Electrical Resistivity Tomography of Claypan Soils in Southeastern Kansas

Claypan soils cover approximately 10 million acres across several states in the central United States. The soils are characterized by a highly impermeable clay layer within the profile that impedes water flow and root growth. While some claypan soils can be productive, they must be carefully managed to avoid reductions to crop productivity due to root restrictions, water, and nutrient limitations. Clay soils are usually resistant to erosion but may exacerbate erosion of the silt-loam topsoil. Soil production potential is the capacity of soil to produce at a given level (yield per acre). The productive capacity is tied to soil characteristics, which can be highly variable within a field. In this project, we have used imagery analysis to study the aerial images and terrain of fields during different productive times of the year to identify where soil samples should be collected for more discrete analysis. Soil samples provide valuable information; however, the amount of data obtained from a relatively small area within a field does not provide sufficient information to delineate the subsurface characteristics. To address the limitations of sampling, we have also employed the use of yield maps collected from commercial yield monitors on production-scale combines and surface electrical conductivity measurements (Sassenrath and Kulesza, 2017). Soil conductivity is a measurement of how well a representative volume of soil conducts electricity. Soil conductivity is a function of the soil clay content, moisture content, and other measurable soil properties (Kitchen et al., 2003); as such, it has become a valuable tool for mapping in-field variability. The main advantage of a soil conductivity measurement is that the entire surface of a field can be imaged. The disadvantage of a soil conductivity measurement is that data are only collected near the surface (10 – 30 inches) and the measurements are relative measurements. This means that the conductivity mappers can identify changes in soil properties, but they cannot directly tell researchers what caused these changes. Electrical resistivity tomography (ERT) is a popular near-surface geophysical measurement for geophysical and engineering applications. The term “near-surface” generally means down to around 30 feet in the subsurface. Electrical resistivity is the reciprocal measurement of electrical conductivity; therefore, both systems measure differences in the same soil properties. ERT measurements are different than surface electrical conductivity measurements because ERT collects a “slice” of data into the subsurface, as opposed to only changes at the surface area. Relative measurements, similar to those collected in an electrical conductivity survey, are collected; however, in ERT studies the data are mathematically inverted to yield the true electrical resistivity of the soil with depth. This allows an interpretation of the changing soil properties with depth to reduce the required amount of sampling. A disadvantage of an ERT survey is that the data acquisition is stationary so mapping an entire field is not feasible. We have used a coupled process of imagery and terrain analysis, yield maps, and electrical conductivity measurements to guide the locations of ERT surveys in this project (Tucker-Kulesza et al. 2017)

Characterization of Claypan Soils in Southeastern Kansas

Soil erosion reduces topsoil depth. In areas with a claypan, removal of productive topsoil reduces crop yield where the claypan layer is near the surface. The topsoil and claypan layer each have unique characteristics that impact crop production and within-field variability. To better understand these differences, the soil from an area of low crop yield and high crop yield were collected and laboratory tests were performed to determine the soil classification and undrained shear strength. Understanding the soil properties and the interaction between the topsoil and claypan layers may aid in under­standing the process by which topsoil is being eroded

Tracing the Mass during Low-Mass Star Formation. II. Modelling the Submillimeter Emission from Pre-Protostellar Cores

We have modeled the emission from dust in pre-protostellar cores, including a self-consistent calculation of the temperature distribution for each input density distribution. Model density distributions include Bonnor-Ebert spheres and power laws. The Bonnor-Ebert spheres fit the data well for all three cores we have modeled. The dust temperatures decline to very low values (\Td \sim 7 K) in the centers of these cores, strongly affecting the dust emission. Compared to earlier models that assume constant dust temperatures, our models indicate higher central densities and smaller regions of relatively constant density. Indeed, for L1544, a power-law density distribution, similar to that of a singular, isothermal sphere, cannot be ruled out. For the three sources modeled herein, there seems to be a sequence of increasing central condensation, from L1512 to L1689B to L1544. The two denser cores, L1689B and L1544, have spectroscopic evidence for contraction, suggesting an evolutionary sequence for pre-protostellar cores.Comment: 22 pages, 9 figures, Ap. J. accepted, uses emulateapj5.st

Reconstructing the density and temperature structure of prestellar cores from <i>Herschel</i> data: a case study for B68 and L1689B

Utilizing multiwavelength dust emission maps acquired with Herschel, we reconstruct local volume density and dust temperature profiles for the prestellar cores B68 and L1689B using an inverse-Abel transform-based technique. We present intrinsic radial dust temperature profiles of starless cores directly from dust continuum emission maps disentangling the effect of temperature variations along the line of sight, which were previously limited to the radiative transfer calculations. The reconstructed dust temperature profiles show a significant drop in the core center, a flat inner part, and a rising outward trend until the background cloud temperature is reached. The central beam-averaged dust temperatures obtained for B68 and L1689B are 9.3 ± 0.5 K and 9.8 ± 0.5 K, respectively, which are lower than the temperatures of 11.3 K and 11.6 K obtained from direct SED fitting. The best mass estimates derived by integrating the volume density profiles of B68 and L1689B are 1.6 M⊙ and 11 M⊙, respectively. Comparing our results for B68 with the near-infrared extinction studies, we find that the dust opacity law adopted by the HGBS project, κλ = 0.1 × (λ/300 μm)-2 cm2 g-1 agrees to within 50% with the dust extinction constraints

The 9.7 and 18 um silicate absorption profiles towards diffuse and molecular cloud lines-of-sight

Studying the composition of dust in the interstellar medium (ISM) is crucial in understanding the cycle of dust in our galaxy. The mid-infrared spectral signature of amorphous silicates, the most abundant dust species in the ISM, is studied in different lines-of-sight through the Galactic plane, thus probing different conditions in the ISM. We have analysed 10 spectra from the Spitzer archive, of which 6 lines-of-sight probe diffuse interstellar medium material and 4 probe molecular cloud material. The 9.7 um silicate absorption features in 7 of these spectra were studied in terms of their shape and strength. In addition, the shape of the 18 um silicate absorption features in 4 of the diffuse sightline spectra were analysed. The 9.7 um silicate absorption bands in the diffuse sightlines show a strikingly similar band shape. This is also the case for all but one of the 18 um silicate absorption bands observed in diffuse lines-of-sight. The 9.7 um bands in the 4 molecular sightlines show small variations in shape. These modest variations in the band shape are inconsistent with the interpretation of the large variations in {\tau}_9.7/E(J-K) between diffuse and molecular sightlines in terms of silicate grain growth. Instead, we suggest that the large changes in {\tau}_9.7 / E(J-K) must be due to changes in E(J-K).Comment: 14 pages, 19 figures, accepted for publication in A&

Single Molecule PCR Reveals Similar Patterns of Non-Homologous DSB Repair in Tobacco and Arabidopsis

DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1–20 bp) deletions occurred at a minority (25–45%) of repair junctions. Approximately ∼1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ

Planck 2013 results. XI. All-sky model of thermal dust emission

This paper presents an all-sky model of dust emission from the Planck 353, 545, and 857 GHz, and IRAS 100 \u3bcm data. Using a modified blackbody fit to the data we present all-sky maps of the dust optical depth, temperature, and spectral index over the 353-3000 GHz range. This model is a good representation of the IRAS and Planck data at 5\u2032 between 353 and 3000 GHz (850 and 100 \u3bcm). It shows variations of the order of 30% compared with the widely-used model of Finkbeiner, Davis, and Schlegel. The Planck data allow us to estimate the dust temperature uniformly over the whole sky, down to an angular resolution of 5\u2032, providing an improved estimate of the dust optical depth compared to previous all-sky dust model, especially in high-contrast molecular regions where the dust temperature varies strongly at small scales in response to dust evolution, extinction, and/or local production of heating photons. An increase of the dust opacity at 353 GHz, \u3c4353/NH, from the diffuse to the denser interstellar medium (ISM) is reported. It is associated with a decrease in the observed dust temperature, Tobs, that could be due at least in part to the increased dust opacity. We also report an excess of dust emission at H i column densities lower than 1020 cm-2 that could be the signature of dust in the warm ionized medium. In the diffuse ISM at high Galactic latitude, we report an anticorrelation between \u3c4353/NH and Tobs while the dust specific luminosity, i.e., the total dust emission integrated over frequency (the radiance) per hydrogen atom, stays about constant, confirming one of the Planck Early Results obtained on selected fields. This effect is compatible with the view that, in the diffuse ISM, Tobs responds to spatial variations of the dust opacity, due to variations of dust properties, in addition to (small) variations of the radiation field strength. The implication is that in the diffuse high-latitude ISM \u3c4353 is not as reliable a tracer of dust column density as we conclude it is in molecular clouds where the correlation of \u3c4353 with dust extinction estimated using colour excess measurements on stars is strong. To estimate Galactic E(B-V) in extragalactic fields at high latitude we develop a new method based on the thermal dust radiance, instead of the dust optical depth, calibrated to E(B-V) using reddening measurements of quasars deduced from Sloan Digital Sky Survey data. \ua9 2014 ESO

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease

Type 1 diabetes: translating mechanistic observations into effective clinical outcomes

Type 1 diabetes remains an important health problem, particularly in Western countries where the incidence has been increasing in younger children(1). In 1986, Eisenbarth described Type 1 diabetes as a chronic autoimmune disease. Work over the past 3 ½ decades has identified many of the genetic, immunologic, and environmental factors that are involved in the disease and have led to hypotheses concerning its pathogenesis. Based on these findings, clinical trials have been conducted to test these hypotheses but have had mixed results. In this review, we discuss the findings that have led to current concepts of the disease mechanisms, how this understanding has prompted clinical studies, and the results of these studies. The findings from preclinical and clinical studies support the original proposed model for how type 1 diabetes develops, but have also suggested that this disease is more complex than originally thought and will require broader treatment approaches