The dominant role of structure for solute transport in soil: experimental evidence and modelling of structure and transport in a field experiment

International audienceA classical transport experiment was performed in a field plot of 2.5 m2 using the dye tracer brilliant blue. The measured tracer distribution demonstrates the dominant role of the heterogeneous soil structure for solute transport. As with many other published experiments, this evidences the need of considering the macroscopic structure of soil to predict flow and transport. We combine three different approaches to represent the relevant structure of the specific situation of our experiment: i) direct measurement, ii) statistical description of heterogeneities and iii) a conceptual model of structure formation. The structure of soil layers was directly obtained from serial sections in the field. The sub-scale heterogeneity within the soil horizons was modelled through correlated random fields with estimated correlation lengths and anisotropy. Earthworm burrows played a dominant role at the transition between the upper soil horizon and the subsoil. A model based on percolation theory is introduced that mimics the geometry of earthworm burrow systems. The hydraulic material properties of the different structural units were obtained by direct measurements where available and by a best estimate otherwise. From the hydraulic structure, the 3-dimensional velocity field of water was calculated by solving Richards' Equation and solute transport was simulated. The simulated tracer distribution compares reasonably well with the experimental data. We conclude that a rough representation of the structure and a rough representation of the hydraulic properties might be sufficient to predict flow and transport, but both elements are definitely required

Understanding the Ultra-Rare Disease Autosomal Dominant Leukodystrophy: an Updated Review on Morpho-Functional Alterations Found in Experimental Models

Autosomal dominant leukodystrophy (ADLD) is an ultra-rare, slowly progressive, and fatal neurodegenerative disorder associated with the loss of white matter in the central nervous system (CNS). Several years after its first clinical description, ADLD was found to be caused by coding and non-coding variants in the LMNB1 gene that cause its overexpression in at least the brain of patients. LMNB1 encodes for Lamin B1, a protein of the nuclear lamina. Lamin B1 regulates many cellular processes such as DNA replication, chromatin organization, and senescence. However, its functions have not been fully characterized yet. Nevertheless, Lamin B1 together with the other lamins that constitute the nuclear lamina has firstly the key role of maintaining the nuclear structure. Being the nucleus a dynamic system subject to both biochemical and mechanical regulation, it is conceivable that changes to its structural homeostasis might translate into functional alterations. Under this light, this review aims at describing the pieces of evidence that to date have been obtained regarding the effects of LMNB1 overexpression on cellular morphology and functionality. Moreover, we suggest that further investigation on ADLD morpho-functional consequences is essential to better understand this complex disease and, possibly, other neurological disorders affecting CNS myelination

Characterisation of the structural heterogeneity of the soil layer by using in situ 2D and 3D electrical resistivity measurements

Introduction Soil structure i. e. the arrangement of soil particles in space (Guérif, 1987) is one important factor of physic quality of soils. In the agricultural context, this structure is modified at several space and time scales by different constraints or processes: tillage, compaction by traffic, natural effects. We need methods to characterize its in situ state. They already exist but they are destructive and time consuming. Recent works (Besson et al., 2004) have shown that a compacte..

Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases

The transcription factor NF-E2 p45-related factor 2 (NRF2; encoded by NFE2L2) and its principal negative regulator, the E3 ligase adaptor Kelch-like ECH-associated protein 1 (KEAP1), are critical in the maintenance of redox, metabolic and protein homeostasis, as well as the regulation of inflammation. Thus, NRF2 activation provides cytoprotection against numerous pathologies including chronic diseases of the lung and liver; autoimmune, neurodegenerative and metabolic disorders; and cancer initiation. One NRF2 activator has received clinical approval and several electrophilic modifiers of the cysteine-based sensor KEAP1 and inhibitors of its interaction with NRF2 are now in clinical development. However, challenges regarding target specificity, pharmacodynamic properties, efficacy and safety remain.This work was supported by grants SAF2015-71304-REDT and SAF2016-76520-R from the Spanish Ministry Economy and Competitiveness; P_37_732/2016 REDBRAIN from the European Regional Development Fund; Competitiveness Operational Program 2014–2020; US National Institutes of Health grant R35 CA197222; Cancer Research UK grant C20953/A18644; Medical Research Council grant MR/N009851/1; Biotechnology and Biological Sciences Research Council grant BB/L01923X/1; Tenovus Scotland grant T17/14; and grant 275147 from the Academy of Finland, Sigrid Juselius Foundation and Finnish Cancer Foundation.Peer reviewe

Three-dimensional structure of a highly heterogeneous soil horizon derived by Electrical Resistivity Tomography

Introduction The soil consists in a natural filter of water transfer to the groundwater. Its structure influences water storage and transfer properties or gas diffusivity, which induce major consequences on both environment and agronomy. Knowing the soil structure is thus essential to predict the soil hydraulic functioning and the 3D characterization of the structure at the horizon scale is necessary to describe the hydraulic functioning of the soil. In heterogeneous horizons, the structure (..

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions.

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution

Multiple Scale Reorganization of Electrostatic Complexes of PolyStyrene Sulfonate and Lysozyme

We report on a SANS investigation into the potential for these structural reorganization of complexes composed of lysozyme and small PSS chains of opposite charge if the physicochemical conditions of the solutions are changed after their formation. Mixtures of solutions of lysozyme and PSS with high matter content and with an introduced charge ratio [-]/[+]intro close to the electrostatic stoichiometry, lead to suspensions that are macroscopically stable. They are composed at local scale of dense globular primary complexes of radius ~ 100 {\AA}; at a higher scale they are organized fractally with a dimension 2.1. We first show that the dilution of the solution of complexes, all other physicochemical parameters remaining constant, induces a macroscopic destabilization of the solutions but does not modify the structure of the complexes at submicronic scales. This suggests that the colloidal stability of the complexes can be explained by the interlocking of the fractal aggregates in a network at high concentration: dilution does not break the local aggregate structure but it does destroy the network. We show, secondly, that the addition of salt does not change the almost frozen inner structure of the cores of the primary complexes, although it does encourage growth of the complexes; these coalesce into larger complexes as salt has partially screened the electrostatic repulsions between two primary complexes. These larger primary complexes remain aggregated with a fractal dimension of 2.1. Thirdly, we show that the addition of PSS chains up to [-]/[+]intro ~ 20, after the formation of the primary complex with a [-]/[+]intro close to 1, only slightly changes the inner structure of the primary complexes. Moreover, in contrast to the synthesis achieved in the one-step mixing procedure where the proteins are unfolded for a range of [-]/[+]intro, the native conformation of the proteins is preserved inside the frozen core

Publisher's Note: “Attosecond state-resolved carrier motion in quantum materials probed by soft x-ray XANES” [Appl. Phys Rev. 8, 011408 (2021)]

Recent developments in attosecond technology led to table-top x-ray spectroscopy in the soft x-ray range, thus uniting the element- and state-specificity of core-level x-ray absorption spectroscopy with the time resolution to follow electronic dynamics in real-time. We describe recent work in attosecond technology and investigations into materials such as Si, SiO2, GaN, Al2O3, Ti, and TiO2, enabled by the convergence of these two capabilities. We showcase the state-of-the-art on isolated attosecond soft x-ray pulses for x-ray absorption near-edge spectroscopy to observe the 3d-state dynamics of the semi-metal TiS2 with attosecond resolution at the Ti L-edge (460 eV). We describe how the element- and state-specificity at the transition metal L-edge of the quantum material allows us to unambiguously identify how and where the optical field influences charge carriers. This precision elucidates that the Ti:3d conduction band states are efficiently photo-doped to a density of 1.9 × 1021 cm−3. The light-field induces coherent motion of intra-band carriers across 38% of the first Brillouin zone. Lastly, we describe the prospects with such unambiguous real-time observation of carrier dynamics in specific bonding or anti-bonding states and speculate that such capability will bring unprecedented opportunities toward an engineered approach for designer materials with pre-defined properties and efficiency. Examples are composites of semiconductors and insulators like Si, Ge, SiO2, GaN, BN, and quantum materials like graphene, transition metal dichalcogens, or high-Tc superconductors like NbN or LaBaCuO. Exiting are prospects to scrutinize canonical questions in multi-body physics, such as whether the electrons or lattice trigger phase transitions

Role of Ucp1 enhancer methylation and chromatin remodelling in the control of Ucp1 expression in murine adipose tissue

Aims/hypothesis Increasing the expression of the brown adipose tissue-specific gene uncoupling protein-1 (Ucp1) is a potential target for treating obesity. We investigated the role of DNA methylation and histone modification in Ucp1 expression in adipose cell lines and ex vivo murine adipose tissues. Methods Methylation state of the Ucp1 enhancer was studied using bisulphite mapping in murine adipose cell lines, and tissue taken from cold-stressed mice, coupled with functional assays of the effects of methylation and demethylation of the Ucp1 promoter on gene expression and nuclear protein binding. Results We show that demethylation of the Ucp1 promoter by 5-aza-deoxycytidine increases Ucp1 expression while methylation of Ucp1 promoter–reporter constructs decreases expression. Brown adipose tissue-specific Ucp1 expression is associated with decreased CpG dinucleotide methylation of the Ucp1 enhancer. The lowest CpG dinucleotide methylation state was found in two cyclic AMP response elements (CRE3, CRE2) in the Ucp1 promoter and methylation of the CpG in CRE2, but not CRE3 decreased nuclear protein binding. Chromatin immunoprecipitation assays revealed the presence of the silencing DiMethH3K9 modification on the Ucp1 enhancer in white adipose tissue and the appearance of the active TriMethH3K4 mark at the Ucp1 promoter in brown adipose tissue in response to a cold environment. Conclusions/interpretation The results demonstrate that CpG dinucleotide methylation of the Ucp1 enhancer exhibits tissue-specific patterns in murine tissue and cell lines and suggest that adipose tissue-specific Ucp1 expression involves demethylation of CpG dinucleotides found in regulatory CREs in the Ucp1 enhancer, as well as modification of histone tails