Nano-contact microscopy of supracrystals

Background: Highly ordered three-dimensional colloidal crystals (supracrystals) comprised of 7.4 nm diameter Au nanocrystals (with a 5% size dispersion) have been imaged and analysed using a combination of scanning tunnelling microscopy and dynamic force microscopy. Results: By exploring the evolution of both the force and tunnel current with respect to tip–sample separation, we arrive at the surprising finding that single nanocrystal resolution is readily obtained in tunnelling microscopy images acquired more than 1 nm into the repulsive (i.e., positive force) regime of the probe–nanocrystal interaction potential. Constant height force microscopy has been used to map tip–sample interactions in this regime, revealing inhomogeneities which arise from the convolution of the tip structure with the ligand distribution at the nanocrystal surface. Conclusion: Our combined STM–AFM measurements show that the contrast mechanism underpinning high resolution imaging of nanoparticle supracrystals involves a form of nanoscale contact imaging, rather than the through-vacuum tunnelling which underpins traditional tunnelling microscopy and spectroscopy

Quantum Zakharov Model in a Bounded Domain

We consider an initial boundary value problem for a quantum version of the Zakharov system arising in plasma physics. We prove the global well-posedness of this problem in some Sobolev type classes and study properties of solutions. This result confirms the conclusion recently made in physical literature concerning the absence of collapse in the quantum Langmuir waves. In the dissipative case the existence of a finite dimensional global attractor is established and regularity properties of this attractor are studied. For this we use the recently developed method of quasi-stability estimates. In the case when external loads are $C^\infty$ functions we show that every trajectory from the attractor is $C^\infty$ both in time and spatial variables. This can be interpret as the absence of sharp coherent structures in the limiting dynamics.Comment: 27 page

The sources and dynamics of fine-grained sediment degrading the Freshwater Pearl Mussel (Margaritifera margaritifera) beds of the River Torridge, Devon, UK

The Freshwater Pearl Mussel (Margaritifera margaritifera) is an endangered organism across its entire range. It has a complex life cycle and stringent habitat requirements and is therefore an indicator species for the general ecosystem health of host rivers. Whereas historical intensive pearl fishing contributed to population declines, excess nutrient and sediment loss associated with current land use pressures in host river catchments, including modern intensive farming practices, are now highlighted as primary contributory factors. Accordingly, this study investigated the sources and dynamics of fine-grained sediment sampled in the mussel beds of the River Torridge, SW England. Sediment source fingerprinting using a combination of colorimetric and radiometric tracers to construct different composite signatures revealed the importance of roads both as a sediment source and delivery pathway for fine-grained sediment mobilised from fields predominantly supporting lowland livestock farming. Grassland fields with evidence of soil poaching were highlighted as important sediment sources, but equally, riparian woodland was also identified as important, especially during the latter stages of consecutive runoff events when its rainfall buffering capacity was exceeded. Bed sediment storage levels (median up to 393 g m−2) were found to be low (41st percentile) compared to typical values reported by a recent strategic scale survey across England and Wales, whereas elevated turbidity peaks were shown to be long duration (days) in conjunction with consecutive days of rainfall and corresponding runoff events. Hysteresis patterns varied but were generally clockwise during the largest runoff events associated with consecutive rain days; again, suggesting mobilisation of sediment from proximal woodland sources following exceedance of rainfall buffering capacity. In combination, the data assembled by this study provides a basis for planning sediment control measures for protecting the Freshwater Pearl Mussel (FPM) beds from excessive fine-grained sediment inputs associated with the intensive use of primarily grazing land

Travelling waves for the Gross-Pitaevskii equation II

The purpose of this paper is to provide a rigorous mathematical proof of the existence of travelling wave solutions to the Gross-Pitaevskii equation in dimensions two and three. Our arguments, based on minimization under constraints, yield a full branch of solutions, and extend earlier results, where only a part of the branch was built. In dimension three, we also show that there are no travelling wave solutions of small energy.Comment: Final version accepted for publication in Communications in Mathematical Physics with a few minor corrections and added remark

Immune responses during COVID-19 infection

Over the past 16 years, three coronaviruses (CoVs), severe acute respiratory syndrome CoV (SARS-CoV) in 2002, Middle East respiratory syndrome CoV (MERS-CoV) in 2012 and 2015, and SARS-CoV-2 in 2020, have been causing severe and fatal human epidemics. The unpredictability of coronavirus disease-19 (COVID-19) poses a major burden on health care and economic systems across the world. This is caused by the paucity of in-depth knowledge of the risk factors for severe COVID-19, insufficient diagnostic tools for the detection of SARS-CoV-2, as well as the absence of specific and effective drug treatments. While protective humoral and cellular immune responses are usually mounted against these betacoronaviruses, immune responses to SARS-CoV2 sometimes derail towards inflammatory tissue damage, leading to rapid admissions to intensive care units. The lack of knowledge on mechanisms that tilt the balance between these two opposite outcomes poses major threats to many ongoing clinical trials dealing with immunostimulatory or immunoregulatory therapeutics. This review will discuss innate and cognate immune responses underlying protective or deleterious immune reactions against these pathogenic coronaviruses

The Stromal Processing Peptidase of Chloroplasts is Essential in Arabidopsis, with Knockout Mutations Causing Embryo Arrest after the 16-Cell Stage

Stromal processing peptidase (SPP) is a metalloendopeptidase located in the stroma of chloroplasts, and it is responsible for the cleavage of transit peptides from preproteins upon their import into the organelle. Two independent mutant Arabidopsis lines with T-DNA insertions in the SPP gene were analysed (spp-1 and spp-2). For both lines, no homozygous mutant plants could be detected, and the segregating progeny of spp heterozygotes contained heterozygous and wild-type plants in a ratio of 2∶1. The siliques of heterozygous spp-1 and spp-2 plants contained many aborted seeds, at a frequency of ∼25%, suggesting embryo lethality. By contrast, transmission of the spp mutations through the male and female gametes was found to be normal, and so gametophytic effects could be ruled out. To further elucidate the timing of the developmental arrest, mutant and wild-type seeds were cleared and analysed by Nomarski microscopy. A significant proportion (∼25%) of the seeds in mutant siliques exhibited delayed embryogenesis compared to those in wild type. Moreover, the mutant embryos never progressed normally beyond the 16-cell stage, with cell divisions not completing properly thereafter. Heterozygous spp mutant plants were phenotypically indistinguishable from the wild type, indicating that the spp knockout mutations are completely recessive and suggesting that one copy of the SPP gene is able to produce sufficient SPP protein for normal development under standard growth conditions

Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation

Galactomannans are hemicellulosic polysaccharides composed of a (1 → 4)-linked β-D-mannan backbone substituted with single-unit (1 → 6)-α-linked D-galactosyl residues. Developing fenugreek (Trigonella foenum-graecum) seeds are known to accumulate large quantities of galactomannans in the endosperm, and were thus used here as a model system to better understand galactomannan biosynthesis and its regulation. We first verified the specific deposition of galactomannans in developing endosperms and determined that active accumulation occurred from 25 to 38 days post anthesis (DPA) under our growth conditions. We then examined the expression levels during seed development of ManS and GMGT, two genes encoding backbone and side chain synthetic enzymes. Based on transcript accumulation dynamics for ManS and GMGT, cDNA libraries were constructed using RNA isolated from endosperms at four ages corresponding to before, at the beginning of, and during active galactomannan deposition. DNA from these libraries was sequenced using the 454 sequencing technology to yield a total of 1.5 million expressed sequence tags (ESTs). Through analysis of the EST profiling data, we identified genes known to be involved in galactomannan biosynthesis, as well as new genes that may be involved in this process, and proposed a model for the flow of carbon from sucrose to galactomannans. Measurement of in vitro ManS and GMGT activities and analysis of sugar phosphate and nucleotide sugar levels in the endosperms of developing fenugreek seeds provided data consistent with this model. In vitro enzymatic assays also revealed that the ManS enzyme from fenugreek endosperm preferentially used GDP-mannose as the substrate for the backbone synthesis

Nearly inviscid Faraday waves

Many powerful techniques from Hamiltonian mechanics are available for the study of ideal hydrodynamics. This article explores some of the consequences of including small viscosity in a study of surface gravity-capillary waves excited by the vertical vibration of a container. It is shown that in this system, as in others, the addition of small viscosity provides a singular perturbation of the ideal fluid system, and that as a result its effects are nontrivial. The relevance of existing studies of ideal fluid problems is discussed from this point of view

Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae

Response of cell wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus

Main conclusion: Methyl-jasmonate induces large increases in p-coumarate linked to arabinoxylan in Brachypodium and in abundance of GT61 and BAHD family transcripts consistent with a role in synthesis of this linkage. Jasmonic acid (JA) signalling is required for many stress responses in plants, inducing large changes in the transcriptome, including up-regulation of transcripts associated with lignification. However, less is known about the response to JA of grass cell walls and the monocot-specific features of arabinoxylan (AX) synthesis and acylation by ferulic acid (FA) and para-coumaric acid (pCA). Here, we show that methyl-jasmonate (MeJA) induces moderate increases in FA monomer, > 50% increases in FA dimers, and five–sixfold increases in pCA ester-linked to cell walls in Brachypodium callus. Direct measurement of arabinose acylated by pCA (Araf-pCA) indicated that most or all the increase in cell-wall pCA was due to pCA ester-linked to AX. Analysis of the RNA-seq transcriptome of the callus response showed that these cell-wall changes were accompanied by up-regulation of members of the GT61 and BAHD gene families implicated in AX decoration and acylation; two BAHD paralogues were among the most up-regulated cell-wall genes (seven and fivefold) after 24 h exposure to MeJA. Similar responses to JA of orthologous BAHD and GT61 transcripts are present in the RiceXPro public expression data set for rice seedlings, showing that they are not specific to Brachypodium or to callus. The large response of AX-pCA to MeJA may, therefore, indicate an important role for this linkage in response of primary cell walls of grasses to JA signalling