Ex vivo culture of patient tissue and examination of gene delivery

Gene therapy has emerged as a realistic prospect for the treatment of cancer due to its potential for selective tumour cell targeting. The greatest challenge gene delivery vectors face is the ability to safely and efficiently deliver genes into target cells. The overall objectives of this thesis are to evaluate the efficacy of various gene delivery methods in a clinically relevant tumour model and to also investigate potential strategies for tumour selective delivery. We began with the development of a tumour slice model system using patient waste tissue. This model involves the use of fresh human tumour tissue, cut into thin slices and maintained ex vivo and is universally applicable to gene delivery methods, using a real-time luminescence detection method to assess gene delivery. The nature of the ex vivo culture system permitted examination of specific physiological variables, the influence of intratumoural factors and tissue specific effects on vector expression. Adenoviral vectors under the control of the human CXCR4 promoter demonstrated a 'tumour on' and 'normal off' expression profile when compared with the ubiquitously active CMV promoter when tested in patient tumour tissue. In addition, we developed an ex vivo system of changing oxygenation using the hypoxia inducer, cobalt, to mimic the transient hypoxic conditions found in solid tumours. We found that Adenoviral transgene expression was robust in the cycling hypoxic conditions relevant to solid tumours and re-oxygenation of chronically hypoxic tissue enhanced transgene expression. Finally, we demonstrated an AAV-based tumour targeting strategy using a tumour-selective promoter allowing for the efficient targeting of AAV vectors to cancer cells and the sparing of normal tissue in both murine metastatic liver tumours models and patient tissue. The thesis highlights the importance of indepth preclinical assessment of novel therapeutics and may serve as a platform for further testing of novel gene delivery approaches.

Biomethane production from grass silage: laboratory assessment to maximise yields

On-farm biogas production is typically associated with forage maize as the biomass source. Digesters are designed and operated with the focus of optimising the conditions for this feedstock. Thus, such systems may not be ideally suited to the digestion of grass. Ireland has ca. 3.85 million ha of grassland. Annual excess grass, surplus to livestock requirements, could potentially fuel an anaerobic digestion industry. Biomethane associated with biomass from 1.1 % of grassland in Ireland, could potentially generate over 10 % renewable energy supply in transport. This study aims to identify and optimise technologies for the production of biomethane from grass silage. Mono-digestion of grass silage and co-digestion with slurry, as would occur on Irish farms, is investigated in laboratory trials. Grass silage was shown to have 7 times greater methane potential than dairy slurry on a fresh weight basis (107 m3 t-1 v 16 m3 t-1). However, comprehensive trace element profiles indicated that cobalt, iron and nickel are deficient in mono-digestion of grass silage at a high organic loading rate (OLR) of 4.0 kg VS m-3 d-1. The addition of a slurry co-substrate was beneficial due to its wealth of essential trace elements. To stimulate hydrolysis of high lignocellulose grass silage, particle size reduction (physical) and rumen fluid addition (biological) were investigated. In a continuous trial, digestion of grass silage of <1 cm particle size achieved a specific methane yield of 371 L CH4 kg-1 VS when coupled with rumen fluid addition. The concept of demand driven biogas was also examined in a two-phase digestion system (leaching with UASB). When demand for electricity is low it is recommended to disconnect the UASB from the system and recirculate rumen fluid to increase volatile fatty acid (VFA) and soluble chemical oxygen demand (SCOD) production whilst minimising volatile solids (VS) destruction. At times of high demand for electricity, connection of the UASB increases the destruction of volatiles and associated biogas production. The above experiments are intended to assess a range of biogas production options from grass silage with a specific focus on maximising methane yields and provide a guideline for feasible design and operation of on-farm digesters in Ireland.

Potential impacts of leakage from deep CO2 geosequestration on overlying freshwater aquifers.

Carbon Capture and Storage may use deep saline aquifers for CO(2) sequestration, but small CO(2) leakage could pose a risk to overlying fresh groundwater. We performed laboratory incubations of CO(2) infiltration under oxidizing conditions for >300 days on samples from four freshwater aquifers to 1) understand how CO(2) leakage affects freshwater quality; 2) develop selection criteria for deep sequestration sites based on inorganic metal contamination caused by CO(2) leaks to shallow aquifers; and 3) identify geochemical signatures for early detection criteria. After exposure to CO(2), water pH declines of 1-2 units were apparent in all aquifer samples. CO(2) caused concentrations of the alkali and alkaline earths and manganese, cobalt, nickel, and iron to increase by more than 2 orders of magnitude. Potentially dangerous uranium and barium increased throughout the entire experiment in some samples. Solid-phase metal mobility, carbonate buffering capacity, and redox state in the shallow overlying aquifers influence the impact of CO(2) leakage and should be considered when selecting deep geosequestration sites. Manganese, iron, calcium, and pH could be used as geochemical markers of a CO(2) leak, as their concentrations increase within 2 weeks of exposure to CO(2).

Radioactive in situ hybridization for detecting diverse gene expression patterns in tissue.

Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we present a radioactive in situ hybridization method modified from Clayton et al. (1988)(1) that has been working successfully in our lab for many years, especially for adult vertebrate brains(2-5). The long complementary RNA (cRNA) probes to the target sequence allows for detection of low abundance transcripts(6,7). Incorporation of radioactive nucleotides into the cRNA probes allows for further detection sensitivity of low abundance transcripts and quantitative analyses, either by light sensitive x-ray film or emulsion coated over the tissue. These detection methods provide a long-term record of target gene expression. Compared with non-radioactive probe methods, such as DIG-labeling, the radioactive probe hybridization method does not require multiple amplification steps using HRP-antibodies and/or TSA kit to detect low abundance transcripts. Therefore, this method provides a linear relation between signal intensity and targeted mRNA amounts for quantitative analysis. It allows processing 100-200 slides simultaneously. It works well for different developmental stages of embryos. Most developmental studies of gene expression use whole embryos and non-radioactive approaches(8,9), in part because embryonic tissue is more fragile than adult tissue, with less cohesion between cells, making it difficult to see boundaries between cell populations with tissue sections. In contrast, our radioactive approach, due to the larger range of sensitivity, is able to obtain higher contrast in resolution of gene expression between tissue regions, making it easier to see boundaries between populations. Using this method, researchers could reveal the possible significance of a newly identified gene, and further predict the function of the gene of interest.

D-Amino acid peptide residualizing agents bearing N-hydroxysuccinimido- and maleimido-functional groups and their application for trastuzumab radioiodination.

INTRODUCTION: Proteins that undergo receptor-mediated endocytosis are subject to lysosomal degradation, requiring radioiodination methods that minimize loss of radioactivity from tumor cells after this process occurs. To accomplish this, we developed the residualizing radioiodination agent N(ϵ)-(3-[(*)I]iodobenzoyl)-Lys(5)-N(α)-maleimido-Gly(1)-D-GEEEK (Mal-D-GEEEK-[(*)I]IB), which enhanced tumor uptake but also increased kidney activity and necessitates generation of sulfhydryl moieties on the protein. The purpose of the current study was to synthesize and evaluate a new D-amino acid based agent that might avoid these potential problems. METHODS: N(α)-(3-iodobenzoyl)-(5-succinimidyloxycarbonyl)-D-EEEG (NHS-IB-D-EEEG), which contains 3 D-glutamates to provide negative charge and a N-hydroxysuccinimide function to permit conjugation to unmodified proteins, and the corresponding tin precursor were produced by solid phase peptide synthesis and subsequent conjugation with appropriate reagents. Radioiodination of the anti-HER2 antibody trastuzumab using NHS-IB-D-EEEG and Mal-D-GEEEK-IB was compared. Paired-label internalization assays on BT474 breast carcinoma cells and biodistribution studies in athymic mice bearing BT474M1 xenografts were performed to evaluate the two radioiodinated D-peptide trastuzumab conjugates. RESULTS: NHS-[(131)I]IB-D-EEEG was produced in 53.8%±13.4% and conjugated to trastuzumab in 39.5%±7.6% yield. Paired-label internalization assays with trastuzumab-NHS-[(131)I]IB-D-EEEG and trastuzumab-Mal-D-GEEEK-[(125)I]IB demonstrated similar intracellular trapping for both conjugates at 1h ((131)I, 84.4%±6.1%; (125)I, 88.6%±5.2%) through 24h ((131)I, 60.7%±6.8%; (125)I, 64.9%±6.9%). In the biodistribution experiment, tumor uptake peaked at 48 h (trastuzumab-NHS-[(131)I]IB-D-EEEG, 29.8%±3.6%ID/g; trastuzumab-Mal-D-GEEEK-[(125)I]IB, 45.3%±5.3%ID/g) and was significantly higher for (125)I at all time points. In general, normal tissue levels were lower for trastuzumab-NHS-[(131)I]IB-D-EEEG, with the differences being greatest in kidneys ((131)I, 2.2%±0.4%ID/g; (125)I, 16.9%±2.8%ID/g at 144 h). CONCLUSION: NHS-[(131)I]IB-D-EEEG warrants further evaluation as a residualizing radioiodination agent for labeling internalizing antibodies/fragments, particularly for applications where excessive renal accumulation could be problematic.

Global oceanic emission of ammonia: Constraints from seawater and atmospheric observations

Current global inventories of ammonia emissions identify the ocean as the largest natural source. This source depends on seawater pH, temperature, and the concentration of total seawater ammonia (NHx(sw)), which reflects a balance between remineralization of organic matter, uptake by plankton, and nitrification. Here we compare [NHx(sw)] from two global ocean biogeochemical models (BEC and COBALT) against extensive ocean observations. Simulated [NHx(sw)] are generally biased high. Improved simulation can be achieved in COBALT by increasing the plankton affinity for NHx within observed ranges. The resulting global ocean emissions is 2.5 TgN a−1, much lower than current literature values (7–23 TgN a−1), including the widely used Global Emissions InitiAtive (GEIA) inventory (8 TgN a−1). Such a weak ocean source implies that continental sources contribute more than half of atmospheric NHx over most of the ocean in the Northern Hemisphere. Ammonia emitted from oceanic sources is insufficient to neutralize sulfate aerosol acidity, consistent with observations. There is evidence over the Equatorial Pacific for a missing source of atmospheric ammonia that could be due to photolysis of marine organic nitrogen at the ocean surface or in the atmosphere. Accommodating this possible missing source yields a global ocean emission of ammonia in the range 2–5 TgN a−1, comparable in magnitude to other natural sources from open fires and soils.

Bioaccumulation Trends of Ten Metals in a Pelagic Food Web of Lake Champlain

Many metals have serious toxic effects when ingested by aquatic organisms, and the process of bioaccumulation intensifies this problem. A better understanding of bioaccumulation trends of anthropogenically introduced metals in freshwater food webs is necessary for the development of effective management strategies to protect aquatic organisms, as well as organisms (including humans) that consume top-predator fish in these food webs. Various fish species representing different trophic levels of a pelagic food chain were sampled from Lake Champlain (VT/NY). Atomic absorption spectrometry (AAS) was used to determine levels of chromium, copper, cobalt, cadmium, lead, zinc, nickel, rubidium, cesium and potassium in the fish samples. Metal concentrations for chromium, cobalt, nickel, cesium, cadmium (<5.0 ppm) and lead (<10.0 ppm) were found to be all below detection limits. Carbon and nitrogen isotopic ratios were analyzed to determine the trophic relationship of each fish species. Stable isotope and AAS metal data were used in tandem to produce linear regressions for each metal against trophic level to assess biomagnification. Both potassium and zinc showed no biomagnification because they are homeostatically regulated essential trace metals. Copper was under the detection limits for all fish species with the exception of the sea lamprey; but showed a significant biodiminution among the invertebrates and lamprey. Rubidium, a rarely studied metal, was shown to increase with trophic level in a marginally significant linear relationship suggesting biomagnification is possible where more trophic levels are sampled.

Phase transitions in epitaxial Ba0.5Sr0.5TiO3 thin films

Ba0.5Sr0.5TiO3 (BST) thin-film capacitor structures with various thicknesses, (50-1200 nm) and different strain conditions (on lanthanum strontium cobalt oxide La0.5Sr0.5CoO3 and strontium ruthenate SrRuO3 buffer layers) were made using pulsed laser deposition, and characterized by x-ray diffraction. The out-of-plane lattice parameter was followed as a function of temperature within the 100-300 K temperature interval. The phase sequence (cubic-tetragonal-orthorhombic-rhombohedral) known to exist in the bulk analog is shown to be strongly affected by both the stress conditions imposed by the buffer layer and the thickness of the BST film itself. Thus, no phase transition was found for the in-plane compressed BST films. On the stress-free BST films, on the contrary, more phase transitions were observed. It appeared that the complexity of structural phase transitions increased as the film thickness in this system was reduced.

El conjunto de azulejos nazaríes de principios del siglo XV del Museo Arqueológico de Córdoba

En este trabajo se analiza la iconografía y se concreta la datación y el origen del conjunto de treinta y cinco azulejos nazaríes decorados en cobalto y reflejo metálico procedentes de la que hemos identificado como capilla de Santiago en la antigua iglesia de San Bartolomé, erigida en la Judería de Córdoba tras el asalto de 1391. Se plantea, asimismo, que Diego Fernández Abencaçin, judeoconverso y alfaqueque mayor del rey y presumiblemente el comitente de la capilla funeraria, fue quien adquirió los azulejos. Hasta ahora, la única interpretación de las escenas figuradas que los decoran apuntaba a una supuesta representación de alegorías de los sentidos; no obstante, la comparación con ejemplos paralelos, el estudio de la indumentaria de los personajes y el estilo nos lleva a identificarlas como materialización de los gustos y aficiones de las clases privilegiadas a comienzos del s. XV: el amor cortés, la caza, la fauna, los ministriles –especialmente el ciego acompañado de lazarillo–, las danzarinas y los catadores de vino; costumbres que el alfaqueque conoció durante sus estancias en la corte y en el desempeño de sus obligaciones, no sólo como redentor de cautivos cristianos, sino como trujimán y enviado del infante don Fernando –futuro rey de Aragón– durante la campaña de Antequera ante la corte nazarita de Granada y en las treguas posteriorment e firmadas con Yusuf III, lo que ha posibilitado concretar la datación de los azulejos entre 1410 y 1415.

Polynuclear metal complexes obtained from the task-specific ionic liquid betainium bistriflimide

The task-specific ionic liquid betainium bis(trifluoromethylsulfonyl)imide, [Hbet][Tf2N], was used to dissolve metal oxides and hydroxides. The crystal structures of the resulting metal betaine bistriflimide complexes exhibit a rich structural variety. A trimeric structure was found for the cobalt(II) compound, [Co-3(bet)(8)(Hbet)(2)(H2O)(2)][Tf2N](9)[Hbet], a tetrameric structure for the manganese(II) and zinc(II) compound, [Mn-4(bet)(10)(H2O)(4)][Tf2N](8) and [Zn-4(bet)(10)(H2O)(2)][Tf2N](8), respectively, a pentameric structure for the nickel(II) compound, [Ni-5(bet)(12)(H2O)(6)][Tf2N](10), an oxo-hydroxo-cluster formation for the lead(II) compound, [(Pb4O)Pb(OH)(bet)(8)(Tf2N)3] [Tf2N](4)center dot MeOH, and a polymeric structure for the silver(I) compound, [Ag-2(bet)(2)(Tf2N)Ag-2(bet)(2)][Tf2N](3). The zwitterionic nature of the betaine ligand and the weakly coordinating ability of the bis(trifluoromethylsulfonyl)imide [Tf2N]- anion facilitates the incorporation of metal ions into oligonuclear and polynuclear metal complexes.

The structure of [Co(H-tptz)Cl-3] center dot H2O (tptz=2,4,6-tri(2-pyridyl)-1,3,5-triazine) prepared by crystallization from the ionic liquid, N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide

The structure of tris-chloro[2,6-bis(2'-pyridyl)-4-(2'-pyridinium)-1,3,5-triazine]cobalt(II) monohydrate, [Co(C18H13N6)Cl-3]center dot H2O (C2/c (No. 15), a = 7.783(11), b = 22.42(3), c = 11.001(15) angstrom, beta = 90.05(2)degrees), crystallized from the open air reaction of CoCl2 and 2,4,6-tri(2-pyridyl)-1,3,5-triazine in the ionic liquid, N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide is reported. The structure consists of six coordinate cobalt in an octahedral geometry bonded to the tridentate tptz ligand and three chlorines. The non-coordinating pyridyl group in the tptz ligand is protonated (with the protonated nitrogen crystallographically disordered over two possible sites), providing overall charge neutrality for the complex.

The efficacy of lead shielding in megavoltage radiotherapy.

The dose received by anatomical structures which are apparently shielded by lead blocks during a course of megavoltage radiotherapy may not be negligible. The dose has three main components; there is that due to radiation transmitted through the shielding block, that due to radiation scattered within the patient and that due to radiation scattered prior to reaching the patient and so circumventing the shield. A calculation method which separates the three components has been investigated and the results have been compared with measurements in a wide range of test situations for both cobalt-60 and 6 MV photon beams. The method of calculation predicts the dose behind the shielding block with acceptable accuracy in all the conditions investigated.

Task-specific ionic liquid for solubilizing metal oxides

Protonated betaine bis(trifluoromethylsulfonyl) imide is an ionic liquid with the ability to dissolve large quantities of metal oxides. This metal-solubilizing power is selective. Soluble are oxides of the trivalent rare earths, uranium(VI) oxide, zinc(II) oxide, cadmium( II) oxide, mercury( II) oxide, nickel( II) oxide, copper(II) oxide, palladium(II) oxide, lead(II) oxide, manganese( II) oxide, and silver( I) oxide. Insoluble or very poorly soluble are iron(III), manganese(IV), and cobalt oxides, as well as aluminum oxide and silicon dioxide. The metals can be stripped from the ionic liquid by treatment of the ionic liquid with an acidic aqueous solution. After transfer of the metal ions to the aqueous phase, the ionic liquid can be recycled for reuse. Betainium bis( trifluoromethylsulfonyl) imide forms one phase with water at high temperatures, whereas phase separation occurs below 55.5 degrees C ( temperature switch behavior). The mixtures of the ionic liquid with water also show a pH-dependent phase behavior: two phases occur at low pH, whereas one phase is present under neutral or alkaline conditions. The structures, the energetics, and the charge distribution of the betaine cation and the bis( trifluoromethylsulfonyl) imide anion, as well as the cation-anion pairs, were studied by density functional theory calculations.

Structural and magnetic properties of sol-gel Co2xNi0.5-xZn0.5-xFe2O4 thin films

Nanocrystalline Co2xNi0.5-xZn0.5-xFe2O4 (x = 0-0.5) thin films have been synthesized with various grain sizes by a sol-gel method on polycrystalline silicon substrates. The morphology as well as magnetic and microwave absorption properties of the films calcined at 1073 K were studied using X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, and vibrating sample magnetometry. All films were uniform with out microcracks . The Co content in the Co-Ni-Zn films resulted in a grain size ranging from 15 to 32 nm while it ranged from 33 to 49 nm in the corresponding powders. Saturation and remnant magnetization increased with increase in grain size, while coercivity demonstrated a drop due to multidomain behavior of crystallites for a given value of x. Saturation magnetization increased and remnant magnetization had a maximum as a function of grain size in dependent of x. In turn, coercivity increased with x independent of grain size. Complex permittivity of the Co-Ni-Zn ferrite films was measured in the frequency range 2-15 GHz. The highest hysteretic heating rate in the temperature range 315-355 K was observed in CoFe2O4. The maximum absorption band shifted from 13 to 11GHz as cobalt content increased from x = 0.1 to 0.2.

Voltage-activated currents in cardiac myocytes of the blue mussel, Mytilus edulis

Voltage-sensitive ionic currents were identified and characterised in ventricular myocytes of the bivalve mollusc, Mytilus edulis, using the whole-cell patch-clamp technique. Two outward currents could be distinguished. A potassium A current (I-A) activated at - 30 mV from a holding potential of - 60 mV. This transient current was inactivated by holding the cells at a potential of - 40 mV and was also blocked by applying 4-aminopyridine (3 mM) to the external bath solution. A second current was identified as a delayed rectifier (I-K). This also activated at - 30 mV but exhibited a sustained time course and was still activated at a holding potential of - 40 mV. Both outward currents were reduced in the presence of tetraethylammonium ions (30 mM). A small number of heart cells also showed an inward sodium current (I-Na). This current appeared at potentials more positive than - 50 mV, reached a maximum at - 20 mV, and decreased with further depolarisation. I-Na was inactivated at a holding potential of - 40 mV and was blocked by tetrodotoxin (1 mu M). A second inward current had a sustained time course and was not inactivated by holding the cell at a potential of -40 mV, and was also not abolished by tetrodotoxin. This current peaked at 0 mV, decreasing with further depolarisation. Furthermore, it was enhanced by the addition of barium ions (3 mM) to the bath and was blocked by external cobalt (2 mM) or nifedipine (15 mu M) These findings are consistent with this being an L-type calcium current (I-Ca) The possible physiological roles of these currents in M. edulis heart are discussed. (C) 1999 Elsevier Science Inc. All rights reserved.