Allele-specific RNA N 6-methyladenosine modifications reveal functional genetic variants in human tissues.

An intricate network of cis- and trans-elements acts on RNA N 6-methyladenosine (m6A), which in turn may affect gene expression and, ultimately, human health. A complete understanding of this network requires new approaches to accurately measure the subtle m6A differences arising from genetic variants, many of which have been associated with common diseases. To address this gap, we developed a method to accurately and sensitively detect transcriptome-wide allele-specific m6A (ASm6A) from MeRIP-seq data and applied it to uncover 12,056 high-confidence ASm6A modifications from 25 human tissues. We also identified 1184 putative functional variants for ASm6A regulation, a subset of which we experimentally validated. Importantly, we found that many of these ASm6A-associated genetic variants were enriched for common disease-associated and complex trait-associated risk loci, and verified that two disease risk variants can change m6A modification status. Together, this work provides a tool to detangle the dynamic network of RNA modifications at the allelic level and highlights the interplay of m6A and genetics in human health and disease.

Adaptive and maladaptive introgression in grapevine domestication.

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning-based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.

Genomic conservation of crop wild relatives: A case study of citrus.

Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.

Population comparative genomics discovers gene gain and loss during grapevine domestication.

Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.

Phased Telomere-to-Telomere Reference Genome and Pangenome Reveal an Expansion of Resistance Genes during Apple Domestication.

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Previous versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the highly heterozygous genome, which impeded genetic studies and breeding programs in apple. In this study, we assembled a haplotype-resolved telomere-to-telomere reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on twelve assemblies from wild and cultivated apples to investigate different types of resistance gene analogs (RGAs). Our results revealed the dynamics of the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Interestingly, our analyses demonstrated a higher prevalence of RGAs in cultivated apples than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Other types of structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR (TNL), NB-ARC-LRR (NL), and CC-NB-ARC-LRR (CNL) genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding programs.

Epigenetic Reprogramming Drives Epithelial Disruption in Chronic Obstructive Pulmonary Disease.

Chronic obstructive pulmonary disease (COPD) remains a major public health challenge that contributes greatly to mortality and morbidity worldwide. Although it has long been recognized that the epithelium is altered in COPD, there has been little focus on targeting it to modify the disease course. Therefore, mechanisms that disrupt epithelial cell function in patients with COPD are poorly understood. In this study, we sought to determine whether epigenetic reprogramming of the cell-cell adhesion molecule E-cadherin, encoded by the CDH1 gene, disrupts epithelial integrity. By reducing these epigenetic marks, we can restore epithelial integrity and rescue alveolar airspace destruction. We used differentiated normal and COPD-derived primary human airway epithelial cells, genetically manipulated mouse tracheal epithelial cells, and mouse and human precision-cut lung slices to assess the effects of epigenetic reprogramming. We show that the loss of CDH1 in COPD is due to increased DNA methylation site at the CDH1 enhancer D through the downregulation of the ten-eleven translocase methylcytosine dioxygenase (TET) enzyme TET1. Increased DNA methylation at the enhancer D region decreases the enrichment of RNA polymerase II binding. Remarkably, treatment of human precision-cut slices derived from patients with COPD with the DNA demethylation agent 5-aza-2'-deoxycytidine decreased cell damage and reduced air space enlargement in the diseased tissue. Here, we present a novel mechanism that targets epigenetic modifications to reverse the tissue remodeling in human COPD lungs and serves as a proof of concept for developing a disease-modifying target.

Compact In Situ Electrochemical NMR with Wireless and Anti-interference Strategy in Multiscenario Applications.

The integration of electrochemistry with nuclear magnetic resonance (NMR) spectroscopy recently offers a powerful approach to understanding oxidative metabolism, detecting reactive intermediates, and predicting biological activities. This combination is particularly effective as electrochemical methods provide excellent mimics of metabolic processes, while NMR spectroscopy offers precise chemical analysis. NMR is already widely utilized in the quality control of pharmaceuticals, foods, and additives and in metabolomic studies. However, the introduction of additional and external connections into the magnet has posed challenges, leading to signal deterioration and limitations in routine measurements. Herein, we report an anti-interference compact in situ electrochemical NMR system (AICISENS). Through a wireless strategy, the compact design allows for the independent and stable operation of electrochemical NMR components with effective interference isolation. Thus, it opens an avenue toward easy integration into in situ platforms, applicable not only to laboratory settings but also to fieldwork. The operability, reliability, and versatility were validated with a series of biomimetic assessments, including measurements of microbial electrochemical systems, functional foods, and simulated drug metabolisms. The robust performance of AICISENS demonstrates its high potential as a powerful analytical tool across diverse applications.

The interplay of hydrogen sulfide and microRNAs in cardiovascular diseases: insights and future perspectives.

Hydrogen sulfide (H2S) is recognized as the third gasotransmitter, after nitric oxide (NO) and carbon monoxide (CO). It is known for its cardioprotective properties, including the relaxation of blood vessels, promotion of angiogenesis, regulation of myocardial cell apoptosis, inhibition of vascular smooth muscle cell proliferation, and reduction of inflammation. Additionally, abnormal H2S generation has been linked to the development of cardiovascular diseases (CVD), such as pulmonary hypertension, hypertension, atherosclerosis, vascular calcification, and myocardial injury. MicroRNAs (miRNAs) are non-coding, conserved, and versatile molecules that primarily influence gene expression by repressing translation and have emerged as biomarkers for CVD diagnosis. Studies have demonstrated that H2S can ameliorate cardiac dysfunction by regulating specific miRNAs, and certain miRNAs can also regulate H2S synthesis. The crosstalk between miRNAs and H2S offers a novel perspective for investigating the pathophysiology, prevention, and treatment of CVD. The present analysis outlines the interactions between H2S and miRNAs and their influence on CVD, providing insights into their future potential and advancement.

Chromatic correction for super multi-view 3D display based on diffraction theory.

The traditional analysis method for super multi-view 3D display based on geometric optics, which approximates the lenticular lenses as a series of pinhole structures, ignored the chromatic aberration. In this paper, the optimization method based on diffraction theory is proposed for super multi-view 3D display, where the wavefronts are evaluated accurately by the forward propagation method, and the chromatic aberration of the synthetic viewpoint image is reduced dramatically by the backward reconstruction optimization method (BROM). The optical experiment is performed to verify the feasibility of the method, which is consistent with numerical simulation results. It is proved that the proposed method simulates the physical propagation process of super multi-view 3D display and improves the reconstructed image quality. In the future, it can be used to achieve the super multi-view 3D light field technology with low crosstalk.

Elongin B promotes breast cancer progression by ubiquitinating tumor suppressor p14/ARF.

Elongin B (ELOB), a pivotal element in the ELOB/c-Cullin2/5-SOCS-box E3 ubiquitin-protein ligase complex, plays a significant role in catalyzing the ubiquitination and subsequent degradation of a broad spectrum of target proteins. Notably, it is documented to facilitate these processes. However, the regulatory role of ELOB in breast cancer remains ambiguous. In this study, through bio-informatic analysis of The Cancer Genome Atlas and Fudan University Shanghai Cancer Center database, we demonstrated that ELOB was over-expressed in breast cancer tissues and was related to unfavorable prognosis. Additionally, pathway enrichment analysis illustrated that high expression of ELOB was associated with multiple cancer promoting pathways, like cell cycle, DNA replication, proteasome and PI3K - Akt signaling pathway, indicating ELOB as a potential anticancer target. Then, we confirmed that both in vivo and in vitro, the proliferation of breast cancer cells could be significantly suppressed by the down-regulation of ELOB. Mechanically, immunoprecipitation and in vivo ubiquitination assays prompted that, as the core element of Cullin2-RBX1-ELOB E3 ligase (CRL2) complex, ELOB regulated the ubiquitination and the subsequent degradation of oncoprotein p14/ARF. Moreover, the anticancer efficacy of erasing ELOB could be rescued by simultaneous knockdown of p14/ARF. Finally, through analyzing breast cancer tissue microarrays and western blot of patient samples, we demonstrated that the expression of ELOB in tumor tissues was elevated in compared to adjacent normal tissues. In conclusion, ELOB is identified to be a promising innovative target for the drug development of breast cancer by promoting the ubiquitination and degradation of oncoprotein p14/ARF.

A novel derivative synchronous fluorescence method for the rapid, non-destructive and intuitive differentiation of denitrifying bacteria.

It is challenging to differentiate bacteria residing in the same habitat by direct observation. This difficulty impedes the harvest, application and manipulation of functional bacteria in environmental engineering. In this study, we developed a novel method for rapid differentiation of living denitrifying bacteria based on derivative synchronous fluorescence spectroscopy, as exemplified by three heterotrophic nitrification-aerobic denitrification bacteria having the maximum nitrogen removal efficiencies greater than 90%. The intact bacteria and their living surroundings can be analyzed as an integrated target, which eliminates the need for the complex pre-processing of samples. Under the optimal synchronous scanning parameter (Δλ = 40 nm), each bacterium possesses a unique fluorescence spectral structure and the derivative synchronous fluorescence technique can significantly improve the spectral resolution compared to other conventional fluorescence methods, which enables the rapid differentiation of different bacteria through derivative synchronous fluorescence spectra as fast as 2 min per spectrum. Additionally, the derivative synchronous fluorescence technique can extract the spectral signals contributed by bacterial extracellular substances produced in the biological nitrogen removal process. Moreover, the results obtained from our method can reflect the real-time denitrification properties of bacteria in the biological nitrogen removal process of wastewater. All these merits highlight derivative synchronous fluorescence spectroscopy as a promising analytic method in the environmental field.

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

Viewing angle enhancement for integral imaging display using two overlapped panels.

Integral imaging three-dimensional (3D) display relies on display panel to provide visual information, but the intrinsic trade-off between the wide viewing angle and high resolution refrains its application in high-throughput 3D display. We propose a method to enhance the viewing angle without sacrificing the resolution by using two overlapped panels. The additionally introduced display panel is composed of two parts: the information area and the transparent area. The transparent area loaded with blank information enables light passing through without any modulation, while the opaque information area is loaded with element image array (EIA) for 3D display. The configuration of the introduced panel can block crosstalk from the original 3D display and establish a new and viewable perspective. Experimental results show that the horizontal viewing angle can be effectively extended from 8° to 16°, demonstrating the feasibility and effectiveness of our proposed method. This method provides the 3D display system with a higher space-bandwidth product, making it a potential technique to be applied for high information-capacity display, including integral imaging and holography.

Dual convolutional neural network for aberration pre-correction and image quality enhancement in integral imaging display.

This paper proposes a method that utilizes a dual neural network model to address the challenges posed by aberration in the integral imaging microlens array (MLA) and the degradation of 3D image quality. The approach involves a cascaded dual convolutional neural network (CNN) model designed to handle aberration pre-correction and image quality restoration tasks. By training these models end-to-end, the MLA aberration is corrected effectively and the image quality of integral imaging is enhanced. The feasibility of the proposed method is validated through simulations and optical experiments, using an optimized, high-quality pre-corrected element image array (EIA) as the image source for 3D display. The proposed method achieves high-quality integral imaging 3D display by alleviating the contradiction between MLA aberration and 3D image resolution reduction caused by system noise without introducing additional complexity to the display system.

Depth of field expansion method for integral imaging based on diffractive optical element and CNN.

In lens-based display systems, lens aberrations and depth of field (DoF) limitation often lead to blurring and distortion of reconstructed images; Meanwhile, expanding the display DoF will face a trade-off between horizontal resolution and axial resolution, restricting the achievement of high-resolution and large DoF three-dimensional (3D) displays. To overcome these constraints and enhance the DoF and resolution of reconstructed scenes, we propose a DoF expansion method based on diffractive optical element (DOE) optimization and image pre-correction through a convolutional neural network (CNN). This method applies DOE instead of the conventional lens and optimizes DOE phase distribution using the Adam algorithm, achieving depth-invariant and concentrated point spread function (PSF) distribution throughout the entire DoF range; Simultaneously, we utilize a CNN to pre-correct the original images and compensate for the image quality reduction introduced by the DOE. The proposed method is applied to a practical integral imaging system, we effectively extend the DoF of the DOE to 400 mm, leading to a high-resolution 3D display in multiple depth planes. To validate the effectiveness and practicality of the proposed method, we conduct numerical simulations and optical experiments.

SUMOylation of RALY promotes vasculogenic mimicry in glioma cells via the FOXD1/DKK1 pathway.

Human malignant gliomas are the most common and aggressive primary malignant tumors of the human central nervous system. Vasculogenic mimicry (VM), which refers to the formation of a tumor blood supply system independently of endothelial cells, contributes to the malignant progression of glioma. Therefore, VM is considered a potential target for glioma therapy. Accumulated evidence indicates that alterations in SUMOylation, a reversible post-translational modification, are involved in tumorigenesis and progression. In the present study, we found that UBA2 and RALY were upregulated in glioma tissues and cell lines. Downregulation of UBA2 and RALY inhibited the migration, invasion, and VM of glioma cells. RALY can be SUMOylated by conjugation with SUMO1, which is facilitated by the overexpression of UBA2. The SUMOylation of RALY increases its stability, which in turn increases its expression as well as its promoting effect on FOXD1 mRNA. The overexpression of FOXD1 promotes DKK1 transcription by activating its promoter, thereby promoting glioma cell migration, invasion, and VM. Remarkably, the combined knockdown of UBA2, RALY, and FOXD1 resulted in the smallest tumor volumes and the longest survivals of nude mice in vivo. UBA2/RALY/FOXD1/DKK1 axis may play crucial roles in regulating VM in glioma, which may contribute to the development of potential strategies for the treatment of gliomas.

Inherent structures of water using fully ab initio simulations.

Using fully ab initio molecular dynamics simulations based on the SCAN functional, we study the inherent structure of water and its temperature dependence. Our results show three types of translational ordering of the second oxygen coordination shell. With this as a criterion, the local structures in water are classified into three types, here named structures I, II, and III. In structure I, the second shell loses its translational ordering, while in structures II and III it presents a translational ordering similar to that in ice II (or ice V) and ice III, respectively. However, the tetrahedral orientational ordering distribution and bond-angle distribution in structures II and III are different from those in ice II (or ice V) and ice III. This indicates that the local atomic structures of liquid water and crystalline ice are not identical, although they have similar translational ordering. The temperature dependence of the inherent structure suggests that the density maximum of water originates from the competition not only between structures I and III, but also between structures II and III. These results provide fully ab initio evidence for the mixture model of water.

Investigation of the mechanical and transport properties of InGeX3 (X = S, Se and Te) monolayers using density functional theory and machine learning.

Recently, novel 2D InGeTe3 has been successfully synthesized and attracted attention due to its excellent properties. In this study, we investigated the mechanical properties and transport behavior of InGeX3 (X = S, Se and Te) monolayers using density functional theory (DFT) and machine learning (ML). The key physical parameters related to mechanical properties, including Poisson's ratio, elastic modulus, tensile strength and critical strain, were revealed. Using a ML method to train DFT data, we developed a neuroevolution-potential (NEP) to successfully predict the mechanical properties and lattice thermal conductivity. The fracture behavior predicted using NEP-based MD simulations in a large supercell containing 20 000 atoms could be verified using DFT. Due to the effects of size, these predicted physical parameters have a slight difference between DFT and ML methods. At 300 K, these monolayers exhibited a low thermal conductivity with the values of 13.27 ± 0.24 W m-1 K-1 for InGeS3, 7.68 ± 0.30 W m-1 K-1 for InGeSe3, and 3.88 ± 0.09 W m-1 K-1 for InGeTe3, respectively. The Boltzmann transport equation (BTE) including all electron-phonon interactions was used to accurately predict the electron mobility. Compared with InGeS3 and InGeSe3, the InGeTe3 monolayer showed flexible mechanical behavior, low thermal conductivity and high mobility.

In Situ Investigations on Structural Evolutions during the Facile Synthesis of Cubic α-MoC1-x Catalysts.

Cubic α-phase molybdenum carbides (α-MoC1-x) exhibit great potential in hydrogen production at low temperatures due to their excellent activity in water dissociation. However, the design strategies of α-MoC1-x are severely restricted by the harsh synthesis conditions, which involve multistep ammonification and carburization or the utilization of a significant amount of noble metals. Herein, high-purity α-MoC1-x synthesis in a one-step carburization process was achieved with the assistance of a trace amount of Rh (0.02%). The structural evolution of Mo species during phase transition was monitored via qualitative and quantitative analysis by in situ X-ray diffraction (XRD) and in situ X-ray absorption spectroscopy (XAS), respectively. Environmental transmission electron microscopy (ETEM) was used to follow the visual changes. We reveal that the reduction of monoclinic MoO3 to cubic oxygen-deficient Mo oxide (MoOx) at low temperatures owing to the promoted H2 activation on Rh sites is vital to the following carbon atom insertion and transformation to α-MoC1-x, making the carburization follow the topological route. The systematic analysis of the relationship between the reduction behavior and the structural evolution supplies a feasible strategy for the α-MoC1-x synthesis, and in situ characterizations shed light on controlling the phase transformation during carburization.

Label-Free Fluorescent Nanofilm Sensor Based on Surface Plasmon Coupled Emission: In Situ Monitoring the Growth of Metal-Organic Frameworks.

We have proposed a universal label-free fluorescent nanofilm sensor based on surface plasmon coupled emission (SPCE). A metal-dye-dielectric (MDD) structure was fabricated to mediate the label-free monitoring based on SPCE. The nonfluorescent dielectric film smartly borrowed the fluorescence signal from the bottom dye layer and led to a new SPCE response through the adjacent metal film. The fluorescence emission angle and polarization strongly depended on the thickness of the nonfluorescent dielectric film on the MDD structure. As a demonstration, the growth of a two-dimensional zeolitic imidazolate framework film (ZIF-L) was in situ monitored in the liquid phase by MDD-SPCE for the first time. The label-free fluorescent sensors are facilely prepared by a spin coating technique, with the potential to be widely spread for in situ studies, especially toward nanomaterial growth processes.