Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.

Mosquito-borne flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), are a growing public health concern. Systems-level analysis of how flaviviruses hijack cellular processes through virus-host protein-protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. We used affinity purification-mass spectrometry (AP-MS) to compare flavivirus-host interactions for two viruses (DENV and ZIKV) in two hosts (human and mosquito). Conserved virus-host PPIs revealed that the flavivirus NS5 protein suppresses interferon stimulated genes by inhibiting recruitment of the transcription complex PAF1C and that chemical modulation of SEC61 inhibits DENV and ZIKV replication in human and mosquito cells. Finally, we identified a ZIKV-specific interaction between NS4A and ANKLE2, a gene linked to hereditary microcephaly, and showed that ZIKV NS4A causes microcephaly in Drosophila in an ANKLE2-dependent manner. Thus, comparative flavivirus-host PPI mapping provides biological insights and, when coupled with in vivo models, can be used to unravel pathogenic mechanisms.

Cell Taxonomy: a curated repository of cell types with multifaceted characterization.

Single-cell studies have delineated cellular diversity and uncovered increasing numbers of previously uncharacterized cell types in complex tissues. Thus, synthesizing growing knowledge of cellular characteristics is critical for dissecting cellular heterogeneity, developmental processes and tumorigenesis at single-cell resolution. Here, we present Cell Taxonomy (https://ngdc.cncb.ac.cn/celltaxonomy), a comprehensive and curated repository of cell types and associated cell markers encompassing a wide range of species, tissues and conditions. Combined with literature curation and data integration, the current version of Cell Taxonomy establishes a well-structured taxonomy for 3,143 cell types and houses a comprehensive collection of 26,613 associated cell markers in 257 conditions and 387 tissues across 34 species. Based on 4,299 publications and single-cell transcriptomic profiles of ∼3.5 million cells, Cell Taxonomy features multifaceted characterization for cell types and cell markers, involving quality assessment of cell markers and cell clusters, cross-species comparison, cell composition of tissues and cellular similarity based on markers. Taken together, Cell Taxonomy represents a fundamentally useful reference to systematically and accurately characterize cell types and thus lays an important foundation for deeply understanding and exploring cellular biology in diverse species.

Association mechanism between Arabidopsis immune coreceptor BAK1 and Pseudomonas syringae effector HopF2.

Brassinosteroid activated kinase 1 (BAK1) is a cell-surface coreceptor which plays multiple roles in innate immunity of plants. HopF2 is an effector secreted by the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 into Arabidopsis and suppresses host immune system through interaction with BAK1 as well as its downstream kinase MKK5. The association mechanism of HopF2 to BAK1 remains unclear, which prohibits our understanding and subsequent interfering of their interaction for pathogen management. Herein, we found the kinase domain of BAK1 (BAK1-KD) is sufficient for HopF2 association. With a combination of hydrogen/deuterium exchange mass spectrometry and mutational assays, we found a region of BAK1-KD N-lobe and a region of HopF2 head subdomain are critical for intermolecular interaction, which is also supported by unbiased protein-protein docking with ClusPro and kinase activity assay. Collectively, this research presents the interaction mechanism between Arabidopsis BAK1 and P. syringae HopF2, which could pave the way for bactericide development that blocking the functioning of HopF2 toward BAK1.

Transcranial Direct Current Stimulation (tDCS) over the left dorsolateral prefrontal cortex reduced attentional bias toward natural emotional sounds.

Previous research has indicated that the left dorsolateral prefrontal cortex (DLPFC) exerts an influence on attentional bias toward visual emotional information. However, it remains unclear whether the left DLPFC also play an important role in attentional bias toward natural emotional sounds. The current research employed the emotional spatial cueing paradigm, incorporating natural emotional sounds of considerable ecological validity as auditory cues. Additionally, high-definition transcranial direct current stimulation (HD-tDCS) was utilized to examine the impact of left dorsolateral prefrontal cortex (DLPFC) on attentional bias and its subcomponents, namely attentional engagement and attentional disengagement. The results showed that (1) compared to sham condition, anodal HD-tDCS over the left DLPFC reduced the attentional bias toward positive and negative sounds; (2) anodal HD-tDCS over the left DLPFC reduced the attentional engagement toward positive and negative sounds, whereas it did not affect attentional disengagement away from natural emotional sounds. Taken together, the present study has shown that left DLPFC, which was closely related with the top-down attention regulatory function, plays an important role in auditory emotional attentional bias.

BrainBase: a curated knowledgebase for brain diseases.

Brain is the central organ of the nervous system and any brain disease can seriously affect human health. Here we present BrainBase (https://ngdc.cncb.ac.cn/brainbase), a curated knowledgebase for brain diseases that aims to provide a whole picture of brain diseases and associated genes. Specifically, based on manual curation of 2768 published articles along with information retrieval from several public databases, BrainBase features comprehensive collection of 7175 disease-gene associations spanning a total of 123 brain diseases and linking with 5662 genes, 16 591 drug-target interactions covering 2118 drugs/chemicals and 623 genes, and five types of specific genes in light of expression specificity in brain tissue/regions/cerebrospinal fluid/cells. In addition, considering the severity of glioma among brain tumors, the current version of BrainBase incorporates 21 multi-omics datasets, presents molecular profiles across various samples/conditions and identifies four groups of glioma featured genes with potential clinical significance. Collectively, BrainBase integrates not only valuable curated disease-gene associations and drug-target interactions but also molecular profiles through multi-omics data analysis, accordingly bearing great promise to serve as a valuable knowledgebase for brain diseases.

Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

Transcriptomic profiling is critical to uncovering functional elements from transcriptional and post-transcriptional aspects. Here, we present Gene Expression Nebulas (GEN, https://ngdc.cncb.ac.cn/gen/), an open-access data portal integrating transcriptomic profiles under various biological contexts. GEN features a curated collection of high-quality bulk and single-cell RNA sequencing datasets by using standardized data processing pipelines and a structured curation model. Currently, GEN houses a large number of gene expression profiles from 323 datasets (157 bulk and 166 single-cell), covering 50 500 samples and 15 540 169 cells across 30 species, which are further categorized into six biological contexts. Moreover, GEN integrates a full range of transcriptomic profiles on expression, RNA editing and alternative splicing for 10 bulk datasets, providing opportunities for users to conduct integrative analysis at both transcriptional and post-transcriptional levels. In addition, GEN provides abundant gene annotations based on value-added curation of transcriptomic profiles and delivers online services for data analysis and visualization. Collectively, GEN presents a comprehensive collection of transcriptomic profiles across multiple species, thus serving as a fundamental resource for better understanding genetic regulatory architecture and functional mechanisms from tissues to cells.

Sub-surface Imaging of Porous GaN Distributed Bragg Reflectors via Backscattered Electrons.

In this article, porous GaN distributed Bragg reflectors (DBRs) were fabricated by epitaxy of undoped/doped multilayers followed by electrochemical etching. We present backscattered electron scanning electron microscopy (BSE-SEM) for sub-surface plan-view imaging, enabling efficient, non-destructive pore morphology characterization. In mesoporous GaN DBRs, BSE-SEM images the same branching pores and Voronoi-like domains as scanning transmission electron microscopy. In microporous GaN DBRs, micrographs were dominated by first porous layer features (45 nm to 108 nm sub-surface) with diffuse second layer (153 nm to 216 nm sub-surface) contributions. The optimum primary electron landing energy (LE) for image contrast and spatial resolution in a Zeiss GeminiSEM 300 was approximately 20 keV. BSE-SEM detects porosity ca. 295 nm sub-surface in an overgrown porous GaN DBR, yielding low contrast that is still first porous layer dominated. Imaging through a ca. 190 nm GaN cap improves contrast. We derived image contrast, spatial resolution, and information depth expectations from semi-empirical expressions. These theoretical studies echo our experiments as image contrast and spatial resolution can improve with higher LE, plateauing towards 30 keV. BSE-SEM is predicted to be dominated by the uppermost porous layer's uppermost region, congruent with experimental analysis. Most pertinently, information depth increases with LE, as observed.

Video telehealth emotional awareness and expression therapy for older U.S. military veterans with chronic pain: A pilot study.

OBJECTIVES: Emotional Awareness and Expression Therapy (EAET) targets trauma and emotional conflict to reduce or eliminate chronic pain, but video telehealth administration is untested. This uncontrolled pilot assessed acceptability, feasibility, and preliminary efficacy of group-based video telehealth EAET (vEAET) for older veterans with chronic musculoskeletal pain. METHODS: Twenty veterans were screened, and 16 initiated vEAET, delivered as one 60-minute individual session and eight 90-minute group sessions. Veterans completed posttreatment satisfaction ratings and pain severity (primary outcome), pain interference, anxiety, depression, functioning, social connectedness, shame, and anger questionnaires at baseline, posttreatment, and 2-month follow-up. RESULTS: Satisfaction was high, and veterans attended 7.4 (SD = 0.6) of 8 group sessions; none discontinued treatment. Veterans attained significant, large reductions in pain severity from baseline to posttreatment (p < .001, Hedges' g = -1.54) and follow-up (p < .001, g = -1.20); 14 of 16 achieved clinically significant (≥ 30%) pain reduction, and 3 achieved 90-100% pain reduction. Secondary outcomes demonstrated significant, medium-to-large improvements. CONCLUSIONS: In this small sample, vEAET produced better attendance, similar benefits, and fewer dropouts than in-person EAET in prior studies. Larger, controlled trials are needed. CLINICAL IMPLICATIONS: Group vEAET appears feasible and highly effective for older veterans with chronic pain.

Three-Photon Excitation of InGaN Quantum Dots.

We demonstrate that semiconductor quantum dots can be excited efficiently in a resonant three-photon process, while resonant two-photon excitation is highly suppressed. Time-dependent Floquet theory is used to quantify the strength of the multiphoton processes and model the experimental results. The efficiency of these transitions can be drawn directly from parity considerations in the electron and hole wave functions in semiconductor quantum dots. Finally, we exploit this technique to probe intrinsic properties of InGaN quantum dots. In contrast to nonresonant excitation, slow relaxation of charge carriers is avoided, which allows us to measure directly the radiative lifetime of the lowest energy exciton states. Since the emission energy is detuned far from the resonant driving laser field, polarization filtering is not required and emission with a greater degree of linear polarization is observed compared to nonresonant excitation.

Preparation and application of high-brightness red carbon quantum dots for pH and oxidized L-glutathione dual response.

Carbon dots (CDs) with red fluorescence emission are highly desirable for use in bioimaging and trace- substance detection, with potential applications in biotherapy, photothermal therapy, and tumor visualization. Most CDs emit green or blue fluorescence, thus limiting their applicability. We report a novel fluorescent detection platform based on high-brightness red fluorescence emission carbon dots (R-CDs) co-doped with nitrogen and bromine, which exhibit pH and oxidized L-glutathione (GSSG) dual-responsive characteristics. The absolute quantum yield of the R-CDs was as high as 11.93%. We discovered that the R-CDs were able to detect acidic pH in live cells and zebrafish owing to protonation and deprotonation. In addition, GSSG was detected in vitro over a broad linear range (8-200 µM) using the R-CDs with excitation-independent emission. Furthermore, cell imaging and bioimaging experiments demonstrated that the R-CDs were highly cytocompatible and could be used as fluorescent probes to target lysosomes and nucleolus. These studies highlight the promising prospects of R-CDs as biosensing tools for bioimaging and trace-substance detection applications.

Nitrogen-doped orange emitting carbon dots for ß-carotene detection and lysosomal imaging.

ß-Carotene is a natural antioxidant that has an indispensable effect on the growth and immunity of the human body. For intracellular and in vitro detection of ß-carotene, N-doped carbon quantum dots (O-CDs) were prepared by co-heating carbonization of 1,5-naphthalenediamine and nitric acid in ethanol solvent for 2 h at 200 °C. O-CDs have longer wavelength orange light emission, with an optimal excitation peak of 470 nm and an optimal emission peak of 590 nm. According to the principle of the internal filtering effect on which the detection system is based, O-CDs present a good linear relationship with ß-carotene within a wide range of 0-2000 µM, and the R2 coefficient of the linear regression equation is 0.999. In addition, O-CDs showed targeting of lysosomes in cell imaging and could be used to detect intracellular lysosomal movement. These experiments show that O-CDs can be used for in vivo and in vitro detection of ß-carotene and can serve as a potential substitute to commercial lysosome targeting probes.

Superhybrid Mode-Enhanced Optical Torques on Mie-Resonant Particles.

Circularly polarized light carries spin angular momentum, so it can exert an optical torque on the polarization-anisotropic particle by the spin momentum transfer. Here, we show that giant positive and negative optical torques on Mie-resonant (gain) particles arise from the emergence of superhybrid modes with magnetic multipoles and electric toroidal moments, excited by linearly polarized beams. Anomalous positive and negative torques on particles (doped with judicious amount of dye molecules) are over 800 and 200 times larger than the ordinary lossy counterparts, respectively. Meanwhile, a rotational motor can be configured by switching the s- and p-polarized beams, exhibiting opposite optical torques. These giant and reversed optical torques are unveiled for the first time in the scattering spectrum, paving another avenue toward exploring unprecedented physics of hybrid and superhybrid multipoles in metaoptics and optical manipulations.

Inverse Optical Torques on Dielectric Nanoparticles in Elliptically Polarized Light Waves.

Elliptically polarized light waves carry the spin angular momentum (SAM), so they can exert optical torques on nanoparticles. Usually, the rotation follows the same direction as the SAM due to momentum conservation. It is counterintuitive to observe the reversal of optical torque acting on an ordinary dielectric nanoparticle illuminated by an elliptically or circularly polarized light wave. Here, we demonstrate that negative optical torques, which are opposite to the direction of SAM, can ubiquitously emerge when elliptically polarized light waves are impinged on dielectric nanoparticles obliquely. Intriguingly, the rotation can be switched between clockwise and counterclockwise directions by controlling the incident angle of light. Our study suggests a new playground to harness polarization-dependent optical force and torque for advancing optical manipulations.

Metabolomic Study on Iohexol-Induced Nephrotoxicity in Rats Based on NMR and LC-MS Analyses.

Iohexol, the raw material of nonionic X-ray computed tomography (X-CT) contrast medium, is usually injected into the vein before CT angiography diagnosis. It is used for angiography, urography, and lymphography. With the advantages of low contrast density and good tolerance, it is currently one of the most popular contrast media. However, the renal toxicity of iohexol seriously affects its safety use. Therefore, it is of great importance to identify new potential diagnostic biomarkers and therapeutic targets in the process of contrast medium-induced acute kidney injury (CI-AKI) in order to safely use iohexol in clinical practice. In this study, in order to understand the metabolic mechanism of CI-AKI, ultra-high-performance liquid chromatography/quadrupole-Orbitrap-mass spectrometry and 1H NMR-based metabolomic techniques were utilized to study the metabolic spectra of kidney, plasma, and urine from CI-AKI rats, and a total of 30 metabolites that were closely related to kidney injury were screened out, which were mainly related to 9 metabolic pathways. The results further indicated that iohexol might intensify kidney dysfunction in vivo by disrupting the metabolic pathways in the body, especially through blocking energy metabolism, amino acid metabolism, and promoting inflammatory reactions.

Chronic Pain in Older Adults: A Neuroscience-Based Psychological Assessment and Treatment Approach.

Chronic pain remains a serious healthcare challenge, particularly for older adults who suffer substantial disability and are susceptible to serious risks from pain medications and invasive procedures. Psychotherapy is a promising option for older adults with chronic pain, since it does not contribute to medical or surgical risks. However, standard psychotherapies for chronic pain, including cognitive-behavioral therapy (CBT), acceptance and commitment therapy, and mindfulness-based interventions, produce only modest and time-limited benefits for older adults. In this article, we describe a novel, evidence-based psychological assessment and treatment approach for older adults with chronic pain, including a detailed case example. The approach begins with reviewing patients' pain, psychosocial, and medical histories to elicit evidence of a subtype of chronic pain called centralized (primary, nociplastic, or psychophysiologic) pain, which is highly influenced and may even be caused by life stress, emotions, and alterations in brain function. Patients then undertake a novel psychotherapy approach called emotional awareness and expression therapy (EAET) that aims to reduce or eliminate centralized pain by resolving trauma and emotional conflicts and learning healthy communication of adaptive emotions. Our published preliminary clinical trial (n = 53) indicated that EAET produced statistically significant and large effect size advantages over CBT in pain reduction and marginally greater improvements in pain interference than CBT for older adults with chronic musculoskeletal pain. Geriatric mental healthcare providers may learn this assessment and treatment approach to benefit many of their patients with chronic pain.

Ultra-bright carbon quantum dots for rapid cell staining.

Cellular imaging using carbon dots is an important research method in several fields. Herein, green-emissive carbon quantum dots (G-CDs) with a pretty high absolute quantum yield (QY) were fabricated via a one-step solvothermal method by using m-phenylenediamine and concentrated hydrochloric acid. G-CDs displayed strong green fluorescence with excitation/emission peaks at 460/500 nm, and their absolute quantum yield was as high as 58.65%. Further experiments suggested that the G-CDs we prepared have good solubility, excellent biocompatibility, and the capacity of rapidly imaging HeLa and 4T1 cells. Over expectations, the G-CDs could penetrate cells in only 10 s and the confocal images showed that the G-CDs could target the nucleus of cells. Moreover, by using 920 nm as the excitation wavelength, two-photon imaging has been successfully applied to 4T1 cells, overcoming the inherent limitations of single-photon imaging. The extremely high absolute quantum efficiency, ultra-fast imaging speed, and two-photon imaging capability make the G-CDs have good application potential in biomedical analysis and the clinical diagnostic field.

Rapid discovery of potential ADR compounds from injection of total saponins from Panax notoginseng using data-independent acquisition untargeted metabolomics.

Injection of total saponins from Panax notoginseng (ISPN) is a modern preparation derived from traditional Chinese medicine (TCM) and is widely applied in the treatment of cardiovascular, cerebrovascular, ophthalmology, and endocrine system diseases. With the increase in the clinical application of ISPN, its adverse drug reactions (ADRs) and related safety issues have attracted much attention. In the present study, a data-independent acquisition (DIA) strategy was proposed to comprehensively characterize the saponins contained in ISPN based on the ultra-high-performance liquid chromatography/quadrupole-Orbitrap MS (UHPLC/Q-Orbitrap MS) platform. As many as 276 saponins were detected, and 250 compounds were identified or tentatively identified based on the retention times and MS/MS data. Furthermore, a metabolomic strategy was utilized to discover the discriminative saponins between normal and ADR batches. The results showed that six saponins, including ginsenoside Rh4, ginsenoside Rk3, ginsenoside Rg5, ginsenoside Rk1, ginsenoside Rg6, and 20(S)-ginsenoside Rh2, were significantly different between the two groups. According to cytotoxicity analysis and degranulation detection of RBL-2H3 cells, ginsenoside Rg5, ginsenoside Rk1, and 20(S)-ginsenoside Rh2 were considered the potential compounds responsible for clinical ADRs, ultimately. In addition, the quantitative analysis showed that the content of these three compounds in ISPN samples with ADRs was generally higher than that in samples without ADRs. This study demonstrated that it is advisable to screen out potential markers related to ADRs for developing the quality standard of ISPN by the integration of untargeted metabolomic analysis and cell biology study, and thus reduce its ADRs in the clinic.

Design, Synthesis and Biological Evaluation of N-phenylindole Derivatives as Pks13 Inhibitors againstMycobacterium tuberculosis.

Polyketide synthase 13 (Pks13), an essential enzyme for the survival of Mycobacterium tuberculosis (Mtb), is an attractive target for new anti-TB agents. In our previous work, we have identified 2-phenylindole derivatives against Mtb. The crystallography studies demonstrated that the two-position phenol was solvent-exposed in the Pks13-TE crystal structure and a crucial hydrogen bond was lost while introducing bulkier hydrophobic groups at indole N moieties. Thirty-six N-phenylindole derivatives were synthesized and evaluated for antitubercular activity using a structure-guided approach. The structure-activity relationship (SAR) studies resulted in the discovery of the potent Compounds 45 and 58 against Mtb H37Rv, with an MIC value of 0.0625 µg/mL and 0.125 µg/mL, respectively. The thermal stability analysis showed that they bind with high affinity to the Pks13-TE domain. Preliminary ADME evaluation showed that Compound 58 displayed modest human microsomal stability. This report further validates that targeting Pks13 is a valid strategy for the inhibition of Mtb and provides a novel scaffold for developing leading anti-TB compounds.

Extraordinary Multipole Modes and Ultra-Enhanced Optical Lateral Force by Chirality.

Strong mode coupling and Fano resonances arisen from exceptional interaction between resonant modes in single nanostructures have raised much attention for their advantages in nonlinear optics, sensing, etc. Individual electromagnetic multipole modes such as quadrupoles, octupoles, and their counterparts from mode coupling (toroidal dipole and nonradiating anapole mode) have been well investigated in isolated or coupled nanostructures with access to high Q factors in bound states in the continuum. Albeit the extensive study on ordinary dielectric particles, intriguing aspects of light-matter interactions in single chiral nanostructures is lacking. Here, we unveil that extraordinary multipoles can be simultaneously superpositioned in a chiral nanocylinder, such as two toroidal dipoles with opposite moments, and electric and magnetic sextupoles. The induced optical lateral forces and their scattering cross sections can thus be either significantly enhanced in the presence of those multipoles with high-Q factors, or suppressed by the bound states in the continuum. This work for the first time reveals the complex correlation between multipolar effects, chiral coupling, and optical lateral force, providing a distinct way for advanced optical manipulation.

Momentum-Topology-Induced Optical Pulling Force.

We report an ingenious mechanism to obtain robust optical pulling force by a single plane wave via engineering the topology of light momentum in the background. The underlying physics is found to be the topological transition of the light momentum from a usual convex shape to a starlike concave shape in the carefully designed background, such as a photonic crystal structure. The principle and results reported here shed insightful concepts concerning optical pulling, and pave the way for a new class of advanced optical manipulation technique, with potential applications of drug delivery and cell sorting.