Polyanion-mediated mineralization — a kinetic analysis of the calcium-carrier hypothesis in the phytoflagellatePleurochrysis carterae

Summary Polyanions are postulated intermediates in biomineralization because they sequester large numbers of calcium ions and occur in high concentrations at mineralizing foci in distantly related organisms. In this study mineral ion and polyanion metabolism was examined inPleurochrysis carterae to determine whether polyanions function as intermediate calcium-carriers during coccolith (mineralized scale) formation. In this organism mineralization occurs intracellularly in coccolith-forming saccules, and mature coccoliths are extruded through the plasma membrane into the coccosphere. The polyanions (acidic polysaccharides known as PS-1 and PS-2) are synthesized in medial Golgi cisternae and transported to the coccolith-forming saccule prior to the onset of mineral deposition; they also cover the mineral surface of mature coccoliths. Pulse-chase experiments with⁴⁵Ca²⁺ and¹⁴CO₃ ^– show the calcium uptake into the coccolith-forming saccule is much slower than carbonate uptake. The extended intracellular half-life of calcium ions destined for the coccosphere suggests that calcium is initially sequestered in more distal Golgi elements (perhaps in association with the polyanions) and enters the coccolith-forming saccule only after passage through the endomembrane system. This is consistent with previous cytochemical studies showing that the polyanions are complexed with calcium prior to mineral deposition. It has been suggested that polyanions may be degraded at the mineralization front in order to free calcium ions for precipitation with available carbonate or phosphate ions. However, this study demonstrates that the polyanions are not degraded; essentially all PS-1 and PS-2 are eventually secreted with the mineral phase into the coccosphere. The kinetics of mineral ion and polyanion secretion are consistent with a polyanion-mediated calcium transport; however, the manner in which calcium might be sequestered by and freed from the polyanions is still obscure.Abbreviations PS-1/2/3 polysaccharide 1/2/3 - EDTA ethylenediaminetetraacetic acid - TCA trichloroacetic acid     

Stability and amino acid preferences of type VIII reverse turn: the most common turn in peptides?

Free energies of the alpha(r)beta and betabeta conformations of 14 tetrapeptides, based on the sequence SALN and protein X-ray structures, were calculated using molecular dynamics simulations and MM-PBSA calculations. The alphaalpha conformations of five of the tetrapeptides were also studied. SALN has been earlier shown by molecular dynamics simulations and NMR spectroscopy to have a tendency to form an alpha(r)beta turn. The gas-phase energy of the molecular mechanical force field (CHARMM), the electrostatic and non-polar solvation free energies and solute entropies were used to explain the free energy differences of the alphaalpha, betabeta and alpha(r)beta conformations of the peptides. The alpha(r)beta conformation of SALN and SATN was predicted to be slightly more stable than the extended conformation (betabeta), in agreement with experimental results. The SALN mutants SAIN, SAVN, SATN, SSIN and MSHV, were also predicted to be potential alpha(r)beta turn-forming peptides. We report also revised positional potentials for the type VIII turn, based on a non-homologous set of protein structures. This protein databank analysis confirms the main results of the earlier analyses and reveals several new amino acid residues with a significant positional preference. The results of this work led us to suggest that the alpha(r)beta turn may be the most common turn type in peptides. Such turns may be readily formed in aqueous solution and thereby play important roles in the protein folding process by serving as an initiation point for structure formation.     

The comparative kinetic analysis of Acetocell and Lignoboost® lignin pyrolysis: the estimation of the distributed reactivity models

The non-isothermal pyrolysis kinetics of Acetocell (the organosolv) and Lignoboost? (kraft) lignins, in an inert atmosphere, have been studied by thermogravimetric analysis. Using isoconversional analysis, it was concluded that the apparent activation energy for all lignins strongly depends on conversion, showing that the pyrolysis of lignins is not a single chemical process. It was identified that the pyrolysis process of Acetocell and Lignoboost? lignin takes place over three reaction steps, which was confirmed by appearance of the corresponding isokinetic relationships (IKR). It was found that major pyrolysis stage of both lignins is characterized by stilbene pyrolysis reactions, which were subsequently followed by decomposition reactions of products derived from the stilbene pyrolytic process. It was concluded that non-isothermal pyrolysis of Acetocell and Lignoboost? lignins can be best described by n-th (n>1) reaction order kinetics, using the Weibull mixture model (as distributed reactivity model) with alternating shape parameters.     

Notch and NF-κB signaling pathways in the biology of classical Hodgkin lymphoma

Classical Hodgkin lymphoma (cHL) is now recognized as a B-cell-derived lymphoma which is characterized by only about 1% malignant pathognomonic Hodgkin and Reed-Sternberg (HRS) cells and an abundant infiltrate of reactive bystander cells. HRS cells are unique with respect to their lost B-cell-specific gene expression pattern and recurrent genetic lesions. Aberrant activity of Notch signaling, a highly conserved developmental pathway, acts as a negative regulator of the B cell program in HRS cells and thereby contributes to their reprogramming. Another striking feature and the major pathogenetic mechanism in HRS cells is constitutive NF-κB activation. A number of aberrations that contribute to canonical NF-κB activity in HRS cells have been described such as genetic lesions, deregulated receptor signaling and Epstein-Barr virus (EBV) infection. The importance of Notch and NF-κB signaling for cHL pathogenesis, their potential cross-talk and implications for future therapeutic applications are being discussed.     

Computational analysis of the oscillatory dynamics in the processes of CO₂ assimilation and photorespiration

The computational analysis of the model system consisting of the processes of CO₂ assimilation and photorespiration shows the appearance of sustained oscillations in the system which might reflect their presence in photosynthesizing cells. Concentrations of CO₂ and O₂ oscillate in opposite phases causing Rubisco switching continuously between the carboxylase (CO₂ assimilation) and the oxygenase (photorespiration) reactions. The results of modeling are consistent with carbon isotopic and other observed data. They show that the oscillation period varies from about 1 s to 3 s depending on the values of parameters taken. Too high concentrations of O₂ suppress the oscillations.     

Genetic and epidemiologic analysis of hereditary diseases of the nervous system in the cities of Volgograd and Volzhskiĭ

A genetic epidemiological study of hereditary diseases of the nervous system (HDNS) was conducted in the cities of Volgograd and Volzhsky for the first time. In total, 1 323 500 individuals were examined including the populations of Volgograd and Volzhsky (1 012 800 and 310 700 persons, respectively). The prevalence of neurological diseases with autosomal dominant (AD), autosomal recessive (AR), and X-linked recessive inheritance was estimated. These data were compared with the estimates previously obtained for different population of the Russian Federation. A decrease was found in general HDNS load in Volgograd and Volzhsky. The compared populations were shown to differ in a contribution of AD, AR, and X-linked recessive diseases into the HDNS load formation. The possible effect of population dynamics factors on the HDNS load structure is discussed.     

Naiveté and an aquatic-terrestrial dichotomy in the effects of introduced predators

There is much evidence that suggests that freshwater systems are more sensitive to introduced predators than are terrestrial or marine systems. We argue here that this dichotomy reflects widespread naiveté toward introduced predators among freshwater prey. Continental terrestrial animals are seldom naive toward novel predators owing to the homogenizing effects of historical biotic interchanges. Comparable biotic interchanges might have also precluded prey naiveté in most marine systems. By contrast, freshwater systems exhibit persistent large- and small-scale heterogeneity in predation regimes. This heterogeneity promotes naiveté at multiple spatial scales in freshwater prey, thereby producing a systemic vulnerability to introduced predators that is not seen in continental terrestrial or marine systems.     

The theoretical analysis of kinetic behaviour of “hysteretic” allosteric enzymes. I. The kinetic manifestations of slow conformational change of an oligomeric enyzme in the Monod,Wyman and Changeux model

The curves of the time (t) dependent product (Pr) accumulation for Monod, Wyman & Changeux model (1965), where the rate of installation of equilibrium between two conformational states of oligomeric enzyme (R ? T) is comparable to that of enzymatic process, are theoretically analysed. It is assumed that the complexes of R and T forms are in rapid equilibrium with the free components. The character of the effective rate constant of conformational transition R ? T and the value of τ (where τ is the intercept of the linear part of the kinetic curve of [Pr] versus t with the time axis) versus the substrate concentration is analysed. It is also shown that slow conformational transition R ? T can be manifested by an unusual shape for Monod et al. model plots of initial velocity of the enzyme reaction v. the substrate concentration (these curves can clearly display expressed inflection points and Hill's cooperativity coefficient less than unity).     

Definition of the binding mode of a new class of phosphoinositide 3-kinase α-selective inhibitors using in vitro mutagenesis of non-conserved amino acids and kinetic analysis

The binding mechanism of a new class of lipid-competitive, ATP non-competitive, p110α isoform-selective PI3K (phosphoinositide 3-kinase) inhibitors has been elucidated. Using the novel technique of isoform reciprocal mutagenesis of non-conserved amino acids in the p110α and p110β isoforms, we have identified three unique binding mechanisms for the p110α-selective inhibitors PIK-75, A-66S and J-32. Each of the inhibitor's p110α-isoform-selective binding was found to be due to interactions with different amino acids within p110. The PIK-75 interaction bound the non-conserved region 2 amino acid p110α Ser(773), A-66S bound the region 1 non-conserved amino acid p110α Gln(859), and J-32 binding had an indirect interaction with Lys(776) and Ile(771). The isoform reciprocal mutagenesis technique is shown to be an important analytical tool for the rational design of isoform-selective inhibitors.     

Diversity and ecology of desmids of peat bogs in the Jizerské hory Mts

The present study focuses on diversity and ecological preferences of desmids in peat bogs in the Jizerské hory Mts (Czech Republic). Altogether 76 desmid algae taxa have been recorded at 18 sites of the study area during our investigation in 2003–2006. Taxa Actinotaenium crassiusculum (De Bary) Teiling, Hyalotheca dissiliens var. tatrica Racib., Staurastrum avicula var. subarcuatum (Wolle) West & G. S. West, S. borgeanum Schmidle, S. simonyi var. semicirculare Coesel, Staurodesmus extensus var. isthmosus (Heimerl) Coesel, S. extensus var. vulgaris (Eichler & Racib.) Croasdale and S. spencerianus (Mask.) Teiling are new for the Czech Republic. In addition, several rare and remarkable taxa were also encountered. The species richness was relatively high in comparison to similar localities in the Czech Republic. Desmid distribution was influenced by pH and conductivity. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

A continuous spectrophotometric assay and nonlinear kinetic analysis of methionine γ-lyase catalysis

In this article, we present a new, easy-to-implement assay for methionine γ-lyase (MGL)-catalyzed γ-elimination reactions of l-methionine and its analogues that produce α-ketobutyrate (α-KB) as product. The assay employs ultraviolet–visible (UV–Vis) spectrophotometry to continuously monitor the rate of formation of α-KB by its absorbance at 315 nm. We also employ a nonlinear data analysis method that obviates the need for an “initial slope” determination, which can introduce errors when the progress curves are nonlinear. The spectrophotometric assay is validated through product analysis by ¹H NMR (nuclear magnetic resonance), which showed that under the conditions of study l-methionine (l-met) and l-methionine sulfone (l-met sulfone) substrates were converted to α-KB product with greater than 99% yield. Using this assay method, we determined for the first time the Michaelis–Menten parameters for a recombinant form of MGL from Porphyromonas gingivalis, obtaining respective k_cat and K_m values of 328 ± 8 min⁻¹ and 1.2 ± 0.1 mM for l-met γ-elimination and 2048 ± 59 min⁻¹ and 38 ± 2 mM for l-met sulfone γ-elimination reactions. We envisage that this assay method will be useful for determining the activity of MGL γ-elimination reactions that produce α-KB as the end product.     

Comprehensive analysis and characterization of the TCR α chain sequences in the common marmoset

The common marmoset (Callithrix jacchus) is useful as a nonhuman primate model of human diseases. Although the marmoset model has great potential for studying autoimmune diseases and immune responses against pathogens, little information is available regarding the genes involved in adaptive immunity. Here, we identified one TCR α constant (TRAC), 46 TRAJ (joining), and 35 TRAV (variable) segments from marmoset cDNA. Marmoset TRAC, TRAJ, and TRAV shared 80%, 68–100%, and 79–98% identity with their human counterparts at the amino acid level, respectively. The amino acid sequences were less conserved in TRAC than in TCRβ chain constant (TRBC). Comparative analysis of TRAV between marmosets and humans showed that the rates of synonymous substitutions per site (d _S ) were not significantly different between the framework regions (FRs) and complementarity determining regions (CDRs), whereas the rates of nonsynonymous substitutions per site (d _N ) were significantly lower in the FRs than in CDRs. Interestingly, the d _N values of the CDRs were greater for TRBV than TRAV. These results suggested that after the divergence of Catarrhini from Platyrrhini, amino acid substitutions were decreased in the FRs by purifying selection and occurred more frequently in CDRβ than in CDRα by positive selection, probably depending on structural and functional constraints. This study provides not only useful information facilitating the investigation of adaptive immunity using the marmoset model but also new insight into the molecular evolution of the TCR heterodimer in primate species.     

Temperature- and seed-batch-related variation in the kinetic behaviour of phytochrome under ‘high-irradiance-response’ conditions

The characteristics of the high-irradiance response (HIR) of plant photomorphogenesis are thought to be the result of the interaction of both the light and dark reactions of phytochrome. Thus any variation in the rates of the dark reactions may be expected to lead to variation in the characteristics of the HIR. We report here substantial differences in the rates of the dark reactions between different seed batches of a single species (Sinapis alba L.), and also between different organs of seedlings from each of the batches of seed. Calculations of phytochrome dynamics from the measured dark-reaction rates show that the behaviour of Pfr under HIR conditions will vary considerably according to seed batch and seedling organ. Much larger differences in dark-reaction rates, and the resulting phytochrome dynamics, were found between 25° and 10° C. These lead to the prediction that the HIR will be much reduced at the lower temperature, and may be absent in some cases.Abbreviations and symbols HIR high-irradiance response - Pfr far-red-absorbing form of phytochrome - Pr red-absorbing form of phytochrome - Ptot total phytochrome, Pr+Pfr - _ss Pfr/Ptot ratio which immediately establishes the phytochrome steady state     

The use of cluster and discriminant analysis in the investigations of the role of trace metals in the pathogenesis of Parkinson’s disease

X-ray fluorescence microscopy was applied for two-dimensional elemental analysis of substantia nigra (SN) tissue. The samples representing Parkinson’s disease (PD) and control cases were examined at HASYLAB beamline L and at ESRF beamline ID22. Two-dimensional mapping of P, S, Cl, K, Ca, Fe, Cu, Zn, Se and Br was done with the spatial resolution of 15 and 5 μm. The masses per unit area of elements in neuromelanin reach nerve cells of SN were determined.The elemental data were processed using two multivariate techniques, namely cluster and discriminant analysis. The statistical methods were used for data reduction, both unsupervised and supervised classification as well as for the creation of a model that would simplify case identification based on the elemental analysis of SN tissue. The results of cluster analysis confirmed the statistical significance of the differences in elemental composition of PD and control SN nerve cells. Based on the results of discriminant analysis, the elements (P, Cl, Fe, Cu and Zn) that played the greatest role in the process of differentiation between neurons from examined groups were determined.     

Role of termites in the restoration of soils and plant richness on bowé in West Africa

Bowé (hardened ferricrete soils formed by erosion, drought or deforestation) are often associated with termite mounds, but little is known about these mounds and their role in the restoration of soils and plant biodiversity on bowé. This study examined termite mounds on bowé and their effects on soil depth and plant richness. Sixty-four sampling plots were laid out randomly on bowé sites with mounds and on adjacent bowé sites without mounds. The height and circumference of each mound were measured. Species inventories were made and soil depth measured in each plot. Linear mixed effects and generalised mixed effects models with Poisson error distribution were used to assess the variation in soil depth and plant species richness in mound and nonmound microsites. Two types of mounds (small vs. large) associated with different termite species were observed on bowé, with the small mounds being most common. Plots with either large or small mounds had deeper soils and higher plant richness than the adjacent plots without mounds. Conservation of termite mounds is important for restoring soils and plant richness on bowé, and termite mounds should be taken into consideration in biodiversity and soil management strategies for bowé.     

Ultrasonic analysis of kinetic mechanism of hydrolysis of cellobiose by β-glucosidase

High-resolution ultrasonic spectroscopy (HR–US) was applied for real-time analysis of enzymatic hydrolysis of cellobiose by a β-glucosidase from Aspergillus niger (Novozyme 188) at 50 °C and pH 4.9. This technique is noninvasive, it does not require optical transparency and is suitable to continuously monitor the time dependence of the reaction progress in a broad range of experimental conditions. The time profiles of the amount of glucose released and the reaction rate were obtained from the time profile of ultrasonic velocity. The results are in good agreement with a discontinuous glucose assay (hexokinase method). The kinetic parameters of the reaction were estimated by fitting the ultrasonic time profiles of the reaction rates to several inhibition models. In addition, the equilibrium constant for the reaction of hydrolysis of cellobiose and the molar Gibbs free energy of hydrolysis were determined from the ultrasonic time profiles of concentration of glucose in the reverse reaction (glucose condensation). The results suggest the existence of more complex mechanisms regulating the activity of cellobiase than the combination of simple inhibitions. An extended kinetic model based on two sites for the competitive inhibitor (glucose) is proposed.