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PubMed2003

Biosorption of cadmium, copper, lead and zinc by inactive biomass of Pseudomonas Putida.

The accumulation of Cd(II), Cu(II), Pb(II) and Zn(II) at mg L(-1) concentration levels by inactive freeze-dried biomass of Pseudomonas Putida has been investigated. These metals could be efficiently removed from diluted aqueous solutions. A contact time of 10 min was sufficient to reach equilibrium. The pH has a strong effect on metal biosorption and the optimal pH values were 6.0, 5.0-6.0, 6.0-6.5 and 7.0-7.5 for Cd(II), Cu(II), Pb(II) and Zn(II) respectively. Under these conditions there was 80% removal for all metals studied. The process of biosorption can be described by a Langmuir-type adsorption model. This model accounts for 98% of the data variance. The K(A) and q(max) parameters for each metal are strongly correlated (at confidence levels greater than 98%) with the metal acidity, quantified by the constant of the corresponding M(OH)(+) complex, thus confirming previous assertions by other authors.

Adsorption↗

PubMed1985

Enzyme-linked immunosorbent assay for the detection of antibodies to bovine viral diarrhea virus in bovine sera.

A specific and sensitive enzyme-linked immunosorbent assay (ELISA) was established for the detection of antibodies to bovine viral diarrhea virus (BVDV) in bovine sera. Polyethylene-glycol concentrated, equilibrium density gradient purified BVDV was used as test antigen at an optimal amount of 1 microgram/well, whereas the optimal concentration of conjugate was at 1/2000 dilution. The standardized test encountered no non-specific reaction with test sera at a starting dilution of 1/10. A total of 50 bovine serum samples was assayed for the presence of antibodies against BVDV by ELISA and serum neutralization test (SNT). A positive correlation between the 2 tests was found. However, ELISA could be as much as 500-fold more sensitive than SNT in detecting low levels of BVDV antibodies.

Abortion, Veterinary↗

PubMed2006

Preparation of UDP-galacturonic acid using UDP-sugar pyrophosphorylase.

UDP-galacturonic acid, the activated form of galacturonic acid (GalUA), is synthesized both de novo and by salvage pathways. The UDP-GalUA pyrophosphorylase gene involved in the salvage pathway has not been identified. Here we show that UDP-sugar pyrophosphorylase from Pisum sativum with a broad specificity has UDP-GalUA pyrophosphorylase activity. The enzyme catalyzed the formation of UDP-GalUA and pyrophosphate from GalUA 1-phosphate and UTP with an equilibrium constant value of 0.24. The recombinant UDP-sugar pyrophosphorylase had optimal pH of 6.0, and the apparent K(m) values for GalUA 1-phosphate, UTP, UDP-GalUA, and pyrophosphate were 2.27, 1.15, 0.70, and 1.26 mM, respectively. In the presence of inorganic pyrophosphatase, the recombinant enzyme produced UDP-GalUA in an 84% yield (based on the GalUA 1-phosphate substrate) on a preparative scale. Thus, this UDP-sugar pyrophosphorylase is useful for the highly efficient production of UDP-GalUA for studies on pectin biosynthesis.

Catalysis↗

PubMed1978

Characterization of DNA binding protein from rat liver chromatin which decreases during growth.

A nuclear nonhistone protein which decreases in chromatin during growth (Yeoman, L. C., et al. (1975) Cancer Res. 35, 1249) has been isolated in high purity from the chromatin of normal rat liver nuclei by gel electrophoresis and column chromatography. This protein, designated BA (Yeoman, L.C., et al. (1973) Biochem Biophys. Res. Commun. 53, 1067), has a molecular weight of 31 000, an acidic to basic amino acid composition ratio of 0.9, and contains one tryptophan residue per molecule. Hydrazinolysis indicated protein BA has a lysine carboxyl terminus; however, the amino terminal is blocked as no reaction occurred with dansyl chloride. Maps of tryptic peptides of protein BA contained 46 spots. Protein BA binding to various DNAs was examined by the nitrocellulose filter assay. Binding was slightly enhanced by 2mM Mn2+ion; Mg2+, however, decreased binding. Binding was optimal at neutral pH and an ionic strength of 0.2 M [NaCl]. Equilibrium competition binding studies indicated a binding preference of protein BA for dA-dT rich DNA.

Aging↗

PubMed2000

Mutagenesis of E477 or K505 in the B' domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage.

A type II topoisomerase is essential for decatenating DNA replication products, and it accomplishes this task by passing one DNA duplex through a transient break in a second duplex. The B' domain of topoisomerase II contains three highly conserved motifs, EGDSA, PL(R/K)GK(I/L/M)LNVR, and IMTD(Q/A)DXD. We have investigated these motifs in topoisomerase II beta by mutagenesis, and report that they play a critical role in establishing the DNA cleavage-religation equilibrium. In addition, the mutations E477Q (EGDSA) and K505E (PLRGKILNVR) increase the optimal magnesium ion concentration for strand passage, without affecting the Mg(2+) dependence of ATP hydrolysis. It is likely that the binding affinity of the magnesium ion(s) specifically required for DNA cleavage has been reduced by these mutations. The crystal structure of yeast topo II indicates that residues E477 and K505 may help to position the three aspartate residues of the IMTD(Q/A)DXD motif for magnesium ion coordination, and we propose two possible locations for the magnesium ion binding site(s). These observations are consistent with a previous model in which the B' domain is positioned such that these acidic residues lie next to the active site tyrosine residue. A magnesium ion bound by these aspartate residues could therefore mediate the DNA cleavage-religation reaction.

Adenosine Triphosphate↗

PubMed2005

Exploring the Jahn-Teller and pseudo-Jahn-Teller conical intersections in the ethane radical cation.

We report a theoretical account on the static and dynamic aspects of the Jahn-Teller (JT) and pseudo-Jahn-Teller (PJT) interactions in the ground and first excited electronic states of the ethane radical cation. The findings are compared with the experimental photoionization spectrum of ethane. The present theoretical approach is based on a model diabatic Hamiltonian and with the parameters derived from ab initio calculations. The optimized geometry of ethane in its electronic ground state (1A1g) revealed an equilibrium staggered conformation belonging to the D3d symmetry point group. At the vertical configuration, the ethane radical cation belongs to this symmetry point group. The ground and low-lying electronic states of this radical cation are of 2Eg, 2A1g, 2Eu, and 2A2u symmetries. Elementary symmetry selection rule suggests that the degenerate electronic states of the radical cation are prone to the JT distortion when perturbed along the degenerate vibrational modes of eg symmetry. The 2A1g state is estimated to be approximately 0.345 eV above the 2Eg state and approximately 2.405 eV below the 2Eu state at the vertical configuration. The symmetry selection rule also suggests PJT crossings of the 2A1g and the 2Eg electronic states of the radical cation along the vibrational modes of eg symmetry and such crossings appear to be energetically favorable also. The irregular vibrational progressions, with numerous shoulders and small peaks, observed below 12.55 eV in the experimental recording are manifestations of the dynamic (E x e)-JT effect. Our findings revealed that the PJT activity of the degenerate vibrational modes is particularly strong in the 2Eg-2A1g electronic manifold which leads to a broad and diffuse structure of the observed photoelectron band.

Journal Article↗

PubMed2006

Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

Essential biological processes require that proteins bind to a set of specific DNA sites with tuned relative affinities. We focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of DNA elasticity on the rigid base pair level. Combining existing parametrizations of elastic potentials for DNA, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker for elastically optimized subsequences in protein-DNA co-crystals. We test our approach in an application to the bacteriophage 434 repressor. In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site. Elastic optimization involves all deformation modes and is mainly due to the adapted equilibrium structure of the operator, while sequence-dependent elasticity plays a minor role. These qualitative observations are robust with respect to current parametrization uncertainties. Predictions for relative affinities mediated by indirect readout depend sensitively on the chosen parametrization. Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures. The software written for the presented analysis is included as Supplementary Data.

Base Pairing↗

PubMed2003

Acid-base homeostasis with the high convective dialysis treatments.

The feedback between metabolic acid production and dialytic base gain ensures a neutral acid-base balance in patients on renal replacement therapy (RRT). Despite acid not accumulating continuously, clinical studies demonstrated that normalizing pre-dialysis serum bicarbonate results in nutritional and osteodystrophy improvements. Full correction of acidosis is not an easy task in dialysis patients because it depends on both some intrinsic characteristics of patients and dialysis prescriptions. Thus, a large variation in the result is often recorded among dialysis populations and in acid-base studies. Highly convective dialysis treatments make the individualization of dialytic parameters easier than conventional dialysis. Up to now, few clinical data have been published. However, knowledge of and the quantification of the kinetic phenomena that govern the buffer transfer during a session of these high performance treatments can provide a rational approach to the optimal dialysis prescription.

Acid-Base Equilibrium↗

PubMed2005

Logic backbone of a transcription network.

A great part of the effort in the study of coarse-grained models of transcription networks concentrates on their dynamical features. In this Letter, we consider their equilibrium properties, showing that the backbone underlying the dynamic descriptions is an optimization problem. It involves N variables, the gene expression levels, and M constraints, the effects of transcriptional regulation. In the case of Boolean variables and constraints, we investigate the structure of the solutions and derive phase diagrams. Notably, the model exhibits a connectivity transition between a regime of simple gene control, where the input genes control O(1) other genes, and a regime of complex control, where some core input genes control O(N) others.

Algorithms↗

PubMed1981

Purification and Characteristics of Sorbitol-6-phosphate Dehydrogenase from Loquat Leaves.

To study the role of sorbitol-6-phosphate dehydrogenase in sorbitol synthesis in leaves of Rosaceous plants, properties of the enzyme and its presence in several plants in the family was investigated. The activity of the enzyme, which catalyzes an NADP-dependent oxidation of the substrate to glucose-6-phosphate, was detected in leaves of Prunus mume, Prunus persica, Rhaphiolepsis indica, Sorbus aucuparia, Cydonia oblonga, Photinia glabra, Sorbaria kirilowii, and Spiraea thunbergii.The enzyme was purified about 60-fold from leaves of loquat (Eriobotrya japonica) using affinity chromatography with Blue Sepharose. Neither mannitol-1-phosphate nor fructose-6-phosphate served as substrate. Molecular weight of the enzyme was calculated to be 65,000 at pH 8.0 by gel filtration. Since sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a peptide of 33,000 daltons, the enzyme was assumed to be a dimer at pH 8.0 K(m) values for sorbitol-6-phosphate, glucose-6-phosphate, NADP, and NADPH were 2.22 millimolar, 11.6 millimolar, 13.5 micromolar, and 1.61 micromolar, respectively. Equilibrium constant for sorbitol-6-phosphate oxidation was 5.12 x 10(-10). Optimal pH for sorbitol-6-phosphate oxidation was 9.8. The enzyme showed its maximum activity within a broad pH range between 7 and 9 for glucose-6-phosphate reduction. The enzyme was more effective in the direction of glucose-6-phosphate reduction than in the reverse direction at neutral pH. Thus, it is suggested that the enzyme catalyzes sorbitol synthesis from glucose-6-phosphate during photosynthesis in leaves of Rosaceous plants.

Journal Article↗

PubMed1983

Characterization of the binding of DL-[3H]-2-amino-4-phosphonobutyrate to L-glutamate-sensitive sites on rat brain synaptic membranes.

The binding of DL-[3,4-3H] 2-amino-4-phosphonobutyric acid DL[3H]-APB to rat whole brain synaptic membranes was investigated. Binding was linear with membrane protein concentration, and optimal at physiological pH and temperature. The association rate was rapid, achieving equilibrium within 10 min. Prolonged incubations (greater than 20 min) revealed additional sites, which apparently possessed identical binding characteristics to those detected with 10 min incubations. Binding of DL-[3H]-APB was enriched in synaptic membrane fractions, and assessment of the regional distribution, indicated greatest binding in those areas with a rich glutamatergic innervation. The binding of DL-[3H]-APB in HEPES-KOH buffer exhibited an absolute requirement for Cl-. The addition of Ca2+ resulted in a further enhancement of binding. Saturation analysis revealed the presence of specific glutamate-sensitive DL-[3H]-APB binding sites, with a KD = 1.26 microM and Bmax = 12.08 pmol mg-1 protein. A Hill plot revealed a slope slightly greater than unity, which could possibly be a reflection of a contribution to binding of a further site which is relatively insensitive to glutamate. Analysis of 60 min incubation data indicated an approximately 3 fold increase in the capacity of the system, but a relatively unchanged KD. Examination of the pharmacological specificity of binding, showed that for both agonist and antagonist molecules, the L-enantiomers were invariably more active than the D-forms. For example, the L-(+)-2-amino-4-phosphonobutyrate isomer was 15 times more active than the D-(-)-form in inhibiting the binding of DL-[3H]-APB. This is in close agreement with the ability of these compounds to produce depression of synaptic transmission. The most potent inhibitor of binding was quisqualate. It is suggested that APB may interact with a quisqualate-preferring class of excitatory amino acid receptors, possibly localised predominantly on presynaptic terminals.

Aminobutyrates↗

PubMed1999

Purification and characterization of a novel 5-oxoprolinase (without ATP-hydrolyzing activity) from Alcaligenes faecalis N-38A.

A novel type of 5-oxoprolinase was found in a cell extract of strain N-38A, which was later identified as Alcaligenes faecalis. The enzyme in the cell extract was purified to a homogeneous state with a yield of 16.6%. The molecular weight of the purified enzyme was estimated to be 47,000 by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, suggesting that the enzyme is a monomeric protein. The enzyme specifically catalyzed a decyclization of L-pyroglutamate without hydrolyzing ATP and also without any requirements for metal ions such as Mg2+ and K+. The optimal pH for the decyclization was 7.4. The reaction was reversible. The equilibrium constant of the reaction, Keq = [L-glutamate]/[L-pyroglutamate], was evaluated to be approximately 0. 035, which indicates that the reaction tends to form L-pyroglutamate. The amino-terminal amino acid sequence of the enzyme was H-Glu-Pro-Arg-Leu-Asp-Thr-Ser-Gln-Leu-Tyr-Ala-Asp-Val-His-Phe-. No protein with a similar sequence was found in the DNASIS database. Based on these data, it was strongly suggested that the enzyme described here is a novel type of 5-oxoprolinase.

Journal Article↗

PubMed1990

Binding of [125I]iodipine to parathyroid cell membranes: evidence of a dihydropyridine-sensitive calcium channel.

The parathyroid cell is unusual, in that an increase in extracellular calcium concentrations inhibits PTH release. Calcium channels are glycoproteins that span cell membranes and allow entry of extracellular calcium into cells. We have demonstrated that the calcium channel agonist (+)202-791, which opens calcium channels, inhibits PTH release and that the antagonist (-)202-791, which closes calcium channels, stimulates PTH release. To identify the calcium channels responsible for these effects, we used a radioligand that specifically binds to calcium channels. Bovine parathyroid cell membranes were prepared and incubated under reduced lighting with [125I] iodipine (SA, 2000 Ci/mmol), which recognizes 1,4-dihydropyridine-sensitive calcium channels. Bound ligand was separated from free ligand by rapid filtration through Whatman GF/B filters. Nonspecific binding was measured by the inclusion of nifedipine at 10 microM. Specific binding represented approximately 40% of the total binding. The optimal temperature for [125I] iodipine binding was 4 C, and binding reached equilibrium by 30 min. The equilibrium dissociation constant (Kd) was approximately 550 pM, and the maximum number of binding sites was 780 fmol/mg protein. Both the calcium channel agonist (+)202-791 and antagonist (-)202-791 competitively inhibited [125I] iodipine binding, with 50% inhibition concentrations of 20 and 300 nM, respectively. These data indicate the presence of dihydropyridine-sensitive calcium channels on parathyroid cell membranes.

Animals↗

PubMed2006

In vitro assessment of plasma protein binding of 20(R)-ginsenoside Rh2 by equilibrium dialysis and LC-MS analysis: a case of species differences.

20(R)-Ginsenoside Rh2 is isolated from Chinese traditional ginsengs with main antitumor effects. To support its pharmacokinetic study which was essential for the pre-clinical research for new drug development, in this paper, 20(R)-Rh2 plasma protein binding was assessed in vitro at four concentration levels (50, 100, 200, 400 ng/ml) both in rat and human plasma using equilibrium dialysis and followed by LC-MS analysis. The method was optimized against some influencing factors during both experimental procedures. And it was validated to be specific, sensitive, accurate, precise and of satisfactory recovery. The results showed the binding fractions were about 70% for rats and 27% for human within four concentration levels. It exhibited a significant species difference between human and rats for the plasma protein binding of 20(R)-Rh2.

Animals↗

PubMed1993

Characterization and subtype identification of the Na(+)-H+ exchanger in bovine corneal epithelium.

Amiloride analogues with N5-alkyl substitutions are specific high-affinity ligands for the Na(+)-H+ exchanger in various tissues. As a means to characterize the Na(+)-H+ exchanger in the bovine corneal epithelium, we determined the binding properties of [3H] methylisobutylamiloride (MIA) to a fraction enriched in plasma membrane from this tissue. [3H]MIA bound to these membranes in a time, -a temperature-, and -a pH-dependent manner. The binding was optimal at 4 degrees C and at pH 8.5 and it reached equilibrium at 60 min. Under these conditions, specific binding, which was inhibitable by excess unlabeled MIA, was about 85%. Scatchard analysis of this specific binding revealed a single saturable binding component with a Kd of 61 nM and a Bmax of 271 pmoles/mg protein. Inhibition of [3H]MIA specific binding by amiloride analogues showed the following order of potency: MIA > dimethylamiloride (DMA) > benzamil > amiloride. Na+ did not compete with MIA for binding. The effectiveness of clonidine, an alpha 2 agonist, and cimetidine, an H2 receptor antagonist, as inhibitors of Na(+)-H+ exchange activity was also determined because these compounds are used to distinguish between the exchanger subtypes. At concentrations higher than those needed for receptor interaction, clonidine was more effective than cimetidine in decreasing MIA binding. The activity of Na(+)-H+ exchanger, which was measured as the uptake of 22Na+ in the presence of an outwardly directly H+ gradient, was also inhibited by DMA, benzamil and amiloride with the same order of potency as obtained in the binding studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Amiloride↗

PubMed2000

Fundamental cryobiology of rat immature and mature oocytes: hydraulic conductivity in the presence of Me(2)SO, Me(2)SO permeability, and their activation energies.

The hydraulic conductivity in the presence of dimethyl sulfoxide Me(2)SO (L(p)(Me(2)SO)), Me(2)SO (P(Me(2)SO)) permeability and reflection coefficient (sigma) of immature (germinal vesicle; GV) and mature (metaphase II; MII) rat oocytes were determined at various temperatures. A temperature controlled micropipette perfusion technique was used to conduct experiments at five different temperatures (30, 20, 10, 4, and -3 degrees C). Kedem and Katchalsky membrane transport theory was used to describe the cell volume kinetics. The cell volumetric changes of oocytes were calculated from the measurement of two oocyte diameters, assuming a spherical shape. The activation energies (E(a)) of L(p)(Me(2)SO) and P(Me(2)SO) were calculated using the Arrhenius equation. Activation energies of L(p)(Me(2)SO) for GV and MII oocytes were 34.30 Kcal/mol and 16.29 Kcal/mol, respectively; while the corresponding E(a)s of P(Me(2)SO) were 19.87 Kcal/mol and 21.85 Kcal/mol, respectively. These permeability parameters were then used to calculate cell water loss in rat oocytes during cooling at subzero temperatures. Based on these values, the predicted optimal cooling rate required to maintain extra- and intracellular water in near equilibrium for rat GV stage oocytes was found to be between 0.05 degrees C/min and 0. 025; while for rat MII oocytes, the corresponding cooling rate was 1 degrees C/min. These data suggest that standard cooling rates used for mouse oocytes (e.g., 0.5-1 degrees C/min) can also be employed to cryopreserve rat MII oocytes. However, the corresponding cooling rate required to avoid damage must be significantly slower for the GV stage rat oocyte. J. Exp. Zool. 286:523-533, 2000.

Animals↗

PubMed1992

[Model of therapeutic programming in NIDDM diabetes].

The usual choice of therapy in NIDDM diabetes, using oral anti-diabetic compounds, insulin or associated treatments, is based on the results of treatment evaluated empirically using glycemic profiles. As a contribution to the search for a method of choosing a treatment which is based on laboratory data and can restore metabolic equilibrium as quickly as possible using the most efficacious drug at an optimal dose, the paper reports a method of assessing the severity of diabetes according to mean daily glucose concentrations, the degree of instability in relation to the standard deviation, and proposes a sensitivity test to SU which indicates the choice of therapy, together with an insulin sensitivity test which is useful for evaluated the optimal dose. Sensitivity to SU evaluated using this method is not dependent on the degree of severity of diabetes. With regard to its practical use for prescribing treatment the test is highly predictive in positive cases since it is extremely sensitive, while its low specificity does not rule out its use in cases of resistance. The analysis of the results obtained after treatment which was not indicated by the sensitivity tests but based on personal experience and the comparison of the two methods shows that a high percentage of patients received inadequate therapy either due to the prescription of the wrong type of treatment or an incorrect dosage.

Blood Glucose↗

PubMed2005

[Adsorption behavior of cadmium in phaeozem and burozem].

The study on the thermodynamics and kinetics of Cd2+ adsorption in phaeozem and burozem showed that within the test range, Cd2+ adsorption was increased with its increasing initial concentration, and phaeozem had a much higher Cd2+ adsorption capacity than burozem. When the Cd2+ concentration in adsorption equilibrium was 20 mg x kg(-1), the amount of adsorbed Cd2+ was 1 485.2 mg x kg(-1) in phaeozem, but 700.6 mg x kg(-1) in burozem. The adsorption isotherm of Cd2+ in the two soils could significantly conform to Langmuir, Freundlich and Henry equations, while Temkin equation was not applicable to describe the isothermal adsorption process of Cd2+ in phaeozem and burozem. The maximum adsorption of Cd2+ in phaeozem and burozem was 5939.3 and 2 790 mg x kg(-1), respectively, according to Langmuir formulation. The Cd2+ adsorption in test soils was a rapid reaction, with 90% of Cd2+ adsorption in the first 2 min and reached equilibrium in 15-30 min. First-order dynamic equation was the optimal model to describe the kinetics of Cd2+ adsorption, while the other models in point were Elovich and Two-constant equations. The adsorption rate of Cd2+ in test soils was increased with its increasing initial concentration, but decreased with its increasing adsorbed amount. Under low concentrations of Cd2+, the decrease of its adsorption rate with time was more quickly in phaeozem than in burozem.

Adsorption↗