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Abstract Maize seedlings are grown in Hostun sand with two different gradings and two different densities. The root-soil system is imaged daily for the first 8 days of plant growth with X-ray computed tomography. Segmentation, skeletonisation and digital image correlation techniques are used to analyse the evolution of the root system architecture, the displacement fields and the local strain fields due to plant growth in the soil. It is found that root thickness and root length density do not depend on the initial soil configuration. However, the depth of the root tip is strongly influenced by the initial soil density, and the number of laterals is impacted by grain size, which controls pore size, capillary rise and thus root access to water. Consequently, shorter root axes are observed in denser sand and fewer second order roots are observed in coarser sands. In all soil configurations tested, root growth induces shear strain in the soil around the root system, and locally, in the vicinity of the first order roots axis. Root-induced shear is accompanied by dilative volumetric strain close to the root body. Further away, the soil experiences dilation in denser sand and compaction in looser sand. These results suggest that the increase of porosity close to the roots can be caused by a mix of shear strain and steric exclusion.

Neuronal development orchestrates the formation of an enormous number of synapses that connect the nervous system. In developing presynapses, the core active zone structure has been found to assemble through liquid–liquid phase separation. Here, we find that the phase separation of Caenorhabditis elegans SYD-2/Liprin-α, a key active zone scaffold, is controlled by phosphorylation. We identify the SAD-1 kinase as a regulator of SYD-2 phase separation and determine presynaptic assembly is impaired in sad-1 mutants and increased by overactivation of SAD-1. Using phosphoproteomics, we find SAD-1 phosphorylates SYD-2 on 3 sites that are critical to activate phase separation. Mechanistically, SAD-1 phosphorylation relieves a binding interaction between 2 folded domains in SYD-2 that inhibits phase separation by an intrinsically disordered region (IDR). We find synaptic cell adhesion molecules localize SAD-1 to nascent synapses upstream of active zone formation. We conclude that SAD-1 phosphorylates SYD-2 at developing synapses, activating its phase separation and active zone assembly.

The recycling of biogenic silica (bSiO 2 ) produced by diatoms is a vital process sustaining a significant fraction of primary production in the oceans. The efficiency with which bSiO 2 dissolves controls the availability of nutrient silicon in the water column, and modulates the export of organic carbon to the deep sea. Environmental conditions during biomineralization (temperature, nutrient availability, light, etc.) affect the silicification and weathering resistance of diatom frustules, while ecosystem processes, including grazing and aggregation, are determining factors for the recycling of bSiO 2 in the water column. Bacterial colonization of dead diatoms leads to the decomposition of the protective organic layers allowing for the dissolution of bSiO 2 to begin. The dissolution rate of diatom frustules is a function of the physicochemical properties of both the silica (e.g., specific surface area, degree of hydration and condensation, impurities) and the aqueous medium (e.g., temperature, pH, pressure, electrolyte composition). In sediments, the dissolution of bSiO 2 is controlled by the presence of lithogenic minerals, aging processes and the build up of dSi in the pore waters. In particular, interactions between lithogenic silicate minerals and bSiO 2 may initiate rapid diagenetic alterations that favor the preservation of bSiO 2 .

Nutrient enrichment is a major global change component that often disrupts the relationship between aboveground biodiversity and ecosystem functions by promoting species dominance, altering trophic interactions, and reducing ecosystem stability. Emerging evidence indicates that nutrient enrichment also reduces soil biodiversity and weakens the relationship between belowground biodiversity and ecosystem functions, but the underlying mechanisms remain largely unclear. Here, we explore the effects of nutrient enrichment on soil properties, soil biodiversity, and multiple ecosystem functions through a 13-year field experiment. We show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon (C) availability, is the primary factor negatively affecting the relationship between soil diversity and ecosystem multifunctionality. Nitrogen and phosphorus additions significantly reduce soil pH, diversity of bacteria, fungi and nematodes, as well as an array of ecosystem functions related to C and nutrient cycling. Effects of nutrient enrichment on microbial diversity also have negative consequences at higher trophic levels on the diversity of microbivorous nematodes. These results indicate that nutrient-induced acidification can cascade up its impacts along the soil food webs and influence ecosystem functioning, providing novel insight into the mechanisms through which nutrient enrichment influences soil community and ecosystem properties.Nutrient enrichment is a major global change component. Here the authors show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon availability, modulates soil biodiversity-function relationships

We report a unique multiyear L-band microwave radiometry dataset collected at the Maqu site on the eastern Tibetan Plateau and demonstrate its utilities in advancing our understandings of microwave observations of land surface processes. The presented dataset contains measurements of L-band brightness temperature by an ELBARA-III microwave radiometer in horizontal and vertical polarization, profile soil moisture and soil temperature, turbulent heat fluxes, and meteorological data from the beginning of 2016 till August 2019, while the experiment is still continuing. Auxiliary vegetation and soil texture information collected in dedicated campaigns are also reported. This dataset can be used to validate the Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) satellite based observations and retrievals, verify radiative transfer model assumptions and validate land surface model and reanalysis outputs, retrieve soil properties, as well as to quantify land-atmosphere exchanges of energy, water and carbon and help to reduce discrepancies and uncertainties in current Earth System Models (ESM) parameterizations. Measurement cases in winter, pre-monsoon, monsoon and post-monsoon periods are presented.

Corrigendum associated with this Article: Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy. Nature Structural & Molecular Biology, 16 (9) 890-898. 2009 doi: 10.1038/nsmb.1627

Thioredoxins (Trxs) are oxidoreductase enzymes, present in all organisms, that catalyze the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single-molecule level. Here we use single-molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different Trx enzymes. All Trxs show a characteristic Michaelis-Menten mechanism that is detected when the disulfide bond is stretched at low forces, but at high forces, two different chemical behaviors distinguish bacterial-origin from eukaryotic-origin Trxs. Eukaryotic-origin Trxs reduce disulfide bonds through a single-electron transfer reaction (SET), whereas bacterial-origin Trxs show both nucleophilic substitution (SN2) and SET reactions. A computational analysis of Trx structures identifies the evolution of the binding groove as an important factor controlling the chemistry of Trx catalysis.

The kinetics of biomass formation, D-xylose utilization, and mixed substrate utilization were determined in a chemostat using the yeast Candida shehatae. The maximum growth rate of C. shehatae grown aerobically on D-xylose was 0.42 h-1 and the Monod constant, Ks, was 0.06 g L-1. The biomass yield, Y(x/s), ranged from 0.40 to 0.50 g g-1 over a dilution rate range of 0.2-0.3 h-1, when C. shehatae was grown on pure D-xylose. Mixtures of D-xylose and glucose (approximately 1:1) were simultaneously utilized over a dilution rate from 0.15 to 0.35 h-1 at pH 3.5 and 4.5, but pH 3.5 reduced micromax and reduced the dilution rate range over which D-xylose was utilized in the presence of glucose. At pH 4.5, micromax was not reduced with the mixed sugar feed and the overall or lumped Ks value was not significantly increased (0.058 g L-1 vs 0.06 g L-1), when compared to a pure D-xylose feed. Kinetic data indicate that C. shehatae is an excellent candidate for chemostat production of value added products from renewable carbon sources, since simultaneous mixed substrate utilization was observed over a wide range of growth rates on a 1:1 mixture of glucose and D-xylose

The influence of various colors of soil cover (mulch) on the far-red/red (FR/R) ratio in upwardly reflected light and on concentrations of chlorophyll (Chl) and light-harvesting Chl protein (LHC-II) were measured under field conditions. The FR/R ratios above green surfaces were higher than over white surfaces. Even though plants (Gossypium hirsutum L. cv PD-1) were grown in full sunlight, those that received higher FR/R ratios in upwardly reflected light were taller and had thinner leaves with higher concentrations of Chl and LHC-II. A controlled environment experiment showed FR/R control of Chl and LHC-II concentrations. The results illustrate the importance of spectral distribution of reflected light on plant growth and a potential means of altering the chemistry of leaf crops under field conditions

Nanostructures refer to materials that have relevant dimensions on the nanometer length scales and reside in the mesoscopic regime between isolated atoms and molecules in bulk matter. These materials have unique physical properties that are distinctly different from bulk materials. This title provides systematic coverage of basic nanomaterials science including materials assembly and synthesis, characterization, and application. Aimed at both beginners and experts, it balances the chemistry aspects of nanomaterials with physical principles. It also highlights nanomaterial-based architectures including assembled or self-assembled systems. Filled with in-depth discussion of important applications of nano-architectures as well as potential applications ranging from physical to chemical and biological systems, the book should prove a useful reference or text for scientists involved with nanostructures.