Multiple Scale Homogenisation of Nutrient Movement and Crop Growth in Partially Saturated Soil

In this paper, we use multiple scale homogenisation to derive a set of averaged macroscale equations that describe the movement of nutrients in partially saturated soil that contains growing potato tubers. The soil is modelled as a poroelastic material, which is deformed by the growth of the tubers, where the growth of each tuber is dependent on the uptake of nutrients via a sink term within the soil representing root nutrient uptake. Special attention is paid to the reduction in void space, resulting change in local water content and the impact on nutrient diffusion within the soil as the tubers increase in size. To validate the multiple scale homogenisation procedure, we compare the system of homogenised equations to the original set of equations and find that the solutions between the two models differ by [Formula: see text]. However, we find that the computation time between the two sets of equations differs by several orders of magnitude. This is due to the combined effects of the complex three-dimensional geometry and the implementation of a moving boundary condition to capture tuber growth.

Imaging microstructure of the barley rhizosphere: particle packing and root hair influences

Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three-dimensional pore structure at a fine scale is scarce and often contradictory. Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (<250 μm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron-based X-ray computed tomography to visualise pore structure at the soil-root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1 mm of the root surface. Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions. A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.

Investigation of microvascular morphological measures for skeletal muscle tissue oxygenation by image-based modelling in three dimensions

The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, especially for skeletal muscle during exercise. Traditionally, microvascular oxygen supply capability is assessed by the analysis of morphological measures on transverse cross-sections of muscle, e.g. capillary density or capillary-to-fibre ratio. In this work, we investigate the relationship between microvascular structure and muscle tissue oxygenation in mice. Phase contrast imaging was performed using synchrotron radiation computed tomography (SR CT) to visualize red blood cells (RBCs) within the microvasculature in mouse soleus muscle. Image-based mathematical modelling of the oxygen diffusion from the RBCs into the muscle tissue was subsequently performed, as well as a morphometric analysis of the microvasculature. The mean tissue oxygenation was then compared with the morphological measures of the microvasculature. RBC volume fraction and spacing (mean distance of any point in tissue to the closest RBC) emerged as the best predictors for muscle tissue oxygenation, followed by length density (summed RBC length over muscle volume). The two-dimensional measures of capillary density and capillary-to-fibre ratio ranked last. We, therefore, conclude that, in order to assess the states of health of muscle tissue, it is advisable to rely on three-dimensional morphological measures rather than on the traditional two-dimensional measures.

Determination of macro-scale soil properties from pore-scale structures: model derivation

In this paper, we use homogenization to derive a set of macro-scale poro-elastic equations for soils composed of rigid solid particles, air-filled pore space and a poro-elastic mixed phase. We consider the derivation in the limit of large deformation and show that by solving representative problems on the micro-scale we can parametrize the macro-scale equations. To validate the homogenization procedure, we compare the predictions of the homogenized equations with those of the full equations for a range of different geometries and material properties. We show that the results differ by [Formula: see text] for all cases considered. The success of the homogenization scheme means that it can be used to determine the macro-scale poro-elastic properties of soils from the underlying structure. Hence, it will prove a valuable tool in both characterization and optimization.

Quantification of root water uptake in soil using X-ray computed tomography and image-based modelling

Spatially averaged models of root-soil interactions are often used to calculate plant water uptake. Using a combination of X-ray computed tomography (CT) and image-based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X-ray CT at 2, 4, 6, 8 and 12 d after transplanting. The roots were segmented using semi-automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image-based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image-based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image-based models with <2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.

Fluid flow in porous media using image-based modelling to parametrize Richards' equation

The parameters in Richards' equation are usually calculated from experimentally measured values of the soil-water characteristic curve and saturated hydraulic conductivity. The complex pore structures that often occur in porous media complicate such parametrization due to hysteresis between wetting and drying and the effects of tortuosity. Rather than estimate the parameters in Richards' equation from these indirect measurements, image-based modelling is used to investigate the relationship between the pore structure and the parameters. A three-dimensional, X-ray computed tomography image stack of a soil sample with voxel resolution of 6 μm has been used to create a computational mesh. The Cahn-Hilliard-Stokes equations for two-fluid flow, in this case water and air, were applied to this mesh and solved using the finite-element method in COMSOL Multiphysics. The upscaled parameters in Richards' equation are then obtained via homogenization. The effect on the soil-water retention curve due to three different contact angles, 0°, 20° and 60°, was also investigated. The results show that the pore structure affects the properties of the flow on the large scale, and different contact angles can change the parameters for Richards' equation.

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm-3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling.

Image-based modelling of nutrient movement in and around the rhizosphere

In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model.

Assessing the influence of the rhizosphere on soil hydraulic properties using X-ray computed tomography and numerical modelling

Understanding the dynamics of water distribution in soil is crucial for enhancing our knowledge of managing soil and water resources. The application of X-ray computed tomography (CT) to the plant and soil sciences is now well established. However, few studies have utilized the technique for visualizing water in soil pore spaces. Here this method is utilized to visualize the water in soil in situ and in three-dimensions at successive reductive matric potentials in bulk and rhizosphere soil. The measurements are combined with numerical modelling to determine the unsaturated hydraulic conductivity, providing a complete picture of the hydraulic properties of the soil. The technique was performed on soil cores that were sampled adjacent to established roots (rhizosphere soil) and from soil that had not been influenced by roots (bulk soil). A water release curve was obtained for the different soil types using measurements of their pore geometries derived from CT imaging and verified using conventional methods, such as pressure plates. The water, soil, and air phases from the images were segmented and quantified using image analysis. The water release characteristics obtained for the contrasting soils showed clear differences in hydraulic properties between rhizosphere and bulk soil, especially in clay soil. The data suggest that soils influenced by roots (rhizosphere soil) are less porous due to increased aggregation when compared with bulk soil. The information and insights obtained on the hydraulic properties of rhizosphere and bulk soil will enhance our understanding of rhizosphere biophysics and improve current water uptake models.

Multiscale models of colloidal dispersion of particles in nematic liquid crystals

We use homogenization theory to develop a multiscale model of colloidal dispersion of particles in nematic liquid crystals under weak-anchoring conditions. We validate the model by comparing it with simulations by using the Landau-de Gennes free energy and show that the agreement is excellent. We then use the multiscale model to study the effect that particle anisotropy has on the liquid crystal: spherically symmetric particles always reduce the effective elastic constant. Asymmetric particles introduce an effective alignment field that can increase the Fredericks threshold and decrease the switch-off time.

Multiscale modelling of hydraulic conductivity in vuggy porous media

Flow in both saturated and non-saturated vuggy porous media, i.e. soil, is inherently multiscale. The complex microporous structure of the soil aggregates and the wider vugs provides a multitude of flow pathways and has received significant attention from the X-ray computed tomography (CT) community with a constant drive to image at higher resolution. Using multiscale homogenization, we derive averaged equations to study the effects of the microscale structure on the macroscopic flow. The averaged model captures the underlying geometry through a series of cell problems and is verified through direct comparison to numerical simulations of the full structure. These methods offer significant reductions in computation time and allow us to perform three-dimensional calculations with complex geometries on a desktop PC. The results show that the surface roughness of the aggregate has a significantly greater effect on the flow than the microstructure within the aggregate. Hence, this is the region in which the resolution of X-ray CT for image-based modelling has the greatest impact.

High resolution synchrotron imaging of wheat root hairs growing in soil and image based modelling of phosphate uptake

· Root hairs are known to be highly important for uptake of sparingly soluble nutrients, particularly in nutrient deficient soils. Development of increasingly sophisticated mathematical models has allowed uptake characteristics to be quantified. However, modelling has been constrained by a lack of methods for imaging live root hairs growing in real soils. · We developed a plant growth protocol and used Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) to uncover the three-dimensional (3D) interactions of root hairs in real soil. We developed a model of phosphate uptake by root hairs based directly on the geometry of hairs and associated soil pores as revealed by imaging. · Previous modelling studies found that root hairs dominate phosphate uptake. By contrast, our study suggests that hairs and roots contribute equally. We show that uptake by hairs is more localized than by roots and strongly dependent on root hair and aggregate orientation. · The ability to image hair-soil interactions enables a step change in modelling approaches, allowing a more realistic treatment of processes at the scale of individual root hairs in soil pores.

Photorefractive control of surface plasmon polaritons in a hybrid liquid crystal cell

We present a photorefractive hybrid liquid crystal system that allows strong photorefractive effects on surface plasmon polaritons. We demonstrate its capability to couple energy between two 1.03 eV surface plasmon polariton modes with an efficiency of 25.3±2.3%. We present the energy and grating pitch dependence of the diffraction and a model that can qualitatively explain them.

Human immunodeficiency virus-infected patients with prior Pneumocystis pneumonia exhibit increased serologic reactivity to several major surface glycoprotein clones

Recombinant clones of the carboxyl terminus of the major surface glycoprotein (MsgC) of Pneumocystis jirovecii are useful for analyzing serologic responses in humans. However, there is no standardized set of antigens in general use, which could lead to conflicting results. We have previously shown that human immunodeficiency virus type 1 (HIV-1)-infected patients with prior Pneumocystis pneumonia (PcP+) responded more frequently and more strongly to a clone of MsgC than did HIV-1-infected patients without PcP (PcP-). Here we test three new clones of MsgC to determine the effect of antigenic sequence variation on immune reactivity in blood donors and HIV-infected patients previously analyzed for reactivity to our original MsgC clone. In Western blot analyses, PcP+ patients exhibited the highest frequency of reactivity to each MsgC clone, and the frequency of reactivity with all four MsgC clones together was significantly higher in sera from PcP+ patients than in sera from the other patient groups. Furthermore, in an enzyme-linked immunosorbent assay we found that the PcP+ population had the highest level of reactivity to two of the four clones tested. One of the new clones could distinguish between PcP+ and PcP- populations, and two MsgC clones could distinguish blood donors from the other patient populations. The results show that inherent differences in MsgC amino acid sequence can affect recognition by antibodies independently of variations in protein length or patient population, and the utility of a clone depends on its sequence and on the populations tested.

Effects of two nipple drinker types with different flow rates on the productive performance of broiler chickens during summerlike growing conditions

Three trials were conducted to study the effects of a high flow volume (2.3 mL/s) nipple waterer (HFN) versus a low flow volume (.4 mL/s) nipple waterer (LFN) on the productive performance of broiler chickens as measured by average body weight (kilograms), average feed conversion (kilograms:kilogram), and percentage mortality rate. Equal numbers of male and female birds were used during Trial 1; only male birds were used during Trials 2 and 3. All trials were conducted during the summer months. An attempt was made during Trial 2 to expose the birds to artificial heat stress. No differences were seen during any of the trials in feed conversion between the two treatments. In Trial 1 the only significant difference (P less than or equal to .05) exhibited was in average male body weight (1.87 kg HFN; 1.84 kg LFN). A highly significant difference (P less than or equal to .01) was seen in average body weight (1.75 kg HFN; 1.64 kg LFN) during Trial 2. Average body weight difference during Trial 3 was highly significant at 42 days of age but not at Day 49. Mortality rate figures during Trial 2 indicate a highly significant difference during the 38-day period prior to heat stress (2.2% LFN; .4% HFN), and significant difference during the heat stress period (38 to 44 days; 2.9% LFN; 1.5% HFN). During Trial 3 mortality rate differences were significant by 49 days (20.6% LFN; 11.4% HFN) although there was no difference at 42 days.(ABSTRACT TRUNCATED AT 250 WORDS)

The effect of age of breeder hens on residual yolk fat, and serum glucose and triglyceride concentrations of day-old broiler chicks

The fat content and the concentrations of glucose and triglyceride in day-old chicks hatched from 27 and 60 wk-old broiler-breeder hens were determined from pooled samples of residual yolk and blood serum, respectively. Serum glucose and triglyceride levels were unaffected (P greater than .05) by breeder age, although there was a linear (P less than .001; r = .67) relationship between these characteristics and chick weight. Yolk fat, adjusted for chick weight, was on the average 13% greater (P less than .05) in chicks from old breeders than chicks from young breeder hens. Yolk wet weight was not affected (P greater than .05) by breeder age. Results indicate that breeder age may affect chick performance through alterations in the fat content of residual yolk.

An intronic 10-base-pair deletion in a class II A beta gene affects RNA processing

Several biologically important examples of posttranscriptionally regulated genes have recently been described (T. Gerster, D. Picard, and W. Schaffner, Cell 45:45-52, 1986; R. Reeves, T.S. Elton, M.S. Nissen, D. Lehn, and K.R. Johnson, Proc. Natl. Acad. Sci. USA 84:6531-6535, 1987; H.A. Young, L. Varesio, and P. Hwu, Mol. Cell. Biol. 6:2253-2256, 1986). Little is known, however, regarding sequences that mediate posttranscriptional RNA stability. Characterization in our laboratory of a mutant murine B lymphoma, M12.C3, revealed a posttranscriptional defect affecting the synthesis of a major histocompatibility complex class II gene (A beta d) whose product normally controls both the specificity and magnitude of the immune response. Molecular studies revealed that the mutation responsible for diminished A beta d gene expression was an intronic deletion of 10 base pairs (bp) located 99 bp 5' of the third exon. This deletion lies in a region not known to be critical for accurate and efficient splicing. Furthermore, sequence analysis of amplified A beta-specific cDNA demonstrated that the small number of A beta d transcripts produced in the mutant cells was correctly spliced. It appears that the mechanism by which this intronic 10-bp deletion acts to decrease RNA stability is unlikely to be at the level of RNA splicing.

Statistical association of dietary components with Simonsiella species residing in normal human mouths

Members of the genus Simonsiella, aerobic, multicellular filamentous gliding bacteria, were detected in swabbings from the palates of 32% of 212 human subjects free of gross oral pathologies. Nutritional evaluations for 142 of the subjects showed a significantly greater daily intake among 53 Simonsiella carriers for 13 dietary variables, including four fat components, but there was no significantly greater daily intake for any of the carbohydrate components. Overall, there was a general excess dietary intake by Simonsiella carriers. The mean dietary intake of the carriers was numerically greater than that of the noncarriers for 70 of 74 dietary variables.

Isolation, characterization, and numerical taxonomy of Simonsiella strains from the oral cavities of cats, dogs, sheep, and humans

Forty-nine strains of the gliding prokaryote Simonsiella were isolated from the oral cavities of cats (8), dogs (19), sheep (4), and humans (18) in Southern California by a direct isolation procedure using a complex serum-enriched medium. The numerical taxonomic analysis (unweighted pair-group method using arithmetric averages) of 57 differential traits for each strain was based on standard bacteriological diagnostic tests and included the molar guanine-plus-cytosine contents of the DNA and the relative percentages of fatty acid contents reported earlier. The resulting phenogram clustered the strains of Simonsiella into groups that correlated with sources of origin. The study included the neotype strain of Simonsiella crassa (ATCC 27504, ICPB 3651, NCTC 10283) of Australian sheep origin. The strains isolated from dogs, sheep, and humans form clusters of organisms that appear to have become adapted to live in and possibly to have evolved with their respective "hosts". In our judgment, these source-of-origin clusters represent different "ecospecies".

Fatty acid composition of Simonsiella strains

Gas-liquid chromatography of methyl esters of bound fatty acids extracted from the cells of 48 Simonsiella strains showed that these aerobic, gliding, multicellular-filamentous bacteria have fatty acid profiles of the pattern considered typical of Gram-negative eubacteria. All strains contained predominantly tetradecanoic acid (29.5%), 9-hexadecenoic acid (22.2%), an unidentified acid with an equivalent chain length of approximately 20 carbon atoms (15.8%), and dodecanoic acid (11.4%). Discriminant analysis of the mean relative percentages of 12 fatty acids correctly assigned 94% of the strains to groups based on their source of origin (i.e., the oral cavities of sheep, cat, human or dog); the relative amounts of only 3 of the fatty acids (9-octadecenoic acid, hexadecanoic acid, and tetradecanoic acid) provided most of this discrimination.