Description and critical appraisal of principal components analysis (PCA) methodology applied to pulsed-field gel electrophoresis profiles of methicillin-resistant Staphylococcus aureus isolates

Principal components analysis (PCA) has been described for over 50 years; however, it is rarely applied to the analysis of epidemiological data. In this study PCA was critically appraised in its ability to reveal relationships between pulsed-field gel electrophoresis (PFGE) profiles of methicillin- resistant Staphylococcus aureus (MRSA) in comparison to the more commonly employed cluster analysis and representation by dendrograms. The PFGE type following SmaI chromosomal digest was determined for 44 multidrug-resistant hospital-acquired methicillin-resistant S. aureus (MR-HA-MRSA) isolates, two multidrug-resistant community-acquired MRSA (MR-CA-MRSA), 50 hospital-acquired MRSA (HA-MRSA) isolates (from the University Hospital Birmingham, NHS Trust, UK) and 34 community-acquired MRSA (CA-MRSA) isolates (from general practitioners in Birmingham, UK). Strain relatedness was determined using Dice band-matching with UPGMA clustering and PCA. The results indicated that PCA revealed relationships between MRSA strains, which were more strongly correlated with known epidemiology, most likely because, unlike cluster analysis, PCA does not have the constraint of generating a hierarchic classification. In addition, PCA provides the opportunity for further analysis to identify key polymorphic bands within complex genotypic profiles, which is not always possible with dendrograms. Here we provide a detailed description of a PCA method for the analysis of PFGE profiles to complement further the epidemiological study of infectious disease. © 2005 Elsevier B.V. All rights reserved.

Refractive index sensing properties of long-period fibre grating with sol-gel derived coatings

Long-period fibre gratings (LPGs) have previously been used to detect quantities such as temperature, strain and refractive index (RI). The responsivity to surrounding refractive index means that, potentially, LPGs could be realised as optical biosensors for applications in biochemical and biomedical application areas. We report here to our best knowledge the first investigation on refractive index sensing properties of LPGs with sol-gel derived titanium and silicon oxide coatings. It is revealed that the RI sensitivity of an LPG is affected by both the thickness and the index value of the coating; the coating with higher index and thickness will enhance the LPG RI sensitivity significantly. The surrounding refractive index induced LPG resonance shift has been evaluated over the LPGs’ most sensitive RI region from 1.42 to 1.44. We have identified that, in this region, the uncoated LPG has an RI sensitivity of (-673.0±0.4)nm/uri (unit of refractive index) while the LPG coated with titanium oxide exhibits a sensitivity as high as (-1067.15±0.04)nm/uri.

Characterisation of Aeromonas strains and species by pulsed field gel electrophoresis and principal components analysis

Aeromonas genomes were investigated by restriction digesting chromosomal DNA with the endonuclease XbaI, separation of restriction fragments by pulsed field gel electrophoresis (PFGE) and principal components analysis (PCA) of resulting separation patterns. A. salmonicida salmonicida were unique amongst the isolates investigated. Separation profiles of these isolates were similar and all characterised by a distinct absence of bands in the 250kb region. Principal components analysis represented these strains as a clearly defined homogeneous group separated by insignificant Euclidian distances. However, A. salmonicida achromogenes isolates in common with those of A. hydrophila and A. sobria were shown by principal components analysis to be more heterogeneous in nature. Fragments from these isolates were more uniform in size distribution but as demonstrated by the Euclidian distances attained through PCA potentially characteristic of each strain. Furthermore passaging of Aeromonas isolates through an appropriate host did not greatly modify fragment separation profiles, indicative of the genomic stability of test aeromonads and the potential of restriction digesting/PFGE/PCA in Aeromonas typing.

Analysis of plasmid profiles of Aeromonas salmonicida isolates by pulsed field gel electrophoresis

Plasmid constitutions of Aeromonas salmonicida isolates were characterised by flat-bed and pulsed field gel electrophoresis. Resolution of plasmids by pulsed field gel electrophoresis was greater and more consistent than that achieved by flat-bed gel electrophoresis. The number of plasmids separated by pulsed field gel electrophoresis varied between A. salmonicida isolates, with five being the most common number present in the isolates used in this study. Plasmid profiles were diverse and the reproducibility of the distances migrated facilitated the use of principal components analysis for the characterisation of the isolates. Isolates were grouped according to the number of plasmids supported. Further principal components analysis of groups of isolates supporting five and seven plasmids showed a spatial separation of plasmids based upon distance migrated. Principal components analysis of plasmid profiles and antimicrobial minimum inhibitory concentrations could not be correlated suggesting that resistance to antimicrobial agents is not associated with either one plasmid or a particular plasmid constitution.

The degradation of gel-spun poly(beta-hydroxybutyrate) fibrous matrix

Poly(β-hydroxybutyrate), (PHB), is a biologically produced, biodegradable thennoplastic with commercial potential. In this work the qualitative and quantitative investigations of the structure and degradation of a previously unstudied, novel, fibrous form of PHB, were completed. This gel-spun PHB fibrous matrix, PHB(FM), which has a similar appearance to cotton wool, possesses a relatively complex structure which combines a large volume with a low mass and has potential for use as a wound scaffolding device. As a result of the intrinsic problems presented by this novel structure, a new experimental procedure was developed to analyze the degradation of the PHB to its monomer hydroxybutyric acid, (HBA). This procedure was used in an accelerated degradation model which accurately monitored the degradation of the undegraded and degraded fractions of a fibrous matrix and the degradation of its PHB component. The in vitro degradation mechanism was also monitored using phase contrast and scanning electron microscopy, differential scanning calorimetry, fibre diameter distributions and Fourier infra-red photoacoustic spectroscopy. The accelerated degradation model was used to predict the degradation of the samples in the physiological model and this provided a clearer picture as to the samples potential biodegradation as medical implantation devices. The degradation of the matrices was characterized by an initial penetration of the degradative medium and weakening of the fibre integrity due to cleavage of the ester linkages, this then led to the physical collapse of the fibres which increased the surface area to volume ratio of the sample and facilitated its degradation. Degradation in the later stages was reduced due to the experimental kinetics, compaction and degradation resistant material, most probably the highly crystalline regions of the PHB. The in vitro degradation of the PHB(FM) was influenced by blending with various polysaccharides, copolymerizing with poly(~-hydroxyvalerate), (PHV), and changes to the manufacturing process. The degradation was also detennined to be faster than that of conventional melt processed PHB based samples. It was concluded that the material factors such as processing, sample size and shape affected the degradation of PHB based samples with the major factor of sample surface area to volume ratio being of paramount importance in determining the degradation of a sample.

Characterizing the hierarchical structures of bioactive sol-gel silicate glass and hybrid scaffolds for bone regeneration

Bone is the second most widely transplanted tissue after blood. Synthetic alternatives are needed that can reduce the need for transplants and regenerate bone by acting as active temporary templates for bone growth. Bioactive glasses are one of the most promising bone replacement/regeneration materials because they bond to existing bone, are degradable and stimulate new bone growth by the action of their dissolution products on cells. Sol-gel-derived bioactive glasses can be foamed to produce interconnected macropores suitable for tissue ingrowth, particularly cell migration and vascularization and cell penetration. The scaffolds fulfil many of the criteria of an ideal synthetic bone graft, but are not suitable for all bone defect sites because they are brittle. One strategy for improving toughness of the scaffolds without losing their other beneficial properties is to synthesize inorganic/organic hybrids. These hybrids have polymers introduced into the sol-gel process so that the organic and inorganic components interact at the molecular level, providing control over mechanical properties and degradation rates. However, a full understanding of how each feature or property of the glass and hybrid scaffolds affects cellular response is needed to optimize the materials and ensure long-term success and clinical products. This review focuses on the techniques that have been developed for characterizing the hierarchical structures of sol-gel glasses and hybrids, from atomicscale amorphous networks, through the covalent bonding between components in hybrids and nanoporosity, to quantifying open macroporous networks of the scaffolds. Methods for non-destructive in situ monitoring of degradation and bioactivity mechanisms of the materials are also included. © 2012 The Royal Society.

A comparative study of the structure of sodium borophosphates made by sol-gel and melt-quench methods

The atomic scale structure of sodium borophosphates made by the sol-gel method is compared to those made by the melt-quench method. It is found that although the sol-gel generated materials have a higher tendency towards crystallization, they nevertheless show a qualitatively similar crystallization trend with composition to their melt-quench analogues; the progressive introduction of boron oxide into the phosphate network initially inhibits then promotes crystallization. At the composition associated with the most stable amorphous sodium borophosphate (20 mol% boron oxide), it is found that the atomic scale structure of the sol-gel synthesized network glass is almost identical to that of the corresponding melt-quenched one.

Bioactive glass sol-gel foam scaffolds:evolution of nanoporosity during processing and in situ monitoring of apatite layer formation using small- and wide-angle X-ray scattering

Recent work has highlighted the potential of sol-gel-derived calcium silicate glasses for the regeneration or replacement of damaged bone tissue. The work presented herein provides new insight into the processing of bioactive calcia-silica sol-gel foams, and the reaction mechanisms associated with them when immersed in vitro in a simulated body fluid (SBF). Small-angle X-ray scattering and wide-angle X-ray scattering (diffraction) have been used to study the stabilization of these foams via heat treatment, with analogous in situ time-resolved data being gathered for a foam immersed in SBF. During thermal processing, pore sizes have been identified in the range of 16.5-62.0 nm and are only present once foams have been heated to 400 degrees C and above. Calcium nitrate crystallites were present until foams were heated to 600 degrees C; the crystallite size varied from 75 to 145 nm and increased in size with heat treatment up to 300 degrees C, then decreased in size down to 95 rim at 400 degrees C. The in situ time-resolved data show that the average pore diameter decreases as a function of immersion time in SBF, as calcium phosphates grow on the glass surfaces. Over the same time, Bragg peaks indicative of tricalcium phosphate were evident after only 1-h immersion time, and later, hydroxycarbonate apatite was also seen. The hydroxycarbonate apatite appears to have preferred orientation in the (h,k,0) direction.

Effect of calcium source on structure and properties of sol-gel derived bioactive glasses

The aim was to determine the most effective calcium precursor for synthesis of sol-gel hybrids and for improving homogeneity of sol-gel bioactive glasses. Sol-gel derived bioactive calcium silicate glasses are one of the most promising materials for bone regeneration. Inorganic/organic hybrid materials, which are synthesized by incorporating a polymer into the sol-gel process, have also recently been produced to improve toughness. Calcium nitrate is conventionally used as the calcium source, but it has several disadvantages. Calcium nitrate causes inhomogeneity by forming calcium-rich regions, and it requires high temperature treatment (>400 C) for calcium to be incorporated into the silicate network. Nitrates are also toxic and need to be burnt off. Calcium nitrate therefore cannot be used in the synthesis of hybrids as the highest temperature used in the process is typically 40-60 C. Therefore, a different precursor is needed that can incorporate calcium into the silica network and enhance the homogeneity of the glasses at low (room) temperature. In this work, calcium methoxyethoxide (CME) was used to synthesize sol-gel bioactive glasses with a range of final processing temperatures from 60 to 800 C. Comparison is made between the use of CME and calcium chloride and calcium nitrate. Using advanced probe techniques, the temperature at which Ca is incorporated into the network was identified for 70S30C (70 mol % SiO, 30 mol % CaO) for each of the calcium precursors. When CaCl was used, the Ca did not seem to enter the network at any of the temperatures used. In contrast, Ca from CME entered the silica network at room temperature, as confirmed by X-ray diffraction, Si magic angle spinning nuclear magnetic resonance spectroscopy, and dissolution studies. CME should be used in preference to calcium salts for hybrid synthesis and may improve homogeneity of sol-gel glasses.

Evaluating transglutaminase crosslinked collagen gel systems for hard and soft tissue repair

Tissue Transglutaminase (TG2) and FXIIIa, members of the transglutaminase (TG) family, catalyses a transamidating reaction and form covalent bond between or within proteins. In bone development, both enzymes expressions correlate with the initial of the mineralisation process by osteoblasts and chondrocytes. Exogenous TG2 also promotes maturation of chondrocytes and mineralisation in pre-osteoblasts. To understand the role of endogenous TG2 in osteoblast mineralisation, the TG2 expression was examined during the human osteoblast (HOB) mineralisation. The expression of the endogenous TG2 increased during the mineralisation, yet, its expression was not essential for mineral deposition due to the compensation effect by other members in the TG family. The extracellular transamidating activity of HOBs was found increased during mineralisation and a shift from FXIIIa dominant- to TG2-dominant crosslinking activity was suggested after differentiation. However, the transamidating activity of both TG2 and FXIIIa were not critical for cell mineralisation. On the other hand, Exogenous TG2 was found to enhance wild type HOB and TG2 knockdown HOB mineral deposition. The transamidating activity of TG2 was not required but most likely a close conformation was essential for this enhancement. Results also demonstrated that exogenous TG2 may activate the ß-catenin pathway through LRP5 receptor thus contribute in cell mineralisation. This enhancement could be abolished by addition of ß-catenin inhibitors. Finally, using of TG2 crosslinked collagen gel for bone and cornea repair was evaluated. Crosslinked collagen gel showed promising results in improving HOB mineralisation, human corneal fibroblast (hCF) proliferation and migration. These effects might be resulted from the trapped TG2 within the collagen matrix and the alteration of matrix topography by TG2.

Refractive index sensing properties of long-period fibre grating with sol-gel derived coatings

Long-period fibre gratings (LPGs) have previously been used to detect quantities such as temperature, strain and refractive index (RI). The responsivity to surrounding refractive index means that, potentially, LPGs could be realised as optical biosensors for applications in biochemical and biomedical application areas. We report here to our best knowledge the first investigation on refractive index sensing properties of LPGs with sol-gel derived titanium and silicon oxide coatings. It is revealed that the RI sensitivity of an LPG is affected by both the thickness and the index value of the coating; the coating with higher index and thickness will enhance the LPG RI sensitivity significantly. The surrounding refractive index induced LPG resonance shift has been evaluated over the LPGs’ most sensitive RI region from 1.42 to 1.44. We have identified that, in this region, the uncoated LPG has an RI sensitivity of (-673.0±0.4)nm/uri (unit of refractive index) while the LPG coated with titanium oxide exhibits a sensitivity as high as (-1067.15±0.04)nm/uri.

Autonomous volume transitions of a polybase triblock copolymer gel in a chemically driven pH-oscillator

A pH-responsive ABA triblock copolymer, comprising poly(methyl methacrylate)-b/ock-poly(2-(diethylamino)ethyl methacrylate)-block-poly(methyl methacrylate) [PMMA-b-PDEA-b-PMMA], has been cast Into thin films with a well-defined microstructure. Small Angle X-ray Scattering (SAXS) and Atomic Force Microscopy (AFM) studies confirm that this copolymer forms a hydrogel consisting of PMMA spheres embedded within a polybase PDEA matrix, with the PMMA domains acting as physical cross-links. The hydrogel has a pH-reversible coil-globule transition at around pH 4.5. This responsive physical property was exploited by immersing a sample of copolymer hydrogel in an aqueous solution containing a cyclic pH-oscillating reaction, whereby the pH was continuously oscillated above and below the transition pH so as to induce autonomous volume transitions. The changes in microscopic and macroscopic length scales correlate closely during (de)swelling cycles, with affine behaviour occurring over five orders of magnitude. Copyright © 2007 WILEY-VCH Verlag GmbH & Co. KGaA,.

Monte Carlo and molecular dynamics simulations of methane in potassium montmorillonite clay hydrates at elevated pressures and temperatures

The structure and dynamics of methane in hydrated potassium montmorillonite clay have been studied under conditions encountered in sedimentary basin and compared to those of hydrated sodium montmorillonite clay using computer simulation techniques. The simulated systems contain two molecular layers of water and followed gradients of 150 barkm-1 and 30 Kkm-1 up to a maximum burial depth of 6 km. Methane particle is coordinated to about 19 oxygen atoms, with 6 of these coming from the clay surface oxygen. Potassium ions tend to move away from the center towards the clay surface, in contrast to the behavior observed with the hydrated sodium form. The clay surface affinity for methane was found to be higher in the hydrated K-form. Methane diffusion in the two-layer hydrated K-montmorillonite increases from 0.39×10-9 m2s-1 at 280 K to 3.27×10-9 m2s-1 at 460 K compared to 0.36×10-9 m2s-1 at 280 K to 4.26×10-9 m2s-1 at 460 K in Na-montmorillonite hydrate. The distributions of the potassium ions were found to vary in the hydrates when compared to those of sodium form. Water molecules were also found to be very mobile in the potassium clay hydrates compared to sodium clay hydrates. © 2004 Elsevier Inc. All All rights reserved.