Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton.

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a "genome shock", leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (Gossypium hirsutum and Gossypium barbadense, AADD) and its extant AA (Gossypium arboreum) and DD (Gossypium raimondii) progenitors. We observed distinct DHS distributions between G. arboreum and G. raimondii. In contrast, the DHSs of the two subgenomes of G. hirsutum and G. barbadense showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids Gossypium darwinii and G. hirsutum var. yucatanense, but absent from a resynthesized hybrid of G. arboreum and G. raimondii, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative cis-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.

Dielectric function and interband critical points of compressively strained ferroelectric K0.85Na0.15NbO3 thin film with monoclinic and orthorhombic symmetry.

The dielectric function and interband critical points of compressively strained ferroelectric K0.85Na0.15NbO3 thin film grown by metal-organic vapor phase epitaxy (MOVPE) are studied in broad spectral and temperature ranges by spectroscopic ellipsometry (SE). The temperature dependence of the measured pseudodielectric functions is strongly affected by a structural phase transition from the monoclinic Mc-phase to the orthorhombic c-phase at about 428 K. Using a parametric optical constant model, the corresponding dielectric functions as well as the interband optical transitions of the film are determined in the spectral range of 0.73-6.00 eV. Standard critical point (SCP) analysis of the 2nd derivatives of the dielectric functions identified three and four critical points for monoclinic and orthorhombic symmetries, respectively. A systematic redshift of the threshold energies with increasing temperatures was observed.

Chemoproteomic Profiling of Erastin-Interacting Proteins.

Ferroptosis is an iron-related cell death caused by irregular lipid peroxidation that has been implicated with a variety of disease. Erastin is a canonical ferroptosis inducer that is known to function by inhibiting system Xc- and cystine transport; however, the global interactome of erastin in cells remains unexplored. In this work, we employed a quantitative chemoproteomic approach to profile direct interacting proteins of erastin in living cells using a multifunctional photo-cross-linking probe. A number of novel erastin-interacting proteins were identified, including a serine hydrolase, ABHD6, whose overexpression showed a potentiating impact on ferroptosis. Further biochemical experiments revealed that erastin can allosterically activate ABHD6's activity to produce more arachidonic acids and elevate the level of lipid reactive oxygen species. Collectively, our work provided a global portrait of erastin-interacting proteins and discovered ABHD6 as a new ferroptosis regulator.

Revealing protein trafficking by proximity labeling-based proteomics.

Protein trafficking is a fundamental process with profound implications for both intracellular and intercellular functions. Proximity labeling (PL) technology has emerged as a powerful tool for capturing precise snapshots of subcellular proteomes by directing promiscuous enzymes to specific cellular locations. These enzymes generate reactive species that tag endogenous proteins, enabling their identification through mass spectrometry-based proteomics. In this comprehensive review, we delve into recent advancements in PL-based methodologies, placing particular emphasis on the label-and-fractionation approach and TransitID, for mapping proteome trafficking. These methodologies not only facilitate the exploration of dynamic intracellular protein trafficking between organelles but also illuminate the intricate web of intercellular and inter-organ protein communications.

Motion prediction of tumbling uncooperative spacecraft during proximity operations.

The relative attitude estimation between chasers and uncooperative targets is an important prerequisite for executing in orbit service (OOS) tasks. Only by efficiently obtaining relative pose parameters can chasers design close-range rendezvous trajectories close to uncooperative targets. The focus of this article is on active systems, such as TOF cameras or LIDAR. This paper proposes an attitude estimation scheme to obtain relative attitude parameters between uncooperative targets. This scheme utilizes LIDAR to obtain three-dimensional point clouds of non-cooperative targets, extracts key points and simplifies the number of point clouds through joint farthest point sampling and point cloud feature analysis, and then uses point fast feature histograms (FPFHs) and robust iterative closest point algorithms to achieve point cloud registration between every two frames. Finally, a filtering framework was designed, whose scheme is an extended Kalman filter designed for updating measurements of relative position, velocity, attitude, and angular velocity estimation. The experimental results show that this method can effectively achieve point cloud registration for close range rotation and translation motion, and can estimate the motion state of the target.

Expression of cholesterol synthesis and steroidogenic markers in females of the Chinese brown frog (Rana dybowskii) during prespawning and prehibernation.

The oviduct of the Chinese brown frog (Rana dybowskii) expands in prehibernation rather than in prespawning, which is one of the physiological phenomena that occur in the preparation for hibernation. Steroid hormones are known to regulate oviductal development. Cholesterol synthesis and steroidogenesis may play an important role in the expansion of the oviduct before hibernation. In this study, we investigated the expression patterns of the markers that are involved in the de novo steroid synthesis pathway in the oviduct of R. dybowskii during prespawning and prehibernation. According to histological analysis, the oviduct of R. dybowskii contains epithelial cells, glandular cells, and tubule lumens. During prehibernation, oviductal pipe diameter and weight were significantly larger than during prespawning. 3-Hydroxy-3-methylglutaryl CoA reductase (HMGCR), low-density lipoprotein receptor (LDLR), steroidogenic acute regulatory protein (StAR), cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), and steroidogenic factor 1 (SF-1) were detected in epithelial cells in prehibernation and glandular cells during prespawning. HMGCR, LDLR, StAR, and P450scc protein expression levels were higher in prehibernation than during prespawning, but the SF-1 protein expression level did not significantly differ. HMGCR, LDLR, StAR, P450scc (CYP11A1), and SF-1 (NR5A1) mRNA expression levels were significantly higher in prehibernation compared with prespawning. The transcriptome results showed that the steroid synthesis pathway was highly expressed during prehibernation. Existing results indicate that the oviduct is able to synthesize steroid hormones using cholesterol, and that steroid hormones may affect the oviductal functions of R. dybowskii.

Ag nanoparticle modified porous Si microspheres as high-performance anodes for Li-ion batteries.

This study aimed to address the challenges associated with silicon (Si) anode materials in Li-ion batteries, such as their large volume effect and poor electrical conductivity. To overcome these limitations, a novel composite microsphere called pSi/Ag was developed using quartz waste through a combination of high-energy ball-milling, spray drying, and magnesiothermic reduction techniques. The morphology and structure of the pSi/Ag composite were thoroughly characterized using various methods, including X-ray diffraction, field-emission scanning electron microscopy, and transmission electron microscopy. The results revealed that the Ag nanoparticles were uniformly dispersed within the porous micron-sized Si sphere particles, leading to enhanced electrochemical performance compared to pure porous silicon that did not undergo the spray drying process. The use of micron-sized Si prevented the excessive formation of the solid electrolyte interphase film, and the pSi/Ag-5 anode, prepared with 5 wt% AgNO3 as a precursor, demonstrated an impressive initial Coulombic efficiency of 92.8%. Moreover, a high specific capacity of 1251.4 mA h g-1 over 300 cycles at a current density of 4000 mA g-1 was attributed to the improved conductivity provided by the Ag nanoparticles in the Si matrix. The straightforward synthesis method employed in this study to produce pSi/Ag presents a promising approach for the future development of high-performance silicon anodes in Li-ion batteries.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus.

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Proteomic Analysis Reveals the Association between the Pathways of Glutathione and α-Linolenic Acid Metabolism and Lanthanum Accumulation in Tea Plants.

Lanthanum can affect the growth and development of the tea plant. Tieguanyin (TGY) and Shuixian (SX) cultivars of Camellia sinensis were selected to explore the mechanism underlying the accumulation of lanthanum (tea plants' most accumulated rare earth element) through proteomics. Roots and fresh leaves of TGY and SX with low- and high-accumulation potential for lanthanum, respectively, were studied; 845 differentially expressed proteins (DEPs) were identified. Gene ontology analysis showed that DEPs were involved in redox processes and related to molecular functions. Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis showed that DEPs were associated with glutathione (GSH) and α-linolenic acid metabolism, plant pathogen interaction, and oxidative phosphorylation. Thirty-seven proteins in the GSH metabolism pathway showed significant differences, wherein 18 GSH S-transferases showed differential expression patterns in the root system. Compared with the control, expression ratios of GST (TEA004130.1) and GST (TEA032216.1) in TGY leaves were 6.84 and 4.06, respectively, after lanthanum treatment; these were significantly higher than those in SX leaves. The LOX2.1 (TEA011765.1) and LOX2.1 (TEA011776.1) expression ratios in the α-linolenic acid metabolic pathway were 2.44 and 6.43, respectively, in TGY roots, which were significantly higher than those in SX roots. The synthesis of specific substances induces lanthanum-associated defense responses in TGY, which is of great significance for plant yield stability.

In Situ Construction of Near-Infrared Response Hybrid Up-Conversion Photocatalyst for Degrading Organic Dyes and Antibiotics.

Unique nonlinear optical properties for converting low-energy incident light into high-energy radiation enable up-conversion materials to be employed in photocatalytic systems. An efficient near-infrared (NIR) response photocatalyst was successfully fabricated through a facile two-step method to load BiOBr on the Nd3+, Er3+@NaYF4 (NE@NYF) up-conversion material. The NE@NYF can transform NIR into visible and UV light and promote charge-energy transfer in the semiconductor. Consequently, the as-obtained photocatalysts exhibit excellent photodegradation performance for rhodamine B dye (RhB) and tetracycline (TC) organic pollutants. About 98.9% of the RhB was decomposed within 60 min with the 20% NE@NYF-B sample, outperforming the pristine BiOBr (61.9%). In addition, the 20% NE@NYF-B composite could decompose approximately 72.7% of the organic carbon during a 10 h reaction, which was almost two-fold more than that of BiOBr. Meanwhile, a possible charge transfer mechanism is proposed based on the recombination of electron-hole pairs and reactive oxygen species. This work provides a rational hybrid structure photocatalyst for improving photocatalytic performance in the broadband spectrum and provides a new strategy for NIR light utilization.

Plasma-Enhanced Chemical-Vapor-Deposition Synthesis of Photoredox-Active Nitrogen-Doped Carbon from NH3 and CH4 Gases.

Earth's primordial atmosphere was rich in ammonia and methane. To understand the evolution of the atmosphere, these two gases were used to make photoredox-active nitrogen-doped carbon (NDC). Photocatalysts such as NDC might play an important role in the development of geological and atmospheric chemistry during the Archean era. This study describes the synthesis of NDC directly from NH3 and CH4 gases. The photocatalyst product can be used to selectively synthesize imines by photo-oxidization of amines, producing H2 O2 simultaneously in the photoreduction reaction. Our findings shed light on the chemical evolution of the Earth.

Chemoproteomic Profiling of an Ibrutinib Analogue Reveals its Unexpected Role in DNA Damage Repair.

Ibrutinib is an FDA-approved drug to treat B-lymphoid malignancies, which functions mechanistically as a covalent inhibitor for Bruton's tyrosine kinase (BTK). During the course of screening more potent and selective BTK inhibitors, we discovered that MM2-48, an ibrutinib analogue that contains the alkynyl amide functional group in place of the acrylamide warhead, exhibits a much stronger cytotoxicity. Comparative chemoproteomic profiling of the targets of ibrutinib and MM2-48 revealed that the alkynyl amide warhead exhibits much higher reactivity in proteomes. Unexpectedly, MM2-48 covalently targets a functional cysteine in a BRCA2 and CDKN1A-interacting protein, BCCIP, and significantly inhibits DNA damage repair. Our findings suggest that simultaneous inhibition of BTK activity and DNA damage repair might be a more effective therapeutic strategy for combating B-cell malignancies.

Spiral spectrum of high-order elliptic Gaussian vortex beams in a non-Kolmogorov turbulent atmosphere.

In a free space optical communication system based on vortex beams, the effects of spread and crosstalk caused by atmospheric turbulence should not be ignored. The orbital angular momentum (OAM) spectrum of the signal based on elliptic Gaussian beam (EGB) after propagation through non-Kolmogorov turbulent atmosphere are deduced, and a theoretical model of the spiral spectrum of EGB propagating through turbulent atmosphere is obtained. Numerically calculated OAM modes detection and crosstalk probability under different ellipticity parameters. The results show that the ellipticity parameter has a significant impact on the OAM spectral distribution of EGB and the transmission characteristics after turbulent atmosphere. The selection of appropriate ellipticity parameter can correspondingly reduce the degradation and crosstalk caused by turbulent atmosphere. We also compared a Laguerre-Gaussian beam (LGB) with EGB and pointed out the advantages and limitations of these two kinds of beams. The research results may be useful in the field of short distance optical communication and OAM-based multiplex communication.

A Novel Model for Landslide Displacement Prediction Based on EDR Selection and Multi-Swarm Intelligence Optimization Algorithm.

With the widespread application of machine learning methods, the continuous improvement of forecast accuracy has become an important task, which is especially crucial for landslide displacement predictions. This study aimed to propose a novel prediction model to improve accuracy in landslide prediction, based on the combination of multiple new algorithms. The proposed new method includes three parts: data preparation, multi-swarm intelligence (MSI) optimization, and displacement prediction. In the data preparation, the complete ensemble empirical mode decomposition (CEEMD) is adopted to separate the trend and periodic displacements from the observed cumulative landslide displacement. The frequency component and residual component of reconstructed inducing factors that related to landslide movements are also extracted by the CEEMD and t-test, and then picked out with edit distance on real sequence (EDR) as input variables for the support vector regression (SVR) model. MSI optimization algorithms are used to optimize the SVR model in the MSI optimization; thus, six predictions models can be obtained that can be used in the displacement prediction part. Finally, the trend and periodic displacements are predicted by six optimized SVR models, respectively. The trend displacement and periodic displacement with the highest prediction accuracy are added and regarded as the final prediction result. The case study of the Shiliushubao landslide shows that the prediction results match the observed data well with an improvement in the aspect of average relative error, which indicates that the proposed model can predict landslide displacements with high precision, even when the displacements are characterized by stepped curves that under the influence of multiple time-varying factors.

Reliable resistive switching of epitaxial single crystalline cubic Y-HfO2 RRAMs with Si as bottom electrodes.

Previous studies have mainly focused on the resistive switching (RS) of amorphous or polycrystalline HfO2-RRAM. The RS of single crystalline HfO2 films has been rarely reported. Yttrium doped HfO2 (YDH) thin films were fabricated and successful Y incorporation into HfO2 was confirmed by x-ray photoemission spectroscopy. A pure cubic phase of YDH and an abrupt YDH/Si interface were obtained and verified by x-ray diffraction, Raman spectroscopy and transmission electron microscopy. A Pt/YDH/n++-Si heterostructure using Si as the bottom electrode was fabricated, which shows stable RS with an ON/OFF ratio of 100 and a reliable data retention (104 s). The electron transport mechanism was investigated in detail. It indicates that hopping conduction is dominating when the device is at a high resistance state, while space charge limited conduction acts as the dominant factor at a low resistance state. Such behavior, which is different from devices using TiN or Ti as electrodes, was attributed to the Y doping and specific YDH/Si interface. Our results demonstrate a proof of concept study to use highly doped Si as bottom electrodes along with single crystalline YDH as insulator layer for such RRAM applications as wireless sensors and synaptic simulation.

Thermal Infrared Imagery Integrated with Terrestrial Laser Scanning and Particle Tracking Velocimetry for Characterization of Landslide Model Failure.

A laboratory model test is an effective method for studying landslide risk mitigation. In this study, thermal infrared (TIR) imagery, a modern no-contact technique, was introduced and integrated with terrestrial laser scanning (TLS) and particle tracking velocimetry (PTV) to characterize the failure of a landslide model. The characteristics of the failure initiation, motion, and region of interest, including landslide volume, deformation, velocity, surface temperature changes, and anomalies, were detected using the integrated monitoring system. The laboratory test results indicate that the integrated monitoring system is expected to be useful for characterizing the failure of landslide models. The preliminary results of this study suggest that a change in the relative TIR signal (ΔTIR) can be a useful index for landslide detection, and a decrease in the average value of the temperature change ( Δ T I R ¯ ) can be selected as a precursor to landslide failure.

Fast and Automatic Reconstruction of Semantically Rich 3D Indoor Maps from Low-quality RGB-D Sequences.

Semantically rich indoor models are increasingly used throughout a facility's life cycle for different applications. With the decreasing price of 3D sensors, it is convenient to acquire point cloud data from consumer-level scanners. However, most existing methods in 3D indoor reconstruction from point clouds involve a tedious manual or interactive process due to line-of-sight occlusions and complex space structures. Using the multiple types of data obtained by RGB-D devices, this paper proposes a fast and automatic method for reconstructing semantically rich indoor 3D building models from low-quality RGB-D sequences. Our method is capable of identifying and modelling the main structural components of indoor environments such as space, wall, floor, ceilings, windows, and doors from the RGB-D datasets. The method includes space division and extraction, opening extraction, and global optimization. For space division and extraction, rather than distinguishing room spaces based on the detected wall planes, we interactively define the start-stop position for each functional space (e.g., room, corridor, kitchen) during scanning. Then, an interior elements filtering algorithm is proposed for wall component extraction and a boundary generation algorithm is used for space layout determination. For opening extraction, we propose a new noise robustness method based on the properties of convex hull, octrees structure, Euclidean clusters and the camera trajectory for opening generation, which is inapplicable to the data collected in the indoor environments due to inevitable occlusion. A global optimization approach for planes is designed to eliminate the inconsistency of planes sharing the same global plane, and maintain plausible connectivity between the walls and the relationships between the walls and openings. The final model is stored according to the CityGML3.0 standard. Our approach allows for the robust generation of semantically rich 3D indoor models and has strong applicability and reconstruction power for complex real-world datasets.

Positioning Locality Using Cognitive Directions Based on Indoor Landmark Reference System.

Locality descriptions are generally communicated using reference objects and spatial relations that reflect human spatial cognition. However, uncertainty is inevitable in locality descriptions. Positioning locality with locality description, with a mapping mechanism between the qualitative and quantitative data, is one of the important research issues in next-generation geographic information sciences. Spatial relations play an important role in the uncertainty of positioning locality. In indoor landmark reference systems, the nearest landmarks can be selected when describing localities by using direction relations indoors. By using probability operation, we combine a set of uncertainties, that is, near and direction relations to positioning locality. Some definitions are proposed from cognitive and computational perspectives. We evaluate the performance of our method through indoor cognitive experiments. Test results demonstrate that a positioning accuracy of 3.55 m can be achieved with the semantically derived direction relationships in indoor landmark reference systems.

High-efficiency and flexible generation of vector vortex optical fields by a reflective phase-only spatial light modulator.

The scheme for generating vector optical fields should have not only high efficiency but also flexibility for satisfying the requirements of various applications. However, in general, high efficiency and flexibility are not compatible. Here we present and experimentally demonstrate a solution to directly, flexibly, and efficiently generate vector vortex optical fields (VVOFs) with a reflective phase-only liquid crystal spatial light modulator (LC-SLM) based on optical birefringence of liquid crystal molecules. To generate the VVOFs, this approach needs in principle only a half-wave plate, an LC-SLM, and a quarter-wave plate. This approach has some advantages, including a simple experimental setup, good flexibility, and high efficiency, making the approach very promising in some applications when higher power is need. This approach has a generation efficiency of 44.0%, which is much higher than the 1.1% of the common path interferometric approach.

Indoors Locality Positioning Using Cognitive Distances and Directions.

Spatial relationships are crucial to spatial knowledge representation, such as positioning localities. However, minimal attention has been devoted to positioning localities indoors with locality description. Distance and direction relations are generally used when positioning localities, namely, translating descriptive localities into spatially explicit ones. We propose a joint probability function to model locality distribution to address the uncertainty of positioning localities. The joint probability function consists of distance and relative direction membership functions. We propose definitions and restrictions for the use of the joint probability function to make the locality distribution highly practical. We also evaluate the performance of our approach through indoor experiments. Test results demonstrate that a positioning accuracy of 3.5 m can be achieved with the semantically derived spatial relationships.