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At least 721 records · Page 40Linked to original sources
PubMed2005

Iron salts in solid state and in frozen solutions as dosimeters for low irradiation temperatures.

The aim of this work is to study the irradiation of iron salts in solid state (heptahydrated ferrous sulfate) and in frozen acid solutions. The study is focused on finding their possible use as dosimeters for low temperature irradiations and high doses. The analysis of the samples was made by UV-visible and Mössbauer spectroscopies. The output signal was linear from 0 to 10 MGy for the solid samples, and 0-600 Gy for the frozen solutions. The obtained data is reproducible and easy to handle. For these reasons, heptahydrate iron sulfate is a suitable dosimeter for low temperature and high irradiation doses, in solid state, and in frozen solution.

Cold Temperature↗
PubMed2005

Ligand-induced thermostability in proteins: thermodynamic analysis of ANS-albumin interaction.

A comparative thermodynamic study of the interaction of anilinonaphthalene sulfonate (ANS) derivatives with bovine serum albumin (BSA) was performed by using differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). The chemically related ligands, 1,8-ANS and 2,6-ANS, present a similar affinity for BSA with different binding energetics. The analysis of the binding driving forces suggests that not only hydrophobic effect but also electrostatic interactions are relevant, even though they have been extensively used as probes for non-polar domains in proteins. Ligand association leads to an increase in protein thermostability, indicating that both dyes interact mainly with native BSA. ITC data show that 1,8-ANS and 2,6-ANS have a moderate affinity for BSA, with an association constant of around 1-9x10(5) M(-1) for the high-affinity site. Ligand binding is disfavoured by conformational entropy. The theoretical model used to simulate DSC data satisfactorily reproduces experimental thermograms, validating this approach as one which provides new insights into the interaction between one or more ligands with a protein. By comparison with 1,8-ANS, 2,6-ANS appears as a more "inert" probe to assess processes which involve conformational changes in proteins.

Anilino Naphthalenesulfonates↗
PubMed2006

Reaction times in discriminations of varying difficulty: decision modulated by arousal.

Pigeons discriminated the hue of a spot of light that appeared in discrete trials. A green spot always signaled food ("green S+") and so did a red spot of constant hue ("red S+"), but on most trials a different red hue appeared and no food was given for pecks ("red S-"). The hue of red S- stayed the same during blocks of up to twelve sessions, but it changed from block to block. During a final group of sessions red S- was omitted and the percent reinforcement to the two S+ stimuli was varied. Major findings were that (1) percent response (Pct(R)) to S- varied with S+/S- similarity, describing a typical ogival psychometric function; (2) Reaction times (RTs) to both red and green S+s were minimal when the red discrimination was impossible (that is, when red S+ and S- were identical); (3) RTs to red S+ were greatest during discriminations of intermediate difficulty; (4) as Pct(R) declined during the learning of a difficult discrimination, RTs increased to red S+ as well as red S-. Most aspects of the data were reproduced by simulations with a quantitative model that incorporated reinforcement-based decision and arousal processes.

Animals↗
PubMed2006

CombiMatrix oligonucleotide arrays: genotyping and gene expression assays employing electrochemical detection.

Electrochemical detection has been developed and assay performances studied for the CombiMatrix oligonucleotide microarray platform that contains 12,544 individually addressable microelectrodes (features) in a semiconductor matrix. The approach is based on the detection of redox active chemistries (such as horseradish peroxidase (HRP) and the associated substrate TMB) proximal to specific microarray electrodes. First, microarray probes are hybridized to biotin-labeled targets, second, the HRP-streptavidin conjugate binds to biotin, and enzymatic oxidation of the electron donor substrate then occurs. The detection current is generated due to electro-reduction of the HRP reaction product, and it is measured with the CombiMatrix ElectraSense Reader. Performance of the ElectraSense platform has been characterized using gene expression and genotyping assays to analyze: (i) signal to concentration dependence, (ii) assay resolution, (iii) coefficients of variation, (CV) and (iv) array-to-array reproducibility and data correlation. The ElectraSense platform was also compared to the standard fluorescent detection, and good consistency was observed between these two different detection techniques. A lower detection limit of 0.75 pM was obtained for ElectraSense as compared to the detection limit of 1.5 pM obtained for fluorescent detection. Thus, the ElectraSense platform has been used to develop nucleic acid assays for highly accurate genotyping of a variety of pathogens including bio-threat agents (such as Bacillus anthracis, Yersinia pestis, and other microorganisms including Escherichia coli, Bacillus subtilis, etc.) and common pathogens of the respiratory tract (e.g. influenza A virus).

Bacteriophage lambda↗
PubMed2006

A comparison of liquid chromatography, capillary electrophoresis, and mass spectrometry methods to determine xyloglucan structures in black currants.

Different separation (HPAEC, RP-HPLC, CE) and identification (MALDI-TOF-MS, ESI-MS(n)) techniques were compared to analyse oligosaccharides obtained after incubation of xyloglucan with endo-glucanase. It was possible to analyse xyloglucan oligosaccharides with each technique. Several techniques, including off line (HPAEC-MALDI-TOF-MS) or online (CE-ESI-MS(n), RP-HPLC-ESI-MS(n)) connection provided complementary information on xyloglucan structure. Online CE-MS and RP-HPLC-MS are described for the first time in xyloglucan analysis. Advantages and disadvantages of the techniques for different purposes such as structural characterisation of oligosaccharides or oligosaccharide profiling are discussed. Black currant xyloglucans had a rather simple XXXG-type structure with galactose and fucose containing side chains.

Carbohydrate Sequence↗
PubMed2004

Cytometric bead array: a multiplexed assay platform with applications in various areas of biology.

The introduction of flow cytometric bead-based technology has added a new approach for investigators to simultaneously measure multiple analytes in biological and environmental samples. This new technology allows for (1) evaluation of multiple analytes in a single sample; (2) utilization of minimal sample volumes to glean data; (3) reproducibility and results comparative with previous experiments; (4) direct comparison with existing assays; and (5) a more rapid evaluation of multiple samples in a single platform. The cytometric bead array (CBA) system enables simultaneous measurement of multiple analytes in sample volumes too small for traditional immunoassays. Results have been presented for the analysis of a variety of human cytokines. In addition, the technology allows for the design and creation of assays to measure a variety of analytes including inflammatory mediators, chemokines, immunoglobulin isotypes, intracellular signaling molecules, apoptotic mediators, adhesion molecules, and antibodies. New initiatives put forward by the Human Genome Project and the FDA require the development and use of assays for the rapid simultaneous quantitation of multiple analytes. The CBA technology provides the ability to quantify multiple proteins within a given sample, with precision and consistency.

Anaphylatoxins↗
PubMed2007

3D heart model for computer simulations in cardiac surgery.

For a satisfactory computer simulation, a model, which imitates a natural situation, is needed. The Human heart is an irregular 3D object and thus difficult to reproduce. Basic data was taken from Visible Human Dataset (VHD), National Library of Medicine. The heart area was cut out of the original cross-sections and different tissues segmented. All the slices also had to be aligned to assure precise overlapping of the structures. A 3D computer heart model with the resolution of 1mm was designed. The heart model was dedicated to simulations of heat transfer during heart surgery however, it is applicable also to other medical simulations.

Cardiac Surgical Procedures↗
PubMed2006

Biochemical profiling in silico--predicting substrate specificities of large enzyme families.

A general high-throughput method for in silico biochemical profiling of enzyme families has been developed based on covalent docking of potential substrates into the binding sites of target enzymes. The method has been tested by systematically docking transition state--analogous intermediates of 12 substrates into the binding sites of 20 alpha/beta hydrolases from 15 homologous families. To evaluate the effect of side chain orientations to the docking results, 137 crystal structures were included in the analysis. A good substrate must fulfil two criteria: it must bind in a productive geometry with four hydrogen bonds between the substrate and the catalytic histidine and the oxyanion hole, and a high affinity of the enzyme-substrate complex as predicted by a high docking score. The modelling results in general reproduce experimental data on substrate specificity and stereoselectivity: the differences in substrate specificity of cholinesterases toward acetyl- and butyrylcholine, the changes of activity of lipases and esterases upon the size of the acid moieties, activity of lipases and esterases toward tertiary alcohols, and the stereopreference of lipases and esterases toward chiral secondary alcohols. Rigidity of the docking procedure was the major reason for false positive and false negative predictions, as the geometry of the complex and docking score may sensitively depend on the orientation of individual side chains. Therefore, appropriate structures have to be identified. In silico biochemical profiling provides a time efficient and cost saving protocol for virtual screening to identify the potential substrates of the members of large enzyme family from a library of molecules.

Binding Sites↗
PubMed2006

Photocatalytic degradation of pollutants from Elcogas IGCC power station effluents.

The aim of this work is to improve the quality of water effluents coming from Elcogas IGCC power station (Puertollano, Spain) with the purpose of fulfilling future more demanding normative, using heterogeneous photocatalytic oxidation processes (UV/H(2)O(2)/TiO(2) or ZnO). The efficiency of photocatalytic degradation for the different catalysts (TiO(2) and ZnO) was determined from the analysis of the following parameters: cyanides, formates and ammonia content. In a first stage, the influence of two parameters (initial concentration of H(2)O(2) and amount of catalyst) on the degradation kinetics of cyanides and formates was studied based on a factorial experimental design. pH was always kept in a value >9.5 to avoid gaseous HCN formation. The degradation of cyanides and formates was found to follow pseudo-first order kinetics. Experimental kinetic constants were fitted using neural networks (NNs). The mathematical model reproduces experimental data within 90% of confidence and allows the simulation of the process for any value of parameters in the experimental range studied. Moreover, a measure of the saliency of the input variables was made based upon the connection weights of the neural networks, allowing the analysis of the relative relevance of each variable with respect to the others. Results showed that the photocatalytic process was effective, being the degradation rate of cyanides about five times higher when compared to removal of formates. Finally, the effect of lowering pH on the degradation of formates was evaluated after complete cyanides destruction was reached (10 min of reaction). Under the optimum conditions (pH 5.2, [H(2)O(2)]=40 g/l; [TiO(2)]=2g/l), 100% of cyanides and 92% of initial NH(3) concentration are degraded after 10 min, whereas 35 min are needed to degrade 98% of formates.

Catalysis↗
PubMed2006

Phi-analysis at the experimental limits: mechanism of beta-hairpin formation.

The 37-residue Formin-binding protein, FBP28, is a canonical three-stranded beta-sheet WW domain. Because of its small size, it is so insensitive to chemical denaturation that it is barely possible to determine accurately a denaturation curve, as the transition spans 0-7 M guanidinium hydrochloride (GdmCl). It is also only marginally stable, with a free energy of denaturation of just 2.3 kcal/mol at 10 degrees Celsius so only small changes in energy upon mutation can be tolerated. But these properties and relaxation times for folding of 25 micros-400 micros conspire to allow the rapid acquisition of accurate and reproducible kinetic data for Phi-analysis using classical temperature-jump methods. The transition state for folding is highly polarized with some regions having Phi-values of 0 and others 1, as readily seen in chevron plots, with Phi-values of 0 having the refolding arms overlaying and those of 1 the unfolding arms superimposable. Good agreement is seen with transition state structures identified from independent molecular dynamics (MD) simulations at 60, 75, and 100 degrees Celsius, which allows us to explore further the details of the folding and unfolding pathway of FBP28. The first beta-turn is near native-like in the transition state for folding (experimental) and unfolding (MD and experiment). The simulations show that there are transient contacts between the aromatic side-chains of the beta-strands in the denatured state and that these interactions provide the driving force for folding of the first beta-hairpin of this three-stranded sheet. Only after the backbone hydrogen bonds are formed between beta1 and beta2 does a hydrogen bond form to stabilize the intervening turn, or the first beta-turn.

Amino Acid Sequence↗
PubMed2006

The human IgE-encoding transcriptome to assess antibody repertoires and repertoire evolution.

Upon encounter with antigen, the B lymphocyte population responds by producing a diverse set of antigen-specific antibodies of various isotypes. The vast size of the responding populations makes it very difficult to study clonal evolution and repertoire composition occurring during these processes in humans. Here, we have explored an approach utilizing the H-EPSILON-encoding transcriptome to investigate aspects of repertoire diversity during the season of antigen exposure. We show through sequencing of randomly picked transcripts that the sizes of patients' repertoires are relatively small. This specific aspect of the transcriptome allows us to construct evolutionary trees pinpointing features of somatic hypermutation as it occurs in humans. Despite the small size of the repertoires, they are highly diverse with respect to VDJ gene usage, suggesting that the H-EPSILON-encoding transcriptome is a faithful mimic of other class-switched isotypes. Importantly, it is possible to use antibody library and selection technologies to define the specificity of clonotypes identified by random sequencing. The small size of the H-EPSILON-encoding transcriptome of peripheral blood B cells, the simple identification of clonally related sets of genes in this population, and the power of library and selection technologies ensure that this approach will allow us to investigate antibody evolution in human B lymphocytes of known specificity. As H-EPSILON repertoires show many of the hallmarks of repertoires encoding other isotypes, we suggest that studies of this type will have an impact on our understanding of human antibody evolution even beyond that occurring in the IgE-producing B cell population.

Amino Acid Sequence↗
PubMed2005

Diffusion versus network models as descriptions for the spread of prion diseases in the brain.

In this paper we will discuss different modeling approaches for the spread of prion diseases in the brain. Firstly, we will compare reaction-diffusion models with models of epidemic diseases on networks. The solutions of the resulting reaction-diffusion equations exhibit traveling wave behavior on a one-dimensional domain, and the wave speed can be estimated. The models can be tested for diffusion-driven (Turing) instability, which could present a possible mechanism for the formation of plaques. We also show that the reaction-diffusion systems are capable of reproducing experimental data on prion spread in the mouse visual system. Secondly, we study classical epidemic models on networks, and use these models to study the influence of the network topology on the disease progression.

Animals↗
PubMed2004

Integrative plasmid vector for constructing single-copy reporter systems to study gene regulation in Rhizobium meliloti and related species.

The integrative system of phage 16-3 of Rhizobium meliloti 41 was shown to function in several bacterial species belonging to the Rhizobium, Bradyrhizobium, Azorhizobium, and Agrobacterium genera. It might also function in many other bacterial species provided that both the target site (attB) and the required host factor(s) are present. Here we report on the construction of a new integrative vector that can be utilized in gene regulation studies. It provides an opportunity to create a single-copy set-up for characterizing DNA-protein interactions in vivo, in a wide range of bacteria. To demonstrate the usefulness of the vector, transcription repression by binding of the C repressor protein of phage 16-3 to wild type operators was studied. The assay system provided highly reproducible quantitative data on repression.

Agrobacterium tumefaciens↗
PubMed2006

Development of a pressure nociceptive threshold testing device for evaluation of analgesics in cats.

A pressure analgesiometric device was developed for unrestrained cats. Eleven cats were studied. Stimulation was via three rounded pins within a bracelet on the forearm. The pins were advanced by manual bladder inflation. Bladder pressure was measured using a strain gauge pressure transducer. The threshold was recorded at the behavioural end point. Thresholds were measured at 5 and 15min intervals for 2-4h, after removal/replacement of the cuff, for 120min after SC butorphanol (0.4mg/kg), and with mild skin inflammation at the testing site. Data were analysed using ANOVA. Pressure thresholds in untreated cats were around 150mmHg. The minimum interval for testing was established as 15min. Data were reproducible over 4h and beyond 24h. Thresholds in 5 cats increased (P<0.05) above baseline for 45min after butorphanol with a maximum increase of 270+/-182mmHg at 10min. Thresholds decreased with inflammation. The method appears suitable for feline analgesia investigations.

Analgesics↗
PubMed2005

High resolution infrared spectra and rovibrational analysis of the coupled nu2/nu5 bands of D3Si35Cl. Equilibrium rotational constants.

The Fourier transform infrared spectrum of monoisotopic D3Si35Cl in the region of the nu2/nu5 band system was recorded with a resolution of 2.4x10(-3) cm-1. More than 9000 lines of the strongly Coriolis x,y-coupled bands, (nu2)0=701.936, and (nu5)0=688.898 cm-1, have been assigned, among them 276 forbidden but perturbation allowed transitions around avoided crossings according to Delta(k-l)=+/-3 mechanisms. Three different models taking into account redundancies in the framework of unitary equivalent reductions of the rovibrational Hamiltonian have been employed to fit the data. All three models reproduced consistently the full data set employing 28 refined parameters with an rms deviation of 0.31x10(-3) cm-1. The equivalence of the parameter sets was established by the agreement of parameter sums obtained with the different models. The analysis of the avoided crossings, together with the fit of the forbidden lines, allowed an independent determination of the ground state parameters A0 and D(K)0. Combined with existing data for nu1, nu3, nu4, and nu6, the present results allowed the determination of experimental values, Ae=1.4371895(94) and Be=0.19823049(59) cm-1. The experimental results are compared with those of previous ab initio calculations of the anharmonic force field.

Models, Chemical↗
PubMed2004

Recombinant LipL32 antigen-based single serum dilution ELISA for detection of canine leptospirosis.

A recombinant antigen-based single serum dilution enzyme-linked immunosorbent assay (ELISA) was developed to measure the specific antibody activity in sera of dogs with leptospirosis. The recombinant antigen developed and used in the assay was specific for the pathogenic serovars of Leptospira. A linear relationship was found to exist between the predicted antibody titres at a single working dilution of 1:1000 and the corresponding observed serum titres as determined by the standard serial-dilution method. Regression analysis was used to determine a standard curve from which an equation can be derived that allows demonstration of the mentioned correlation. The equation was then used to convert the corrected absorbance readings of the single working dilution directly into the predicted ELISA antibody titres. The assay was proved to be sensitive, specific and accurate as compared to the standard microscopic agglutination test (MAT).

Agglutination Tests↗
PubMed2004

Animal models of type I allergy using recombinant allergens.

Various animal models including guinea pigs, monkeys, dogs, rats, and mice have been established in an attempt to provide insights into the complex immunological and pathophysiological mechanisms of human type I allergic diseases. The detailed knowledge of the murine genome, the various components of the murine immune system, and the generation of engineered mice has made the murine system the most attractive among all animal models. The availability of multitude technologies and reagents to characterize and manipulate immunological pathways and mediators adds to the outstanding opportunities to assess the pathology of allergic diseases and to develop novel therapeutic strategies in mice. Numerous sensitization protocols with food and aero-allergens are used to establish an allergic/asthma-like phenotype in mice. Requirements for an appropriate murine model include a close resemblance to the pathology of the disease in humans, the objective measurement of the physiologic parameters, as well as reliability and reproducibility of the experimental data. With respect to reproducible experimental conditions, it has been recognized that extract preparations from natural allergen sources can vary in their allergen-content and -composition. This might influence the degree of sensitization or the outcome of treatment strategies in dependence of the applied extract preparation. The use of recombinant allergens in experimental in vivo and in vitro systems can overcome these problems. Another aspect, that has become obvious from the experimental studies, is that allergens can differ in their immunogenicity as well as in their capacity to act as tolerogens. Therefore, it seems important that the efficacy of the different allergen-molecules to act as therapeutic agents is individually examined. In this review, examples of animal models are described, in which recombinant allergens have been used for sensitization and/or treatment of allergic responses and how they have been used to enhance our understanding of the pathology of allergic diseases.

Allergens↗
PubMed1996

Comparison of impedance cardiography with thermodilution and direct Fick methods for noninvasive measurement of stroke volume and cardiac output during incremental exercise in patients with ischemic cardiomyopathy.

In the last decade, an inexpensive and simple noninvasive method (i.e., transthoracic electrical bioimpedance cardiography, has been tested in healthy subjects and patients with various heart disease for measuring stroke volume and cardiac output at rest and/or during exercise. However, the results are still controversial, especially when measurements are obtained during exercise and data on reproducibility during exercise are lacking. Twenty-five consecutive patients (20 men and 5 women, mean age 48 +/- 9 years) in sinus rhythm with documented coronary artery disease and a previous myocardial infarct were studied. Patients were divided into 2 groups. Group A had ischemic cardiomyopathy, characterized by left ventricular (LV) enlargement and LV ejection fraction depression (35 +/- 8%). Group B had normal LV dimensions and ejection fraction (62 +/- 9%). After a familiarization study, all patients underwent an exercise test with gas exchange analysis and hemodynamic measurements. Stroke volume and cardiac output were simultaneously obtained at rest and at the end of each work rate stage with 3 methods: impedance, thermodilution, and direct Fick. Group A reached a lower peak oxygen uptake (56%), peak work load (60%), and peak systolic blood pressure (69%) than group B. Cardiac output and stroke volume were significantly greater at submaximal and peak exercise in group B than in group A (p < 0.0001). There were no significant differences in stroke volume and cardiac output in the 3 techniques at any matched work rate. There was no significant difference between measurements obtained by 2 experienced observers or between those obtained on 2 exercise tests performed on 2 different days. These results demonstrate that impedance cardiography is a noninvasive, simple, accurate, and reproducible method of measurement of cardiac output and stroke volume over a wide range of workloads.

Cardiac Catheterization↗