds. Steady-state fluorescence, circular dichroism and hydrophobic dye binding experiments cumulatively suggest that Ehis-AsnRS undergoes a two-state transition during unfolding. Shifting of the transition mid-point with increasing protein concentration further illustrate that dissociation and unfolding processes are coupled indicating the absence of any detectable folded monomer. Conclusion: This article indicates that GdnHCl induced denaturation of Ehis-AsnRS is a two – state process and does not involve any intermediate; unfolding occurs directly from native dimer to unfolded monomer. The solvent exposure of the tryptophan residues is biphasic, indicating selective quenching. Ehis-AsnRS also exhibits a structural as well as functional stability over a wide range of pH.

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