Effect of Bioactive and Antimicrobial Nanoparticles on Properties and Applicability of Dental Adhesives

The aim of the study was to examine the applicability of bioactive and antibacterial nanoparticles to an experimental adhesive. The adhesive (60 wt% BisGMA, 15 wt% TEGDMA, 25 wt% HEMA) was mixed with combinations of 5 wt% methacryl-functionalized polyhedral oligomeric silsesquioxane (MA-POSS) and one kind of bioactive/antibacterial nanoparticles: 1 wt% core-shell silica-silver nanoparticle (SiO₂@Ag), 1 wt% bioactive glass with bismuth (BAG-Bi) or 1 wt% calcium phosphate (CAP). Pure adhesive served as control. The physicochemical (degree of conversion (DC), linear shrinkage (LS), shear and complex viscosity, water sorption (WS), sol fraction (SF)), biological (antimicrobial effect) and bioactive (mineral precipitation) properties were investigated. DC and LS remained unchanged. The combination of BAG-Bi/MA-POSS resulted in a significantly increased WS and SF compared to control. In addition, the combination of CAP/MA-POSS slightly increased the shear viscosity of the adhesive. The addition of the nanoparticles did not influence the antimicrobial effects compared to the pure adhesive. Improved mineral inducing capacity could be detected in all nanoparticle combinations. The combination of bioactive and/or antibacterial nanoparticles showed improved mineral inducing capacity, but no antibacterial properties. The material properties were not or only slightly affected.

Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA

We showcase the high potential of the 2'-cyanoethoxymethyl (CEM) methodology to synthesize RNAs with naturally occurring modified residues carrying stable isotope (SI) labels for NMR spectroscopic applications. The method was applied to synthesize RNAs with sizes ranging between 60 to 80 nucleotides. The presented approach gives the possibility to selectively modify larger RNAs (>60 nucleotides) with atom-specifically ¹³C/¹⁵N-labelled building blocks. The method harbors the unique potential to address structural as well as dynamic features of these RNAs with NMR spectroscopy but also using other biophysical methods, such as mass spectrometry (MS), or small angle neutron/X-ray scattering (SANS, SAXS).

Influence of urban area on the water quality of the Campo River basin, Paraná State, Brazil

The Campo River basin is located on the third plateau of the Paraná State or trap plateau of Paraná, at the middle portion between the rivers Ivaí and Piquiri, southern Brazil, between the coordinates 23° 53 and 24° 10’ South Latitude and 52° 15’ and 52° 31’ West Longitude. The basin has 384 Km² area, being 247 km2 in the municipality of Campo Mourão and 137 km2 in the municipality of Peabiru, in Paraná State. The Campo River is a left bank tributary of the Mourão River, which flows into the Ivaí River. The objective of this study was to monitor water quality in the Km 119 River and the Campo River, tributaries of the Mourão River, with monthly collection of water samples to determine pH, temperature, turbidity, biochemical oxygen demand, dissolved oxygen, fecal coliforms, total solids, total nitrogen, ammoniacal nitrogen, nitrite, nitrate and total phosphorus. The results obtained were compared with the indices established by the environmental legislation and applied in the determination of the Water Quality Index (WQI) used by the Water Institute of Paraná State, regulating environmental agency. Poor water quality in these rivers presents a worrying scenario for the region, since this river is the main source of water supply for the public system. Results of organic matter, fecal coliforms and total phosphorus were higher than the limits established by Resolution CONAMA 357/2005 to river class 2, specially at downstream of the Km 119 River and the Campo River, due to the significant influence of the urban anthropic activity by the lack of tertiary treatment and also rural by the lack of basic sanitation in this area. Results of WQI of Km 119 River and do Campo River indicated that water quality can be classified as average in 71% and good in 29% of the sites evaluated.

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter estimation for model fitting. We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient C code. A variety of parameter estimation algorithms as well as frequentist and Bayesian methods for uncertainty analysis have been implemented and used on a range of applications that lead to publications.

AVAILABILITY AND IMPLEMENTATION

The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org.

CONTACT

andreas.raue@fdm.uni-freiburg.de

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[Differential diagnosis of myeloproliferative neoplasms. Quantitative NF-E2 immunohistochemistry for differentiating between essential thrombocythemia and primary myelofibrosis]

BACKGROUND

Besides essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) the myeloproliferative neoplasms (MPN) defined by the World Health Organization (WHO) comprise the entity of unclassifiable MPNs (MPN, U). The exact differential diagnosis of the specific MPN entities can be challenging particularly at early stages of the diseases. So far, pathologists have had to rely only on histomorphological evaluation of bone marrow biopsies in combination with laboratory data because helpful ancillary tests are not yet available. Even molecular tests, such as JAK2 mutation analysis are not helpful particularly in the differential diagnosis of ET and PMF because both entities are associated with the V617F mutation in 50 % of the cases. Recently overexpression of the transcription factor NF-E2 in MPN was described.

MATERIALS AND METHODS

A collective of samples consisting of 163 bone marrow biopsies including 139 MPN cases was stained immunohistochemically for NF-E2 and analyzed regarding the subcellular localization of NF-E2 in erythroid progenitor cells. The results were compared between the MPN entities as well as the controls and statistical analyses were conducted.

RESULTS AND DISCUSSION

This study showed that NF-E2 immunohistochemistry and analysis of the proportion of nuclear positive erythroblasts of all erythroid precursor cells can help to distinguish between ET and PMF even in early stages of the diseases. An MPN, U case showing a proportion of more than 20 % nuclear positive erythroblasts can be classified as a PMF with 92 % accuracy.

Comprehensive estimation of input signals and dynamics in biochemical reaction networks

Motivation: Cellular information processing can be described mathematically using differential equations. Often, external stimulation of cells by compounds such as drugs or hormones leading to activation has to be considered. Mathematically, the stimulus is represented by a time-dependent input function.

Parameters such as rate constants of the molecular interactions are often unknown and need to be estimated from experimental data, e.g. by maximum likelihood estimation. For this purpose, the input function has to be defined for all times of the integration interval. This is usually achieved by approximating the input by interpolation or smoothing of the measured data. This procedure is suboptimal since the input uncertainties are not considered in the estimation process which often leads to overoptimistic confidence intervals of the inferred parameters and the model dynamics.

Results: This article presents a new approach which includes the input estimation into the estimation process of the dynamical model parameters by minimizing an objective function containing all parameters simultaneously. We applied this comprehensive approach to an illustrative model with simulated data and compared it to alternative methods. Statistical analyses revealed that our method improves the prediction of the model dynamics and the confidence intervals leading to a proper coverage of the confidence intervals of the dynamic parameters. The method was applied to the JAK-STAT signaling pathway.

Availability: MATLAB code is available on the authors' website http://www.fdmold.uni-freiburg.de/~schelker/.

Contact:max.schelker@fdm.uni-freiburg.de

Supplementary Information: Additional information is available at Bioinformatics Online.

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

MOTIVATION

Mathematical description of biological reaction networks by differential equations leads to large models whose parameters are calibrated in order to optimally explain experimental data. Often only parts of the model can be observed directly. Given a model that sufficiently describes the measured data, it is important to infer how well model parameters are determined by the amount and quality of experimental data. This knowledge is essential for further investigation of model predictions. For this reason a major topic in modeling is identifiability analysis.

RESULTS

We suggest an approach that exploits the profile likelihood. It enables to detect structural non-identifiabilities, which manifest in functionally related model parameters. Furthermore, practical non-identifiabilities are detected, that might arise due to limited amount and quality of experimental data. Last but not least confidence intervals can be derived. The results are easy to interpret and can be used for experimental planning and for model reduction.

AVAILABILITY

An implementation is freely available for MATLAB and the PottersWheel modeling toolbox at http://web.me.com/andreas.raue/profile/software.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

An error model for protein quantification

MOTIVATION

Quantitative experimental data is the critical bottleneck in the modeling of dynamic cellular processes in systems biology. Here, we present statistical approaches improving reproducibility of protein quantification by immunoprecipitation and immunoblotting.

RESULTS

Based on a large data set with more than 3600 data points, we unravel that the main sources of biological variability and experimental noise are multiplicative and log-normally distributed. Therefore, we suggest a log-transformation of the data to obtain additive normally distributed noise. After this transformation, common statistical procedures can be applied to analyze the data. An error model is introduced to account for technical as well as biological variability. Elimination of these systematic errors decrease variability of measurements and allow for a more precise estimation of underlying dynamics of protein concentrations in cellular signaling. The proposed error model is relevant for simulation studies, parameter estimation and model selection, basic tools of systems biology.

AVAILABILITY

Matlab and R code is available from the authors on request. The data can be downloaded from our website www.fdm.uni-freiburg.de/~ckreutz/data.

Data-based identifiability analysis of non-linear dynamical models

MOTIVATION

Mathematical modelling of biological systems is becoming a standard approach to investigate complex dynamic, non-linear interaction mechanisms in cellular processes. However, models may comprise non-identifiable parameters which cannot be unambiguously determined. Non-identifiability manifests itself in functionally related parameters, which are difficult to detect.

RESULTS

We present the method of mean optimal transformations, a non-parametric bootstrap-based algorithm for identifiability testing, capable of identifying linear and non-linear relations of arbitrarily many parameters, regardless of model size or complexity. This is performed with use of optimal transformations, estimated using the alternating conditional expectation algorithm (ACE). An initial guess or prior knowledge concerning the underlying relation of the parameters is not required. Independent, and hence identifiable parameters are determined as well. The quality of data at disposal is included in our approach, i.e. the non-linear model is fitted to data and estimated parameter values are investigated with respect to functional relations. We exemplify our approach on a realistic dynamical model and demonstrate that the variability of estimated parameter values decreases from 81 to 1% after detection and fixation of structural non-identifiabilities.

Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cells

Sesquiterpene lactones are known for their anti-inflammatory activity which has been proven in various assays on DNA, mRNA and protein level. Here we report on the change in the gene expression profile in TNF-alpha stimulated human 293 cells after treatment with parthenolide using a cDNA microarray analysis. Twenty-one of 7028 genes were found to be up- and 18 down-regulated. They encode for chemoattractants, immune system proteins, glycoproteins, metabolism, serine proteinases, and transcription factors. Confirmatory analyses were carried out using quantitative real-time RT-PCR (TaqMan). Additional studies with selected genes revealed the concentration-dependent influence of parthenolide on the expression of these genes.

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways

Complex cellular networks regulate regeneration, detoxification and differentiation of hepatocytes. By combining experimental data with mathematical modelling, systems biology holds great promises to elucidate the key regulatory mechanisms involved and predict targets for efficient intervention. For the generation of high-quality quantitative data suitable for mathematical modelling a standardised in vitro system is essential. Therefore the authors developed standard operating procedures for the preparation and cultivation of primary mouse hepatocytes. To reliably monitor the dynamic induction of signalling pathways, the authors established starvation conditions and evaluated the extent of starvation-associated stress by quantifying several metabolic functions of cultured primary hepatocytes, namely activities of glutathione-S-transferase, glutamine synthetase, CYP3A as well as secretion of lactate and urea into the culture medium. Establishment of constant metabolic activities after an initial decrease compared with freshly isolated hepatocytes showed that the cultured hepatocytes achieve a new equilibrium state that was not affected by our starving conditions. To verify the highly reproducible dynamic activation of signalling pathways in the in vitro system, the authors examined the JAK-STAT, SMAD, PI3 kinase, MAP kinase, NF-kappaB and Wnt/beta-catenin signalling pathways. For the induction of gp130, JAK1 and STAT3 phosphorylation IL6 was used, whereas TGFbeta was applied to activate the phosphorylation of SMAD1, SMAD2 and SMAD3. Both Akt/PKB and ERK1/2 phosphorylation were stimulated by the addition of hepatocyte growth factor. The time-dependent induction of a pool of signalling competent beta-catenin was monitored in response to the inhibition of GSK3beta. To analyse whether phosphorylation is actually leading to transcriptional responses, luciferase reporter gene constructs driven by multiple copies of TGFbeta-responsive motives were applied, demonstrating a dose-dependent increase in luciferase activity. Moreover, the induction of apoptosis by the TNF-like cytokine Fas ligand was studied in the in vitro system. Thus, the mouse hepatocyte in vitro system provides an important basis for the generation of high-quality quantitative data under standardised cell culture conditions that is essential to elucidate critical hepatocellular functions by the systems biology approach.

Synthesis of glycosyl amino acids by light-induced coupling of photoreactive amino acids with glycosylamines and 1-C-aminomethyl glycosides

The glycosylamines of O-acetyl-protected GlcNAc and chitobiose, as well as two partially unprotected 1-C-aminomethyl glucosides, were photochemically coupled with orthogonally protected N-aspartyl-5-bromo-7-nitroindoline derivatives. The reactions proceeded under neutral conditions by irradiation with near-UV light. The glycosyl asparagines with N- or C-glycosyl linkages were afforded in 60-85% yield on a 10-70 mg scale. Moreover, the ability of a highly photoreactive N-glutamyl-4-methoxy-7-nitroindoline derivative to acylate amino saccharides was tested. Upon irradiation in the presence of a dimeric 1-C-aminomethyl glycoside, or a glycosylamine, the corresponding glycosyl glutamines were obtained in 50% and 30% yield, respectively. Preparations of the photoreactive aspartates and the 1-C-aminomethyl glycosides are also described.

Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers

Systems biology is an approach to the analysis and prediction of the dynamic behaviour of biological networks through mathematical modelling based on experimental data. The current lack of reliable quantitative data, especially in the field of signal transduction, means that new methodologies in data acquisition and processing are needed. Here, we present methods to advance the established techniques of immunoprecipitation and immunoblotting to more accurate and quantitative procedures. We propose randomisation of sample loading to disrupt lane correlations and the use of normalisers and calibrators for data correction. To predict the impact of each method on improving the data quality we used simulations. These studies showed that randomisation reduces the standard deviation of a smoothed signal by 55% +/- 10%, independently from most experimental settings. Normalisation with appropriate endogenous or external proteins further reduces the deviation from the true values. As the improvement strongly depends on the quality of the normaliser measurement, a criteria-based normalisation procedure was developed. Our approach was experimentally verified by application of the proposed methods to time course data obtained by the immunoblotting technique. This analysis showed that the procedure is robust and can significantly improve the quality of experimental data.

Molecular, immunological and clinical properties of mutated hepatitis B viruses

Hepatitis B virus (HBV) is at the origin of severe liver diseases like chronic active hepatitis, liver cirrhosis and hepatocellular carcinoma. There are some groups of patients with high risk of generation of HBV mutants: infected infants, immunosuppressed individuals (including hemodialysis patients), patients treated with interferon and lamivudine for chronic HBV infection. These groups are the target for molecular investigations reviewed in this paper. The emergence of lamivudine- or other antiviral-resistant variants, rises concern regarding long term use of these drugs. Infection or immunization with one HBV subtype confers immunity to all subtypes. However, reinfection or reactivation of latent HBV infection with HBV mutants have been reported in patients undergoing transplant and those infected with HIV. Mutations of the viral genome which are not replicative incompetent can be selected in further course of infection or under prolonged antiviral treatment and might maintain the liver disease. Four open reading frames (ORF) which are called S-gene, C-gene, X-gene and P-gene were identified within the HBV genome. Mutations may affect each of the ORFs. Mutated S-genes were described to be responsible for HBV-infections in successfully vaccinated persons, mutated C-genes were found to provoke severe chronic liver diseases, mutated X-genes could cause serious medical problems in blood donors by escaping the conventional test systems and mutated P-genes were considered to be the reason for chemotherapeutic drug resistance. This paper reviews molecular, immunological and clinical aspects of the HBV mutants.

Fibronectin and laminin binding of eighteen Clostridium species

The ability of Clostridium difficile, Clostridium perfringens, Clostridium sporogenes and fifteen other Clostridium species to bind to human serum fibronectin or laminin was tested by using protein-coated latex particles. Three groups of Clostridium species were formed, namely the pseudomembranous colitis-causing species Clostridium difficile, the gas gangrene-causing Clostridium species and other Clostridium species, which are infrequently found in human infections. Significantly more strains of gas gangrene-causing Clostridium species, and strains of Clostridium species other than Clostridium difficile recognized fibronectin or laminin than did Clostridium difficile. Experiments with monoclonal antibodies revealed the specificity of the bacterial binding to fibronectin or laminin.

Adherence properties of Bacteroides vulgatus, the preponderant colonic organism of adult humans

Bacteroides vulgatus is the predominant intestinal bacterium of adult humans. The adhesins of this species were studied by using haemagglutination of rabbit erythrocytes and inhibition of this haemagglutination. Eleven haemagglutinating strains were tested after incubation with chicken albumin, bovine serum albumin, human serum fibronectin, fibronectin fragment and N-acetyl neuraminic acid, and after they had been heated, treated with NaIO4, trypsin and D(+)-mannose. Rabbit erythrocytes treated with neuraminidase served as controls. Four different types of adhesins could be distinguished as characterized by different substrate specificities.

Effects of acute viral respiratory tract infections in patients with cystic fibrosis

To determine the effects of acute viral respiratory infections (ARI) in cystic fibrosis (CF) we studied all episodes of ARI in ten patients over a 2 year period. A daily diary card was kept on which they recorded all illnesses, including specific upper and lower respiratory symptoms, antibiotic use, and daily peak flow measurements. Recording of concurrent similar illnesses in other household members aided in confirming the onset of ARI, as did a home viral culturing technique and serial serum antibody levels against specific viral types. A total of 80% of the 35 recorded onsets of ARI (1.75/yr/subject) were confirmed by one or more of these methods. Five subjects with moderate to severe pulmonary function scores at the outset of the study had significantly greater decreases in PEFR during ARI episodes (42.4%) than those with milder disease (15.4%), and it took them significantly longer to recover to their baseline measurements (22 days vs. 15 days respectively). The majority of hospital admissions for pulmonary exacerbations were preceded by viral infections (7/8).

A trial of metaproterenol by metered-dose inhaler and two spacers in preschool asthmatics

Because most young children have difficulty in coordination for correct use of metered-dose inhalers (MDI), a trial of two spacer devices attached to MDIs was performed. In 13 children with asthma, aged 2-5 years old, a collapsible bag (Inspir-Ease) and a tube spacer (Aerochamber) were tested in a double-blind crossover trial with metaproterenol (1,300 micrograms). Respiratory resistance was measured by the forced oscillation method. Thirty minutes after metaproterenol administration there was a significant decrease in resistance with both spacers, while no significant change occurred after placebo administration. There was no difference in degree of bronchodilation between the two spacers. It is concluded that metaproterenol can be safely and effectively administered to preschool asthmatics by an MDI with spacer devices.

The preventive effect and duration of action of nedocromil sodium and cromolyn sodium on exercise-induced asthma (EIA) in adults

Nedocromil sodium, 4 mg, from a metered-dose inhaler, cromolyn sodium, (cr) 20 mg, from a Spinhaler, and placebo (pl) were compared in their efficacy and duration of action in preventing exercise-induced asthma. Twelve patients with asthma performed treadmill exercise tests 20 minutes, 2 hours, and 4 hours after a single dose of drug in a double-blind, crossover trial. Both active drugs were significantly better than pl at 20 minutes. Two hours after drug administration, only cr was significantly different from pl. The direct comparison between nedocromil and cr demonstrated no significant difference on FEV1, and the only significant difference was with forced expiratory flow between 25% and 75% of vital capacity at 2 hours. It is concluded that at these clinically recommended doses, both drugs are equally effective in preventing exercise-induced asthma with cr possibly having a somewhat longer duration of action.

A longitudinal study of bronchodilator responsiveness in cystic fibrosis

The prevalence of bronchodilator responsiveness was evaluated in 20 outpatients with cystic fibrosis (CF) every 1 to 3 months for a 1-yr period and in 20 patients with CF during a hospital admission. All but 1 subject (95%) showed a significant bronchodilator response at least once on an outpatient basis; nonhospitalized subjects were responsive 49% of the time. Bronchodilator responsiveness was unrelated to long-term pulmonary severity or indexes of atopy but it was significantly influenced by season of the year; 70% of the population was responsive in winter compared with 25% in summer. Bronchodilator responsiveness increased during hospital admission together with improvement in baseline values; 23% of the population was responsive during the first 3 days compared with 80% by the end of the second week of admission. After discharge, a reverse pattern occurred, with decrease in bronchodilator responsiveness and a fall in baseline values. However, in some patients, bronchodilator responsiveness was lost when baseline values were still at their best. Bronchodilator responsiveness in CF tends to undulate with pulmonary exacerbations of the disease.

Normal values for forced oscillatory respiratory resistance in children

Forced oscillatory respiratory resistance was measured in 138 healthy children aged 2- to 16-years-old using a commercial unit. Regression analysis was performed using the resistance measurements obtained at frequencies of 6 Hz and 26 Hz and averages of measurements obtained at frequencies of from 6-26 Hz, 6-10 Hz, and 22-26 Hz. The analysis suggested that regression curves and 95% confidence intervals obtained using a quadratic model with height as the independent variable provided the best prediction of normal values and their ranges. Three independent sets of resistance measurements, which were obtained for all 138 subjects, were used to calculate the average individual coefficients of variation (CV) for the five resistance parameters noted above; these ranged from 9 to 13%. This analysis suggested that the expected CV of repeated measurements would be about 10%. Finally, values from 13 children who had asthma with mild bronchial obstruction (FEV1 less than 80% of predicted) were compared with the normal values derived from the regression curves. Values from all but two of the children fell within the reference intervals, suggesting that FEV1 may be a more sensitive measure of obstruction than forced oscillatory resistance. The main applications of this new approach may be in the evaluation of young children, in following individual patients, and in bronchodilation and bronchial challenge tests.