Ba/Ca ratios in benthic foraminifera from recent core tops

The carbon isotope ratio (delta13C) and cadmium content (Cd/Ca) of benthic foraminifera shells have been used to reconstruct deep-water circulation patterns of the glacial oceans. These tracers co-vary with phosphorus in the modern ocean because they are nearly quantitatively regenerated from sinking biological debris in the upper water column. Hence they can be used to reconstruct the distribution of labile nutrients in glacial water masses. Independent constraints on glacial deep-ocean circulation patterns could be provided by a tracer of the distribution of silica and alkalinity, the deeply regenerated constituents of planktonic hard parts. Barium shares key aspects of its behaviour with these refractory nutrients because it is removed from solution in surface waters and incorporated into sinking particles which slowly dissolve deep in the water column and in the sediments. The fractionation of Ba between deep-water masses of the major ocean basins is largely controlled by thermohaline circulation patterns, so Ba conforms to different boundary conditions from Cd and 13C. As Ba substitutes into trigonal carbonates, it is a potential palaeoceano-graphic tracer if the Ba content of foraminifera shells reflects ambient dissolved Ba concentrations. Here we present data from Recent core-top benthic foraminifera which indicate that the Ba content of some recent calcitic benthic foraminifera does co-vary with bottom-water Ba.

Analyzation of marine snow and fecal pellets collected in sediment trap CBi-2 off Cape Blanc, Mauritania

We analyzed size-specific dry mass, sinking velocity, and apparent diffusivity in field-sampled marine snow, laboratory-made aggregates formed by diatoms or coccolithophorids, and small and large zooplankton fecal pellets with naturally varying content of ballast materials. Apparent diffusivity was measured directly inside aggregates and large (millimeter-long) fecal pellets using microsensors. Large fecal pellets, collected in the coastal upwelling off Cape Blanc, Mauritania, showed the highest volume-specific dry mass and sinking velocities because of a high content of opal, carbonate, and lithogenic material (mostly Saharan dust), which together comprised ~80% of the dry mass. The average solid matter density within these large fecal pellets was 1.7 g cm**-3, whereas their excess density was 0.25 ± 0.07 g cm**-3. Volume-specific dry mass of all sources of aggregates and fecal pellets ranged from 3.8 to 960 µg mm**-3, and average sinking velocities varied between 51 and 732 m d**-1. Porosity was >0.43 and >0.96 within fecal pellets and phytoplankton-derived aggregates, respectively. Averaged values of apparent diffusivity of gases within large fecal pellets and aggregates were 0.74 and 0.95 times that of the free diffusion coefficient in sea water, respectively. Ballast increases sinking velocity and, thus, also potential O2 fluxes to sedimenting aggregates and fecal pellets. Hence, ballast minerals limit the residence time of aggregates in the water column by increasing sinking velocity, but apparent diffusivity and potential oxygen supply within aggregates are high, whereby a large fraction of labile organic carbon can be respired during sedimentation.

Communities and microhabitats of living benthic foraminifera from the tropical East Atlantic

Living (Rose Bengal stained) benthic foraminifera were collected with a multicorer from six stations between 2°N and 12°S off West Africa. The foraminiferal communities in the investigated area reflect the direct influence of different productivity regimes, and are characterized by spatially and seasonally varying upwelling activity. At five stations, foraminiferal abundance coincides well with the gradient of surface productivity. However, at one station off the Congo River, the influence of strong fresh water discharge is documented. Although this station lies directly in the center of an upwelling area, foraminiferal standing stocks are surprisingly low. It is suggested that the Congo discharge may induce a fractionation of the organic matter into small and light particles of low nutritional content, by contrast to the relatively fast-sinking aggregates found in the centers of high productivity areas. Quality and quantity of the organic matter seem to influence the distribution of microhabitats as well. The flux of organic carbon to the sea-floor controls the sequence of degradation of organic matter in sediment and the position of different redox fronts. The vertical foraminiferal stratification within sediment closely parallels the distribution of oxygen and nitrate in porewater, and reflects different nutritive strategies and adaptation to different types of organic matter. The epifauna and shallow infauna colonize oxygenated sediments where labile organic matter is available. The intermediate infauna (M. barleeanum) is linked to the zone of nitrate reduction in sediments where epifaunal and shallow infaunal species are not competitive anymore, and must feed on bacterial biomass or on metabolizable nutritious particles produced by bacterial degradation of more refractory organic matter. The deep infauna shows its maximum distribution in anoxic sediments, where no easily metabolizable organic matter is available.

Polymerizable Peptide Monomers for the Targeted and Intracellular Delivery of Cancer Therapeutics

Thesis (Ph.D.)--University of Washington, 2016-06

Recombinant probiotics for treatment and prevention of enterotoxigenic Escherichia coli diarrhea

Background & Aims: We have developed a therapeutic strategy for gastrointestinal infections that is based on molecular mimicry of host receptors for bacterial toxins on the surface of harmless gut bacteria. The aim of this study was to apply this to the development of a recombinant probiotic for treatment and prevention of diarrheal disease caused by enterotoxigenic Escherichia coli strains that produce heat-labile enterotoxin. Methods: This was achieved by expressing glycosyltransferase genes from Neisseria meningitidis or Campylobacter jejuni in a harmless Escherichia coli strain (CWG:308), resulting in the production of a chimeric lipopolysaccharide capable of binding heat-labile enterotoxin with high avidity. Results: The strongest heat-labile enterotoxin binding was achieved with a construct (CWG308:pLNT) that expresses a mimic of lacto-N-neotetraose, which neutralized ≥ 93.8% of the heat-labile enterotoxin activity in culture lysates of diverse enterotoxigenic Escherichia coli strains of both human and porcine origin. When tested with purified heat-labile enterotoxin, it was capable of adsorbing approximately 5% of its own weight of toxin. Weaker toxin neutralization was achieved with a construct that mimicked the ganglioside GM2. Preabsorption with, or coadministration of, CWG308:pLNT also resulted in significant in vivo protection from heat-labile enterotoxin-induced fluid secretion in rabbit ligated ileal loops. Conclusions: Toxin-binding probiotics such as those described here have considerable potential for prophylaxis and treatment of enterotoxigenic Escherichia coli-induced travelers' diarrhea.

Plant-based immunocontraceptive control of wildlife - "potentials, limitations, and possums"

Possums (Trichosurus vulpecula), originally introduced from Australia, are spread over 90% of New Zealand and cause major economic and environmental damage. Immunocontraception has been suggested as a humane means to control them. Marsupial-specific reproductive antigens expressed at high levels in edible transgenic plant tissue might provide a safe, effective, and cheap oral delivery bait for immuno-contraceptive control. As proof of concept, female possums vaccinated with immunocontraceptive antigens showed reduced fertility, and possums fed with potato-expressed heat labile toxin-B (LT-B) had mucosal and systemic immune responses to the antigen. This demonstrated that immunocontraception was effective in possums and that oral delivery in edible plant material might be possible. Nuclear transformation with reporter genes showed that transgenic carrot roots accumulate high levels of foreign protein in edible tissues, indicating their potential as a delivery vector. However, prior to attempts at large scale production, more effective immunocontraceptive antigen-adjuvant formulations are probably required before plant-based immunocontraception can become a major tool for immunocontraceptive control of overabundant vertebrate pests. (c) 2004 Elsevier Ltd. All rights reserved.

Spatial patterns of aerobic and anaerobic mineralization rates and oxygen penetration dynamics in coral reef sediments

Oxygen consumption rates (OCR), aerobic mineralization and sulfate reduction rates (SRR) were studied in the permeable carbonate reef sediments of Heron Reef, Australia. We selected 4 stations with different hydrodynamic regimes for this study. In situ oxygen penetration into the sediments was measured with an autonomous microsensor profiler. Areal OCR were quantified from the measured oxygen penetration depth and volumetric OCR. Oxygen penetration and dynamics (median penetration depths at the 4 stations ranged between 0.3 and 2.2 cm), OCR (median 57 to 196 mmol C m(-2) d(-1)), aerobic mineralization (median 24 to 176 mmol C m(-2) d(-1)) and SRR (median 9 to 42 mmol C m(-2) d(-1)) were highly variable between sites. The supply of oxygen by pore water advection was a major cause for high mineralization rates by stimulating aerobic mineralization at all sites. However, estimated bottom water filtration rates could not explain the differences in volumetric OCR and SRR between the 4 stations. This suggests that local mineralization rates are additionally controlled by factors other than current driven pore water advection, e.g. by the distribution of the benthic fauna or by local differences in labile organic carbon supply from sources such as benthic photosynthesis. Carbon mineralization rates were among the highest reported for coral reef sediments, stressing the role of these sediments in the functioning of the reef ecosystem.

Dde as a protecting group for carbohydrate synthesis

Oligosaccharide synthesis using aminosugars requires the presence of a suitable amino protecting group. A number of protecting groups are currently used, and while many display favorable properties, most agents available still suffer from certain disadvantages. This report details the use of a hydrazine labile aminosugar protecting group, N -[1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl] (Dde), which can be introduced and removed in a facile and cost-effective manner.

Limitations on bioassays in macronutrient deficiency determination

Short-term nutrient bioassays can be used to assess labile nutrient availability in soils. These bioassays rely on a high number of plants and small soil volumes to exploit labile soil resources rapidly and assess potential nutrient deficiency. A comparison of the Neubauer bioassay with conventional pot trial assessment of P and S availability in a Yellow Kurosol was undertaken. Changes in labile soil nutrients and enzyme activity after bioassay assessment were also measured. The Neubauer bioassay was able to detect increased labile P availability following P fertiliser application to the soil. This corresponded with response to added P in a longer-term pot trial using maize. As expected, phosphatase activity increased following the bioassay and labile P was depleted by the plants. However, although a longer-term pot trial demonstrated the Yellow Kurosol was responsive to S fertilisation, labile S pools were sufficiently large that the short-term Neubauer bioassay detected no difference in S availability to plants. Both soil sulphatase activity and labile soil S were elevated following the bioassay. The short period of contact between the roots of the bioassay and the soil may have limited S uptake and therefore the ability of the bioassay to identify a S responsive soil. When using bioassay techniques to assess labile nutrient availability, it is critical that the size of the labile nutrient pool present be considered for each element, and that the period of contact between the bioassay and soil being tested is long enough for plant uptake to lower the nutrient supply to a level that limits further uptake.

Evidence for sensitisation of DNA to oxidative damage during isolation

The oxidative base lesion 8-oxo-deoxyguanosine (8-oxo-dG) has been identified in DNA isolated from normal tissue and may occur at elevated levels during disease. However, the use of phenol during DNA extraction may artificially elevate the detected levels of this lesion. Herein, we have performed a comparative methodological study using both pronase E and phenol extraction techniques; native or oxidatively stressed DNA was isolated to determine the validity of each extraction technique for the subsequent determination of 8-oxo-dG. Whilst the yields of DNA were comparable, after pronase E extraction there was no detectable induction of 8-oxo-dG in reextracted naked DNA or peripheral blood mononuclear cell DNA that had been oxidatively stressed. However, phenol extraction enhanced the basal levels of 8-oxo-dG detected, and also induced a significant increase in levels of the modified base after exposure to oxidative stress. The latter was dependent on the presence of foetal calf serum in the extracellular medium. We have confirmed that phenol extraction sensitises native DNA to subsequent oxidative damage. In addition, this work shows that the extent of sensitisation occurring during phenol extraction varies with the degree of oxidative damage already incurred and infers that labile guanine sites generated during oxidative stress may be detected as 8-oxo-dG residues after phenol extraction.

The co-ordination chemistry of tellurium and related selenium ligands

2-(2-pyridyl)phenyl(p-ethoxyphenyl)tellurium(II), (RR1Te) reacts with HgC12 at room temperature to give white HgCl2.RR1Te. On setting aside, or on warming the reaction mixture a yellow material, [R1HgCl.(RTeCl)2] is formed. Multinuclear NMR(125Te, 199Hg, 1H) and mass spectroscopy confirm the formulation, and confirm the ease of transfer of the p-ethoxyphenyl group (R1) between the metal centres. The crystal structure of the yellow material consists of two discrete RTeCl molecules together with a R1HgCl molecule. There is no dative bond formation between these species, hence the preferred description of the formation of an inclusion complex. The reaction of RR1Te with Copper(I) chloride in the cold gives an air sensitive yellow product Cu3Cl3(RR1Te)2(0.5CH3CN); under reflux in air changes to the green Cu2Cl(RR1Te)(0.5 EtOH). By contrast, the reaction of RR1Te with acetonitrile solution of Copper(II) salts under mild conditions affords the white materials CuCl(RR1Te) and CuBr(RR1Te)H2O. RR1Te reacts with PdCl2 and PtCl2 to give materials albeit not well defined, can be seen as intermediates to the synthesis of inorganic phase of the type M3XTe2XCl2X. Paramagnetism is associated with some of the palladium and platinum products. The 195Pt NMR measurement in DMSO establishes the presence of six platinum species, which are assigned to Pt(IV), Pt(III) or Pt(II). The reactions show that in the presence of PdCl2 or PtCl2 both R and R1 are very labile. The reaction of RHgCl(R= 2-(2-pyridyl)phenyl) with SeX4(X= Cl, Br) gives compounds which suggest that both Trans-metallation and redox processes are involved. By varying reaction conditions materials which appear to be intermediates in the trans-metallation process are isolated. Potentially bidentate tellurium ligands having molecular formula RTe(CH2)nTeR,Ln, (R= Ph,(t-Bu). C6H4, n = 5,10) are prepared. Palladium and Platinum complexes containing these ligands are prepared. Also complex Ph3SnC1L(L = p-EtO.C6H4) is prepared.

Assessing interactions of linear and nonlinear neuronal sources using MEG beamformers:a proof of concept

Objective: This study aimed to explore methods of assessing interactions between neuronal sources using MEG beamformers. However, beamformer methodology is based on the assumption of no linear long-term source interdependencies [VanVeen BD, vanDrongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng 1997;44:867-80; Robinson SE, Vrba J. Functional neuroimaging by synthetic aperture magnetometry (SAM). In: Recent advances in Biomagnetism. Sendai: Tohoku University Press; 1999. p. 302-5]. Although such long-term correlations are not efficient and should not be anticipated in a healthy brain [Friston KJ. The labile brain. I. Neuronal transients and nonlinear coupling. Philos Trans R Soc Lond B Biol Sci 2000;355:215-36], transient correlations seem to underlie functional cortical coordination [Singer W. Neuronal synchrony: a versatile code for the definition of relations? Neuron 1999;49-65; Rodriguez E, George N, Lachaux J, Martinerie J, Renault B, Varela F. Perception's shadow: long-distance synchronization of human brain activity. Nature 1999;397:430-3; Bressler SL, Kelso J. Cortical coordination dynamics and cognition. Trends Cogn Sci 2001;5:26-36]. Methods: Two periodic sources were simulated and the effects of transient source correlation on the spatial and temporal performance of the MEG beamformer were examined. Subsequently, the interdependencies of the reconstructed sources were investigated using coherence and phase synchronization analysis based on Mutual Information. Finally, two interacting nonlinear systems served as neuronal sources and their phase interdependencies were studied under realistic measurement conditions. Results: Both the spatial and the temporal beamformer source reconstructions were accurate as long as the transient source correlation did not exceed 30-40 percent of the duration of beamformer analysis. In addition, the interdependencies of periodic sources were preserved by the beamformer and phase synchronization of interacting nonlinear sources could be detected. Conclusions: MEG beamformer methods in conjunction with analysis of source interdependencies could provide accurate spatial and temporal descriptions of interactions between linear and nonlinear neuronal sources. Significance: The proposed methods can be used for the study of interactions between neuronal sources. © 2005 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

The analysis of organic matter in oil-shales

The organic matter in five oil shales (three from the Kimmeridge Clay sequence, one from the Oxford Clay sequence and one from the Julia Creek deposits in Australia) has been isolated by acid demineralisation, separated into kerogens and bitumens by solvent extraction and then characterised in some detail by chromatographic, spectroscopic and degradative techniques. Kerogens cannot be characterised as easily as bitumens because of their insolubility, and hence before any detailed molecular information can be obtained from them they must be degraded into lower molecular weight, more soluble components. Unfortunately, the determination of kerogen structures has all too often involved degradations that were far too harsh and which lead to destruction of much of the structural information. For this reason a number of milder more selective degradative procedures have been tested and used to probe the structure of kerogens. These are: 1. Lithium aluminium hydride reduction. - This procedure is commonly used to remove pyrite from kerogens and it may also increase their solubility by reduction of labile functional groups. Although reduction of the kerogens was confirmed, increases in solubility were correlated with pyrite content and not kerogen reduction. 2. O-methylation in the presence of a phase transfer catalyst. - By the removal of hydrogen bond interactions via O-methylation, it was possible to determine the contribution of such secondary interactions to the insolubility of the kerogens. Problems were encountered with the use of the phase transfer catalyst. 3. Stepwise alkaline potassium permanganate oxidation. - Significant kerogen dissolution was achieved using this procedure but uncontrolled oxidation of initial oxidation products proved to be a problem. A comparison with the peroxytrifluoroaceticacid oxidation of these kerogens was made. 4. Peroxytrifluoroacetic acid oxidation. - This was used because it preferentially degrades aromatic rings whilst leaving any benzylic positions intact. Considerable conversion of the kerogens into soluble products was achieved with this procedure. At all stages of degradation the products were fully characterised where possible using a variety of techniques including elemental analysis, solution state 1H and 13C nuclear magnetic resonance, solid state 13C nuclear magnetic resonance, gel-permeationchromatography, gas chromatography-mass spectroscopy, fourier transform infra-red spectroscopy and some ultra violet-visible spectroscopy.

Chemical modification of smectite clays

Today, speciality use organoclays are being developed for an increasingly large number of specific applications. Many of these, including use in cosmetics, polishes, greases and paints, require that the material be free from abrasive impurities so that the product retains a smooth `feel'. The traditional `wet' method preparation of organoclays inherently removes abrasives naturally present in the parent mineral clay, but it is time-consuming and expensive. The primary objective of this thesis was to explore the alternative `dry' method (which is both quicker and cheaper but which provides no refining of the parent clay) as a process, and to examine the nature of the organoclays produced, for the production of a wide range of commercially usable organophilic clays in a facile way. Natural Wyoming bentonite contains two quite different types of silicate surface (that of the clay mineral montmorillonite and that of a quartz impurity) that may interact with the cationic surfactant added in the `dry' process production of organoclays. However, it is oil shale, and not the quartz, that is chiefly responsible for the abrasive nature of the material, although air refinement in combination with the controlled milling of the bentonite as a pretreatment may offer a route to its removal. Ion exchange of Wyoming bentonite with a long chain quaternary ammonium salt using the `dry' process affords a partially exchanged, 69-78%, organoclay, with a monolayer formation of ammonium ions in the interlayer. Excess ion pairs are sorbed on the silicate surfaces of both the clay mineral and the quartz impurity phases. Such surface sorption is enhanced by the presence of very finely divided, super paramagnetic, Fe2O3 or Fe(O)(OH) contaminating the surfaces of the major mineral components. The sorbed material is labile to washing, and induces a measurable shielding of the 29Si nuclei in both clay and quartz phases in the MAS NMR experiment, due to an anisotropic magnetic susceptibility effect. XRD data for humidified samples reveal the interlamellar regions to be strongly hydrophobic, with the by-product sodium chloride being expelled to the external surfaces. Many organic cations will exchange onto a clay. The tetracationic cyclophane, and multipurpose receptor, cyclobis(paraquat-p-phenylene) undergoes ion exchange onto Wyoming bentonite to form a pillared clay with a very regular gallery height. The major plane of the cyclophane is normal to the silicate surfaces, thus allowing the cavity to remain available for complexation. A series of group VI substituted o-dimethoxybenzenes were introduced, and shown to participate in host/guest interactions with the cyclophane. Evidence is given which suggests that the binding of the host structure to a clay substrate offers advantages, not only of transportability and usability but of stability, to the charge-transfer complex which may prove useful in a variety of commercial applications. The fundamental relationship between particle size, cation exchange capacity and chemical composition of clays was also examined. For Wyoming bentonite the extent of isomorphous substitution increases with decreasing particle size, causing the CEC to similarly increase, although the isomorphous substitution site: edge site ratio remains invarient throughout the particle size range studied.

The central role of the neutrophil in ischaemic/reperfusion injury

Inadequate blood flow to an organ, ischaemia, may lead to both local and remote tissue injury characterized by oedema, increased microvascular permeability to protein and degradation of connective tissue components. This damage is probably caused by the accumulation and inappropriate activation of neutrophils which occurs when the tissue is reperfused. To test this hypothesis a number of in vitro models of the sequential stages of ischaemia/reperfusion injury were examined. Methods were initially developed to examine the adhesion of neutrophils to monolayers of a cultured endothelial cell line (ECV304) after periods of hypoxia and reoxygenation. Neutrophil migration in response to factors secreted by the treated endothelial cells was then assessed. The genesis of an inappropriate oxidative burst by the neutrophil upon exposure to endothelial chemoattractants and adhesion molecules was also measured. Finally to appraise how tissue function might be affected by endothelial cell hypoxia the contractility of vascular smooth muscle was examined. Neutrophil adhesion to ECV304 cells, which had been hypoxic for 4 hours and then reoxygenated for 30 minutes, was significantly increased. This response was probably initiated by reactive oxygen species (ROS) generated by the endothelial cells. Blockage of their production by allopurinol reduced the heightened adhesion. Similarly removal of ROS by superoxide dismutase or catalase also attenuated adhesion. ROS generation in turn caused the release of a soluble factor (s) which induced a conformational change on the neutrophil surface allowing it to bind to the intercellular adhesion molecule 1 (ICAM-1) on the endothelial cell. Soluble factor (s) from hypoxia/reoxygenated endothelial cells also had a powerful neutrophil chemoattractant ability. When neutrophils were exposed to both hypoxic/reoxygenated endothelial cells and the soluble factor (s) released by them a large oxidative burst was elicited. This response was greatest immediately after reoxygenation and one hour later was diminishing suggesting at least one of the components involved was labile. Analysis of the supernatant from hypoxic/reoxygenated endothelial cell cultures and studies using inhibitors of secretion suggested platelet activating factor (PAF) may be a major component in this overall sequence of events. Lesser roles for IL-8, TNF and LTB4 were also suggested. The secretory products from hypoxia/reoxygenated endothelial cells also affected smooth muscle contractility having an anti-vasoconstrictor or relaxation property, similar to that exerted by PAF.