Significance of Soil Lightness Versus Physicochemical Soil Properties in Semiarid Areas

This is an author's accepted manuscript of an article published in " Arid Land Research and Management"; Volume 28, Issue 4, 2014; copyright Taylor & Francis; available online at: http://www.tandfonline.com/doi/abs/10.1080/15324982.2014.882871Modern agriculture aims to encompass all soil attributes to optimize soil use and minimize environmental impacts. One of those attributes is soil color, which allows determining important soil variables for crop management and soil conservation. In this study, the relationships between lightness and several pedologic, topographic, and soil management variables were determined. One hundred and ten topsoil points were sampled in an area where the Mediterranean climate is the only homogeneous soil forming factor. Soil samples were air dried, crushed, and sieved, and lightness measurements were made using a trichromatic colorimeter. The relationships between lightness and soil-related parameters were carried out by means of bivariate linear correlation, and Mann-Witney and Kruskal-Wallis tests. Soil textural fractions (sand and silt), electrical conductivity and carbonates were statistically significant (p<0.001) and exhibited moderate correlation coefficients (0.32 0.45). Topographic variables (slope and aspect), soil organic carbon, iron, nitrogen, pH, and parent material (marls) exhibited lower effect on lightness. The response of lightness to clay content was highly conditioned by iron content. Stoniness, phosphorous, elevation, and soil management variables (irrigation and land use) were not statistically significant. The results obtained with calcareous samples from semiarid areas showed that soil lightness behavior agree with findings in developed soils, despite of the large differences in soil composition and the heterogeneity of the study area.Moreno-Ramón, H.; Marqués-Mateu, Á.; Ibañez Asensio, S. 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Accelerated boundary integral method for multiphase flow in non-periodic geometries

An accelerated boundary integral method for Stokes flow of a suspension of deformable particles is presented for an arbitrary domain and implemented for the important case of a planar slit geometry. The computational complexity of the algorithm scales as O(N) or $O(N\log N$), where $N$ is proportional to the product of number of particles and the number of elements employed to discretize the particle. This technique is enabled by the use of an alternative boundary integral formulation in which the velocity field is expressed in terms of a single layer integral alone, even in problems with non-matched viscosities. The density of the single layer integral is obtained from a Fredholm integral equation of the second kind involving the double layer integral. Acceleration in this implementation is provided by the use of General Geometry Ewald-like method (GGEM) for computing the velocity and stress fields driven by a set of point forces in the geometry of interest. For the particular case of the slit geometry, a Fourier-Chebyshev spectral discretization of GGEM is developed. Efficient implementations employing the GGEM methodology are presented for the resulting single and the double layer integrals. The implementation is validated with test problems on the velocity of rigid particles and drops between parallel walls in pressure driven flow, the Taylor deformation parameter of capsules in simple shear flow and the particle trajectory in pair collisions of capsules in shear flow. The computational complexity of the algorithm is verified with results from several large scale multiparticle simulations.Comment: Journal of Computational Physics, to appea

Transient Expression of Hemagglutinin Antigen from Low Pathogenic Avian Influenza A (H7N7) in Nicotiana benthamiana

The influenza A virus is of global concern for the poultry industry, especially the H5 and H7 subtypes as they have the potential to become highly pathogenic for poultry. In this study, the hemagglutinin (HA) of a low pathogenic avian influenza virus of the H7N7 subtype isolated from a Swedish mallard Anas platyrhynchos was sequenced, characterized and transiently expressed in Nicotiana benthamiana. Recently, plant expression systems have gained interest as an alternative for the production of vaccine antigens. To examine the possibility of expressing the HA protein in N. benthamiana, a cDNA fragment encoding the HA gene was synthesized de novo, modified with a Kozak sequence, a PR1a signal peptide, a C-terminal hexahistidine (6×His) tag, and an endoplasmic retention signal (SEKDEL). The construct was cloned into a Cowpea mosaic virus (CPMV)-based vector (pEAQ-HT) and the resulting pEAQ-HT-HA plasmid, along with a vector (pJL3:p19) containing the viral gene-silencing suppressor p19 from Tomato bushy stunt virus, was agro-infiltrated into N. benthamiana. The highest gene expression of recombinant plant-produced, uncleaved HA (rHA0), as measured by quantitative real-time PCR was detected at 6 days post infiltration (dpi). Guided by the gene expression profile, rHA0 protein was extracted at 6 dpi and subsequently purified utilizing the 6×His tag and immobilized metal ion adsorption chromatography. The yield was 0.2 g purified protein per kg fresh weight of leaves. Further molecular characterizations showed that the purified rHA0 protein was N-glycosylated and its identity confirmed by liquid chromatography-tandem mass spectrometry. In addition, the purified rHA0 exhibited hemagglutination and hemagglutination inhibition activity indicating that the rHA0 shares structural and functional properties with native HA protein of H7 influenza virus. Our results indicate that rHA0 maintained its native antigenicity and specificity, providing a good source of vaccine antigen to induce immune response in poultry species

Suppression of Methylation-Mediated Transcriptional Gene Silencing by βC1-SAHH Protein Interaction during Geminivirus-Betasatellite Infection

DNA methylation is a fundamental epigenetic modification that regulates gene expression and represses endogenous transposons and invading DNA viruses. As a counter-defense, the geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a betasatellite called DNA β. This study presents evidence that suppression of methylation-mediated TGS by the sole betasatellite-encoded protein, βC1, is crucial to the association of Tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB). We show that TYLCCNB complements Beet curly top virus (BCTV) L2- mutants deficient for methylation inhibition and TGS suppression, and that cytosine methylation levels in BCTV and TYLCCNV genomes, as well as the host genome, are substantially reduced by TYLCCNB or βC1 expression. We also demonstrate that while TYLCCNB or βC1 expression can reverse TGS, TYLCCNV by itself is ineffective. Thus its AC2/AL2 protein, known to have suppression activity in other geminiviruses, is likely a natural mutant in this respect. A yeast two-hybrid screen of candidate proteins, followed by bimolecular fluorescence complementation analysis, revealed that βC1 interacts with S-adenosyl homocysteine hydrolase (SAHH), a methyl cycle enzyme required for TGS. We further demonstrate that βC1 protein inhibits SAHH activity in vitro. That βC1 and other geminivirus proteins target the methyl cycle suggests that limiting its product, S-adenosyl methionine, may be a common viral strategy for methylation interference. We propose that inhibition of methylation and TGS by βC1 stabilizes geminivirus/betasatellite complexes

Rapid Transient Production in Plants by Replicating and Non-Replicating Vectors Yields High Quality Functional Anti-HIV Antibody

Background: The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product. Methodology/Principal Findings: To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV) RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue) of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER). Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO) cell-produced 2G12. Conclusions: Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for biopharmaceutical development and production

Signatures of degraded body tissues and environmental conditions in grave soils from a Roman and an Anglo-Scandinavian age burial from Hungate, York

Despite the importance of human burials in archaeological investigations of past peoples and their lives, the soil matrix that accommodates the remains is rarely considered, attention being focused mainly on visible features. The decomposition of a buried corpse and associated organic matter influences both the organic composition and, directly or indirectly, the microstructure of the burial matrix, producing signatures that could be preserved over archaeological timescales. If preserved, such signatures have potential to reveal aspects of the individual’s lifestyle and cultural practices as well as providing insights into taphonomic processes. Using organic chemical analysis and soil micromorphology we have identified organic signatures and physical characteristics relating to the presence of the body, and its decomposition in grave soils associated with two human skeletons (one Roman age and one Anglo-Scandinavian age) from Hungate, York, UK. The organic signatures, including contributions from body tissues, gut contents, bone degradation and input from microbiota, exhibit spatial variations with respect to anatomical location and features of the immediate burial environment. In the Roman grave broad changes in redox conditions associated with the decomposition of the corpse and disturbance from the excavation and use of an Anglo-Scandinavian age cess pit that partially cuts the grave were evident. Leachate from the cess pit was shown to exacerbate the degradation of the skeletal remains in the regions closest to it, also degrading and depleting spherulites in the soil, through decalcification of the bone and liberation of bone-derived cholesterol into the soil matrix. The findings from this work have implications for future archaeo- and contemporary forensic investigations of buried human remains

Swelling transition of a clay induced by heating

Clays are of paramount importance for soil stability, but also in applications ranging from oil recovery to composites and hydrogels. Generically, clays are divided into two subclasses: macroscopically swelling, ‘active’ clays that have the capacity for taking up large amounts of water to form stable gels, and ‘passive’ or non-swelling clays; the former stabilize soils whereas the latter are known to lead to landslides. However, it has been unclear so far what mechanisms underlie clay swelling. Here, we report the first observation of a temperature-induced transition from a passive to an active, swelling clay. We propose a simple description of the swelling transition; while net attractive interactions are dominant at low temperatures so that the clay particles remain attached to each other in stacks, at higher temperatures it is energetically favourable for the clay to swell due to the entropy that is gained by counterions which are liberated during swelling