DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis.

DNA methylation is a conserved epigenetic modification that is typically associated with silencing of transposable elements and promoter methylated genes. However, some DNA-methylated loci are protected from silencing, allowing transcriptional flexibility in response to environmental and developmental cues. Through a genetic screen in Arabidopsis (Arabidopsis thaliana), we uncovered an antagonistic relationship between the MICRORCHIDIA (MORC) protein and the IMITATION SWITCH (ISWI) complex in regulating the DNA-methylated SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC) reporter. We demonstrate that components of the plant-specific ISWI complex, including CHROMATIN REMODELING PROTEIN11 (CHR11), CHR17, DDT-RELATED PROTEIN4 (DDR4), and DDR5, function to partially derepress silenced genes and transposable elements (TEs), through their function in regulating nucleosome distribution. This action also requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. Genome-wide studies revealed that DDR4 causes changes in nucleosome distribution at numerous loci, a subset of which is associated with changes in DNA methylation and/or transcription. Our work reveals a mechanism for balancing transcriptional flexibility and faithful silencing of DNA-methylated loci. As both ISWI and MORC family genes are widely distributed across plant and animal species, our findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic regulation.

First Study of the

New astronomical observations point to a nucleosynthesis picture that goes beyond what was accepted until recently. The intermediate "i" process was proposed as a plausible scenario to explain some of the unusual abundance patterns observed in metal-poor stars. The most important nuclear physics properties entering i-process calculations are the neutron-capture cross sections and they are almost exclusively not known experimentally. Here we provide the first experimental constraints on the ^{139}Ba(n,γ)^{140}Ba reaction rate, which is the dominant source of uncertainty for the production of lanthanum, a key indicator of i-process conditions. This is an important step towards identifying the exact astrophysical site of stars carrying the i-process signature.

Proton Shell Gaps in N=28 Nuclei from the First Complete Spectroscopy Study with FRIB Decay Station Initiator.

The first complete measurement of the ß-decay strength distribution of _{17}^{45}Cl_{28} was performed at the Facility for Rare Isotope Beams (FRIB) with the FRIB Decay Station Initiator during the second FRIB experiment. The measurement involved the detection of neutrons and γ rays in two focal planes of the FRIB Decay Station Initiator in a single experiment for the first time. This enabled an analytical consistency in extracting the ß-decay strength distribution over the large range of excitation energies, including neutron unbound states. We observe a rapid increase in the ß-decay strength distribution above the neutron separation energy in _{18}^{45}Ar_{27}. This was interpreted to be caused by the transitioning of neutrons into protons excited across the Z=20 shell gap. The SDPF-MU interaction with reduced shell gap best reproduced the data. The measurement demonstrates a new approach that is sensitive to the proton shell gap in neutron rich nuclei according to SDPF-MU calculations.

The rare C9 P167S risk variant for age-related macular degeneration increases polymerization of the terminal component of the complement cascade.

Age-related macular degeneration (AMD) is a complex neurodegenerative eye disease with behavioral and genetic etiology and is the leading cause of irreversible vision loss among elderly Caucasians. Functionally significant genetic variants in the alternative pathway of complement have been strongly linked to disease. More recently, a rare variant in the terminal pathway of complement has been associated with increased risk, Complement component 9 (C9) P167S. To assess the functional consequence of this variant, C9 levels were measured in two independent cohorts of AMD patients. In both cohorts, it was demonstrated that the P167S variant was associated with low C9 plasma levels. Further analysis showed that patients with advanced AMD had elevated sC5b-9 compared to those with non-advanced AMD, although this was not associated with the P167S polymorphism. Electron microscopy of membrane attack complexes (MACs) generated using recombinantly produced wild type or P167S C9 demonstrated identical MAC ring structures. In functional assays, the P167S variant displayed a higher propensity to polymerize and a small increase in its ability to induce hemolysis of sheep erythrocytes when added to C9-depleted serum. The demonstration that this C9 P167S AMD risk polymorphism displays increased polymerization and functional activity provides a rationale for the gene therapy trials of sCD59 to inhibit the terminal pathway of complement in AMD that are underway.

Decoupling absorption and radiative cooling in mid-wave infrared bolometric elements.

We present a spectrally selective, passively cooled mid-wave infrared bolometric absorber engineered to spatially and spectrally decouple infrared absorption and thermal emission. The structure leverages an antenna-coupled metal-insulator-metal resonance for mid-wave infrared normal incidence photon absorption and a long-wave infrared optical phonon absorption feature, aligned closer to peak room temperature thermal emission. The phonon-mediated resonant absorption enables a strong long-wave infrared thermal emission feature limited to grazing angles, leaving the mid-wave infrared absorption feature undisturbed. The two independently controlled absorption/emission phenomena demonstrate decoupling of the photon detection mechanism from radiative cooling and offer a new design approach enabling ultra-thin, passively cooled mid-wave infrared bolometers.

Identification of potent and selective inhibitors of PKR via virtual screening and traditional design.

Protein Kinase RNA-activated (PKR) inhibition is thought to be relevant for immunology due to the potential to reduce macrophage and dendritic cell responses to bacteria and its signaling downstream of TNFα. PKR is also associated with neuroscience indications such as Alzheimer's disease due to its activation by the double stranded DNA (dsDNA) virus HSV1, a virus suggested to be important in the development of AD. Studies exploring the mechanistic role of PKR with existing tool molecules such as the tricyclic oxindole C16 are clouded by the poor selectivity profile of this ATP-competitive, Type I kinase inhibitor. Type II kinase leads such as the benzothiophene or pyrazolopyrimidine scaffolds from literature are equally poor in their selectivity profiles. As such, it became necessary to identify more potent and selective chemical matter to better understand PKR biology. A dual approach was taken. The first step of the strategy included virtual screening of the AbbVie compound collection. A combination of pharmacophore-based and GPU shape-based screening was pursued to identify selective chemical matter from promiscuous leads. The second step of the strategy followed traditional compound design. This step initiated from a literature lead with PKR cross reactivity. Combined, the two parallel efforts led to identification of more selective leads for investigation of PKR biology.

Transfusion of incompatible blood to a patient with alloanti-Sc1.

Sc1 is a high-prevalence blood group antigen that is part of the Scianna blood group system. The clinical significance of Scianna antibodies is not well understood because of their rarity; there are only a handful of cases in the literature. This scarcity of information can make it difficult to decide on the best course of action when transfusing a patient with alloantibodies to Scianna blood group antigens. We describe a case of an 85-year-old woman presenting with melena and a hemoglobin of 66 g/L. Upon request for crossmatched blood, a panreactive antibody was found, later elucidated to be alloanti-Sc1. Because of the urgent nature of the transfusion, the patient was transfused with 2 incompatible, presumed Sc1+, red blood cell units with no evidence of an acute or delayed transfusion reaction. This case has been shared with the International Society of Blood Transfusion Rare Donor Working Party, via their Outcome of Incompatible Transfusion form, and adds to the body of evidence on clinical significance of antibodies to the antigens of the Scianna blood group system.

In Situ Ion Counting for Improved Implanted Ion Error Rate and Silicon Vacancy Yield Uncertainty.

An in situ counted ion implantation experiment improving the error on the number of ions required to form a single optically active silicon vacancy (SiV) defect in diamond 7-fold compared to timed implantation is presented. Traditional timed implantation relies on a beam current measurement followed by implantation with a preset pulse duration. It is dominated by Poisson statistics, resulting in large errors for low ion numbers. Instead, our in situ detection, measuring the ion number arriving at the substrate, results in a 2-fold improvement of the error on the ion number required to generate a single SiV compared to timed implantation. Through postimplantation analysis, the error is improved 7-fold compared to timed implantation. SiVs are detected by photoluminescence spectroscopy, and the yield of 2.98% is calculated through the photoluminescence count rate. Hanbury-Brown-Twiss interferometry is performed on locations potentially hosting single-photon emitters, confirming that 82% of the locations exhibit single photon emission statistics.

Terahertz Pulse Generation with Binary Phase Control in Nonlinear InAs Metasurface.

The effect of terahertz (THz) pulse generation has revolutionized broadband coherent spectroscopy and imaging at THz frequencies. However, THz pulses typically lack spatial structure, whereas structured beams are becoming essential for advanced spectroscopy applications. Nonlinear optical metasurfaces with nanoscale THz emitters can provide a solution by defining the beam structure at the generation stage. We develop a nonlinear InAs metasurface consisting of nanoscale optical resonators for simultaneous generation and structuring of THz beams. We find that THz pulse generation in the resonators is governed by optical rectification. It is more efficient than in ZnTe crystals, and it allows us to control the pulse polarity and amplitude, offering a platform for realizing binary-phase THz metasurfaces. To illustrate this capability, we demonstrate an InAs metalens, which simultaneously generates and focuses THz pulses. The control of spatiotemporal structure using nanoscale emitters opens doors for THz beam engineering and advanced spectroscopy and imaging applications.

Use of diamond sensors for a high-flux, high-rate X-ray pass-through diagnostic.

X-ray free-electron lasers (XFELs) deliver pulses of coherent X-rays on the femtosecond time scale, with potentially high repetition rates. While XFELs provide high peak intensities, both the intensity and the centroid of the beam fluctuate strongly on a pulse-to-pulse basis, motivating high-rate beam diagnostics that operate over a large dynamic range. The fast drift velocity, low X-ray absorption and high radiation tolerance properties of chemical vapour deposition diamonds make these crystals a promising candidate material for developing a fast (multi-GHz) pass-through diagnostic for the next generation of XFELs. A new approach to the design of a diamond sensor signal path is presented, along with associated characterization studies performed in the XPP endstation of the LINAC Coherent Light Source (LCLS) at SLAC. Qualitative charge collection profiles (collected charge versus time) are presented and compared with those from a commercially available detector. Quantitative results on the charge collection efficiency and signal collection times are presented over a range of approximately four orders of magnitude in the generated electron-hole plasma density.

Comparative analysis of the sensitivity of nanometallic thin film thermometers.

Thin film platinum resistive thermometers are conventionally applied for resistance thermometry techniques due to their stability and proven measurement accuracy. Depending upon the required thermometer thickness and temperature measurement, however, performance benefits can be realized through the application of alternative nanometallic thin films. Herein, a comparative experimental analysis is provided on the performance of nanometallic thin film thermometers most relevant to microelectronics and thermal sensing applications: Al, Au, Cu, and Pt. Sensitivity is assessed through the temperature coefficient of resistance, measured over a range of 10-300 K for thicknesses nominally spanning 25-200 nm. The interplay of electron scattering sources, which give rise to the temperature-dependent TCR properties for each metal, are analyzed in the framework of a Mayadas-Shatzkes based model. Despite the prevalence of evaporated Pt thin film thermometers, Au and Cu films fabricated in a similar manner may provide enhanced sensitivity depending upon thickness. These results may serve as a guide as the movement toward smaller measurement platforms necessitates the use of smaller, thinner metallic resistance thermometers.

Highly efficient terahertz photoconductive metasurface detectors operating at microwatt-level gate powers.

Despite their wide use in terahertz (THz) research and technology, the application spectra of photoconductive antenna (PCA) THz detectors are severely limited due to the relatively high optical gating power requirement. This originates from poor conversion efficiency of optical gate beam photons to photocurrent in materials with sub-picosecond carrier lifetimes. Here we show that using an ultra-thin (160 nm), perfectly absorbing low-temperature grown GaAs metasurface as the photoconductive channel drastically improves the efficiency of THz PCA detectors. This is achieved through perfect absorption of the gate beam in a significantly reduced photoconductive volume, enabled by the metasurface. This Letter demonstrates that sensitive THz PCA detection is possible using optical gate powers as low as 5 µW-three orders of magnitude lower than gating powers used for conventional PCA detectors. We show that significantly higher optical gate powers are not necessary for optimal operation, as they do not improve the sensitivity to the THz field. This class of efficient PCA THz detectors opens doors for THz applications with low gate power requirements.

Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.

DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5-methyl-dC (5mC) base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the post-SET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis.

Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion. This enabled us to identify high-confidence differentially methylated regions (hcDMRs) by comparing each test library to over 50 high-quality wild-type controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their effect on DNA methylation. In addition to confirming existing relationships, we revealed unanticipated connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at nonoverlapping regions of CMT2 targeted heterochromatin. Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes and can also be adopted for other genomics datasets.

Perfect absorption in GaAs metasurfaces near the bandgap edge.

Perfect optical absorption occurs in a metasurface that supports two degenerate and critically-coupled modes of opposite symmetry. The challenge in designing a perfectly absorbing metasurface for a desired wavelength and material stems from the fact that satisfying these conditions requires multi-dimensional optimization often with parameters affecting optical resonances in non-trivial ways. This problem comes to the fore in semiconductor metasurfaces operating near the bandgap wavelength, where intrinsic material absorption varies significantly. Here we devise and demonstrate a systematic process by which one can achieve perfect absorption in GaAs metasurfaces for a desired wavelength at different levels of intrinsic material absorption, eliminating the need for trial and error in the design process. Using this method, we show that perfect absorption can be achieved not only at wavelengths where GaAs exhibits high absorption, but also at wavelengths near the bandgap edge. In this region, absorption is enhanced by over one order of magnitude compared a layer of unstructured GaAs of the same thickness.

Vestibular rehabilitation in multiple sclerosis: study protocol for a randomised controlled trial and cost-effectiveness analysis comparing customised with booklet based vestibular rehabilitation for vestibulopathy and a 12 month observational cohort study of the symptom reduction and recurrence rate following treatment for benign paroxysmal positional vertigo.

BACKGROUND: Symptoms arising from vestibular system dysfunction are observed in 49-59% of people with Multiple Sclerosis (MS). Symptoms may include vertigo, dizziness and/or imbalance. These impact on functional ability, contribute to falls and significant health and social care costs. In people with MS, vestibular dysfunction can be due to peripheral pathology that may include Benign Paroxysmal Positional Vertigo (BPPV), as well as central or combined pathology. Vestibular symptoms may be treated with vestibular rehabilitation (VR), and with repositioning manoeuvres in the case of BPPV. However, there is a paucity of evidence about the rate and degree of symptom recovery with VR for people with MS and vestibulopathy. In addition, given the multiplicity of symptoms and underpinning vestibular pathologies often seen in people with MS, a customised VR approach may be more clinically appropriate and cost effective than generic booklet-based approaches. Likewise, BPPV should be identified and treated appropriately. METHODS/ DESIGN: People with MS and symptoms of vertigo, dizziness and/or imbalance will be screened for central and/or peripheral vestibulopathy and/or BPPV. Following consent, people with BPPV will be treated with re-positioning manoeuvres over 1-3 sessions and followed up at 6 and 12 months to assess for any re-occurrence of BPPV. People with central and/or peripheral vestibulopathy will be entered into a randomised controlled trial (RCT). Trial participants will be randomly allocated (1:1) to either a 12-week generic booklet-based home programme with telephone support or a 12-week VR programme consisting of customised treatment including 12 face-to-face sessions and a home exercise programme. Customised or booklet-based interventions will start 2 weeks after randomisation and all trial participants will be followed up 14 and 26 weeks from randomisation. The primary clinical outcome is the Dizziness Handicap Inventory at 26 weeks and the primary economic endpoint is quality-adjusted life-years. A range of secondary outcomes associated with vestibular function will be used. DISCUSSION: If customised VR is demonstrated to be clinically and cost-effective compared to generic booklet-based VR this will inform practice guidelines and the development of training packages for therapists in the diagnosis and treatment of vestibulopathy in people with MS. TRIAL REGISTRATION: ISRCTN Number: 27374299 Date of Registration 24/09/2018 Protocol Version 15 25/09/2019.

Single and double hole quantum dots in strained Ge/SiGe quantum wells.

Even as today's most prominent spin-based qubit technologies are maturing in terms of capability and sophistication, there is growing interest in exploring alternate material platforms that may provide advantages, such as enhanced qubit control, longer coherence times, and improved extensibility. Recent advances in heterostructure material growth have opened new possibilities for employing hole spins in semiconductors for qubit applications. Undoped, strained Ge/SiGe quantum wells are promising candidate hosts for hole spin-based qubits due to their low disorder, large intrinsic spin-orbit coupling strength, and absence of valley states. Here, we use a simple one-layer gated device structure to demonstrate both a single quantum dot as well as coupling between two adjacent quantum dots. The hole effective mass in these undoped structures, m* âˆ¼ 0.08 m 0, is significantly lower than for electrons in Si/SiGe, pointing to the possibility of enhanced tunnel couplings in quantum dots and favorable qubit-qubit interactions in an industry-compatible semiconductor platform.

Interaction between particles with inhomogeneous surface charge distributions: Revisiting the Coulomb fission of dication molecular clusters.

An analytical solution describing the electrostatic interaction between particles with inhomogeneous surface charge distributions has been developed. For particles, each carrying a single charge, the solution equates to the presence of a point charge residing on the surface, which makes it particularly suitable for investigating the Coulomb fission of doubly charged clusters close to the Rayleigh instability limit. For a series of six separate molecular dication clusters, center-of-mass kinetic energy releases have been extracted from experimental measurements of their kinetic energy spectra following Coulomb fission. These data have been compared with Coulomb energy barriers calculated from the electrostatic interaction energies given by this new solution. For systems with high dielectric permittivity, results from the point charge model provide a viable alternative to kinetic energy releases calculated on the assumption of a uniform distribution of surface charge. The equivalent physical picture for the clusters would be that of a trapped proton. For interacting particles with low dielectric permittivity, a uniform distribution of charge provides better agreement with the experimental results.

Comparison of portable blood-warming devices under simulated pre-hospital conditions: a randomised in-vitro blood circuit study.

Pre-hospital transfusion of blood products is a vital component of many advanced pre-hospital systems. Portable fluid warmers may be utilised to help prevent hypothermia, but the limits defined by manufacturers often do not reflect their clinical use. The primary aim of this randomised in-vitro study was to assess the warming performance of four portable blood warming devices (Thermal Angel, Hypotherm X LG, °M Warmer, Buddy Lite) against control at different clinically-relevant flow rates. The secondary aim was to assess haemolysis rates between devices at different flow rates. We assessed each of the four devices and the control, at flow rates of 50 ml.min-1 , 100 ml.min-1 and 200 ml.min-1 , using a controlled perfusion circuit with multisite temperature monitoring. Free haemoglobin concentration, a marker of haemolysis, was measured at multiple points during each initial study run with spectrophotometry. At all flow rates, the four devices provided superior warming performance compared with the control (p < 0.001). Only the °M Warmer provided a substantial change in temperature at all flow rates (mean (95%CI) temperature change of 21.1 (19.8-22.4) °C, 20.4 (19.1-21.8) °C and 19.4 (17.7-21.1) °C at 50 ml.min-1 , 100 ml.min-1 and 200 ml.min-1 , respectively). There was no association between warming and haemolysis with any device (p = 0.949) or flow rate (p = 0.169). Practical issues, which may be relevant to clinical use, also emerged during testing. Our results suggest that there were significant differences in the performance of portable blood warming devices used at flow rates encountered in clinical practice.

Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes.

The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions. In Arabidopsis, AtMORC1, AtMORC2, and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements. Here, we studied Arabidopsis AtMORC4 and AtMORC7. We found that, in contrast to AtMORC1,2,6, they act to suppress a wide set of non-methylated protein-coding genes that are enriched for those involved in pathogen response. Furthermore, atmorc4 atmorc7 double mutants show a pathogen response phenotype. We found that AtMORC4 and AtMORC7 form homomeric complexes in vivo and are concentrated in discrete nuclear bodies adjacent to chromocenters. Analysis of an atmorc1,2,4,5,6,7 hextuple mutant demonstrates that transcriptional de-repression is largely uncoupled from changes in DNA methylation in plants devoid of MORC function. However, we also uncover a requirement for MORC in both DNA methylation and silencing at a small but distinct subset of RNA-directed DNA methylation target loci. These regions are characterized by poised transcriptional potential and a low density of sites for symmetric cytosine methylation. These results provide insight into the biological function of MORC proteins in higher eukaryotes.