Antimicrobial activity of truncated alpha-defensin (human neutrophil peptide (HNP)-1) analogues without disulphide bridges.

Antimicrobial peptides play an important role in host defence, particularly in the oral cavity where there is constant challenge by microorganisms. The a-defensin antimicrobial peptides comprise 30–50% of the total protein in the azurophilic granules of human neutrophils, the most abundant of which is human neutrophil peptide 1 (HNP-1). Despite its antimicrobial activity, a limiting factor in the potential therapeutic use of HNP-1 is its chemical synthesis with the correct disulphide topology. In the present study, we synthesised a range of truncated defensin analogues lacking disulphide bridges. All the analogues were modelled on the C-terminal region of HNP-1 and their antimicrobial activity was tested against a range of microorganisms, including oral pathogens. Although there was variability in the antimicrobial activity of the truncated analogues synthesised, a truncated peptide named 2Abz23S29 displayed a broad spectrum of antibacterial activity, effectively killing all the bacterial strains tested. The finding that truncated peptides, modelled on the C-terminal ß-hairpin region of HNP-1 but lacking disulphide bridges, display antimicrobial activity could aid their potential use in therapeutic interventions.

Development of composite tissue scaffolds containing naturally sourced mircoporous hydroxyapatite

The aims of this work were to investigate the conversion of a marine alga into hydroxyapatite (HA), and furthermore to design a composite bone tissue engineering scaffold comprising the synthesised HA within a porous bioresorbable polymer. The marine alga Phymatolithon calcareum, which exhibits a calcium carbonate honeycomb structure, with a natural architecture of interconnecting permeable pores (microporosity 4-11 mu m), provided the initial raw material for this study. The objective was to convert the alga into hydroxyapatite while maintaining its porous morphology using a sequential pyrolysis and chemical synthesis processes. Semi-quantitative XRD analysis of the post-hydrothermal material (pyrolised at 700-750 degrees C), indicated that the calcium phosphate (CaP) ceramic most likely consisted of a calcium carbonate macroporous lattice, with hydroxyapatite crystals on the surface of the macropores. Cell visibility (cytotoxicity) investigations of osteogenic cells were conducted on the CaP ceramic (i.e., the material post-hydrothermal analysis) which was found to be non-cytotoxic and displayed good biocompatibility when seeded with MG63 cells. Furthermore, a hot press scaffold fabrication technique was developed to produce a composite scaffold of CaP (derived from the marine alga) in a polycaprolactone (PCL) matrix. A salt leaching technique was further explored to introduce macroporosity to the structure (50-200 mu m). Analysis indicated that the scaffold contained both micro/macroporosity and mechanical strength, considered necessary for bone tissue engineering applications. (C) 2008 Published by Elsevier B.V.

A study of the relationship between process conditions and mechanical strength of mineralized red algae in the preparation of a marine-derived bone void filler

Bone void fillers that can enhance biological function to augment skeletal repair have significant therapeutic potential in bone replacement surgery. This work focuses on the development of a unique microporous (0.5-10 mu m) marine-derived calcium phosphate bioceramic granule. It was prepared fro Corallina officinalis, a mineralized red alga, using a novel manufacturing process. This involved thermal processing, followed by a low pressure-temperature chemical synthesis reaction. The study found that the ability to maintain the unique algal morphology was dependent on the thermal processing conditions. This study investigates the effect of thermal heat treatment on the physiochemical properties of the alga. Thermogravimetric analysis was used to monitor its thermal decomposition. The resultant thermograms indicated the presence of a residual organic phase at temperatures below 500 degrees C and an irreversible solid-state phase transition from mg-rich-calcite to calcium oxide at temperatures over 850 degrees C. Algae and synthetic calcite were evaluated following heat treatment in an air-circulating furance at temperatures ranging from 400 to 800 degrees C. The highest levels of mass loss occurred between 400-500 degrees C and 700-800 degrees C, which were attributed to the organic and carbonate decomposition respectively. The changes in mechanical strength were quantified using a simple mechanical test, which measured the bulk compressive strength of the algae. The mechanical test used may provide a useful evaluation of the compressive properties of similar bone void fillers that are in granular form. The study concluded that soak temperatures in the range of 600 to 700 degrees C provided the optimum physiochemical properties as a precursor to conversion to hydroxyapatite (HA). At these temperatures, a partial phase transition to calcium oxide occurred and the original skeletal morphology of the alga remained intact.

A dynamic sampling methodology for plasma etch processes using Gaussian process regression

Plasma etch is a key process in modern semiconductor manufacturing facilities as it offers process simplification and yet greater dimensional tolerances compared to wet chemical etch technology. The main challenge of operating plasma etchers is to maintain a consistent etch rate spatially and temporally for a given wafer and for successive wafers processed in the same etch tool. Etch rate measurements require expensive metrology steps and therefore in general only limited sampling is performed. Furthermore, the results of measurements are not accessible in real-time, limiting the options for run-to-run control. This paper investigates a Virtual Metrology (VM) enabled Dynamic Sampling (DS) methodology as an alternative paradigm for balancing the need to reduce costly metrology with the need to measure more frequently and in a timely fashion to enable wafer-to-wafer control. Using a Gaussian Process Regression (GPR) VM model for etch rate estimation of a plasma etch process, the proposed dynamic sampling methodology is demonstrated and evaluated for a number of different predictive dynamic sampling rules. © 2013 IEEE.

Derivatisable Cyanobactin Analogues: A Semisynthetic Approach

Many natural cyclic peptides have potent and potentially useful biological activities. Their use as therapeutic starting points is often limited by the quantities available, the lack of known biological targets and the practical limits on diversification to fine-tune their properties. We report the use of enzymes from the cyanobactin family to heterocyclise and macrocyclise chemically synthesised substrates so as to allow larger-scale syntheses and better control over derivatisation. We have made cyclic peptides containing orthogonal reactive groups, azide or dehydroalanine, that allow chemical diversification, including the use of fluorescent labels that can help in target identification. We show that the enzymes are compatible and efficient with such unnatural substrates. The combination of chemical synthesis and enzymatic transformation could help renew interest in investigating natural cyclic peptides with biological activity, as well as their unnatural analogues, as therapeutics.

Combining Bio- and Chemo-catalysis for the Sustainable Production of Chemicals

The combination of bio- and chemo-catalysis to form a single synthetic route is a powerful methodology for the improvement of chemical synthesis. The extreme methods of biocatalysis (whole cell and isolated enzyme) fulfill very different roles. Biocatalysis by isolated enzymes enables highly efficient chemical transformations of extremely high selectivity and low contamination; however, conditions and substrates are limited to a narrow range. Whole cell biocatalysis enables the conversion of crude substrates, such as those derived from biomass; however, the products tend to be impure and delivered in dilute aqueous solution. Chemocatalysis is a well-established technique, and the addition of chemical catalysis and chemocatalytic methods to biocatalysis enables synthetic chemists to avoid the shortcomings of a biocatalytic step. For example, in enzymatic catalysis the addition of a chemical catalyst can allow the conversion of a racemic alcohol to an enantiopure, instead of racemic, product. In whole cell biocatalysis chemical reagents can assist the separation, transformation, and further isolation of the functionality of interest. The cooperation of bio- and chemocatalysts enables sustainable production of chemicals that would be impossible using biocatalysis alone, while achieving selectivities and using substrates not currently possible with chemocatalysis alone.

Study of multiferroic materials

The present PhD work aims the research and development of materials that exhibit multiferroic properties, in particular having a significant interaction between ferromagnetism and ferroelectricity; either directly within an intrinsic single phase or by combining extrinsic materials, achieving the coupling of properties through mechanic phenomena of the respective magnetostriction and piezoelectricity. These hybrid properties will allow the cross modification of magnetic and electric polarization states by the application of cross external magnetic and/or electric fields, giving way to a vast area for scientific investigation and potential technological applications in a new generation of electronic devices, such as computer memories, signal processing, transducers, sensors, etc. Initial experimental work consisted in chemical synthesis of nano powders oxides by urea pyrolysis method: A series of ceramic bulk composites with potential multiferroic properties comprised: of LuMnO3 with La0.7Sr0.3MnO3 and BaTiO3 with La0.7Ba0.3MnO3; and a series based on the intrinsic multiferroic LuMn1-zO3 phase modified with of Manganese vacancies. The acquisition of a new magnetron RF sputtering deposition system, in the Physics Department of Aveiro University, contributed to the proposal of an analogous experimental study in multiferroic thin films and multilayer samples. Besides the operational debut of this equipment several technical upgrades were completed like: the design and construction of the heater electrical contacts; specific shutters and supports for the magnetrons and for the substrate holder and; the addition of mass flow controllers, which allowed the introduction of N2 or O2 active atmosphere in the chamber; and the addition of a second RF generator, enabling co-deposition of different targets. Base study of the deposition conditions and resulting thin films characteristics in different substrates was made from an extensive list of targets. Particular attention was given to thin film deposition of magnetic phases La1-xSrxMnO3, La1-xBaxMnO3 and Ni2+x-yMn1-xGa1+y alloy, from the respective targets: La0.7Sr0.3MnO3, La0.7Ba0.3MnO3; and NiGa with NiMn. Main structural characterization of samples was performed by conventional and high resolution X-Ray Diffraction (XRD); chemical composition was determined by Electron Dispersion Spectroscopy (EDS); magnetization measurements recur to a Vibrating Sample Magnetometer (VSM) prototype; and surface probing (SPM) using Magnetic-Force (MFM) and Piezo-Response (PFM) Microscopy. Results clearly show that the composite bulk samples (LuM+LSM and BTO+LBM) feat the intended quality objectives in terms of phase composition and purity, having spurious contents below 0.5 %. SEM images confirm compact grain packaging and size distribution around the 50 nm scale. Electric conductivity, magnetization intensity and magneto impedance spreading response are coherent with the relative amount of magnetic phase in the sample. The existence of coupling between the functional phases is confirmed by the Magnetoelectric effect measurements of the sample “78%LuM+22%LSM” reaching 300% of electric response for 1 T at 100 kHz; while in the “78%BTO+22%LBM” sample the structural transitions of the magnetic phase at ~350 K result in a inversion of ME coefficient the behavior. A functional Magneto-Resistance measurement system was assembled from the concept stage until the, development and operational status; it enabled to test samples from 77 to 350 K, under an applied magnetic field up to 1 Tesla with 360º horizontal rotation; this system was also designed to measure Hall effect and has the potential to be further upgraded. Under collaboration protocols established with national and international institutions, complementary courses and sample characterization studies were performed using Magneto-Resistance (MR), Magneto-Impedance (MZ) and Magneto-Electric (ME) measurements; Raman and X-ray Photoelectron Spectroscopy (XPS); SQUID and VSM magnetization; Scanning Electron Microscopy (SEM) and Rutherford Back Scattering (RBS); Scan Probe Microscopy (SPM) with Band Excitation Probe Spectroscopy (BEPS); Neutron Powder Diffraction (NPD) and Perturbed Angular Correlations (PAC). Additional collaboration in research projects outside the scope of multiferroic materials provided further experience in sample preparation and characterization techniques, namely VSM and XPS measurements were performed in cubane molecular complex compounds and enable to identify the oxidation state of the integrating cluster of Ru ions; also, XRD and EDS/SEM analysis of the acquired targets and substrates implied the devolution of some items not in conformity with the specifications. Direct cooperation with parallel research projects regarding multiferroic materials, enable the assess to supplementary samples, namely a preliminary series of nanopowder Y1-x-yCaxØyMn1O3 and of Eu0.8Y0.2MnO3, a series of micropowder composites of LuMnO3 with La0.625Sr0.375MnO3 and of BaTiO3 with hexagonal ferrites; mono and polycrystalline samples of Pr1-xCaxMnO3, La1-xSrxMnO3 and La1-xCaxMnO3.

Secondary effects of catalytic diesel particulate filters: copper-induced formation of PCDD/Fs.

Potential risks of a secondary formation of polychlorinated dibenzodioxins/furans (PCDD/Fs) were assessed for two cordierite-based, wall-through diesel particulate filters (DPFs) for which soot combustion was either catalyzed with an iron- or a copper-based fuel additive. A heavy duty diesel engine was used as test platform, applying the eight-stage ISO 8178/4 C1 cycle. DPF applications neither affected the engine performance, nor did they increase NO, NO2, CO, and CO2 emissions. The latter is a metric for fuel consumption. THC emissions decreased by about 40% when deploying DPFs. PCDD/F emissions, with a focus on tetra- to octachlorinated congeners, were compared under standard and worst case conditions (enhanced chlorine uptake). The iron-catalyzed DPF neither increased PCDD/F emissions, nor did it change the congener pattern, even when traces of chlorine became available. In case of copper, PCDD/F emissions increased by up to 3 orders of magnitude from 22 to 200 to 12 700 pg I-TEQ/L with fuels of < 2, 14, and 110 microg/g chlorine, respectively. Mainly lower chlorinated DD/Fs were formed. Based on these substantial effects on PCDD/F emissions, the copper-catalyzed DPF system was not approved for workplace applications, whereas the iron system fulfilled all the specifications of the Swiss procedures for DPF approval (VERT).

Melan-A/MART-1-specific CD4 T cells in melanoma patients: identification of new epitopes and ex vivo visualization of specific T cells by MHC class II tetramers.

Over the past decade, many efforts have been made to identify MHC class II-restricted epitopes from different tumor-associated Ags. Melan-A/MART-1(26-35) parental or Melan-A/MART-1(26-35(A27L)) analog epitopes have been widely used in melanoma immunotherapy to induce and boost CTL responses, but only one Th epitope is currently known (Melan-A51-73, DRB1*0401 restricted). In this study, we describe two novel Melan-A/MART-1-derived sequences recognized by CD4 T cells from melanoma patients. These epitopes can be mimicked by peptides Melan-A27-40 presented by HLA-DRB1*0101 and HLA-DRB1*0102 and Melan-A25-36 presented by HLA-DQB1*0602 and HLA-DRB1*0301. CD4 T cell clones specific for these epitopes recognize Melan-A/MART-1+ tumor cells and Melan-A/MART-1-transduced EBV-B cells and recognition is reduced by inhibitors of the MHC class II presentation pathway. This suggests that the epitopes are naturally processed and presented by EBV-B cells and melanoma cells. Moreover, Melan-A-specific Abs could be detected in the serum of patients with measurable CD4 T cell responses specific for Melan-A/MART-1. Interestingly, even the short Melan-A/MART-1(26-35(A27L)) peptide was recognized by CD4 T cells from HLA-DQ6+ and HLA-DR3+ melanoma patients. Using Melan-A/MART-1(25-36)/DQ6 tetramers, we could detect Ag-specific CD4 T cells directly ex vivo in circulating lymphocytes of a melanoma patient. Together, these results provide the basis for monitoring of naturally occurring and vaccine-induced Melan-A/MART-1-specific CD4 T cell responses, allowing precise and ex vivo characterization of responding T cells.

Tetrathiafulvalene and 2,2'-Bipyridine: Bridging both Worlds in the Pursuit of Novel Molecular Materials

The preparation and characterization of two families of building blocks for molecule-based magnetic and conducting materials are described in three projects. In the first project the synthesis and characterization of three bis-imine ligands LI - L3 is reported. Coordination of LI to a series of metal salts afforded the five novel coordination complexes Sn(L4)C4 (I), [Mn(L4)(u-CI)(CI)(EtOH)h (II), [CU(L4)(u-sal) h(CI04)2 (sal = salicylaldehyde anion) (III), [Fe(Ls)2]CI (IV) and [Fe(LI)h(u-O) (V). All complexes have been structurally and magnetically characterized. X-ray diffraction studies revealed that, upon coordination to Lewis acidic metal salts, the imine bonds of LI are susceptible to nucleophilic attack. As a consequence, the coordination complexes (I) - (IV) contain either the cyclised ligand L4 or hydrolysed ligand Ls. In contrast, the dimeric Fe3+ complex (V) comprises two intact ligand LI molecules. In. this complex, the ligand chelates two Fe(III) centres in a bis-bidentate manner through the lone pairs of a phenoxy oxygen and an imine nitrogen atom. Magnetic studies of complexes (II-V) indicate that the dominant interactions between neighbouring metal centres in all of the complexes are antiferromagnetic. In the second project the synthesis and characterization two families of TTF donors, namely the cyano aryl compounds (VI) - (XI) and the his-aryl TTF derivatives (XII) - (XIV) are reported. The crystal structures of compounds (VI), (VII), (IX) and (XII) exhibit regular stacks comprising of neutral donors. The UV -Vis spectra of compounds (VI) - (XIV) present an leT band, indicative of the transfer of electron density from the TTF donors to the aryl acceptor molecules. Chemical oxidation of donors (VI), (VII), (IX) and (XII) with iodine afforded a series of CT salts that where possible have been characterized by single crystal X -ray diffraction. Structural studies showed that the radical cations in these salts are organized in stacks comprising of dimers of oxidized TTF donors. All four salts behave as semiconductors, displaying room temperature conductivities ranging from 1.852 x 10-7 to 9.620 X 10-3 Scm-I. A second series of CT salts were successfully prepared via the technique of electrocrystallization. Following this methodology, single crystals of two CT salts were obtained. The single crystal X-ray structures of both salts are isostructural, displaying stacks formed by trimers of oxidized donors. Variable temperature conductivity measurements carried out on this series of CT salts reveal they also are semiconductors with conductivities ranging from 2.94 x 10-7 to 1.960 X 10-3 S em-I at room temperature. In the third project the synthesis and characterization of a series of MII(hfac)2 coordination complexes of donor ligand (XII) where M2+ = Co2+, Cu2+, Ni2+ and Zn2+ are reported. These complexes crystallize in a head-to-tail arrangement of TTF donor and bipyridine moieties, placing the metal centres and hfac ligands are located outside the stacks. Magnetic studies of the complexes (XV) - (XVIII) indicate that the bulky hfac ligands prevent neighbouring metal centres from assembling in close proximity, and thus they are magnetically isolated.

Luminescence tuning and enhanced nonlinear optical properties of nanocomposites of ZnO–TiO2

In this article we present the spectral and nonlinear optical properties of ZnO–TiO2 nanocomposites prepared by colloidal chemical synthesis. Emission peaks of ZnO–TiO2 nanocomposites change from 340 nm to 385 nm almost in proportion to changes in Eg. The nanocomposites show self-defocusing nonlinearity and good nonlinear absorption behaviour. The nonlinear refractive index and the nonlinear absorption increase with increasing TiO2 volume fraction at 532 nm and can be attributed to the enhancement of exciton oscillator strength. ZnO–TiO2 is a potential nanocomposite material for the tunable light emission and for the development of nonlinear optical devices with a relatively small limiting threshold

Spectral and Nonlinear Optical Characteristics of ZnO Nanocomposites

The spectral and nonlinear optical properties of ZnO based nanocomposites prepared by colloidal chemical synthesis are investigated. Very strong UV emissions are observed from ZnO–Ag, ZnO– Cu and ZnO–SiO2 nanocomposites. The strongest visible emission of a typical ZnO–Cu nanocomposite is over ten times stronger than that of pure Cu due to transition from deep donor level to the copper induced level. The optical band gap of ZnO–CdS and ZnO–TiO2 nanocomposites is tunable and emission peaks changes almost in proportion to changes in band gap. Nonlinear optical response of these nanocomposites is studied using nanosecond laser pulses from a tunable laser in the wavelength range of 450–650 nm at resonance and off-resonance wavelengths. The nonlinear response is wavelength dependent and switching from RSA to SA has been observed at resonant wavelengths. Such a change-over is related to the interplay of plasmon/exciton band bleach and optical limiting mechanisms. The observed nonlinear absorption is explained through two photon absorption followed by weak free carrier absoption, interband absorption and nonlinear scattering mechanisms. The nonlinearity of the silica colloid is low and its nonlinear response can be improved by making composites with ZnO and ZnO–TiO2. The increase of the third-order nonlinearity in the composites can be attributed to the enhancement of exciton oscillator strength. This study is important in identifying the spectral range and the composition over which the nonlinear material acts as an RSA based optical limiter. These nanocomposites can be used as optical limiters and are potential materials for the light emission and for the development of nonlinear optical devices with a relatively small limiting threshold.

Spectral and Nonlinear Optical Characteristics of ZnO Nanocomposites

The spectral and nonlinear optical properties of ZnO based nanocomposites prepared by colloidal chemical synthesis are investigated. Very strong UV emissions are observed from ZnO–Ag, ZnO– Cu and ZnO–SiO2 nanocomposites. The strongest visible emission of a typical ZnO–Cu nanocomposite is over ten times stronger than that of pure Cu due to transition from deep donor level to the copper induced level. The optical band gap of ZnO–CdS and ZnO–TiO2 nanocomposites is tunable and emission peaks changes almost in proportion to changes in band gap. Nonlinear optical response of these nanocomposites is studied using nanosecond laser pulses from a tunable laser in the wavelength range of 450–650 nm at resonance and off-resonance wavelengths. The nonlinear response is wavelength dependent and switching from RSA to SA has been observed at resonant wavelengths. Such a change-over is related to the interplay of plasmon/exciton band bleach and optical limiting mechanisms. The observed nonlinear absorption is explained through two photon absorption followed by weak free carrier absoption, interband absorption and nonlinear scattering mechanisms. The nonlinearity of the silica colloid is low and its nonlinear response can be improved by making composites with ZnO and ZnO–TiO2. The increase of the third-order nonlinearity in the composites can be attributed to the enhancement of exciton oscillator strength. This study is important in identifying the spectral range and the composition over which the nonlinear material acts as an RSA based optical limiter. These nanocomposites can be used as optical limiters and are potential materials for the light emission and for the development of nonlinear optical devices with a relatively small limiting threshold.

Spectral and nonlinear optical characteristics of nanocomposites of ZnO-CdS

In this article, we present the spectral and nonlinear optical properties of ZnO–CdS nanocomposites prepared by colloidal chemical synthesis. The optical band gap (Eg) of the material is tunable between 2.62 and 3.84 eV. The emission peaks of ZnO–CdS nanocomposites change from 385 to 520 nm almost in proportion to changes in Eg. It is possible to obtain a desired luminescence color from UV to green by simply adjusting the composition. The nonlinear optical response of these samples is studied by using nanosecond laser pulses from a tunable laser at the excitonic resonance and off-resonance wavelengths. The nonlinear response is wavelength dependent, and switching from saturable absorption (SA) to reverse SA (RSA) has been observed for samples as the excitation wavelength changes from the excitonic resonance to off-resonance wavelengths. Such a changeover in the sign of the nonlinearity of ZnO–CdS nanocomposites is related to the interplay of exciton bleach and optical limiting mechanisms. The ZnO–CdS nanocomposites show self-defocusing nonlinearity and good nonlinear absorption behavior at off-resonant wavelengths. The nonlinear refractive index and the nonlinear absorption increase with increasing CdS volume fraction at 532 nm. The observed nonlinear absorption is attributed to two photon absorption followed by weak free carrier absorption. The enhancement of the third-order nonlinearity in the composites can be attributed to the concentration of exciton oscillator strength. This study is important in identifying the spectral range and composition over which the nonlinear material acts as a RSA based optical limiter. ZnO–CdS is a potential nanocomposite material for the tunable light emission and for the development of nonlinear optical devices with a relatively small limiting threshold.