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PubMed2006

Identifying fitness and optimal life-history strategies for an asexual filamentous fungus.

Filamentous fungi are ubiquitous and ecologically important organisms with rich and varied life histories, however, there is no consensus on how to identify or measure their fitness. In the first part of this study we adapt a general epidemiological model to identify the appropriate fitness metric for a saprophytic filamentous fungus. We find that fungal fitness is inversely proportional to the equilibrium density of uncolonized fungal resource patches which, in turn, is a function of the expected spore production of a fungus. In the second part of this study we use a simple life history model of the same fungus within a resource patch to show that a bang-bang resource allocation strategy maximizes the expected spore production, a critical fitness component. Unlike bang-bang strategies identified in other life-history studies, we find that the optimal allocation strategy for saprophytes does not entail the use of all of the resources within a patch.

Biological Evolution↗
PubMed1995

The influence of pH on surface properties of lung surfactants.

Protein-lipid interactions at air-liquid interfaces are dependent on electrostatic charges, cations, anions, distribution of protons, and surface potential, which are influenced by pH changes. All of these factors may affect lung surfactant function. To verify the pH dependence of surface activity of pulmonary surfactant, we studied the in vitro effects of pH and Ca2+ on the surface tension-lowering abilities of various surfactants in an oscillating bubble surfactometer. Surface tension measurements were made of mixtures at known pHs or after the replacement of the subphase fluid of surfactant films with buffered saline at various pH values. At the pH range 4.0-7.0, the average equilibrium surface tension (EST)/minimum surface tension (MST) for natural surfactants human amniotic fluid and natural lung surfactant from rabbit lung lavage was 24/2 mN/m. At the same pH range, Exosurf and phospholipids alone had an EST/MST of 44/25 and 44/12 mN/m, respectively. Survanta (SUR) containing SP-B and SP-C and a phospholipid surfactant (KL4) containing a leucine/lysine peptide had an EST/MST of 29/5 and 36/3, respectively. Alkalinization of the subphase (pH > 7.4) significantly decreased the surface tension-lowering ability of SUR (P < 0.01) and to a lesser extent that of KL4 surfactant (P < 0.05), but natural lung surfactants were not significantly affected over a pH range of 3-7.5. These data demonstrate that natural surfactants maintain their optimal surface activities over a broader pH range than do the commercial products because of a lack of SP-A. Careful monitoring of the pH for optimal surface activity is recommended when evaluating surfactant function and the effects of specific inhibitors on this function.

Acid-Base Equilibrium↗
PubMed2005

Chondrogenic differentiation and functional maturation of bovine mesenchymal stem cells in long-term agarose culture.

BACKGROUND: The developmental history of the chondrocyte results in a cell whose biosynthetic activities are optimized to maintain the concentration and organization of a mechanically functional cartilaginous extracellular matrix. While useful for cartilage tissue engineering studies, the limited supply of healthy autologous chondrocytes may preclude their clinical use. Consequently, multipotential mesenchymal stem cells (MSCs) have been proposed as an alternative cell source. OBJECTIVE: While MSCs undergo chondrogenesis, few studies have assessed the mechanical integrity of their forming matrix. Furthermore, efficiency of matrix formation must be determined in comparison to healthy chondrocytes from the same donor. Given the scarcity of healthy human tissue, this study determined the feasibility of isolating bovine chondrocytes and MSCs, and examined their long-term maturation in three-dimensional agarose culture. EXPERIMENTAL DESIGN: Bovine MSCs were seeded in agarose and induced to undergo chondrogenesis. Mechanical and biochemical properties of MSC-laden constructs were monitored over a 10-week period and compared to those of chondrocytes derived from the same group of animals maintained similarly. RESULTS: Our results show that while chondrogenesis does occur in MSC-laden hydrogels, the amount of the forming matrix and measures of its mechanical properties are lower than that produced by chondrocytes under the same conditions. Furthermore, some important properties, particularly glycosaminoglycan content and equilibrium modulus, plateau with time in MSC-laden constructs, suggesting that diminished capacity is not the result of delayed differentiation. CONCLUSIONS: These findings suggest that while MSCs do generate constructs with substantial cartilaginous properties, further optimization must be done to achieve levels similar to those produced by chondrocytes.

Animals↗
PubMed2001

Comparison of diffusive gradients in thin films and equilibrium dialysis for the determination of Al, Fe(III) and Zn complexed with dissolved organic matter.

The distinction between 'free' metals and organically complexed metals in aqueous solutions is important for research involving the mobility or bioavailability of metals in the environment. In this study, the applicability of equilibrium dialysis (molecular weight cut-off = 1000 Da) and diffusive gradients in thin films (DGT) to determine 'free' Al, Fe(III) and Zn in four forest soil solutions was compared. The 'free' metals as measured by both methods, consist of hydrated metal cations and soluble inorganic metal complexes. In addition, dialysis measures any organic complexes < 1000 Da and DGT measures a portion of smaller labile organic complexes. The four soil solutions were prepared by water extraction of an organic soil horizon (H) from a Fimic Anthrosol, and contained either 20 or 75 mg C/l dissolved organic matter at pH 4.0 and pH 7.0. To test the performance of both methods and optimize experimental volume and time, experiments using metal nitrate solutions were carried out. In the solutions at pH 4.0, no significant differences in average 'free' metal contents were found for Al, Fe(III) or Zn. This makes DGT a viable alternative for equilibrium dialysis for the study of the complexation of all three metals in acidic soils. At pH 7.0, again no significant difference between both methods were found for Al and Fe(III), but the DGT results for Zn were significantly higher. This was likely caused by labile organic complexes that were only detected by DGT.

Aluminum↗
PubMed1980

Influence of the position of the double bond in steroid substrates on the efficiency of the proton-transfer reaction by Pseudomonas testosteroni 3-oxo-steroid delta 4-delta 5-isomerase.

Studies of the proton-transfer reaction by Pseudomonas testosteroni 3-oxo steroid Delta(4)-Delta(5)-isomerase with Delta(5(6))- and Delta(5(10))-steroid substrates demonstrate the importance of the position of the double bond for the efficiency of the isomerization process. Thus 3-oxo-Delta(5(6))-substrates have markedly high k(cat.) values, whereas those of 3-oxo-Delta(5(10))-substrates are very low and their apparent K(m) values approach equilibrium dissociation constants. The first step in the isomerization process is: [Formula: see text] which is governed by the k(-1)/k(+1) ratio and is shown to be very similar for the two classes of substrates (3-oxo-Delta(5(6))- and -Delta(5(10))-steroids). They therefore differ in the steps distal to the initial formation of the Michaelis-Menten complex. The use of the deuterated androst-5(6)-ene-3,17-dione substrate enabled us to calculate individual rate constants k(+1) and k(-1) as well as to determine the apparent rate-limiting step in the isomerization process. With the deuterated oestr-5(10)-ene-3,17-dione substrate, no significant isotope effect was observed suggesting that a different rate-limiting step may be operative in this isomerization process. Data are presented that indicate that under optimal concentrations of the efficient androst-5(6)-ene-3,17-dione substrate, the forward reaction for ES complex formation (as defined by k(+1)) is limited only by diffusion and the apparent K(m) does not approach the equilibrium constant, suggesting that the evolution of this enzyme has proceeded close to ;catalytic perfection'.

Androstenedione↗
PubMed1989

Histochemical demonstration of primary amino groups with 2-hydroxy-1-naphthaldehyde (HNA): optimization of the method.

2-hydroxy-1-naphthaldehyde (HNA) was used for the histochemical demonstration of primary amino groups. The Schiff-bases formed exhibited a double-banded maximum absorption at lambda = 420 nm and lambda = 400 nm, respectively. The dependence of the equilibrium of the Schiff-base formation upon the concentration of HNA, the reaction medium, especially upon its pH-value, was investigated with Ehrlich ascites tumour cells and rat liver parenchymal cells. Optimum conditions were elaborated for the histochemical reaction running either in absolute ethanol (HNA-EtOH) or in a mixture of ethanol and acetate buffer pH = 4 (HNA-pH4), the equilibrium of the reactions adjusted after 10 d and 1 d, respectively. The HNA-pH4-method can be used for the histochemical demonstration of primary alpha-, delta-, and epsilon-amino groups of proteins. The HNA-EtOH-method comprises primary amino groups of proteins and of other substances insoluble in absolute ethanol. Both histochemical methods proved to be reproducible.

Amines↗
PubMed1989

Site-specific mutation of Tyr240----Phe in the catalytic chain of Escherichia coli aspartate transcarbamylase. Consequences for kinetic mechanism.

In the catalytic chain of Escherichia coli aspartate transcarbamylase, Tyr240 helps stabilize the T-state conformation by an intrachain hydrogen bond to Asp271. Changes in kinetic characteristics of ATCase that result from disruption of this bond by site-specific mutation of Tyr240----Phe have been investigated by isotopic exchanges at chemical equilibrium. The Tyr240----Phe (Y240F) mutation caused the rate of the [32P] carbamyl phosphate (C-P) in equilibrium Pi exchange to decrease by 2-8-fold, without altering the [14C]Asp in equilibrium N-carbamyl-L-aspartate (C-Asp) rate. The mutation also caused the S0.5 and Hill nH values to decrease in virtually every substrate saturation experiment. Upon increasing the concentrations of the C-P,Pi or C-P,C-Asp reactant-product pairs, inhibition effects observed with the C-P in equilibrium Pi exchange for wild-type enzyme were not apparent with the Y240F mutant enzyme. In contrast, upon increasing the concentrations of the Asp,C-Asp and Asp,Pi pairs, inhibition effects on C-P in equilibrium Pi observed with wild-type enzyme became stronger with the Y240F mutant enzyme. These data indicate that the Tyr240----Phe mutation alters the kinetic mechanism in two different ways: on the reactant side, C-P binding prior to Asp shifts from preferred to compulsory order, and, on the product side, C-Asp and Pi release changes from preferred to nearly random order. These conclusions were also confirmed on a quantitative basis by computer simulations and fitting of the data, which also produced an optimal set of rate constants for the Y240F enzyme. The Arrhenius plot for wild-type holoenzyme was biphasic, but those for catalytic subunits and Y240F enzyme were linear (monophasic). Taken together, the data indicate that the Tyr240----Phe mutation destabilizes the T-state and shifts the equilibrium for the T-R allosteric transition toward the R-state by increasing the rate of T----R conversion.

Aspartate Carbamoyltransferase↗
PubMed1989

The specificity of interaction between S-adenosyl-L-methionine and a nucleolar 2'-O-methyltransferase.

The structural features of S-adenosyl-L-methionine (SAM)3 required for optimal binding to a nucleolar 2'-O-methyltransferase were elucidated using various analogs of SAM with modifications of the amino acid, sugar, sulfonium center, and base portions of the molecule. Equilibrium binding constants for SAM and each analog were determined by a nitrocellulose filter binding assay. To ensure the chiral and chemical purity of the 3H-labeled SAM used in the binding experiments, a cation-exchange HPLC procedure was developed to separate degradation products of SAM such as adenine and 5'-deoxy-5'-methylthioadenosine, as well as to separate the (S,S)-SAM from the biologically inactive (R,S)-SAM stereoisomer. Results from these studies demonstrated that S-adenosyl-L-homocysteine, a product of the methyltransferase reaction, bound equally as well as (S,S)-SAM, indicating that neither the charge nor the methyl group at the sulfonium center of (S,S)-SAM is essential for maximal binding. Other modifications of the sulfonium center demonstrated that a sulfur to carbon atom replacement had little effect on binding affinity, whereas substituting an ethyl group for the methyl group greatly reduced the binding affinity. In addition, the chirality at the sulfonium center was important. The naturally occurring S-chiral form had a 10-fold higher binding affinity than the R-chiral form. No significant stereospecificity was observed relative to the chiral alpha-carbon of the methionine moiety in SAM. The alpha-amino group of methionine and the 6-amino group of adenine were both required for maximal binding, while the loss of the 2'-hydroxyl group on the ribose moiety was not. Taken together, these results defined some of the specific geometric and functional group requirements which affect the specificity of interaction between S-adenosyl-L-methionine and the nucleolar 2'-O-methyltransferase.

Animals↗
PubMed1977

The effect of palmitoyl-coenzyme A on rat heart and liver mitochondria. Oxygen consumption and palmitoylcarnitine formation.

Rat heart and liver mitochondria, respectively, oxidized palmitoyl-CoA and palmitoylcarnitine optimally at 20-30 and 10-20 nmol substrate/mg. The oxidation of palmitoyl-CoA was accompanied by a lag in State 3 respiration that was proportional to the palmitoyl-CoA concentration. The delay in State 3 rates was more prolonged in liver than in heart at comparable palmitoyl-CoA levels. A similar range of palmitoyl-CoA concentrations produced significant inhibition of respiration in mitochondria oxidizing glutamate-malate. The inhibition was not due to a detergent effect of palmitoyl-CoA since addition of carnitine restored State 3 rates. Electron microscopic examination of mitochondria at low palmitoyl-CoA levels revealed normal ultrastructure. At comparable concentrations of palmitoyl-CoA, formation of palmitoylcarnitine by mitochondria from rat heart and liver followed first-order kinetics. The apparent first-order rate constants decreased with increasing palmitoyl-CoA. These results suggest that substrate inhibition may influence the rate of palmitoyl carnitine formation even at physiological concentrations of palmitoyl-CoA. The apparent first-order rate constant at palmitoyl-CoA levels (12 nmol palmitoyl CoA/mg) optimally oxidized by liver mitochondria, was one-third the value of the apparent rate constant measured in heart mitochondria at the identical substrate level. The prolongation in time to reach equilibrium may acocunt for the relatively greater respiratory sensitivity of liver mitochondria to increasing levels of palmitoyl-CoA.

Animals↗
PubMed1994

Quantitative analysis of cytosolic free calcium oscillations in neutrophils by mathematical modelling.

Mathematical models are often used to elucidate mechanisms behind cytosolic Ca2+ oscillations. We have evaluated the use of mathematical modelling to analyse and quantify Ca2+ signal patterns, in single, adherent human neutrophils (PMN) after stimulation by the bacterial peptide N-formyl-methionyl-leucyl-phenylalanine (fMLP). The cells were loaded with Fura-2 and fluctuations in cytosolic Ca2+ recorded with a video based digital imaging system. A new indirect intracellular calibration method was introduced to avoid the uncertainty in obtaining an equilibrium between the extracellular and intracellular calcium concentrations. Two different approaches to mathematical modelling were used. First, we applied a sensitivity analysis with a two-pool model by assuming an optimal situation using reliable a priori estimates of all structural parameters (e.g. Hill coefficients and dissociation constants). We found that the a priori estimates of the other 5 more variable parameters must lie within the range of 25-400% of the postulated true parameter values to be reliable in a parameter estimation method. Small changes (less than 5%) in those variable parameter values induced very different types of signal patterns which may have some relevance in evaluating a possible functional significance to the oscillatory signals. Second, we employed a one-pool, non oscillatory model integrated with a power spectrum method as a tool to quantify the dose dependency between fMLP (1-1000 nM) and parameters describing the biphasic process of calcium signalling and parameters describing only the oscillatory components. We conclude that the frequency of the observed oscillations assembled around one characteristic frequency independent of fMLP concentration, and sinusoidal oscillations were observed most frequently in PMN stimulated to a moderate peak [Ca2+]i level.

Biological Assay↗
PubMed2003

Mass transfer effects in preparative chromatography of eremomycin on polymeric sorbents.

This work is devoted to the study of the regularities of the sorption of the new antibacterial antibiotic eremomycin on carboxylic sorbents. The main sorption kinetic equilibrium and dynamic parameters for realization of one-act preparative chromatographic process were determined and the difference between gel-like and structurally segregated carboxylic cation exchangers was analyzed. The optimal conditions for sorption and complete desorption of eremomycin were found.

Adsorption↗
PubMed2002

Modeling for point-non-point source effluent trading: perspective of non-point sources regulation in China.

In the past decades, little abatement efforts have been implemented on China's non-point source water pollution, and studies aiming at non-point sources regulation were also rare. Watershed abatement trading between point and non-point sources may serve as a cost-effective way to deal with the problem. The inherent uncertainty of non-point emissions, however, could affect the feasibility and outcome of point-non-point effluent trading. The purpose of this paper is to model the watershed point-non-point abatement trading incorporating the uncertainty of non-point source emissions, and to examine its impacts on trading equilibrium and trading ratio. The uncertainties of non-point emissions were taken into consideration by setting an acceptable probability by which the watershed emission constraints were achieved. Using the watershed optimization model, the optimal abatement allocation and trading ratio were explicitly illustrated. It was found that they were affected significantly by the variances of non-point emissions, the reliability requirement assigned to the non-point abatement, and the marginal abatement costs of point and non-point sources. Since the variances of non-point emissions may increase or decrease at the abatement level, the impacts of these factors were discussed in different circumstances. Based on the illumination of the trading model, future directions and implications of point-non-point trading in China were discussed.

Journal Article↗
PubMed1982

Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable.

The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.

Animals↗
PubMed2005

Thorium complexation by hydroxamate siderophores in perturbed multicomponent systems using flow injection electrospray ionization mass spectrometry.

Flow injection electrospray ionization mass spectrometry has been shown to produce simple, characteristic m/z signals for Th-hydroxamate siderophore (desferrioxamine and ferrichrome) complexes, with Th complexed as a simple 4+ ion in the environmentally relevant pH range investigated (pH 5-9). All species of interest for this study were identified optimally in the positive mode; thus, multiple species were analyzed concurrently in a single spectrum. Complexation of Th by the two siderophores was rapid in 1:1 molar aqueous solution, reaching equilibrium before the first measurement was possible at 2 min. However, a significant proportion of the equimolar siderophore remained uncomplexed. Both siderophores rapidly exchanged Th for Fe when equimolar Fe(III) was added to the Th complexes, and only a small proportion of each siderophore remained complexed with Th at equilibrium (7-30 min). The results show a difference in the affinities of the two siderophores for the metals; ferrichrome has a 5-fold higher affinity than desferrioxamine for Th and a 5-fold lower affinity than desferrioxamine for Fe. Also, siderophore-complexed Th interacted strongly with a cation-exchange resin suggesting that, even when complexed by trianionic siderophores, Th mobility will be impeded by interactions with negatively charged binding sites in subsurface environmental matrixes. These results have important implications regarding siderophore-enhanced actinide(IV) mobility in the terrestrial environment.

Calibration↗
PubMed2003

Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory.

We show that the ab initio CASPT2//CASSCF strategy previously used to investigate the ground and excited states of the chromophore of the vision receptor rhodopsin (Rh) in vacuo can be successfully implemented in a QM/MM scheme allowing for CASPT2//CASSCF/AMBER geometry optimization and excited state property evaluation in proteins. Two receptor models (Rh-1 and Rh-2) incorporating different reduced chromophores are investigated. It is shown that Rh-2 features a chromophore equilibrium structure with the correct helicity and a lambdamax that is only 52 nm blue-shifted from the observed value. This result should open the way to a qualitatively correct ab initio QM/MM modeling of the early excited state transient species involved in the vision process.

Imidazoles↗
PubMed2006

Effect of model potential of adsorptive bond on the thermodynamic properties of adsorbed CO molecules on Ni(111) surface.

The effect of anharmonicity on the adsorption of CO molecules on the Ni(111) surface has been investigated. The DFT calculations are used to obtain the effective adsorption potential of the CO molecule on the Ni(111) surface. First, using an appropriate slab model, the geometry of adsorption system corresponding to hcp, fcc, bridge, and on-top sites with p(2 x 2) arrangement and coverage of 0.25 ML is optimized by the DFT calculations using a plane wave basis set and ultrasoft pseudopotentials; this gives the hcp site as the most stable site with De = 185 kJ/mol, for which the equilibrium distance of CO from the surface and C-O bond length on the surface are found to be 1.31 and 1.192 A, respectively. Then, the potential function of adsorption versus adsorptive bond distance was plotted, which is significantly different from that of a harmonic oscillator, i.e., the anharmonicity for the adsorptive bond is significant. Also the harmonic and anharmonic shifts of vibrational frequencies of adsorptive and C-O bonds are calculated to be -22.6 and 7.8 cm(-1), respectively. Hence, two potential models are selected for which their Schrödinger equations are solved analytically, namely the hard repulsion-soft attraction (HS) and Morse potential (MP) models. The adsorption isotherms, internal energy, isochoric heat capacity, and entropy of adsorbed CO molecules have been calculated for the mentioned model potentials and compared with those of the harmonic oscillator (H). As a result, the adsorption isotherms are not considerably sensitive to the model potential. The anharmonicity of CO-Ni bond, which is included in HS and MP models, gives an average deviation in pressure as much as 1.4% for HS and 5.8% for MP, compared to 6.1% for the H model. However, isochoric heat capacity and entropy depend on the model potential significantly, and the differences may be as high as 69% and 55% for isochoric heat capacity and entropy, respectively.

Journal Article↗
PubMed1977

Complex formation between ribosomal protein S1, oligo-and polynucleotides: chain length dependence and base specificity.

In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The complex formation is Mg2+ dependent at low salt concentrations and becomes Mg2+ independent at an ionic strength greater than 90 mM. Oligouridylates of increasing chain length reach an optimal KA of 3-3-10(7) M-1 at a chain length of n=13-14. Protein S1 contains one binding site for long chain oligouridylates, such as U12, and the standard-free-energy change on binding caused by one Pu increment is 0.41 kcal/mol, when n varies between five and fourteen. Complex formation is insensitive to the capacity of the homopolynucleotide bases to form hydrogen bonds. Homopolynuceotides, however, showing a Tm less than 250 in the buffer system used show an increased affinity for S1 compared to poly(A) and poly(C) (Tm greater than 40 degrees). The data are discussed with respect to the proposed binding of protein S1 to the 3-terminal end of the 16S RNA.

Chemical Phenomena↗
PubMed2002

High-beta equilibria of drift-optimized compact stellarators.

Compact stellarator configurations have been obtained with good neoclassical confinement that are stable to both pressure- and current-driven modes for high values of beta. These configurations are drift-optimized tokamak-stellarator hybrids with a high-shear tokamak-like rotational transform profile and /B/ that is approximately poloidally symmetric. The bootstrap current is consistent with the required equilibrium current and, while larger than that in existing stellarators, is typically only a small fraction (1/3-1/5) of that in an equivalent tokamak. These configurations have strong magnetic wells and consequently high interchange stability beta limits up to beta=23%. Because of the reduced bootstrap current, these configurations are stable to low-n ideal MHD kink modes with no wall stabilization for values of beta ( approximately 7%-11%) significantly larger than in an equivalent advanced tokamak.

Journal Article↗