Proteomic profile of the saliva and plasma protein layer adsorbed on Ti–Zr alloy: the effect of sandblasted and acid-etched surface treatment

Abstract

Titanium–zirconium (Ti–Zr) alloy has been widely used as a biomaterial for implant devices, and it is commonly treated by sandblasting followed by acid etching (SLA) to improve biological responses. Although protein adsorption is the first biological response, the effect of this SLA treatment on the proteomic profile of proteins adsorbed from saliva and blood plasma has not been tested. In this study, the proteomic profile was evaluated by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Streptococcus sanguinis was used to test whether the protein layer affects bacterial adhesion. SLA treatment affected the proteomic profile, showing exclusive proteins adsorbed from saliva (14) and plasma (3). However, both groups exhibited close patterns of intensity for common proteins, molecular functions and biological processes mediated by proteins. Interestingly, Ti–Zr_SLA showed higher bacterial adhesion (～1.9 fold over) for the surface coated with plasma proteins. Therefore, SLA treatment of Ti–Zr alloy changed the proteomic profile, which may affect bacterial adhesion.     

Effect of dissolved oxygen and carbon–nitrogen loads on denitrification by an aerobic consortium

Four samples of natural ecosystems and one sample from an activated sludge treatment plant were mixed together and progressively adapted to alternating aerobic/anoxic phases in the presence of nitrate in order to enrich the microflora in aerobic denitrifiers. Aerobic denitrifying performances of this mixed ecosystem at various dissolved oxygen concentrations and various carbon–nitrogen loads were evaluated and compared to those obtained with the aerobic denitrifier Microvirgula aerodenitrificans. The consortium and the pure strain exhibited an aerobic denitrifying activity at air saturation conditions (7 mg dissolved oxygen l^–1), i.e. there was co-respiration of the two electron acceptors with significant specific nitrate reduction rates. Dissolved oxygen concentrations had no influence on denitrifying performances above a defined threshold: 0.35 mg l^–1 for the consortium and 4.5 mg l^–1 for M. aerodenitrificans respectively. Under these thresholds, decreasing the dissolved oxygen concentrations enhanced the denitrifying activity of each culture. The higher the carbon and nitrogen loads, the higher the performance of the aerobic denitrifying ecosystem. However, for M. aerodenitrificans, the nitrate reduction percentage was affected more by variations in nitrogen load than in carbon load. Received: 6 December 1999 / Received revision: 8 March 2000 / Accepted: 10 March 2000     

Effect of influent pH and alkalinity on the removal of chlorophenols in sequential anaerobic–aerobic reactors

This study was carried out to determine the effect of influent pH and alkalinity on the performance of sequential UASB and RBC reactors for the removal of 2-CP and 2,4-DCP from two different simulated wastewaters. The performance of methanogens at low (<6.0) to high (>8.0) pH values and at sufficiently high alkalinity (1500–3500 mg/l as CaCO₃) is described in this paper. Sequential reactors were capable of handling wastewaters with influent pH, 5.5–8.5. However, with influent pH 7.0 ± 0.1 UASB reactor showed best performance for 2-CP (99%) and 2,4-DCP (88%) removals. Increase in alkalinity/COD ratio in the influent (>1.1) caused gradual decrease in the chlorophenol removal in UASB reactors. The UASB reactors could not tolerate wastewater with higher alkalinity/COD ratio (2.6) and showed significant deterioration of its performance in terms of chlorophenols removal achieving only 74.7% 2-CP and 60% 2,4-DCP removals, respectively.     

Rapid detection and high-resolution discrimination of the genus Streptomyces based on 16S–23S rDNA spacer region and denaturing gradient gel electrophoresis

As the leading source of antibiotics, Streptomyces species are the subject of widespread investigation. Many approaches have been tried to aid in the classification of Streptomyces isolates to the genus, species, and strain levels. Genetic methods are more rapid and convenient than classification methods based on phenotypic characteristics, but a method that is universal in detecting all Streptomyces yet selective in detecting only Streptomyces is needed. The highly conserved nature of the 16S rRNA gene (16S rDNA) combined with the need to discriminate between closely related strains results in analyses of ribosomal intergenic spacer (RIS) regions being more productive than analyses of 16S rRNA genes. PCR primers were designed to amplify the RIS region as well as a sufficient length of the 16S rRNA gene to enable phylogenetic analyses of Streptomyces. Improved selectivity and specificity for the amplification of RIS sequences from Streptomyces with environmental samples was demonstrated. The use of RIS–PCR and denaturing gradient gel electrophoresis (DGGE) was shown to be a convenient means to obtain unique genetic “fingerprints” of Streptomyces cultures allowing them to be accurately identified at species, and even strain classification levels. These RIS–PCR and DGGE approaches show potential for the rapid characterization of environmental Streptomyces populations.     

Direct electrochemical immunoassay based on a silica nanoparticles/sol–gel composite architecture for encapsulation of immunoconjugate

A highly hydrophobic and non-toxic colloidal silica nanoparticle/polyvinyl butyral sol–gel composite membrane was prepared on a platinum wire electrode. With diphtheria-toxoid (D-Ag) as a model antigen and encapsulation of diphtheria antibody (D-Ab) in the composite architecture, this membrane could be used for reagentless electrochemical immunoassay. It displayed a porous and homogeneous composite architecture without the aggregation of the immobilized protein molecules. The formation of immunoconjugate by a simple one-step immunoreaction between D-Ag in sample solution and the immobilized D-Ab introduced the change in the potential. Under optimal conditions, the D-Ag analyte could be determined in the linear ranges from 10 to 800 ng ml⁻¹ with a relatively low detection limit of 2.3 ng ml⁻¹ at 3δ. The D-Ag immunosensor exhibited good precision, high sensitivity, acceptable stability, accuracy, and reproducibility. This composite membrane could be used efficiently for the entrapment of different biomarkers and clinical applications.     

Prediction of protein–protein interactions based on PseAA composition and hybrid feature selection

Based on pseudo amino acid (PseAA) composition and a novel hybrid feature selection frame, this paper presents a computational system to predict the PPIs (protein–protein interactions) using 8796 protein pairs. These pairs are coded by PseAA composition, resulting in 114 features. A hybrid feature selection system, mRMR–KNNs–wrapper, is applied to obtain an optimized feature set by excluding poor-performed and/or redundant features, resulting in 103 remaining features. Using the optimized 103-feature subset, a prediction model is trained and tested in the k-nearest neighbors (KNNs) learning system. This prediction model achieves an overall accurate prediction rate of 76.18%, evaluated by 10-fold cross-validation test, which is 1.46% higher than using the initial 114 features and is 6.51% higher than the 20 features, coded by amino acid compositions. The PPIs predictor, developed for this research, is available for public use at http://chemdata.shu.edu.cn/ppi.     

Metabolic flux analysis of Arthrobacter sp. CGMCC 3584 for cAMP production based on C tracer experiments and gas chromatography–mass spectrometry

Arthrobacter sp. CGMCC 3584 are able to produce cAMP from glucose by the purine synthesis pathway via de novo or salvage biosynthesis. In order to gain an improved understanding of its metabolism, ¹³C-labeling experiment and gas chromatography–mass spectrometry (GC–MS) analysis were employed to determine the metabolic network structure and estimate the intracellular fluxes. GC–MS analysis helps to reflect the activity of the intracellular pathways and reactions. The metabolic network mainly contains glycolytic and pentose phosphate pathways, the tricarboxylic acid cycle, and the inactive glyoxylate shunt. Hypoxanthine as a precursor of cAMP and sodium fluoride as an inhibitor of glycolysis were found to increase the cAMP production, as well as the flux through the PP pathway. The effects of adding hypoxanthine and sodium fluoride are discussed based on the enzyme assays and metabolic flux analysis. In conclusion, our results provide quantitative insights into how cells manipulate the metabolic network under different culture conditions and this may be of value in metabolic regulation for desirable production.     

Characteristics and effects of specific peptides on heat-induced aggregation of β-lactoglobulin

A bovine β-lactoglobulin hydrolysate, obtained by the hydrolysis by the Glu specific enzyme Bacillus licheniformis protease (BLP), was fractionated at pH 7.0 into a soluble and an insoluble fraction and characterized by LC-MS. From the 26 peptides identified in the soluble fraction, five peptides (A[f97-112] = [f115-128], AB[f1-45], AB[f135-157], AB[f135-158], and AB[f138-162]) bound to β-lactoglobulin at room temperature. After heating of β-lactoglobulin in the presence of peptides, eight peptides were identified in the pellet formed, three of them belonging to the previously mentioned peptides. Principle component analysis revealed that the binding at room temperature (to β-lactoglobulin) was related to the total hydrophobicity and the total charge of the peptides. The binding to the unfolded protein could not be attributed to distinct properties of the peptides. The presence of the peptides caused a 50% decrease in denaturation enthalpy (from 148 ± 3 kJ/mol for the protein alone to 74 ± 2 kJ/mol in the presence of peptides), while no change in secondary structure or denaturation temperature was observed. At temperatures <85 °C, the addition of peptides resulted in a 30-40% increase of precipitated β-lactoglobulin. At pH < 6, no differences in the amount of aggregated β-lactoglobulin were observed, which indicates the lack of binding of peptides to β-lactoglobulin at those pH values as was also observed by SELDI-TOF-MS. Although only a few peptides were found to participate in aggregation, suggesting specificity, principal component analysis was unable to identify specific properties responsible for this.     

Impacts of Shewanella oneidensis c‐type cytochromes on aerobic and anaerobic respiration

Shewanella are renowned for their ability to utilize a wide range of electron acceptors (EA) for respiration, which has been partially accredited to the presence of a large number of the c-type cytochromes. To investigate the involvement of c-type cytochrome proteins in aerobic and anaerobic respiration of Shewanella oneidensis Mr -1, 36 in-frame deletion mutants, among possible 41 predicted, c-type cytochrome genes were obtained. The potential involvement of each individual c-type cytochrome in the reduction of a variety of EAs was assessed individually as well as in competition experiments. While results on the well-studied c-type cytochromes CymA(SO4591) and MtrC(SO1778) were consistent with previous findings, collective observations were very interesting: the responses of S. oneidensis Mr -1 to low and highly toxic metals appeared to be significantly different; CcoO, CcoP and PetC, proteins involved in aerobic respiration in various organisms, played critical roles in both aerobic and anaerobic respiration with highly toxic metals as EA. In addition, these studies also suggested that an uncharacterized c-type cytochrome (SO4047) may be important to both aerobiosis and anaerobiosis.     

The Effect of Experimental Hyperthyroidism on Characteristics of Actin–Myosin Interaction in Fast and Slow Skeletal Muscles

The molecular mechanism of the failure of contractile function of skeletal muscles caused by oxidative damage to myosin in hyperthyroidism is not fully understood. Using an in vitro motility assay, we studied the effect of myosin damage caused by oxidative stress in experimental hyperthyroidism on the actin–myosin interaction and its regulation by calcium. We found that hyperthyroidism-induced oxidation of myosin is accompanied by a decrease in the sliding velocity of the regulated thin filaments in the in vitro motility assay, and this effect is increased with the duration of the pathological process.     

Effect of inorganic salts and glucose additives on dose–response,melting point and mass density of genipin gel dosimeters

Genipin gel dosimeters are hydrogels infused with a radiation-sensitive material which yield dosimetric information in three dimensions (3D). The effect of inorganic salts and glucose on the visible absorption dose–response, melting points and mass density of genipin gel dosimeters has been experimentally evaluated using 6-MV LINAC photons. As a result, the addition of glucose with optimum concentration of 10% (w/w) was found to improve the thermal stability of the genipin gel and increase its melting point (T_m) by 6 °C accompanied by a slight decrease of dose–response. Furthermore, glucose helps to adjust the gel mass density to obtain the desired tissue-equivalent properties. A drop of T_m was observed when salts were used as additives. As the salt concentration increased, gel T_m decreased. The mass density and melting point of the genipin gel could be adjusted using different amounts of glucose that improved the genipin gel suitability for 3D dose measurements without introducing additional toxicity to the final gel.     

Effect of (+) and (–) Usnic Acid on Physiological,Biochemical, and Cytological Characteristics of Allium fistulosum Seeds

Russian Journal of Plant Physiology - The effect of (+) and (–)-usnic acid (UA) on the physiological, biochemical, and cytological characteristics of Allium fistulosum L. seedlings was...     

Dependence of red blood cell dynamics in microvessel bifurcations on the endothelial surface layer’s resistance to flow and compression

Red blood cells (RBCs) make up 40–45% of blood and play an important role in oxygen transport. That transport depends on the RBC distribution throughout the body, which is highly heterogeneous. That distribution, in turn, depends on how RBCs are distributed or partitioned at diverging vessel bifurcations where blood flows from one vessel into two. Several studies have used mathematical modeling to consider RBC partitioning at such bifurcations in order to produce useful insights. These studies, however, assume that the vessel wall is a flat impenetrable homogeneous surface. While this is a good first approximation, especially for larger vessels, the vessel wall is typically coated by a flexible, porous endothelial glycocalyx or endothelial surface layer (ESL) that is on the order of 0.5–1 µm thick. To better understand the possible effects of this layer on RBC partitioning, a diverging capillary bifurcation is analyzed using a flexible, two-dimensional model. In addition, the model is also used to investigate RBC deformation and RBC penetration of the ESL region when ESL properties are varied. The RBC is represented using interconnected viscoelastic elements. Stokes flow equations (viscous flow) model the surrounding fluid. The flow in the ESL is modeled using the Brinkman approximation for porous media with a corresponding hydraulic resistivity. The ESL’s resistance to compression is modeled using an osmotic pressure difference. One cell passes through the bifurcation at a time, so there are no cell–cell interactions. A range of physiologically relevant hydraulic resistivities and osmotic pressure differences are explored. Decreasing hydraulic resistivity and/or decreasing osmotic pressure differences (ESL resistance to compression) produced four behaviors: (1) RBC partitioning nonuniformity increased slightly; (2) RBC deformation decreased; (3) RBC velocity decreased relative to blood flow velocity; and (4) RBCs penetrated more deeply into the ESL. Decreasing the ESL’s resistance to flow and/or compression to pathological levels could lead to more frequent cell adhesion and clotting as well as impaired vascular regulation due to weaker ATP and nitric oxide release. Potential mechanisms that can contribute to these behaviors are also discussed.

     

Approximate analytical solutions of root surface nutrient uptake flux and rhizosphere solute concentrations北大核心CSCD

Aims We use the Nye-Tinker-Barber model to obtain approximate analytical solutions of the root surface nutrient uptake flux and the rhizosphere solute concentrations. Methods The rhizosphere is divided into the distant field and the close-range field. The outer solution is obtained by the similarity variable method, and the inner solution is obtained by the rescaling method. Expanding the outer solution from root surface and matching it with the inner solution, we finally obtain the approximate analytical solutions of the root surface nutrient uptake flux and rhizosphere solute concentrations based on Nye-Tinker-Barber model. Numerical simulations are performed on the uptake fluxes of six elements (N, K, P, Mg, S and Ca) and the solute concentrations of two elements (N and K). Comparisons are made among the Nye-Tinker-Barber model approximate analytical solutions, Roose’s analytical solutions and the numerical solutions. Important findings The approximate analytical solutions of the root surface uptake fluxes based on the diffusion Nye-Tinker-Barber model are similar to those of the Roose's analytical solutions; both approaches produced higher values than the numerical solutions. The approximate analytical solutions of the rhizosphere N and K concentrations based on the diffusion Nye-Tinker-Barber model are similar to the Roose’s analytical solutions and coincide with the trend of changes in the numerical solutions. The approximate analytical solutions of all elements but N, of the root surface, uptake fluxes based on the convection-diffusion Nye-Tinker-Barber model are more similar to the numerical solutions than the Roose’s analytical solutions, and the approximate analytical solutions of the rhizosphere N and K concentrations are coincide with the trend of changes in the numerical solutions. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All Rights Reserved.     

Effects of the Chaperone Inducer U133 on Sleep–Wake Cycle Temporal Characteristics and Spatial Memory

Journal of Evolutionary Biochemistry and Physiology - U133, a chaperone inducer synthesized on the basis of echinochrome A, has antitumor, antioxidant and neuroprotective activity. The breadth of...     

Development of a protein–ligand-binding site prediction method based on interaction energy and sequence conservation

We present a new method for predicting protein–ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.     

The effects of surface and macromolecular interactions on the kinetics of inactivation of trypsin and α-chymotrypsin

The autolysis of trypsin and α-chymotrypsin is accelerated in the presence of colloidal silica and glass surfaces. It is proposed that adsorption of the enzymes (favoured by electrostatic factors) results in a conformational change that renders the adsorbed enzyme more susceptible to proteolytic attack. Although the adsorbed enzymes are more susceptible to proteolysis, their activity towards low-molecular-weight substrates is not affected, indicating a relatively minor conformational change on adsorption. The rates of autolysis in solution (i.e. in `inert' vessels) are second-order for both trypsin and α -chymotrypsin, with rate constants of 13.0mol<sup>−1</sup>·dm<sup>3</sup>·s<sup>−1</sup> for trypsin (in 50mm-NaCl at pH8.0 at 25°C) and 10.2mol<sup>−1</sup>·dm<sup>3</sup>·s<sup>−1</sup> for α-chymotrypsin (in 0.1m-glycine at pH9.2 at 30°C). In glass vessels or in the presence of small areas of silica surface (as colloidal silica particles), the autolysis of both trypsin and α-chymotrypsin can show first-order kinetics. Under these conditions, saturation of the surface occurs and the fast surface proteolytic reaction controls the overall kinetic order. However, when greater areas of silica surface are present, saturation of the surface does not occur, and, since for a considerable portion of the adsorption isotherm the amount adsorbed is approximately proportional to the concentration in solution, second-order kinetics are again observed. A number of negatively charged macromolecules have been shown similarly to increase the rate of autolysis of trypsin: thus this effect, observed initially with glass and silica surfaces, is of more general occurrence when these enzymes adsorb on or interact with negatively charged surfaces and macromolecules. These observations explain the confusion in the literature with regard to the kinetics of autolysis of α-chymotrypsin, where first-order, second-order and intermediate kinetics have been reported. A further effect of glass surfaces and negatively charged macromolecules is to shift the pH–activity curve of trypsin to higher pH values, as a consequence of the effective decrease in pH in the `microenvironment' of the enzyme associated with the negatively charged surface or macromolecule.     

Metabolic cold adaptation of polar fish based on measurements of aerobic oxygen consumption: fact or artefact? Artefact!

Whether metabolic cold adaptation in polar fish, based on measurements of aerobic standard metabolic rate, is a fact or an artefact has been a dispute since Holeton asked the question in 1974. So far polar fish had been considered to be metabolically cold adapted because they were reported to have a considerably elevated resting oxygen consumption, or standard metabolic rate, compared with oxygen consumption values of tropical or temperate fish extrapolated to similar low polar temperatures. Recent experiments on arctic and Antarctic fish, however, do not show elevated resting aerobic oxygen consumption values, or standard metabolic rate, and hence it is concluded that that metabolic cold adaptation in the traditional sense is an artefact.