Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis

Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.

Comparative Study of Different Methods for the Prediction of Drug− Polymer Solubility

In this study, a comparison of different methods to predict drug−polymer solubility was carried out on binary systems consisting of five model drugs (paracetamol, chloramphenicol, celecoxib, indomethacin, and felodipine) and polyvinylpyrrolidone/vinyl acetate copolymers (PVP/VA) of different monomer weight ratios. The drug−polymer solubility at 25 °C was predicted using the Flory−Huggins model, from data obtained at elevated temperature using thermal analysis methods based on the recrystallization of a supersaturated amorphous solid dispersion and two variations of the melting point depression method. These predictions were compared with the solubility in the low molecular weight liquid analogues of the PVP/VA copolymer (N-vinylpyrrolidone and vinyl acetate). The predicted solubilities at 25 °C varied considerably depending on the method used. However, the three thermal analysis methods ranked the predicted solubilities in the same order, except for the felodipine−PVP system. Furthermore, the magnitude of the predicted solubilities from the recrystallization method and melting point depression method correlated well with the estimates based on the solubility in the liquid analogues, which suggests that this method can be used as an initial screening tool if a liquid analogue is available. The learnings of this important comparative study provided general guidance for the selection of the most suitable method(s) for the screening of drug−polymer solubility.

Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider the applications of nTTM and MD for the description of silicon, and then construct the combined MD-nTTM model. Its development and thorough testing is followed by a comprehensive computational study of fast nonequilibrium processes induced in silicon by an ultrashort laser irradiation. The new model allowed to investigate the effect of laser-induced pressure and temperature of the lattice on the melting kinetics. Two competing melting mechanisms, heterogeneous and homogeneous, were identified in our big-scale simulations. Apart from the classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to the large negative volume of melting of silicon, the material contracts upon the phase transition, relaxes the compressive stresses, and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. A series of simulations for a range of absorbed fluences allowed us to find the threshold fluence value at which homogeneous liquid nucleation starts contributing to the classical heterogeneous propagation of the solid-liquid interface. A series of simulations for a range of the material thicknesses showed that the sample width we chosen in our simulations (800 nm) corresponds to a thick sample. Additionally, in order to support the main conclusions, the results were verified for a different interatomic potential. Possible improvements of the model to account for nonthermal effects are discussed and certain restrictions on the suitable interatomic potentials are found. As a first step towards the inclusion of these effects into MD-nTTM, we performed nanometer-scale MD simulations with a new interatomic potential, designed to reproduce ab initio calculations at the laser-induced electronic temperature of 18946 K. The simulations demonstrated that, similarly to thermal melting, nonthermal phase transition occurs through nucleation. A series of simulations showed that higher (lower) initial pressure reinforces (hinders) the creation and the growth of nonthermal liquid nuclei. For the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with a face-centered cubic crystal structure. The results of this study, therefore, have important implications for interpretation of experimental data on the kinetics of melting process of semiconductors.

Investigation by Combined Solid-State NMR and SAXS Methods of the Morphology and Domain Size in Polystyrene-b-Polyethylene Oxide-b-Polystyrene Triblock Copolymers

The microphase structure of a series of polystyrene-b-polyethylene oxide-b-polystyrene (SEOS) triblock copolymers with different compositions and molecular weights has been studied by solid-state NMR, DSC, wide and small angle X-ray scattering (WAXS and SAXS). WAXS and DSC measurements were used to detect the presence of crystalline domains of polyethyleneoxide (PEO) blocks at room temperature as a function of the copolymer chemical composition. Furthermore, DSC experiments allowed the determination of the melting temperatures of the crystalline part of the PEO blocks. SAXS measurements, performed above and below the melting temperature of the PEO blocks, revealed the formation of periodic structures, but the absence or the weakness of high order reflections peaks did not allow a clear assessment of the morphological structure of the copolymers. This information was inferred by combining the results obtained by SAXS and (1)H NMR spin diffusion experiments, which also provided an estimation of the size of the dispersed phases of the nanostructured copolymers. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48:55-64,2010

Rapid detection of SMARCB1 sequence variation using high resolution melting

Background : Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Methods : Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results : The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions : This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening.

Phase behavior of synthetic amphiphile vesicles investigated by calorimetry and fluorescence methods

The understanding of biological membranes may be improved by investigating physical properties of vesicles from natural or synthetic amphiphiles. The application of vesicles as mimetic agents depends on the knowledgment of their structure and properties. Vesicles having different curvature and size may be obtained using different preparation protocols. We have used differential scanning calorimetry (DSC) and steady-state fluorescence to investigate the gel to liquid-crystal phase transition of vesicles prepared by sonication (SUV) and non-sonication (GUV) of the synthetic dioctadecyldimethylammonium bromide (DODAB) in aqueous solution. DSC thermograms for a non-sonicated dispersion show a well-defined pre- and main transition corresponding to two narrow peaks at 36 and 45°C in the first upscan, while in a second upscan, only the main peak was observed. The sharpness of the peaks indicate a cooperative phase behavior for GUV. For a sonicated DODAB dispersion, the first upscan shows a third peak at 40.3°C, whereas for the second upscan the peaks are not well-defined, indicating a less cooperative phase behavior. Alternatively, the fluorescence quantum yield (Φ f) and the anisotropy (r) of trans, trans, trans-1-[4-(3-carboxypropyl)-phenyl]-6-[4-butylphenyl]-1,3,5-hexatriene (4H4A) and the ratio I 1/I 3 of the first to the third vibronic peaks of the pyrene emission spectrum as function of temperature are used as well to describe the phase behavior of DODAB sonicated and non-sonicated dispersions. It is in good agreement with the DSC results that the cooperativity of the thermotropic process is diminished under sonication of the DODAB dispersion, meaning that sonication changes from homogeneous to heterogeneous populations of the amphiphile aggregates. The pre- and main transitions obtained from these techniques are in fairly good accord with results from the literature.

Methods for qualitative analysis of cefazolin sodium raw material and pharmaceutical product

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Partial melting within the lower crust – Constraints from bulk rock geochemical data and trace element mineral analyses of granulites and migmatites from Central Finland

This PhD thesis concerns geochemical constraints on recycling and partial melting of Archean continental crust. A natural example of such processes was found in the Iisalmi area of Central Finland. The rocks from this area are Middle to Late Archean in age and experienced metamorphism and partial melting between 2.7-2.63 Ga. The work is based on extensive field work. It is furthermore founded on bulk rock geochemical data as well as in-situ analyses of minerals. All geochemical data were obtained at the Institute of Geosciences, University of Mainz using X-ray fluorescence, solution ICP-MS and laser ablation-ICP-MS for bulk rock geochemical analyses. Mineral analyses were accomplished by electron microprobe and laser ablation ICP-MS. Fluid inclusions were studied by microscope on a heating-freezing-stage at the Geoscience Center, University Göttingen. Part I focuses on the development of a new analytical method for bulk rock trace element determination by laser ablation-ICP-MS using homogeneous glasses fused from rock powder on an Iridium strip heater. This method is applicable for mafic rock samples whose melts have low viscosities and homogenize quickly at temperatures of ~1200°C. Highly viscous melts of felsic samples prevent melting and homogenization at comparable temperatures. Fusion of felsic samples can be enabled by addition of MgO to the rock powder and adjustment of melting temperature and melting duration to the rock composition. Advantages of the fusion method are low detection limits compared to XRF analyses and avoidance of wet-chemical processing and use of strong acids as in solution ICP-MS as well as smaller sample volumes compared to the other methods. Part II of the thesis uses bulk rock geochemical data and results from fluid inclusion studies for discrimination of melting processes observed in different rock types. Fluid inclusion studies demonstrate a major change in fluid composition from CO2-dominated fluids in granulites to aqueous fluids in TTG gneisses and amphibolites. Partial melts were generated in the dry, CO2-rich environment by dehydration melting reactions of amphibole which in addition to tonalitic melts produced the anhydrous mineral assemblages of granulites (grt + cpx + pl ± amph or opx + cpx + pl + amph). Trace element modeling showed that mafic granulites are residues of 10-30 % melt extraction from amphibolitic precursor rocks. The maximum degree of melting in intermediate granulites was ~10 % as inferred from modal abundances of amphibole, clinopyroxene and orthopyroxene. Carbonic inclusions are absent in upper-amphibolite facies migmatites whereas aqueous inclusion with up to 20 wt% NaCl are abundant. This suggests that melting within TTG gneisses and amphibolites took place in the presence of an aqueous fluid phase that enabled melting at the wet solidus at temperatures of 700-750°C. The strong disruption of pre-metamorphic structures in some outcrops suggests that the maximum amount of melt in TTG gneisses was ~25 vol%. The presence of leucosomes in all rock types is taken as the principle evidence for melt formation. However, mineralogical appearance as well as major and trace element composition of many leucosomes imply that leucosomes seldom represent frozen in-situ melts. They are better considered as remnants of the melt channel network, e.g. ways on which melts escaped from the system. Part III of the thesis describes how analyses of minerals from a specific rock type (granulite) can be used to determine partition coefficients between different minerals and between minerals and melt suitable for lower crustal conditions. The trace element analyses by laser ablation-ICP-MS show coherent distribution among the principal mineral phases independent of rock composition. REE contents in amphibole are about 3 times higher than REE contents in clinopyroxene from the same sample. This consistency has to be taken into consideration in models of lower crustal melting where amphibole is replaced by clinopyroxene in the course of melting. A lack of equilibrium is observed between matrix clinopyroxene / amphibole and garnet porphyroblasts which suggests a late stage growth of garnet and slow diffusion and equilibration of the REE during metamorphism. The data provide a first set of distribution coefficients of the transition metals (Sc, V, Cr, Ni) in the lower crust. In addition, analyses of ilmenite and apatite demonstrate the strong influence of accessory phases on trace element distribution. Apatite contains high amounts of REE and Sr while ilmenite incorporates about 20-30 times higher amounts of Nb and Ta than amphibole. Furthermore, trace element mineral analyses provide evidence for magmatic processes such as melt depletion, melt segregation, accumulation and fractionation as well as metasomatism having operated in this high-grade anatectic area.

Three dimensional finite element simulation of polymer melting and flow in a single-screw extruder : optimization of screw channel geometry

Single-screw extrusion is one of the widely used processing methods in plastics industry, which was the third largest manufacturing industry in the United States in 2007 [5]. In order to optimize the single-screw extrusion process, tremendous efforts have been devoted for development of accurate models in the last fifty years, especially for polymer melting in screw extruders. This has led to a good qualitative understanding of the melting process; however, quantitative predictions of melting from various models often have a large error in comparison to the experimental data. Thus, even nowadays, process parameters and the geometry of the extruder channel for the single-screw extrusion are determined by trial and error. Since new polymers are developed frequently, finding the optimum parameters to extrude these polymers by trial and error is costly and time consuming. In order to reduce the time and experimental work required for optimizing the process parameters and the geometry of the extruder channel for a given polymer, the main goal of this research was to perform a coordinated experimental and numerical investigation of melting in screw extrusion. In this work, a full three-dimensional finite element simulation of the two-phase flow in the melting and metering zones of a single-screw extruder was performed by solving the conservation equations for mass, momentum, and energy. The only attempt for such a three-dimensional simulation of melting in screw extruder was more than twenty years back. However, that work had only a limited success because of the capability of computers and mathematical algorithms available at that time. The dramatic improvement of computational power and mathematical knowledge now make it possible to run full 3-D simulations of two-phase flow in single-screw extruders on a desktop PC. In order to verify the numerical predictions from the full 3-D simulations of two-phase flow in single-screw extruders, a detailed experimental study was performed. This experimental study included Maddock screw-freezing experiments, Screw Simulator experiments and material characterization experiments. Maddock screw-freezing experiments were performed in order to visualize the melting profile along the single-screw extruder channel with different screw geometry configurations. These melting profiles were compared with the simulation results. Screw Simulator experiments were performed to collect the shear stress and melting flux data for various polymers. Cone and plate viscometer experiments were performed to obtain the shear viscosity data which is needed in the simulations. An optimization code was developed to optimize two screw geometry parameters, namely, screw lead (pitch) and depth in the metering section of a single-screw extruder, such that the output rate of the extruder was maximized without exceeding the maximum temperature value specified at the exit of the extruder. This optimization code used a mesh partitioning technique in order to obtain the flow domain. The simulations in this flow domain was performed using the code developed to simulate the two-phase flow in single-screw extruders.

On the structure of the floating zone in melting

Floating zone melting is used in crystal growth and purification of high melting materials. The use of a reduced gravity environment will remove the constraint imposed on the length of the zone by the hydrostatic pressure. The equilibrium of the fioatmg zone may involve, (1)Hydrostatic forces, when the zone rotates as a whole. (2)Convective driving forces, when the zone is stationary but fluid property gradients appear.(3) Hydrodynamic forces, when some parts of the zone are set into motion with respect to others. The last effects are considered in this paper. The flow pattern of a floating zone held between two discs in relative motion is complicated, and thence the solution of the problem is difficult even assuming a constant property-newtonian liquid Nevertheless, when a small parameter appears m the problem, the complete flow field can be split into zones where simple solutions are found. To illustrate this approach, the spin up from rest of an initially cylindrical floating zone is considered with detail. Here the small parameter is the time elapsed from the impulsive starting of motion. Since the problem which has been considered, as well as some others which can be tackled by use of similar methods, concern the viscous layer close to either plate, they can be simulated experimentally in the ground laboratory with short floating zones. Procedures to produce these zones are indicated.

A Multiplex Real-Time PCR with High Resolution Melting Analysis for the Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.

Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detecting AMR determinants could provide valuable tools for surveillance, epidemiological studies and to inform individual case management. We developed a fast (<1.5 hrs) SYBR-green based real-time PCR method with high resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully-characterized N. gonorrhoeae strains, 19 commensal Neisseria spp., and an additional panel of 193 gonococcal isolates. Results were compared with culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with non-gonococcal Neisseria species and the detection limit was 10(3)-10(4) gDNA copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity 100%, specificity 90%), cefixime (sensitivity 92%, specificity 94%), azithromycin and spectinomycin (both sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations generating resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens but this method can be used to screen collections of gonococcal isolates for AMR more quickly than with current culture-based AMR testing.

Effect of sample geometry on regression rate of the melting interface for carbon steel burned in oxygen

Promoted-ignition testing on carbon steel rods of varying cross-sectional area and shape was performed in high pressure oxygen to assess the effect of sample geometry on the regression rate of the melting interface. Cylindrical and rectangular geometries and three different cross sections were tested and the regression rates of the cylinders were compared to the regression rates of the rectangular samples at test pressures around 6.9 MPa. Tests were recorded and video analysis used to determine the regression rate of the melting interface by a new method based on a drop cycle which was found to provide a good basis for statistical analysis and provide excellent agreement to the standard averaging methods used. Both geometries tested showed the typical trend of decreasing regression rate of the melting interface with increasing cross-sectional area; however, it was shown that the effect of geometry is more significant as the sample's cross sections become larger. Discussion is provided regarding the use of 3.2-mm square rods rather than 3.2-mm cylindrical rods within the standard ASTM test and any effect this may have on the observed regression rate of the melting interface.

Application of Artificial Intelligence Methods to Computer Design of Inorganic Compounds

In this paper the main problems for computer design of materials, which would have predefined properties, with the use of artificial intelligence methods are presented. The DB on inorganic compound properties and the system of DBs on materials for electronics with completely assessed information: phase diagram DB of material systems with semiconducting phases and DB on acousto-optical, electro-optical, and nonlinear optical properties are considered. These DBs are a source of information for data analysis. Using the DBs and artificial intelligence methods we have predicted thousands of new compounds in ternary, quaternary and more complicated chemical systems and estimated some of their properties (crystal structure type, melting point, homogeneity region etc.). The comparison of our predictions with experimental data, obtained later, showed that the average reliability of predicted inorganic compounds exceeds 80%. The perspectives of computational material design with the use of artificial intelligence methods are considered.

Development of a sustained release solid dispersion using swellable polymer by melting method

PURPOSE: This study is to design a sustained release solid dispersion using swellable polymer by melting method. METHODS: Polyethylene glycol 6000 (PEG 6000) and hydroxypropyl methylcellulose 4000 (HPMC 4000) were used in solid dispersion for not only enhancing drug dissolution rate but also sustaining drug release. HPMC 4000 is a common swellable polymer in matrix sustained release dosage form, but could not be used in preparation of solid dispersion by melting method. However, the current study utilized the swelling capability of HPMC 4000 accompanied by the common carrier PEG 6000 in solid dispersion to accomplish the goal. RESULTS: While PEG 6000 acted as a releasing stimulant carrier and provided an environment to facilitate the swelling of HPMC 4000, this swellable polymer could act as a rate-controlling agent. This greatly assisted the dissolution enhancement by changing the crystalline structure of drug to more amorphous form and creating a molecular interaction. CONCLUSIONS: These results suggested that this useful technique can be applied in designing a sustained release solid dispersion with many advantages.

An improved static model for tool deflection in machining of Ti–6Al–4V acetabular shell produced by selective laser melting

Tool deflection during milling operation leads to dimensional error, decreasing surface quality and increasing rejection rate. In this study, tool deflection during the milling of the inner surfaces of Ti–6Al–4V prosthetic acetabular shell produced by selective laser melting (SLM) was modelled. The first purpose of this research is to provide a general static cutting tool deflection model for ball nose cutters where deviation of machine components and tool holder are so small as to be considered negligible. This is because the values of machine component and tool holder deflection were lower than standard tolerances (10 μm) and found to be lower than 1/15 of tool deflection. The second and third objectives of this work involve calculating contact surfaces by determining workpiece and tool geometry and choosing second moment of inertia using a novel cross section method (CSM). Static models for three quasi-analytical methods (QAM) that are simple cantilever beam model (SCBM), two-section model (TWSM) and our three section model (THSM) are presented. THSM showed high accuracy which was validated by 3D finite element method (FEM3D) and experimental measurements. The accuracy of tool deflection calculation using THSM by computing, shank, flute and ball head deflection and also utilizing CSM to determine second moment of inertia showed notable improvements.