http://hdl.handle.net/10197/2707 2013-05-19T16:15:24Z http://hdl.handle.net/10197/3782 Biotransformation of fluorobiphenyl by Cunninghamella elegans Amadio, Jessica; Murphy, Cormac D. The fungus Cunninghamella elegans is a useful model of human catabolism of xenobiotics. In this paper, the biotransformation of fluorinated biphenyls by C. elegans was investigated by analysis of the culture supernatants with a variety of analytical techniques. 4-Fluorobiphenyl was principally transformed to 4-fluoro-4′-hydroxybiphenyl, but other mono- and dihydroxylated compounds were detected in organic extracts by gas chromatography–mass spectrometry. Additionally, fluorinated water-soluble products were detected by 19F NMR and were identified as sulphate and β-glucuronide conjugates. Other fluorobiphenyls (2-fluoro-, 4,4′-difluoro- and 2,3,4,5,6-pentafluoro-biphenyl) were catabolised by C. elegans, yielding mono- and dihydroxylated products, but phase II metabolites were detected from 4,4′-difluorobiphenyl only. 2010-01-01T00:00:00Z http://hdl.handle.net/10197/3781 Bacterial defluorination of 4-fluoroglutamic acid Donnelly, Clár; Murphy, Cormac D. Fluorinated amino acids are used as enzyme inhibitors, mechanistic probes and in the production of pharmacologically active peptides. Because enantiomerically pure 4-fluoroglutamate is difficult to prepare, the selective degradation of the l-isomer is a potentially convenient method of obtaining d-4-fluoroglutamate from the racemate. In this paper, we describe our investigations on the degradation of 4-fluoroglutamate by bacteria. Fluoride ion was detected in resting-cell cultures of a number of bacteria that were incubated with racemic 4-fluoroglutamate. Analysis of the culture supernatants by chiral gas chromatography–mass spectrometry revealed that only the l-isomer was degraded. The degradation of 4-fluoroglutamate was also examined in cell-free extracts of Streptomyces cattleya and Proteus mirabilis, and it was observed that equimolar concentrations of fluoride ion and ammonia were generated. The activity was located in the soluble fraction of cell extracts, thus is not related to the l-2-amino-4-chloro-4-pentenoic acid dehydrochlorinase previously identified in membrane fractions of P. mirabilis. 2007-01-01T00:00:00Z http://hdl.handle.net/10197/3745 Purification and properties of fluoroacetate dehalogenase from Pseudomonas fluorescens DSM 8341 Donnelly, Clár; Murphy, Cormac D. The degradation of fluoroacetate by microorganisms has been established for some time, although only a handful of dehalogenases capable of hydrolyzing the stable C-F bond have been studied. The bacterium Pseudomonas fluorescens DSM 8341 was originally isolated from soil and very readily degraded fluoroacetate, thus it was thought that its dehalogenase might have some desirable properties. The enzyme was purified from cell free extracts and characterised: it is a monomer of 32,500 Da, with a pH optimum of 8 and is stable between pH 4 and 10; its activity is stimulated by some metal ions (Mg2+, Mn2+ and Fe3+), but inhibited by others (Hg2+, Ag2+). The enzyme is specific for fluoroacetate, and the Km for this substrate (0.68 mM) is the lowest determined for enzymes of this type that have been investigated to date. 2009-01-01T00:00:00Z http://hdl.handle.net/10197/3700 Precursor-directed biosynthesis of fluorinated iturin A in Bacillus spp. Moran, Stephen; Rai, Dilip K.; Clark, Benjamin R.; Murphy, Cormac D. Some iturin A-producing strains of Bacillus subtilis will elaborate the novel fluorinated analogue when incubated with 3-fluoro-L-tyrosine. The activity of iturin A is dependent on the D-tyrosine residue and the presence of fluorotyrosine may result in an improvement of the biological properties of this lipopeptide. The fluorinated iturin might also be used as a probe for studying its interaction with biological membranes. 2009-01-01T00:00:00Z http://hdl.handle.net/10197/3699 Biosynthesis of pyrrolylpolyenes in Auxarthron umbrinum Clark, Benjamin R.; Murphy, Cormac D. The biosynthesis of the pyrrolylpolyene rumbrin (1) in the fungus Auxarthron umbrinum was elucidated using feeding studies with labelled precursors. Incorporation of stable isotopes from [15N]-proline, [13C]-methionine and [13C]-acetate confirmed that these were the precursors of the pyrrole moiety, methyl groups, and backbone of rumbrin, respectively. Label-dilution experiments with pyrrole-2-carboxylate confirmed it was a direct precursor in the biosynthesis of rumbrin. Both 3- and 4-chloropyrrolecarboxylates were also accepted as precursors in polyene production. 2009-01-01T00:00:00Z http://hdl.handle.net/10197/3386 Electrophoretic deposition of poly(3-decylthiophene) onto gold-mounted cadmium selenide nanorods Garate, Jose-Antonio; English, Niall J.; Singh, Ajay; Ryan, Kevin M.; Mooney, Damian A.; MacElroy, J. M. Don Molecular mechanisms of electrophoretic deposition (EPD) of poly(3-decylthiophene) (P3DT) molecules onto vertically aligned cadmium selenide arrays have been studied using large-scale, nonequilibrium molecular dynamics (MD), in the absence and presence of static external electric fields. The field application and larger polymer charges accelerated EPD. Placement of multiple polymers at the same lateral displacement from the surface reduced average deposition times due to “crowding”, giving monolayer coverage. These findings were used to develop and validate Brownian dynamics simulations of multilayer polymer EPD in scaled-up systems with larger inter-rod spacings, presenting a generalized picture in qualitative agreement with random sequential adsorption. 2011-09-21T00:00:00Z http://hdl.handle.net/10197/3016 First-principles study of the excited-state properties of coumarin-derived dyes in dye-sensitized solar cells Agrawal, Saurabh; Dev, Pratibha; English, Niall J.; Thampi, Ravindranathan; MacElroy, J. M. Don Using Time-Dependent Density Functional Theory (TD-DFT), we have investigated the optical properties of dye-sensitized solar cells (DSSCs) comprised of TiO2 nanoparticle sensitized with two coumarins, namely, NKX-2311 and NKX-2593. The two sensitizers (dyes) differ only in their linker moieties and are shown to have different absorption spectra when adsorbed on to the TiO2 surface. Knowledge of different light absorption and charge transfer (CT) behavior within these complexes is useful for further improving the photo-dynamics of newer organic dyes presently being designed and investigated worldwide. Moreover, we have also investigated the effect of deprotonation of the sensitizers' carboxylic groups during adsorption on the titania surface and the excited state electronic properties of the resulting species. 2011-06-23T00:00:00Z http://hdl.handle.net/10197/2961 Molecular dynamics study of water in contact with TiO2 rutile-110, 100, 101, 001 and anatase-101, 001 surface Kavathekar, Ritwik S.; Dev, Pratibha; English, Niall J.; MacElroy, J. M. Don We have carried out classical molecular dynamics of various surfaces of TiO2 with its interface with water. We report the geometrical features of the first and second monolayers of water using a Matsui Akaogi (MA) force field for the TiO2 surface and a flexible single point charge model for the water molecules. We show that the MA force field can be applied to surfaces other than Rutile-(110). It was found that water OH bond lengths, H-O-H bond angles and dipole moments do not vary due to the nature of the surface. However, their orientation within the first and second monolayers suggest that planar Rutile-(001) and Anatase-(001) surfaces may play an important role in not hindering removal of the products formed on these surfaces. Also, we discuss the effect of surface termination in order to explain the layering of water molecules throughout the simulation box. 2011-05-19T00:00:00Z http://hdl.handle.net/10197/2745 Characterisation of a modified rotating disk reactor for the cultivation of Staphylococcus epidermidis biofilm Cotter, John J.; O'Gara, James P.; Stewart, Philip S.; Pitts, Betsey; Casey, Eoin Aims:  The purpose of this study was to develop a system that would allow biofilms to be cultivated under strictly defined conditions in terms of dissolved oxygen, fluid shear and to assess whether the method was suitable for the detection of respiratory activity stratification in biofilm samples. Methods:  The system is a modified version a commercially available laboratory biofilm reactor and incorporates a number of features such as the provision of defined levels of dissolved oxygen, constant average shear, enhanced gas–liquid mass transfer, aseptic operation and the ability to remove biofilm for ex situ analysis during or after continuous cultivation. Conclusions:  The system was shown to be effective for the characterization of the effects of dissolved oxygen on a pure culture of Staphylococcus epidermidis. The versatility of the system offers the potential for cultivating pure culture biofilm in defined, controlled conditions and facilitates a range of analyses that can be performed ex situ. Significance and Impact of the Study:  The ability to provide strict regulation of environmental conditions and enhanced transfer of oxygen to the biofilm during cultivation are important, first because oxygen is known to regulate biofilm development in several micro-organisms and second because many conventional biofilm cultivation systems may not provide adequate oxygen supply to the biofilm. 2010-12-01T00:00:00Z http://hdl.handle.net/10197/2744 Oxygen-mediated regulation of biofilm development is controlled by the alternative sigma factor sigma(B) in Staphylococcus epidermidis Cotter, John J.; O'Gara, James P.; Mack, Dietrich; Casey, Eoin Using a modified rotating-disk reactor to sparge oxygen to Staphylococcus epidermidis cultures, we found that oxygen negatively regulates biofilm development by influencing the activity of {sigma}B. Under anaerobic conditions, increased {sigma}B activity activates icaADBC, which encodes enzymes responsible for polysaccharide intercellular adhesin synthesis, by repressing transcription of the negative regulator icaR. 2009-01-01T00:00:00Z http://hdl.handle.net/10197/2743 Treatment of fluoroacetate by a Pseudomonas fluorescens biofilm grown in membrane aerated biofilm reactor Heffernan, Barry; Murphy, Cormac D.; Syron, Eoin; Casey, Eoin Fluorinated organic compounds have widespread applications, and their accumulation in the environment is a concern. Biofilm reactors are an effective technology for the treatment of contaminated wastewater, yet almost no research has been conducted on the effectiveness of biofilms for the biodegradation of fluorinated aliphatic compounds. In this paper we describe experiments undertaken to investigate the degradation of fluoroacetate using a membrane aerated biofilm reactor (MABR) by Pseudomonas fluorescens DSM8341. The concentration of fluoroacetate in the medium influenced biofilm structure, with less dense biofilm observed at lower fluoroacetate loading rates. As biofilm thickness increased, oxygen utilization decreased, probably as a consequence of increased resistance to oxygen transfer. Furthermore, most of the biofilm was anaerobic, since oxygen penetration depth was less than 1000 μm. Biofilm performance, in terms of fluoroacetate removal efficiency, was improved by decreasing the fluoroacetate loading rate, however increasing the intramembrane oxygen pressure had little effect on biofilm performance. A mathematical model showed that while fluoroacetate does not penetrate the entire biofilm, the defluorination intermediate metabolite glycolate does, and consequently the biofilm was not carbon limited at the biofilm−membrane interface where oxygen concentrations were highest. The model also showed the accumulation of the free fluoride ion within the biofilm. Overflow metabolism of glycolate was identified to be most likely a result of a combination of oxygen limitation and free fluoride ion inhibition. The study demonstrated the potential of MABR for treating wastewater streams contaminated with organofluorine compounds. 2009-01-01T00:00:00Z http://hdl.handle.net/10197/2742 Comparison of planktonic and biofilm cultures of Pseudomonas fluorescens DSM 8341 cells grown on fluoroacetate Heffernan, Barry; Murphy, Cormac D.; Casey, Eoin Comparisons between the physiological properties of Pseudomonas fluorescens biofilm cells grown in a tubular biofilm reactor and planktonic cells grown in a chemostat were performed. Fluoroacetate was the sole carbon source for all experiments. The performance of cells was assessed using cell cycle kinetics and by determining specific fluoroacetate utilization rates. Cell cycle kinetics were studied by flow cytometry in conjunction with the fluorescent stain propidium iodide. Determination of the DNA content of planktonic and biofilm cultures showed little difference between the two modes of growth. Cultures with comparable specific glycolate utilization rates had similar percentages of cells in the B phase of the cell cycle, indicating similar growth rates. Specific fluoroacetate utilization rates showed the performance of planktonic cells to be superior to that of biofilm cells, with more fluoroacetate utilized per cell at similar specific fluoroacetate loading rates. A consequence of this decreased biofilm performance was the accumulation of glycolate in the effluent of biofilm cultures. This accumulation of glycolate was not observed in the effluent of planktonic cultures. Spatial stratification of oxygen within the biofilm was identified as a possible explanation for the overflow metabolism of glycolate and the decreased performance of the biofilm cells. 2009-05-01T00:00:00Z http://hdl.handle.net/10197/2729 Rapid depletion of dissolved oxygen in 96 well microtitre plate Staphylococcus epidermidis biofilm assays promotes biofilm development and is influenced by inoculum cell concentration Cotter, John J.; O'Gara, James P.; Casey, Eoin Biofilm-related research using 96-well microtiter plates involves static incubation of plates indiscriminate of environmental conditions, making oxygen availability an important variable which has not been considered to date. By directly measuring dissolved oxygen concentration over time we report here that dissolved oxygen is rapidly consumed in Staphylococcus epidermidis biofilm cultures grown in 96-well plates irrespective of the oxygen concentration in the gaseous environment in which the plates are incubated. These data indicate that depletion of dissolved oxygen during growth of bacterial biofilm cultures in 96-well plates may significantly influence biofilm production. Furthermore higher inoculum cell concentrations are associated with more rapid consumption of dissolved oxygen and higher levels of S. epidermidis biofilm production. Our data reveal that oxygen depletion during bacterial growth in 96-well plates may significantly influence biofilm production and should be considered in the interpretation of experimental data using this biofilm model. 2009-08-01T00:00:00Z http://hdl.handle.net/10197/2716 Phase diagrams of non-ionic microemulsions containing reducing agents and metal salts as bases for the synthesis of bimetallic nanoparticles Magno, Miguel; Angelescu, Daniel G.; Stubenrauch, Cosima Phase diagrams of microemulsions containing metal salt(s) and reducing agent, respectively, were studied in detail. The microemulsions were based on non-ionic surfactants, namely pure tetraethyleneglycol monododecylether, C12E4, and technical grade Brij30. We studied the influence of the metal salts H2PtCl6, Pb(NO3)2, Bi(NO3)3, H2PtCl6 + Pb(NO3)2 (1:1 mixture), and H2PtCl6 + Bi(NO3)3 (1:1 mixture) as well as of the reducing agent NaBH4 on the location of the phase boundaries. The focus was on the water emulsification failure boundary (wefb) where the aqueous phase forms spherical droplets. The temperature shifts of the wefb, which were caused by the presence of the salt(s), are directly related with the shift of the clouding points of the corresponding oil-free systems. The location of the wefb is affected in a complex manner by the pH (the lower the pH the higher the temperature at which the wefb occurred), the ionic strength and by specific salting-in or salting-out effects of the electrolyte ions. The desired overlap of the wefb of the microemulsions containing the metal salt(s) and the reducing agent, respectively, could be achieved by adding NaOH to the C12E4-based microemulsions and by titrating 1-octanol to the Brij30-based microemulsions, respectively. 2009-09-01T00:00:00Z http://hdl.handle.net/10197/2710 Phase diagrams of microemulsions containing reducing agents and metal salts as bases for the synthesis of metallic nanoparticles Najjar, Reza; Stubenrauch, Cosima We studied the phase diagrams of microemulsions with a view to using these systems for the synthesis of metallic Pt, Pb, and Bi nanoparticles as well as of intermetallic Pt/Pb and Pt/Bi nanoparticles. The microemulsions consisted of H2O/salt – n-decane – SDS – 1-butanol. The salt was either one metal precursor (H2PtCl6·6H2O, Pb(NO3)2, or Bi(NO3)3·5H2O), a mixture of two metal precursors (H2PtCl6·6H2O + Pb(NO3)2 or H2PtCl6·6H2O + Bi(NO3)3·5H2O), or the reducing agent (NaBH4). In addition, other salts needed to be added in order to solubilize the metal precursors, to stabilize the reducing agent, and to adjust the ionic strength. Combining the microemulsion (μe1) that contains the metal precursor(s) with the microemulsion (μe2) that contains the reducing agent leads to metallic nanoparticles. To study systematically how the shape and size of the synthesized metallic nanoparticles depend on the size and shape of the respective microemulsion droplets, first of all one has to find those conditions under which μe1 and μe2 have the same structure. For that purpose we determined the water emulsification failure boundary (wefb) of each microemulsion as it is at the wefb where the water droplets are known to be spherical. We found that the ionic strength (I) of the aqueous phase as well as the hard acid and hard base properties of the ions are the key tuning parameters for the location of the wefb. 2008-11-21T00:00:00Z