Co-incidence of Damage and Microbial Patterns Controls Localized Immune Responses in Roots.

Recognition of microbe-associated molecular patterns (MAMPs) is crucial for the plant's immune response. How this sophisticated perception system can be usefully deployed in roots, continuously exposed to microbes, remains a mystery. By analyzing MAMP receptor expression and response at cellular resolution in Arabidopsis, we observed that differentiated outer cell layers show low expression of pattern-recognition receptors (PRRs) and lack MAMP responsiveness. Yet, these cells can be gated to become responsive by neighbor cell damage. Laser ablation of small cell clusters strongly upregulates PRR expression in their vicinity, and elevated receptor expression is sufficient to induce responsiveness in non-responsive cells. Finally, localized damage also leads to immune responses to otherwise non-immunogenic, beneficial bacteria. Damage-gating is overridden by receptor overexpression, which antagonizes colonization. Our findings that cellular damage can "switch on" local immune responses helps to conceptualize how MAMP perception can be used despite the presence of microbial patterns in the soil.

Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes.

Many processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint of mutagenic processes. Of nine clustered mutation signatures identified from >1,000 tumor genomes, three relate to variable APOBEC activity and three are associated with tobacco smoking. An additional signature matches the spectrum of translesion DNA polymerase eta (POLH). In lymphoid cells, these mutations target promoters, consistent with AID-initiated somatic hypermutation. In solid tumors, however, they are associated with UV exposure and alcohol consumption and target the H3K36me3 chromatin of active genes in a mismatch repair (MMR)-dependent manner. These regions normally have a low mutation rate because error-free MMR also targets H3K36me3 chromatin. Carcinogens and error-prone repair therefore redistribute mutations to the more important regions of the genome, contributing a substantial mutation load in many tumors, including driver mutations.

cAMP signaling: a remarkably regional affair.

Louis Pasteur once famously said 'in the fields of observation chance favors only the prepared mind'. Much of chance is being in the right place at the right time. This is particularly true in the crowded molecular environment of the cell where being in the right place is often more important than timing. Although Brownian motion argues that enzymes will eventually bump into substrates, this probability is greatly enhanced if both molecules reside in the same subcellular compartment. However, activation of cell signaling enzymes often requires the transmission of chemical signals from extracellular stimuli to intracellular sites of action. This review highlights new developments in our understanding of cAMP generation and the 3D utilization of this second messenger inside cells.

Classical vs. quantum plasmon-induced molecular transformations at metallic nanojunctions.

Chemical transformations near plasmonic metals have attracted increasing attention in the past few years. Specifically, reactions occurring within plasmonic nanojunctions that can be detected via surface and tip-enhanced Raman (SER and TER) scattering were the focus of numerous reports. In this context, even though the transition between localized and nonlocal (quantum) plasmons at nanojunctions is documented, its implications on plasmonic chemistry remain poorly understood. We explore the latter through AFM-TER-current measurements. We use two molecules: i) 4-mercaptobenzonitrile (MBN) that reports on the (non)local fields and ii) 4-nitrothiophenol (NTP) that features defined signatures of its neutral/anionic forms and dimer product, 4,4'-dimercaptoazobenzene (DMAB). The transition from classical to quantum plasmons is established through our optical measurements: It is marked by molecular charging and optical rectification. Simultaneously recorded force and current measurements support our assignments. In the case of NTP, we observe the parent and DMAB product beneath the probe in the classical regime. Further reducing the gap leads to the collapse of DMAB to form NTP anions. The process is reversible: Anions subsequently recombine into DMAB. Our results have significant implications for AFM-based TER measurements and their analysis, beyond the scope of this work. In effect, when precise control over the junction is not possible (e.g., in SER and ambient TER), both classical and quantum plasmons need to be considered in the analysis of plasmonic reactions.

Far from home: the role of glial mRNA localization in synaptic plasticity.

Neurons and glia are highly polarized cells, whose distal cytoplasmic functional subdomains require specific proteins. Neurons have axonal and dendritic cytoplasmic extensions containing synapses whose plasticity is regulated efficiently by mRNA transport and localized translation. The principles behind these mechanisms are equally attractive for explaining rapid local regulation of distal glial cytoplasmic projections, independent of their cell nucleus. However, in contrast to neurons, mRNA localization has received little experimental attention in glia. Nevertheless, there are many functionally diverse glial subtypes containing extensive networks of long cytoplasmic projections with likely localized regulation that influence neurons and their synapses. Moreover, glia have many other neuron-like properties, including electrical activity, secretion of gliotransmitters and calcium signaling, influencing, for example, synaptic transmission, plasticity and axon pruning. Here, we review previous studies concerning glial transcripts with important roles in influencing synaptic plasticity, focusing on a few cases involving localized translation. We discuss a variety of important questions about mRNA transport and localized translation in glia that remain to be addressed, using cutting-edge tools already available for neurons.

Hitchhiking of Cas9 with nucleus-localized proteins impairs its controllability and leads to efficient genome editing of NLS-free Cas9.

CRISPR-Cas9 is the most commonly used genome-editing tool in eukaryotic cells. To modulate Cas9 entry into the nucleus to enable control of genome editing, we constructed a light-controlled CRISPR-Cas9 system to control exposure of the Cas9 protein nuclear localization signal (NLS). Although blue-light irradiation was found to effectively control the entry of Cas9 protein into the nucleus with confocal microscopy observation, effective gene editing occurred in controls with next-generation sequencing analysis. To further clarify this phenomenon, a CRISPR-Cas9 editing system without the NLS and a CRISPR-Cas9 editing system containing a nuclear export signal were also constructed. Interestingly, both Cas9 proteins could achieve effective editing of target sites with significantly reduced off-target effects. Thus, we speculated that other factors might mediate Cas9 entry into the nucleus. However, NLS-free Cas9 was found to produce effective target gene editing even following inhibition of cell mitosis to prevent nuclear import caused by nuclear membrane disassembly. Furthermore, multiple nucleus-localized proteins were found to interact with Cas9, which could mediate the "hitchhiking" of NLS-free Cas9 into the nucleus. These findings will inform future attempts to construct controllable gene-editing systems and provide new insights into the evolution of the nucleus and compatible protein functions.

Vasa, a regulator of localized mRNA translation on the spindle.

Localized mRNA translation is a biological process that allows mRNA to be translated on-site, which is proposed to provide fine control in protein regulation, both spatially and temporally within a cell. We recently reported that Vasa, an RNA-helicase, is a promising factor that appears to regulate this process on the spindle during the embryonic development of the sea urchin, yet the detailed roles and functional mechanisms of Vasa in this process are still largely unknown. In this review article, to elucidate these remaining questions, we first summarize the prior knowledge and our recent findings in the area of Vasa research and further discuss how Vasa may function in localized mRNA translation, contributing to efficient protein regulation during rapid embryogenesis and cancer cell regulation.

Enhanced localized dipole of Pt-Au single-site catalyst for solar water splitting.

Solar water splitting is regarded as holding great potential for clean fuels production. However, the efficiency of charge separation/transfer of photocatalysts is still too low for industrial application. This paper describes the synthesis of a Pt-Au binary single-site loaded g-C3N4 nanosheet photocatalyst inspired by the concept of the dipole. The existent larger charge imbalance greatly enhanced the localized molecular dipoles over adjacent Pt-Au sites in contrast to the unary counterparts. The superposition of molecular dipoles then further strengthened the internal electric field and thus promoted the charge transportation dynamics. In the modeling photocatalytic hydrogen evolution, the optimal Pt-Au binary site photocatalysts (0.25% loading) showed 4.9- and 2.3-fold enhancement of performance compared with their Pt and Au single-site counterparts, respectively. In addition, the reaction barrier over the Pt-Au binary sites was lowered, promoting the hydrogen evolution process. This work offers a valuable strategy for improving photocatalytic charge transportation dynamics by constructing polynary single sites.

Core/Shell-Like Localized Emission at Atomically Thin Semiconductor-Au Interface.

Localized emission in atomically thin semiconductors has sparked significant interest as single-photon sources. Despite comprehensive studies into the correlation between localized strain and exciton emission, the impacts of charge transfer on nanobubble emission remains elusive. Here, we report the observation of core/shell-like localized emission from monolayer WSe2 nanobubbles at room temperature through near-field studies. By altering the electronic junction between monolayer WSe2 and the Au substrate, one can effectively adjust the semiconductor to metal junction from a Schottky to an Ohmic junction. Through concurrent analysis of topography, potential, tip-enhanced photoluminescence, and a piezo response force microscope, we attribute the core/shell-like emissions to strong piezoelectric potential aided by induced polarity at the WSe2-Au Schottky interface which results in spatial confinement of the excitons. Our findings present a new approach for manipulating charge confinement and engineering localized emission within atomically thin semiconductor nanobubbles. These insights hold implications for advancing the nano and quantum photonics with low-dimensional semiconductors.

Chenodeoxycholic Acid-Loaded Nanoparticles Are Sufficient to Decrease Adipocyte Size by Inducing Mitochondrial Function.

Excess fat accumulation is not only associated with metabolic diseases but also negatively impacts physical appearance and emotional well-being. Bile acid, the body's natural emulsifier, is one of the few FDA-approved noninvasive therapeutic options for double chin (submental fat) reduction. Synthetic sodium deoxycholic acid (NaDCA) causes adipose cell lysis; however, its side effects include inflammation, bruising, and necrosis. Therefore, we investigated if an endogenous bile acid, chenodeoxycholic acid (CDCA), a well-known signaling molecule, can be beneficial without many of the untoward effects. We first generated CDCA-loaded nanoparticles to achieve sustained and localized delivery. Then, we injected them into the subcutaneous fat depot and monitored adipocyte size and mitochondrial function. Unlike NaDCA, CDCA did not cause cytolysis. Instead, we demonstrate that a single injection of CDCA-loaded nanoparticles into the subcutaneous fat reduced the adipocyte size by promoting fat burning and mitochondrial respiration, highlighting their potential for submental fat reduction.

Determining Transmission Characteristics from Shot-Noise-Driven Electroluminescence in Single-Molecule Junctions.

Biased metal-molecule-metal junctions emit light through electroluminescence, a phenomenon at the intersection of molecular electronics and nanoplasmonics. This can occur when the junction plasmon mode is excited by inelastic electron current fluctuations. Here, we simultaneously measure the conductance and electroluminescence intensity from single-molecule junctions with time resolution in a solution environment at room temperature. We use current versus bias data to determine the molecular junction transport parameters and then relate these to the expected current shot noise. We find that the electroluminescence signal accurately matches the theoretical prediction of shot-noise-driven emission in a large fraction of the molecular junctions studied. This introduces a novel experimental method for qualitatively estimating finite-frequency shot noise in single-molecule junctions under ambient conditions. We further demonstrate that electroluminescence can be used to obtain the level alignment of the frontier orbital dominating transport in the molecular junction.

Stability of Plasmonic Mg-MgO Core-Shell Nanoparticles in Gas-Phase Oxidative Environments.

Magnesium is a recent addition to the plasmonic toolbox: nanomaterials that efficiently utilize photons' energy due to their ability to sustain localized surface plasmon resonances. Magnesium nanoparticles protected by a native oxide shell can efficiently absorb light across the solar spectrum, making them a promising photocatalytic material. However, their inherent reactivity toward oxidation may limit the number of reactions in which Mg-MgO can be used. Here, we investigate the stability of plasmonic Mg-MgO core-shell nanoplates under oxidative conditions. We demonstrate that the MgO shell stabilizes the metallic Mg core against oxidation in air at up to 400 °C. Furthermore, we show that the reactivity of Mg-MgO nanoplates with water vapor (3.5 vol % in N2) decreases with temperature, with no oxidation of the Mg core detected from 200 to 400 °C. This work unravels the potential of Mg-MgO nanoparticles for a broad range of catalytic transformations occurring in oxidative environments.

Nanoscale Localized Phonons at Al2O3 Grain Boundaries.

Nanoscale defects like grain boundaries (GBs) would introduce local phonon modes and affect the bulk materials' thermal, electrical, optical, and mechanical properties. It is highly desirable to correlate the phonon modes and atomic arrangements for individual defects to precisely understand the structure-property relation. Here we investigated the localized phonon modes of Al2O3 GBs by combination of the vibrational electron energy loss spectroscopy (EELS) in scanning transmission electron microscope and density functional perturbation theory (DFPT). The differences between GB and bulk obtained from the vibrational EELS show that the GB exhibited more active vibration at the energy range of <50 meV and >80 meV, and further DFPT results proved the wide distribution of bond lengths at GB are the main factor for the emergence of local phonon modes. This research provides insights into the phonon-defect relation and would be of importance in the design and application of polycrystalline materials.

Differences in real-world outcomes by risk classification for localized prostate cancer patients after radiation therapy.

BACKGROUND: Limited real-world evidence exists on the long-term clinical outcomes of patients with localized prostate cancer (LPC) who received external beam radiation therapy (EBRT) as the initial treatment. This study evaluated clinical outcomes of US patients with high-risk LPC (HR-LPC) and low/intermediate-risk LPC (LIR-LPC) who received EBRT. METHODS: This retrospective study using Surveillance, Epidemiology, and End Results-Medicare linked data from 2012 to 2019 included patients ≥ 65 years old who received EBRT as initial therapy. Baseline patient characteristics were summarized, metastasis-free survival (MFS), overall survival, and time to initiation of advanced prostate cancer treatment were compared using Kaplan-Meier (KM) and adjusted Cox proportional hazard (PH) models. 5-year survival probabilities stratified by race/ethnicity (non-Hispanic [NH] White, NH Black, NH Asian, and Hispanic) were assessed. RESULTS: Of 11,313 eligible patients, 41% (n = 4600) had HR-LPC and 59% (n = 6713) had LIR-LPC. Patient characteristics for both groups were comparable, with mean age at EBRT initiation > 70 years, 86% white, and mean follow-up time >40 months. More patients in the HR-LPC than LIR-LPC groups (78% vs 34%) had concurrent androgen deprivation therapy use and for a longer duration (median 10.4 months vs. 7.4 months). A higher proportion of HR-LPC patients developed metastasis, died, or received advanced prostate cancer treatment. Adjusted Cox PH survival analyses showed significantly (p < 0.0001) higher risk of mortality (hazard ratios [HR], 1.57 [1.38, 2.34]), metastasis or death (HR, 1.97 [1.78, 2.17]), and advanced prostate cancer therapy use (HR, 2.57 [2.11, 3.14]) for HR-LPC than LIR-LPC patients. Within 5 years after the initial EBRT treatment, 18%-26% of patients with HR-LPC are expected to have died or developed metastasis. The 5-year MFS rate in the HR-LPC group was lower than the LIR-LPC group across all racial/ethnic subgroups. NH Black patients with HR-LPC had the highest all-cause mortality rate and lowest rate of receiving advanced prostate cancer treatment, compared to other racial/ethnic subgroups. CONCLUSIONS: This real-world study of clinical outcomes in patients with LPC treated with EBRT suggests substantial disease burden in patients with HR-LPC and highlights the need for additional treatment strategies to improve clinical outcomes in patients with HR-LPC.

Fewer systematic prostate core biopsies in clinical stage T1c prostate cancer leads to biochemical recurrence after brachytherapy as monotherapy.

BACKGROUND: After brachytherapy, fewer prostate biopsy cores at diagnosis can underestimate the pathological characteristics of prostate cancer (PCa) with lower concordance, resulting in improper treatment, particularly in patients with low-risk nonpalpable cT1c PCa. The aim of this study was to assess the relationship between the number of biopsy cores at diagnosis and long-term clinical outcomes after brachytherapy for cT1c PCa. METHODS: We reviewed 516 patients with localized cT1c PCa with Gleason scores of 3 + 3 = 6 or 3 + 4 = 7 who underwent brachytherapy as monotherapy without hormonal therapy between January 2005 and September 2014 at our institution. Clinical staging was based on the American Joint Committee on Cancer manual for staging. Thus, the cT1c category is based solely on digital rectal examination. The primary outcome was biochemical recurrence (BCR). Based on the optimized cutoff value for biopsy core number obtained from receiver operating characteristic analysis, patients were divided into the biopsy cores ≤8 (N = 123) and ≥9 (N = 393) groups. The BCR-free survival rate was compared between the groups. Prognostic factors for BCR were evaluated, including age, initial prostate-specific antigen (PSA) level, Gleason score, positive core rate, PSA density, prostate magnetic resonance imaging findings, and biopsy core number. RESULTS: The median patient age was 66.0 years (interquartile range [IQR]: 61.0-71.0 years), and the median follow-up time was 11.1 years (IQR: 9.5-13.3 years). The median number of core biopsies was 12 (IQR: 9-12). The area under the curve was 0.637 (95% confidence interval [CI]: 0.53-0.75), and the optimal biopsy core cutoff value for BCR prediction was 8.5 (sensitivity = 43.5%, specificity = 77.1%). Although fewer patients had Gleason scores of 3 + 4 = 7 (19/123 [15%] vs. 125/393 [32%], p < 0.02) in the biopsy cores ≤8 group, the 10-year BCR-free survival rate was significantly lower in the biopsy cores ≤8 group than in the biopsy cores ≥9 group (93.8% vs. 96.3%, p < 0.05). Multivariate analysis revealed that a lower biopsy core number (hazard ratio: 0.828, 95% CI: 0.71-0.97, p < 0.03) and a Gleason score of 3 + 4 = 7 (hazard ratio: 3.26, 95% CI: 1.37-7.73, p < 0.01) significantly predicted BCR. CONCLUSIONS: A low number of prostate core biopsies results in worse BCR-free survival after brachytherapy as monotherapy in patients with cT1c PCa.

SCHENGEN receptor module drives localized ROS production and lignification in plant roots.

Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.

How delocalized are the polyacenes?

In an attempt to quantify electron delocalization in polyacenes with up to 50 carbon atoms, we have performed self-consistent field calculations in which the π electrons are constrained to occupy highly localized molecular orbitals (HILOs) centered on a maximum of two, six or ten adjacent carbon atoms. We have also performed similar calculations on simple polyacene analogs consisting only of hydrogen atoms and exhibiting electron delocalization in the σ framework. We find that the energetic cost of localizing the π electrons in the polyacenes is roughly 60, 5 or 0.1 kJ/mol per ring atom for the two-, six- and ten-atom HILOs, respectively, and the use of these localized models overestimates the predicted hydrogenation energies of the acenes by roughly 50%, 4% and 0.1%, respectively. We conclude that the chemistry of polyacenes can be modeled well using highly localized descriptions of the π electrons.

Strongly Localized Moiré Exciton in Twisted Homobilayers.

Artificially molding exciton flux is the cornerstone for developing promising excitonic devices. In the emerging hetero/homobilayers, the spatial separated charges prolong exciton lifetimes and create out-plane dipoles, facilitating electrically control exciton flux on a large scale, and the nanoscale periodic moiré potentials arising from twist-angle or/and lattice mismatch can substantially alter exciton dynamics, which are mainly proved in the heterostructures. However, the spatially indirect excitons dynamics in homobilayers without lattice mismatch remain elusive. Here the nonequilibrium dynamics of indirect exciton in homobilayers are systematically investigated. The homobilayers with slightly twist-angle can induce a deep moiré potential (>50 meV) in the energy landscape of indirect excitons, resulting in a strongly localized moiré excitons insulating the transport dynamics from phonons and disorder. These findings provide insights into the exciton dynamics and many-body physics in moiré superlattices modulated energy landscape, with implications for designing excitonic devices operating at room temperature.

Deciphering the Mechanisms of Photo-Enhanced Catalytic Activities in Plasmonic Pd-Au Heteromeric Nanozymes for Colorimetric Analysis.

The growing demand for highly active nanozymes in various fields has led to the development of several strategies to enhance their activity. Plasmonic enhancement, a strategy used in heterogenous catalysis, represents a promising strategy to boost the activity of nanozymes. Herein, Pd-Au heteromeric nanoparticles (Pd-Au dimers) with well-defined heterointerfaces have been explored as plasmonic nanozymes. As a model system, the Pd-Au dimers with integrated peroxidase (POD)-like activity and plasmonic activity are used to investigate the effect of plasmons on enhancing the activity of nanozymes under visible light irradiation. Mechanistic studies revealed that the generation of hot electron-hole pairs plays a dominant role in plasmonic effect, and it greatly enhances the decomposition of H2 O2 to the reactive oxygen species (ROS) intermediates (•OH, •O2 - and 1 O2 ), leading to elevated POD-like activity of the Pd-Au dimers. Finally, the Pd-Au dimers are applied in the plasmon-enhanced colorimetric method for the detection of alkaline phosphatase, exhibiting broad linear range and low detection limit. This study not only provides a straightforward approach for regulating nanozyme activity through plasmonic heterostructures but also sheds light on the mechanism of plasmon-enhanced catalysis of nanozymes.

Recent Advances in the 3D Chiral Plasmonic Nanomaterials.

From the view of geometry, chirality is that an object cannot overlap with its mirror image, which has been a fundamental scientific problem in biology and chemistry since the 19th century. Chiral inorganic nanomaterials serve as ideal templates for investigating chiral transfer and amplification mechanisms between molecule and bulk materials, garnering widespread attentions. The chiroptical property of chiral plasmonic nanomaterials is enhanced through localized surface plasmon resonance effects, which exhibits distinctive circular dichroism (CD) response across a wide wavelength range. Recently, 3D chiral plasmonic nanomaterials are becoming a focal research point due to their unique characteristics and planar-independence. This review provides an overview of recent progresses in 3D chiral plasmonic nanomaterials studies. It begins by discussing the mechanisms of plasmonic enhancement of molecular CD response, following by a detailed presentation of novel classifications of 3D chiral plasmonic nanomaterials. Finally, the applications of 3D chiral nanomaterials such as biology, sensing, chiral catalysis, photology, and other fields have been discussed and prospected. It is hoped that this review will contribute to the flourishing development of 3D chiral nanomaterials.