Measurement of the spatial distribution of mucilage around roots using infrared spectroscopy

Mucilage is a mixture of polysaccharides and some lipids which is secreted by the root tip. It facilitates plant nutrient acquisition, stabilizes aggregates, reduces lubrication during plant growth and may increase rhizosphere water content due to its high water holding capacity. So far there is no method to measure the spatial distribution of mucilage in soil around roots. The aim of this study was to test whether infrared spectroscopy can be applied to quantify gradients of mucilage around roots in soil. The C-H to C-O ratio obtained from infrared spectroscopy measurements is an indicator of soil hydrophobicity. As Mucilage turns hydrophobic after drying we hypothesized that mucilage can be detected by the C-H to C-O ratio measured with infrared spectroscopy. We grew maize plants in rhizoboxes filled with quartz silt. Before measurement the planted containers were dried and the roots were removed from soil. Infrared spectroscopy measurements were conducted with a spatial resolution of 50x50 µm a) radially with increasing distance from the root channel center and b) axially with increasing distance from the root channel tip. In parallel, the contact angle, which also indicates soil hydrophobicity, was quantified in the same locations. Both measurements were additionally conducted on glass slides covered with quartz silt mixed with given concentrations of mucilage. The measurements on the glass slides revealed that the C-H to C-O ratio and the contact angle measurements correlated well with the mucilage concentration in soil. Similarly, the infrared spectroscopy measurements in in the rhizoboxes revealed that radial profiles of mucilage around roots can be quantified: while the C-H to C-O ratio was highest inside the root channels, it decreased to the bulk soil values 0.7 mm in radial direction from the border of the root channel. In axial direction the C-H to C-O ratio did not change significantly, indicating that those compounds causing hydrophobicity of mucilage are not easily degraded by soil microorganisms. We showed that infrared spectroscopy can be applied to measure profiles of mucilage around roots in soil. The radial profiles of mucilage were narrower than those reported for other rhizodeposits which may be explained by the viscosity of mucilage

The DEEP2 Galaxy Redshift Survey: Clustering of Groups and Group Galaxies at z~1

We study the clustering properties of groups and of galaxies in groups in the DEEP2 Galaxy Redshift Survey dataset at z~1. Four clustering measures are presented: 1) the group correlation function for 460 groups with estimated velocity dispersions of sigma>200 km/s, 2) the galaxy correlation for the full galaxy sample, using a flux-limited sample of 9800 objects between 0.7<z<1.0, 3) the galaxy correlation for galaxies in groups, and 4) the group-galaxy cross-correlation function. Using the observed number density and clustering amplitude of the groups, the estimated minimum group dark matter halo mass is M_min~6 10^12 h^-1 M_Sun for a flat LCDM cosmology. Groups are more clustered than galaxies, with a relative bias of b=1.7 +/-0.04 on scales r_p=0.5-15 Mpc/h. Galaxies in groups are also more clustered than the full galaxy sample, with a scale-dependent relative bias which falls from b~2.5 +/-0.3 at r_p=0.1 Mpc/h to b~1 +/-0.5 at r_p=10 Mpc/h. The correlation functions for all galaxies and galaxies in groups can be fit by a power-law on scales r_p=0.05-20 Mpc/h. We empirically measure the contribution to the projected correlation function for galaxies in groups from a `one-halo' term and a `two-halo' term by counting pairs of galaxies in the same or in different groups. The projected cross-correlation between shows that red galaxies are more centrally concentrated in groups than blue galaxies at z~1. DEEP2 galaxies in groups appear to have a shallower radial distribution than that of mock galaxy catalogs made from N-body simulations, which assume a central galaxy surrounded by satellite galaxies with an NFW profile. We show that the clustering of galaxies in groups can be used to place tighter constraints on the halo model than can be gained from using the usual galaxy correlation function alone.Comment: 22 pages, 12 figures, in emulateapj format, accepted to ApJ, minor changes made to match published versio

Colloid transport through soil and other porous media under transient flow conditions—A review

Understanding colloid transport in porous media under transient-flow conditions is crucial in understanding contaminant transport in soil or the vadose zone where flow conditions vary constantly. In this article, we provide a review of experimental studies, numerical approaches, and new technologies available to determine the transport of colloids in transient flow. Experiments indicate that soil structure and preferential flow are primary factors. In undisturbed soils with preferential flow pathways, macropores serve as main conduits for colloid transport. In homogeneously packed soil, the soil matrix often serves as filter. At the macroscale, transient flow facilitates colloid transport by frequently disturbing the force balance that retains colloids in the soil as indicated by the offset between colloid breakthrough peaks and discharge peaks. At the pore-scale and under saturated condition, straining, and attachment at solid–water interfaces are the main mechanisms for colloid retention. Variably saturated conditions add more complexity, such as immobile water zones, film straining, attachment to air–water interfaces, and air–water–solid contact lines. Filter ripening, size exclusion, ionic strength, and hydrophobicity are identified as the most influential factors. Our review indicates that microscale and continuum-scale models for colloid transport under transient-flow conditions are rare, compared to the numerous steady-state models. The few transient flow models that do exist are highly parameterized and suffer from a lack of a priori information of required pore-scale parameters. However, new techniques are becoming available to measure colloid transport in real-time and in a nondestructive way that might help to better understand transient flow colloid transport. This article is categorized under: Science of Water &gt; Hydrological Processes Science of Water &gt; Water Quality

Gene–Environment Interactions at Nucleotide Resolution

Interactions among genes and the environment are a common source of phenotypic variation. To characterize the interplay between genetics and the environment at single nucleotide resolution, we quantified the genetic and environmental interactions of four quantitative trait nucleotides (QTN) that govern yeast sporulation efficiency. We first constructed a panel of strains that together carry all 32 possible combinations of the 4 QTN genotypes in 2 distinct genetic backgrounds. We then measured the sporulation efficiencies of these 32 strains across 8 controlled environments. This dataset shows that variation in sporulation efficiency is shaped largely by genetic and environmental interactions. We find clear examples of QTN:environment, QTN: background, and environment:background interactions. However, we find no QTN:QTN interactions that occur consistently across the entire dataset. Instead, interactions between QTN only occur under specific combinations of environment and genetic background. Thus, what might appear to be a QTN:QTN interaction in one background and environment becomes a more complex QTN:QTN:environment:background interaction when we consider the entire dataset as a whole. As a result, the phenotypic impact of a set of QTN alleles cannot be predicted from genotype alone. Our results instead demonstrate that the effects of QTN and their interactions are inextricably linked both to genetic background and to environmental variation

CHANGE DETECTION BETWEEN DIGITAL SURFACE MODELS FROM AIRBORNE LASER SCANNING AND DENSE IMAGE MATCHING USING CONVOLUTIONAL NEURAL NETWORKS

Airborne photogrammetry and airborne laser scanning are two commonly used technologies used for topographical data acquisition at the city level. Change detection between airborne laser scanning data and photogrammetric data is challenging since the two point clouds show different characteristics. After comparing the two types of point clouds, this paper proposes a feed-forward Convolutional Neural Network (CNN) to detect building changes between them. The motivation from an application point of view is that the multimodal point clouds might be available for different epochs. Our method contains three steps: First, the point clouds and orthoimages are converted to raster images. Second, square patches are cropped from raster images and then fed into CNN for change detection. Finally, the original change map is post-processed with a simple connected component analysis. Experimental results show that the patch-based recall rate reaches 0.8146 and the precision rate reaches 0.7632. Object-based evaluation shows that 74 out of 86 building changes are correctly detected

SLIC SUPERPIXELS FOR OBJECT DELINEATION FROM UAV DATA

Unmanned aerial vehicles (UAV) are increasingly investigated with regard to their potential to create and update (cadastral) maps. UAVs provide a flexible and low-cost platform for high-resolution data, from which object outlines can be accurately delineated. This delineation could be automated with image analysis methods to improve existing mapping procedures that are cost, time and labor intensive and of little reproducibility. This study investigates a superpixel approach, namely simple linear iterative clustering (SLIC), in terms of its applicability to UAV data. The approach is investigated in terms of its applicability to high-resolution UAV orthoimages and in terms of its ability to delineate object outlines of roads and roofs. Results show that the approach is applicable to UAV orthoimages of 0.05&thinsp;m GSD and extents of 100 million and 400 million pixels. Further, the approach delineates the objects with the high accuracy provided by the UAV orthoimages at completeness rates of up to 64&thinsp;%. The approach is not suitable as a standalone approach for object delineation. However, it shows high potential for a combination with further methods that delineate objects at higher correctness rates in exchange of a lower localization quality. This study provides a basis for future work that will focus on the incorporation of multiple methods for an interactive, comprehensive and accurate object delineation from UAV data. This aims to support numerous application fields such as topographic and cadastral mapping

Genotoxic agents promote the nuclear accumulation of annexin A2: role of annexin A2 in mitigating DNA damage

Annexin A2 is an abundant cellular protein that is mainly localized in the cytoplasm and plasma membrane, however a small population has been found in the nucleus, suggesting a nuclear function for the protein. Annexin A2 possesses a nuclear export sequence (NES) and inhibition of the NES is sufficient to cause nuclear accumulation. Here we show that annexin A2 accumulates in the nucleus in response to genotoxic agents including gamma-radiation, UV radiation, etoposide and chromium VI and that this event is mediated by the nuclear export sequence of annexin A2. Nuclear accumulation of annexin A2 is blocked by the antioxidant agent N-acetyl cysteine (NAC) and stimulated by hydrogen peroxide (H2O2), suggesting that this is a reactive oxygen species dependent event. In response to genotoxic agents, cells depleted of annexin A2 show enhanced phospho-histone H2AX and p53 levels, increased numbers of p53-binding protein 1 nuclear foci and increased levels of nuclear 8-oxo-2'-deoxyguanine, suggesting that annexin A2 plays a role in protecting DNA from damage. This is the first report showing the nuclear translocation of annexin A2 in response to genotoxic agents and its role in mitigating DNA damage.Natural Sciences and Engineering Research Council of Canada (NSERC); European Union [PCOFUND-GA-2009-246542]; Foundation for Science and Technology of Portugal; Beatrice Hunter Cancer Research Institute; Terry Fox Foundationinfo:eu-repo/semantics/publishedVersio

Human annexin A6 interacts with influenza a virus protein M2 and negatively modulates infection

Copyright © 2012, American Society for Microbiology. All Rights ReservedThe influenza A virus M2 ion channel protein has the longest cytoplasmic tail (CT) among the three viral envelope proteins and is well conserved between different viral strains. It is accessible to the host cellular machinery after fusion with the endosomal membrane and during the trafficking, assembly, and budding processes. We hypothesized that identification of host cellular interactants of M2 CT could help us to better understand the molecular mechanisms regulating the M2-dependent stages of the virus life cycle. Using yeast two-hybrid screening with M2 CT as bait, a novel interaction with the human annexin A6 (AnxA6) protein was identified, and their physical interaction was confirmed by coimmunoprecipitation assay and a colocalization study of virus-infected human cells. We found that small interfering RNA (siRNA)-mediated knockdown of AnxA6 expression significantly increased virus production, while its overexpression could reduce the titer of virus progeny, suggesting a negative regulatory role for AnxA6 during influenza A virus infection. Further characterization revealed that AnxA6 depletion or overexpression had no effect on the early stages of the virus life cycle or on viral RNA replication but impaired the release of progeny virus, as suggested by delayed or defective budding events observed at the plasma membrane of virus-infected cells by transmission electron microscopy. Collectively, this work identifies AnxA6 as a novel cellular regulator that targets and impairs the virus budding and release stages of the influenza A virus life cycle.This work was supported by the Research Fund for the Control of Infectious Disease (project 09080892) of the Hong Kong Government, the Area of Excellence Scheme of the University Grants Committee (grant AoE/M-12/-06 of the Hong Kong Special Administrative Region, China), the French Ministry of Health, the RESPARI Pasteur Network