Semi-automated assembly of high-quality diploid human reference genomes.

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Micropolarity governs the structural organization of biomolecular condensates.

Membraneless organelles within cells have unique microenvironments that play a critical role in their functions. However, how microenvironments of biomolecular condensates affect their structure and function remains unknown. In this study, we investigated the micropolarity and microviscosity of model biomolecular condensates by fluorescence lifetime imaging coupling with environmentally sensitive fluorophores. Using both in vitro and in cellulo systems, we demonstrated that sufficient micropolarity difference is key to forming multilayered condensates, where the shells present more polar microenvironments than the cores. Furthermore, micropolarity changes were shown to be accompanied by conversions of the layered structures. Decreased micropolarities of the granular components, accompanied by the increased micropolarities of the dense fibrillar components, result in the relocation of different nucleolus subcompartments in transcription-stalled conditions. Our results demonstrate the central role of the previously overlooked micropolarity in the regulation of structures and functions of membraneless organelles.

N6-Methyladenine DNA Modification in the Human Genome.

DNA N6-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N6-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.

RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads.

MOTIVATION: Nanopore direct RNA sequencing (DRS) enables the detection of RNA N6-methyladenosine (m6A) without extra laboratory techniques. A number of supervised or comparative approaches have been developed to identify m6A from Nanopore DRS reads. However, existing methods typically utilize either statistical features of the current signals or basecalling-error features, ignoring the richer information of the raw signals of DRS reads. RESULTS: Here, we propose RedNano, a deep-learning method designed to detect m6A from Nanopore DRS reads by utilizing both raw signals and basecalling errors. RedNano processes the raw-signal feature and basecalling-error feature through residual networks. We validated the effectiveness of RedNano using synthesized, Arabidopsis, and human DRS data. The results demonstrate that RedNano surpasses existing methods by achieving higher area under the ROC curve (AUC) and area under the precision-recall curve (AUPRs) in all three datasets. Furthermore, RedNano performs better in cross-species validation, demonstrating its robustness. Additionally, when detecting m6A from an independent dataset of Populus trichocarpa, RedNano achieves the highest AUC and AUPR, which are 3.8%-9.9% and 5.5%-13.8% higher than other methods, respectively. AVAILABILITY AND IMPLEMENTATION: The source code of RedNano is freely available at https://github.com/Derryxu/RedNano.

Integration of valence and conflict processing through cellular-field interactions in human subgenual cingulate during emotional face processing in treatment-resistant depression.

The subgenual anterior cingulate cortex (sgACC) has been identified as a key brain area involved in various cognitive and emotional processes. While the sgACC has been implicated in both emotional valuation and emotional conflict monitoring, it is still unclear how this area integrates multiple functions. We characterized both single neuron and local field oscillatory activity in 14 patients undergoing sgACC deep brain stimulation for treatment-resistant depression. During recording, patients were presented with a modified Stroop task containing emotional face images that varied in valence and congruence. We further analyzed spike-field interactions to understand how network dynamics influence single neuron activity in this area. Most single neurons responded to both valence and congruence, revealing that sgACC neuronal activity can encode multiple processes within the same task, indicative of multifunctionality. During peak neuronal response, we observed increased spectral power in low frequency oscillations, including theta-band synchronization (4-8 Hz), as well as desynchronization in beta-band frequencies (13-30 Hz). Theta activity was modulated by current trial congruency with greater increases in spectral power following non-congruent stimuli, while beta desynchronizations occurred regardless of emotional valence. Spike-field interactions revealed that local sgACC spiking was phase-locked most prominently to the beta band, whereas phase-locking to the theta band occurred in fewer neurons overall but was modulated more strongly for neurons that were responsive to task. Our findings provide the first direct evidence of spike-field interactions relating to emotional cognitive processing in the human sgACC. Furthermore, we directly related theta oscillatory dynamics in human sgACC to current trial congruency, demonstrating it as an important regulator during conflict detection. Our data endorse the sgACC as an integrative hub for cognitive emotional processing through modulation of beta and theta network activity.

Regulating Benzene Ring Number as Connector in Covalent Organic Framework for Boosting Photosynthesis of H2O2 from Seawater.

Photosynthesis of H2O2 from seawater represents a promising pathway to acquire H2O2, but it is still restricted by the lack of a highly active photocatalyst. In this work, we propose a convenient strategy of regulating the number of benzene rings to boost the catalytic activity of materials. This is demonstrated by ECUT-COF-31 with adding two benzene rings as the connector, which can result in 1.7-fold enhancement in the H2O2 production rate relative to ECUT-COF-30 with just one benzene ring as the connector. The reason for enhancement is mainly due to the release of *OOH from the surface of catalyst and the final formation of H2O2 being easier in ECUT-COF-31 than in ECUT-COF-30. Moreover, ECUT-COF-31 provides a stable photogeneration of H2O2 for 70 h, and a theoretically remarkable H2O2 production of 58.7 mmol per day from seawater using one gram of photocatalyst, while the cost of the used raw material is as low as 0.24 $/g.

Controllable Synthesis of Transferable Ultrathin Bi2Ge(Si)O5 Dielectric Alloys with Composition-Tunable High-κ Properties.

Two-dimensional (2D) alloys hold great promise to serve as important components of 2D transistors, since their properties allow continuous regulation by varying their compositions. However, previous studies are mainly limited to the metallic/semiconducting ones as contact/channel materials, but very few are related to the insulating dielectrics. Here, we use a facile one-step chemical vapor deposition (CVD) method to synthesize ultrathin Bi2SixGe1-xO5 dielectric alloys, whose composition is tunable over the full range of x just by changing the relative ratios of the GeO2/SiO2 precursors. Moreover, their dielectric properties are highly composition-tunable, showing a record-high dielectric constant of >40 among CVD-grown 2D insulators. The vertically grown nature of Bi2GeO5 and Bi2SixGe1-xO5 enables polymer-free transfer and subsequent clean van der Waals integration as the high-κ encapsulation layer to enhance the mobility of 2D semiconductors. Besides, the MoS2 transistors using Bi2SixGe1-xO5 alloy as gate dielectrics exhibit a large Ion/Ioff (>108), ideal subthreshold swing of ∼61 mV/decade, and a small gate hysteresis (∼5 mV). Our work not only gives very few examples on controlled CVD growth of insulating dielectric alloys but also expands the family of 2D single-crystalline high-κ dielectrics.

Enhanced Alkaline Hydrogen Evolution Reaction through Lanthanide-Modified Rhodium Intermetallic Catalysts.

Design of highly efficient electrocatalysts for alkaline hydrogen evolution reaction (HER) is of paramount importance for water electrolysis, but still a considerable challenge because of the slow HER kinetics in alkaline environments. Alloying is recognized as an effective strategy to enhance the catalytic properties. Lanthanides (Ln) are recognized as an electronic and structural regulator, attributed to their unique 4f electron behavior and the phenomenon known as lanthanide contraction. Here, a new class of Rh3Ln intermetallics (IMs) are synthesized using the sodium vapor reduction method. The alloying process induced an upshift of the d-band center and electron transfer from Ln to Rh, resulting in optimized adsorption and dissociation energies for H2O molecules. Consequently, Rh3Tb IMs exhibited outstanding HER activity in both alkaline environments and seawater, displaying an overpotential of only 19 mV at 10 mA cm-2 and a Tafel slope of 22.2 mV dec-1. Remarkably, the current density of Rh3Tb IMs at 100 mV overpotential is 8.6 and 5.7 times higher than that of Rh/C and commercial Pt/C, respectively. This work introduces a novel approach to the rational design of HER electrocatalysis and sheds light on the role of lanthanides in electrocatalyst systems.

Enhanced Alkaline Hydrogen Evolution Reaction via Electronic Structure Regulation: Activating PtRh with Rare Earth Tm Alloying.

Developing high-performance electrocatalysts for alkaline hydrogen evolution reaction (HER) is crucial for producing green hydrogen, yet it remains challenging due to the sluggish kinetics in alkaline environments. Pt is located near the peak of HER volcano plot, owing to its exceptional performance in hydrogen adsorption and desorption, and Rh plays an important role in H2O dissociation. Lanthanides (Ln) are commonly used to modulate the electronic structure of materials and further influence the adsorption/desorption of reactants, intermediates, and products, and noble metal-Ln alloys are recognized as effective platforms where Ln elements regulate the catalytic properties of noble metals. Here Pt1.5Rh1.5Tm alloy is synthesized using the sodium vapor reduction method. This alloy demonstrates superior catalytic activity, being 4.4 and 6.6 times more effective than Pt/C and Rh/C, respectively. Density Functional Theory (DFT) calculations reveal that the upshift of d-band center and the charge transfer induced by alloying promote adsorption and dissociation of H2O, making Pt1.5Rh1.5Tm alloy more favorable for the alkaline HER reaction, both kinetically and thermodynamically.

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data.

MOTIVATION: Oxford Nanopore sequencing has great potential and advantages in population-scale studies. Due to the cost of sequencing, the depth of whole-genome sequencing for per individual sample must be small. However, the existing single nucleotide polymorphism (SNP) callers are aimed at high-coverage Nanopore sequencing reads. Detecting the SNP variants on low-coverage Nanopore sequencing data is still a challenging problem. RESULTS: We developed a novel deep learning-based SNP calling method, NanoSNP, to identify the SNP sites (excluding short indels) based on low-coverage Nanopore sequencing reads. In this method, we design a multi-step, multi-scale and haplotype-aware SNP detection pipeline. First, the pileup model in NanoSNP utilizes the naive pileup feature to predict a subset of SNP sites with a Bi-long short-term memory (LSTM) network. These SNP sites are phased and used to divide the low-coverage Nanopore reads into different haplotypes. Finally, the long-range haplotype feature and short-range pileup feature are extracted from each haplotype. The haplotype model combines two features and predicts the genotype for the candidate site using a Bi-LSTM network. To evaluate the performance of NanoSNP, we compared NanoSNP with Clair, Clair3, Pepper-DeepVariant and NanoCaller on the low-coverage (∼16×) Nanopore sequencing reads. We also performed cross-genome testing on six human genomes HG002-HG007, respectively. Comprehensive experiments demonstrate that NanoSNP outperforms Clair, Pepper-DeepVariant and NanoCaller in identifying SNPs on low-coverage Nanopore sequencing data, including the difficult-to-map regions and major histocompatibility complex regions in the human genome. NanoSNP is comparable to Clair3 when the coverage exceeds 16×. AVAILABILITY AND IMPLEMENTATION: https://github.com/huangnengCSU/NanoSNP.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genetic architecture of source-sink-regulated senescence in maize.

Source and sink interactions play a critical but mechanistically poorly understood role in the regulation of senescence. To disentangle the genetic and molecular mechanisms underlying source-sink-regulated senescence (SSRS), we performed a phenotypic, transcriptomic, and systems genetics analysis of senescence induced by the lack of a strong sink in maize (Zea mays). Comparative analysis of genotypes with contrasting SSRS phenotypes revealed that feedback inhibition of photosynthesis, a surge in reactive oxygen species, and the resulting endoplasmic reticulum (ER) stress were the earliest outcomes of weakened sink demand. Multienvironmental evaluation of a biparental population and a diversity panel identified 12 quantitative trait loci and 24 candidate genes, respectively, underlying SSRS. Combining the natural diversity and coexpression networks analyses identified 7 high-confidence candidate genes involved in proteolysis, photosynthesis, stress response, and protein folding. The role of a cathepsin B like protease 4 (ccp4), a candidate gene supported by systems genetic analysis, was validated by analysis of natural alleles in maize and heterologous analyses in Arabidopsis (Arabidopsis thaliana). Analysis of natural alleles suggested that a 700-bp polymorphic promoter region harboring multiple ABA-responsive elements is responsible for differential transcriptional regulation of ccp4 by ABA and the resulting variation in SSRS phenotype. We propose a model for SSRS wherein feedback inhibition of photosynthesis, ABA signaling, and oxidative stress converge to induce ER stress manifested as programed cell death and senescence. These findings provide a deeper understanding of signals emerging from loss of sink strength and offer opportunities to modify these signals to alter senescence program and enhance crop productivity.

Enhancement of solar blind full band absorption in photodetector with Ga2O3 nanopore and Al nanograting.

In this paper, we presented a novel double-layer light-trapping structure consisting of nanopores and nanograting positioned on both the surface and bottom of a gallium oxide-based solar-blind photodetector. Utilizing the finite element method (FEM), we thoroughly investigated the light absorption enhancement capabilities of this innovative design. The simulation results show that the double-layer nanostructure effectively combines the light absorption advantages of nanopores and nanogratings. Compared with thin film devices and devices with only nanopore or nanograting structures, double-layer nanostructured devices have a higher light absorption, achieving high light absorption in the solar blind area.

The scaffold of neutrophil extracellular traps promotes CCA progression and modulates angiogenesis via ITGAV/NFκB.

Neutrophil extracellular traps (NETs) have garnered attention for their dual role in host defense and tumor promotion. With their involvement documented across a spectrum of tumors, their influence on the progression of cholangiocarcinoma (CCA) is of paramount interest. We employed immunohistochemistry and immunofluorescence to detect NET deposition in CCA tissues. Through in vitro and in vivo investigation, including CCA organoid and transposon-based models in PAD4 KO mice, we explored the effects of NETs on cell proliferation and metastasis. Molecular insights were gained through RNA sequencing, enzyme linked immunosorbent assay, and chromatin immunoprecipitation. Elevated intratumoral NET deposition within CCA tissues was associated with poor survival. The influence of NETs on CCA proliferation, migration and invasion was primarily mediated by NET-DNA. RNA sequencing unveiled the activation of the NFκB signaling pathway due to NET-DNA stimulation. NET-DNA pull-down assay coupled with mass spectrometry revealed the interaction between NET-DNA and αV integrin (ITGAV), culmination in the activation of the NFκB pathway. Furthermore, NET-DNA directly upregulated the expression of VEGF-A in cancer cells. The study unequivocally establishes NETs as facilitators of CCA progression, orchestrating proliferation, metastasis, and angiogenesis through ITGAV/NFκB pathway activation. This novel insight positions NETs as prospective therapeutic targets for managing CCA patients. By implementing a variety of methodologies and drawing intricate connections between NETs, DNA interactions, and signaling pathways, this research expands our comprehension of the complex interplay between the immune system and cancer progression, offering promising avenues for intervention.

Cancer-associated fibroblasts mediate resistance to anti-EGFR therapies in cancer.

Over the last decade, epidermal growth factor receptor (EGFR)-targeted therapies have transformed the treatment landscape for patients with advanced solid tumors. Despite these advances, resistance to anti-EGFR therapies is still a significant clinical challenge. While cell-autonomous mechanisms of resistance are well-documented, they do not fully elucidate the complexity of drug resistance. Cancer-associated fibroblasts (CAFs), key mediators within the tumor microenvironment (TME), have emerged as pivotal players in cancer progression and chemoresistance. Recent evidence implicates CAFs in resistance to anti-EGFR therapies, suggesting they may undermine treatment efficacy. This review synthesizes current data, highlighting the critical role of CAFs in resistance pathogenesis and summarizing recent therapeutic strategies targeting CAFs. We underscore the challenges and advocate for the exploration of CAFs as a potential dual-targeted approach.

Separation of Palladium by an Imine-Linked Cu(I)-Organic Framework.

Selective capture of palladium (Pd) is one of the important works in science due to its high application and low content in the Earth's crust. To this end, we present herein a new Cu(I)-organic framework (ECUT-MOF-1) by introducing pyridine N active sites to chelate Pd(II). ECUT-MOF-1 demonstrated that the maximal adsorption capacity of Pd(II) was 350 mg/g in pH = 3 solution. In addition, kinetic analysis, cycle performance, selectivity, and adsorption mechanisms were also investigated. All of the results suggested its superior application in the recovery of Pd(II).

Extraction of Uranium by a Cheap Phosphite-Derived Polymer under Light Condition.

Uranium, as the main fuel of today's nuclear energy, is crucial to the development of nuclear energy. Therefore, the development of low-cost and powerful adsorbents is very important for the removal or recovery of uranium from uranium-containing solutions. Herein, we report the synthesis of a cheap phosphite-derived polymer for such use. Under visible-light irradiation, this phosphite-derived polymer was found to enable selective adsorption of uranium with an adsorption capacity as high as 1030 mg/g, suggesting its great potential in handling nuclear waste.

Extraction of Uranium by a Pyrazole-Based Porous Organic Polymer.

In this work, we report a pyrazole-based porous organic polymer (namely, ECUT-POP-2) for extraction of uranium. ECUT-POP-2 affords a high uranium extraction capacity of up to 1851 mg/g, excellent selectivity, and good reusability, suggesting its superior application in treating uranium-containing wastewater and acquring nuclear fuel.

Strong Electron Transfer in Covalently Integrating Cu(I)-Organic Frameworks Enabling Effective Radionuclide Capture.

Rational construction of strong electron-transfer materials remains a challenging task. Herein, we show a design rule for the construction of strong electron-transfer materials through covalently integrating electron-donoring Cu(I) clusters and electron-withdrawing triazine monomers together. As expected, Cu-CTF-1 (Cu(I)-triazine framework) was found to enable strong electron transfer up to 0.46|e| from each Cu(I) metal center to each adjacent triazine fragment. This finally leads to good spatial separation in both photogenerated electron-hole pairs and function units for photocatalytic uranium reduction under ambience and no sacrificial agent and to good charge separation of [I+][I5-] for I2 immobilization under extremely rigorous conditions. The results have not only opened up a structural design principle to access electron-transfer materials but also solved several challenging tasks in the field of radionuclide capture and CTFs.

Dual-Color Visual Ratiometric Fluorescence Sensing for H2O and D2O Mixtures Using a Hexanuclear Ln(III) Cluster-Based Metal-Organic Framework.

High-purity heavy water (D2O) is a strategic material owing to its important application in the fields of nuclear energy and scientific research. D2O always tends to get contaminated by H2O owing to its strong hygroscopicity. Herein, a bimetallic hexanuclear Ln(III) cluster-based metal-organic framework (Eu0.5Tb0.5-TZB-MOF) has been synthesized for fluorescence sensing of the D2O-H2O binary mixtures. Eu0.5Tb0.5-TZB-MOF can be used to immediately differentiate D2O or H2O via fluorescent color responses that are obvious to the naked eye and allow for quantitative ratiometric analysis using simple spectrophotometry. Fluorescence titration experiments demonstrate that both trace H2O in D2O and trace D2O in H2O can be quantitatively detected. Mechanistic studies demonstrate that the weaker vibrational quenching of the O-D oscillator compared to the O-H oscillator, in addition to the terbium-to-europium energy transfer, triggered the fluorescence signal response.