The hydrology of a sloping fragiaqualf : a thesis presented in partial fulfilment of the requirements for the degree of Master of Philosophy in Soil Science, Massey University

A field experiment was conducted on a sloping Tokomaru silt loam (Typic Fragiaqualf). This soil has a permeable topsoil, but is underlain with an impermeable fragipan at 500 - 700 mm. Paired runoff plots (100 m2 in area) were constructed, and over a four-year period, rainfall, water table levels and runoff were monitored. Infiltration and saturated hydraulic conductivity were also measured. During the study period, forty surface runoff events occurred with most of these being relatively minor events where less than 1 mm of runoff was generated. Subsurface flow rather than overland flow removed most of the excess rain over winter and early spring. The dominant surface-runoff-generating process was found to be saturation overland flow. Hortonian runoff only occurred when the infiltration capacity was reduced by pugging of the soil surface. When such a treatment was applied to one of the plots, the saturated hydraulic conductivity of the topsoil was reduced from 500 - 1200 mm/day to only 0.8 mm/day. For the damaged plot, 25% (1.8 mm) of the 7.2 mm of rain which fell over a seven hour period became overland flow. This compared to 18% (1.3 mm) of the rain becoming surface runoff on the undamaged plot. Aspects of modelling and simulation are discussed and several rainfall-runoff models are reviewed. A simple, physically-based, finite-difference model for predicting water table behaviour and runoff generation is described. The model uses the Dupuit-Forchheimer assumptions for flow below the water table, and it assumes a constant hydraulic potential between the water table and the surface. Water table behaviour during and following a rainstorm was predicted reasonably accurately. Using hourly rainfall data, the occurrence and magnitude of runoff surface events over a winter/spring period were simulated. The model was also used to illustrate the importance of slope angle in subsurface flow and runoff generation. Over a winter/spring period, a 100 m2 plot with a 10% slope was predicted to have nine days on which overland flow occurred, and subsurface flow rates which sometimes exceeded 30 mm/day. For the same period, a plot with a 2% slope was shown to have much less subsurface flow (with rates not exceeding 10 mm/day), and nineteen days of surface runoff

Cloning and expression of a thermostable α-galactosidase from the thermophilic fungus Talaromyces emersonii in the methylotrophic yeast Pichia pastoris

The first gene (alpha-gal1) encoding an extracellular alpha-Dgalactosidase from the thermophilic fungus Talaromyces emersonii was cloned and characterized. The alpha-gal1 gene consisted of an open reading frame of 1,792 base pairs interrupted by six introns that encoded a mature protein of 452 amino acids, including a 24 amino acid secretory signal sequence. The translated protein had highest identity with other fungal alpha-galactosidases belonging to glycosyl hydrolase family 27. The alpha-gal1 gene was overexpressed as a secretory protein with an N-terminal histidine tag in the methylotrophic yeast Pichia pastoris. Recombinant alpha-Gal1 was secreted into the culture medium as a monomeric glycoprotein with a maximal yield of 10.75 mg/l and purified to homogeneity using Hisbinding nickel-agarose affinity chromatography. The purified enzyme was maximally active at 70 degrees C, pH 4.5, and lost no activity over 10 days at 50 degrees C. alpha-Gal1 followed Michaelis-Menten kinetics (Vmax of 240.3 micronM/min/mg, Km of 0.294 mM) and was inhibited competitively by galactose (Km obs of 0.57 mM, Ki of 2.77 mM). The recombinant T. emersonii alpha-galactosidase displayed broad substrate preference, being active on both oligo- and polymeric substrates, yet had strict specificity for the alpha-galactosidic linkage. Owing to its substrate preference and noteworthy stability, alpha-Gal1 is of particular interest for possible biotechnological applications involving the processing of plant materials.J.S. thanks her supervisor at the University of Jyvaskyla, Emily Knott, for permission to perform her Masters degree research while on exchange at NUT Galway, and for constructive comments on the manuscript. J.S. and A.G. both received scholarships under EU Erasmus/Socrates bilateral agreement. Funding for this research was provided in part to M.G.T. under the National Development Plan, through the Food Institutional Research Measure, administered by the Department of Agriculture, Fisheries and Food, Ireland

Visual drainage assessment: A standardised visual soil assessment method for use in land drainage design in Ireland

peer-reviewedThe implementation of site-specific land drainage system designs is usually disregarded by landowners in favour of locally established ‘standard practice’ land drainage designs. This is due to a number of factors such as a limited understanding of soil–water interactions, lack of facilities for the measurement of soil’s physical or hydrological parameters and perceived time wastage and high costs. Hence there is a need for a site-specific drainage system design methodology that does not rely on inaccessible, time-consuming and/or expensive measurements of soil physical or hydrological properties. This requires a standardised process for deciphering the drainage characteristics of a given soil in the field. As an initial step, a new visual soil assessment method, referred to as visual drainage assessment (VDA), is presented whereby an approximation of the permeability of specific soil horizons is made using seven indicators (water seepage, pan layers, texture, porosity, consistence, stone content and root development) to provide a basis for the design of a site-specific drainage system. Across six poorly drained sites (1.3 ha to 2.6 ha in size) in south-west Ireland a VDA-based design was compared with (i) an ideal design (utilising soil physical measurements to elucidate soil hydraulic parameters) and (ii) a standard design (0.8 m deep drains at a 15 m spacing) by model estimate of water table control and rainfall recharge/drain discharge capacity. The VDA method, unlike standard design equivalents, provided a good approximation of an ideal (from measured hydrological properties) design and prescribed an equivalent land drainage system in the field. Mean modelled rainfall recharge/drain discharge capacity for the VDA (13.3 mm/day) and ideal (12.0 mm/day) designs were significantly higher (P < 0.001, s.e. 1.42 mm/day) than for the standard designs (0.5 mm/day), when assuming a design minimum water table depth of 0.45 m

Linking Hydro-Geophysics and Remote Sensing Technology for Sustainable Water and Agricultural Catchment Management

PosterThe acquisition of sub-surface data for agricultural purposes is traditionally achieved by in situ point sampling in the top 2m over limited target areas (farm scale ~ km2) and time periods. This approach is inadequate for integrated regional (water catchment ~ 100 km2) scale management strategies which require an understanding of processes varying over decadal time scales in the transition zone (~ 10’s m) from surface to bedrock. With global food demand expected to increase by 100% by 2050, there are worldwide concerns that achievement of production targets will be at the expense of water quality. In order to overcome the limitations of the traditional approach, this research programme will combine airborne and ground geophysics with remote sensing technologies to access hydrogeological and soil structure information on Irish Soils at multiple spatial scales. It will address this problem in the context of providing tools for the sustainable management of agricultural intensification envisioned in Food Harvest 2020 and Food Wise 2025 and considering the EU Habitats and Water Framework Directives (WFD), Clean Air Policy and Soil Thematic Strategies. The work will use existing ground based geophysical and hydrogeological data from Teagasc Agricultural Catchment Programme (ACP) and Heavy Soil sites co-located ground and airborne electromagnetic data. Neural Networks training and Machine learning approaches will supplement traditional geophysical workflows. Work will then focus on upscaling results from ACP to WFD catchment scale. This upscaling will require modification of traditional satellite remote sensing conceptual frameworks to analyse heterogeneous, multi-temporal data streams

Quantifying distortions in two-photon remote focussing microscope images using a volumetric calibration specimen

This Document is Protected by copyright and was first published by Frontiers. All rights reserved. it is reproduced with permission.Remote focussing microscopy allows sharp, in-focus images to be acquired at high speed from outside of the focal plane of an objective lens without any agitation of the specimen. However, without careful optical alignment, the advantages of remote focussing microscopy could be compromised by the introduction of depth-dependent scaling artifacts. To achieve an ideal alignment in a point-scanning remote focussing microscope, the lateral (XY) scan mirror pair must be imaged onto the back focal plane of both the reference and imaging objectives, in a telecentric arrangement. However, for many commercial objective lenses, it can be difficult to accurately locate the position of the back focal plane. This paper investigates the impact of this limitation on the fidelity of three-dimensional data sets of living cardiac tissue, specifically the introduction of distortions. These distortions limit the accuracy of sarcomere measurements taken directly from raw volumetric data. The origin of the distortion is first identified through simulation of a remote focussing microscope. Using a novel three-dimensional calibration specimen it was then possible to quantify experimentally the size of the distortion as a function of objective misalignment. Finally, by first approximating and then compensating the distortion in imaging data from whole heart rodent studies, the variance of sarcomere length (SL) measurements was reduced by almost 50%.Medical Research Council (MRC)Engineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC)British Heart Foundation Centre of Research Excellence, Oxfor

Phosphorus and nitrogen losses from temperate permanent grassland on clay-loam soil after the installation of artificial mole and gravel mole drainage

peer-reviewedMole (M) and gravel-mole (GM) drainage systems improve the permeability of soils with high clay contents. They collect and carry away infiltrating water during episodic rainfall events. Characterisation of nutrient fluxes (concentration and flows) in overland flow (OF) and in mole drain flow (MF) across sequential rainfall events is important for environmental assessment of such drainage systems. The objective of this study is to assess the impact of drainage systems on soil nutrient losses. Three treatments were imposed on grazed permanent grassland on a clay loam soil in Ireland (52°30′N, 08°12′W) slope 1.48%: undrained control (C), mole drainage (M) and gravel mole drainage (GM). Plots (100 m × 15 m) were arranged in a randomized complete block design with four replicated blocks. Nitrogen (N) and phosphorus (P) concentrations in OF, MF and groundwater (GW) were measured from each plot over 15 consecutive rainfall events. The results showed that M and GM (P < 0.05) deepened the watertable depth and decreased OF. M and GM increased losses of nitrate-N (22%) and ammonium-N (14%) in GW. Nitrate-N concentrations from all the flow pathways (mean and standard error (s.e.): 0.99 s.e. 0.10 mg L−1) were well below the 11.3 mg L−1 threshold for drinking water. Ammonium-N concentrations from all the flow pathways (mean: 0.64 s.e. 0.14 mg L−1) exceeded drinking water quality standards. On the other hand M and GM lowered total P losses (mean annual losses from C, M and GM: 918, 755 and 853 s.e. 14.1 g ha−1 year−1) by enhancing soil P sorption. Hence M and GM can be implemented on farms under similar management to that described in the present study with a minor impact on N (increased concentration on averaged 18% to GW) and P (reduced by on avenged 114 g ha−1 year−1)

Prebiotics from Marine Macroalgae for Human and Animal Health Applications

The marine environment is an untapped source of bioactive compounds. Specifically, marine macroalgae (seaweeds) are rich in polysaccharides that could potentially be exploited as prebiotic functional ingredients for both human and animal health applications. Prebiotics are non-digestible, selectively fermented compounds that stimulate the growth and/or activity of beneficial gut microbiota which, in turn, confer health benefits on the host. This review will introduce the concept and potential applications of prebiotics, followed by an outline of the chemistry of seaweed polysaccharides. Their potential for use as prebiotics for both humans and animals will be highlighted by reviewing data from both in vitro and in vivo studies conducted to date