Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.

Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention.

HiMT: An integrative toolkit for assembling organelle genomes using HiFi reads.

Chloroplast and mitochondrial genomes, which coexist with the nuclear genome, are extensively used in gene function studies, evolutionary analyses, and targeted breeding. However, assembling these organelle genomes remains challenging due to frequent recombination events and abundant repetitive sequences. Although some assembly tools are available, many are difficult to install or require extensive parameter tuning and computational resources.

Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce Structural Variants Genotyping of Assemblies on Population scales (SVGAP), a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level.

Pore-Size Confinement Strategy in Hierarchical Porous MOFs for Efficient Enzyme Immobilization and Thiol Identification.

Metal-organic frameworks (MOFs) demonstrate considerable potential for enzyme immobilization, yet their applications are often limited by enzyme leakage or denaturation. Herein, we present a strategy for enzyme immobilization using hierarchically porous UiO-66 (a stable microporous MOF) frameworks. By partially replacing the conventional 1,4-benzenedicarboxylic acid (HBDC) linkers with monocarboxylic acids of controlled-chain lengths, we successfully engineered tailored mesopores within the stable microporous UiO-66 structure.

Cellular Identification of Single-Base Mutations in KRAS Gene Fragments Based on Nonhomologous Spectroscopic Data Fusion Modeling.

The sensitivity of KRAS gene mutation detection in colorectal cancer (CRC) can affect prognosis. This study established a nonhomologous spectroscopic data fusion method based on nuclear magnetic resonance (NMR) and laser tweezers Raman spectroscopy (LTRS), in order to analyze the metabolic characteristics of wild-type cells DKS-8 and HEK-3, and their respective mutant cells DLD-1 and HCT-116. Through multivariate statistical analysis, it was found that there were significant differences between mutant and wild-type cells.

Deciphering Pyridinic N-Mediated Inhibition Mode in Platinum Nanozymes for Pesticide Distinction.

Developing high-performance nanozymes with efficient HO activation capacity for biosensing still faces a great challenge. Here, Pt nanoparticles on a porous nitrogen-doped carbon carrier (Pt─N─C) are prepared as efficient nanozymes. By optimizing the pyridinic N content in the carbon carrier, a positive correlation has been found between the pyridinic N content and the peroxidase-like activity of Pt─N─C nanozymes.

Single-Atom Cobalt Sites Efficient Activation of HO With Enhanced O Tolerance for Electrochemiluminescence Sensing of Plasticizers.

Electrochemiluminescence (ECL) based on luminol-HO systems presents significant potential for the accurate and reliable biosensing. However, owing to the overlap of the potential windows for activating HO and dissolved O leads to competitive reactions, which presents a significant challenge for the selective ECL sensing. Herein, single atom Co sites on nitrogen-doped hierarchically porous carbon (Co-NC SAs) as co-reaction accelerators can efficiently activate HO to generate reactive oxygen species for oxidation of luminol and thus achievement of enhanced ECL emission.

Modulating p-d Orbital Hybridization in Mesoporous Medium-Entropy Alloy Nanozymes with Enhanced Peroxidase-Like Activity.

Platinum (Pt)-based nanozymes display exceptional stability and catalytic activity in the activation of HO, making them ideal peroxidase (POD)-like substitutes for immunoassay applications. However, specific catalytic progress is hindered by the excessive orbital overlaps between Pt and oxygen-based intermediates. Herein, a highly efficient mesoporous medium-entropy alloy (m-MEA) nanozyme is reported to selectively enhance POD activity through synergy interaction of multiple elements.

Global Research Trends in Pediatric Acute Respiratory Distress Syndrome: A Bibliometric Analysis from 2014 To 2024.

Background: To assess an overview of research trends, influential studies, and collaborative networks in pediatric acute respiratory distress syndrome (PARDS), identifying key contributions and insights for future research directions.

Methods: Web of Science Core Collection (WoSCC) database was used to conduct the bibliometric analysis. Bibliometric indicators such as publication counts, citation frequencies, authors, countries/regions, institutions and keyword occurrences were analyzed using VOSviewer and CiteSpace and R.

lncRNA CASC9 stabilizes MUC1 by binding to U2AF2 to inhibit cellular ferroptosis and alleviate LPS-induced cell injury.

Background: Sepsis-induced acute lung injury (ALI) is a critical condition with a limited number of treatment options. The regulatory role of long noncoding RNA cancer susceptibility candidate 9 (lncRNA CASC9) in ferroptosis, a specific type of cell death, has been linked to this condition.

Methods: In this study, HPAEpiCs were treated with lipopolysaccharide (LPS) to model sepsis-induced acute lung injury.

Amorphous RuO Nanozymes with an Excellent Catalytic Efficiency Superior to Natural Peroxidases.

Developing efficient peroxidase-like nanozymes to surpass natural enzymes remains a significant challenge. Herein, an amorphous RuO nanozyme with peroxidase-like activity is synthesized for activating HO with a specific activity of 1492.52 U mg, outperforming the crystalline RuO nanozymes by a factor of 22 and far superior to natural peroxidases.

Cu single sites on BO as thyroid peroxidase mimicking for iodotyrosine coupling and pharmaceutical assess.

Designing three-dimensional (3D) catalytic sites in single-atom catalysts (SACs) that mimic thyroid peroxidase (TPO) function for achieving iodotyrosine coupling, although highly desirable for the synthesis of thyroid hormones, poses a great challenge. Herein, we design and synthesize a class of SACs with 3D catalytic centers composed of Cu-N as catalytic sites and BO as binding sites (BO/CuNC) for mimicking TPO in activating HO to facilitate tyrosine iodination and conjugation for producing thyroid hormones. We demonstrate that the as-prepared BO/CuNC not only provides binding sites for HO through hydrogen bond interactions but also possesses catalytic sites to promote an alternative O-O heterolysis process.

Inhibition effect-involved colorimetric sensor array based on PtBi aerogel nanozymes for discrimination of antioxidants.

Nanozymes, as superior alternatives to natural enzymes, frequently employ the inhibition effect in turn-off sensors for analyte detection. However, limited attention has been paid to the inhibition mechanisms between analytes and nanozymes, limiting advancements in nanozyme-based sensing. Benefiting from the synergistic effects between three-dimensional network structure of aerogel and ligand effect triggered electronic regulation, PtBi aerogel nanozymes (PtBi ANs) exhibit superior peroxidase-like activity (293.

SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing.

Genome editing using CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies.

Coupled Homogeneous Hopfield Neural Networks: Simplest Model Design, Synchronization, and Multiplierless Circuit Implementation.

When using a synapse as a coupler to connect neurons, parameter-based synchronization transitions have been investigated. However, the dependence on initial conditions has not been comprehensively discussed in the literature. This work presents an electrical-synapse-coupled model consisting of two homogeneous Hopfield neural networks (HNNs), which is the simplest network-to-network coupling model known for HNN.

Utilizing Target Sequences with Multiple Flanking Protospacer Adjacent Motif (PAM) Sites Reduces Off-Target Effects of the Cas9 Enzyme in Pineapple.

Background/objectives: CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein 9 is now widely used in agriculture and medicine. Off-target effects can lead to unexpected results that may be harmful, and these effects are a common concern in both research and therapeutic applications.

Methods: In this study, using pineapple as the gene-editing material, eighteen target sequences with varying numbers of PAM (Protospacer-Adjacent Motif) sites were used to construct gRNA vectors.

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level.

Nrf2 deficiency aggravates hepatic cadmium accumulation, inflammatory response and subsequent injury induced by chronic cadmium exposure in mice.

Prolonged cadmium (Cd) exposure leads to Cd accumulation and oxidative damage in the liver. Nuclear factor erythroid-derived 2-like 2 (NRF2) plays a vital role in preventing acute hepatic toxicity of Cd. However, the participation of NRF2 in chronic liver injury, especially in the context of chronic Cd exposure, has rarely been investigated.

Nanozymes with Modulable Inhibition Transfer Pathways for Thiol and Cell Identification.

The elementary mechanism and site studies of nanozyme-based inhibition reactions are ambiguous and urgently require advanced nanozymes as mediators to elucidate the inhibition effect. To this end, we develop a class of nanozymes featuring single Cu-N catalytic configurations and B-O sites as binding configurations on a porous nitrogen-doped carbon substrate (B/Cu) for inducing modulable inhibition transfer at the atomic level. The full redistribution of electrons across the Cu-N sites, induced by B-O sites incorporation, yields B/Cu with enhanced peroxidase-like activity versus Cu.

Direct engulfment of synapses by overactivated microglia due to cadmium exposure and the protective role of Nrf2.

Cadmium (Cd), a notorious environmental pollutant, has been linked to neurological disorders, but the underlying mechanism remains elusive. We aimed to explore the role of microglia in Cd-induced synaptic damages at environmentally relevant doses and whether microglia directly engulf synaptic structures. Nrf2 is deeply implicated in the status of microglial activation; therefore, we also investigated whether it is involved in the above process.

The spatiotemporal and paradoxical roles of NRF2 in renal toxicity and kidney diseases.

Over 10% of the global population is at risk to kidney disorders. Nuclear factor erythroid-derived 2-related factor 2 (NRF2), a pivotal regulator of redox homeostasis, orchestrates antioxidant response that effectively counters oxidative stress and inflammatory response in a variety of acute pathophysiological conditions, including acute kidney injury (AKI) and early stage of renal toxicity. However, if persistently activated, NRF2-induced transcriptional cascade may disrupt normal cell signaling and contribute to numerous chronic pathogenic processes such as fibrosis.

Oxygen-bridged W-Pd atomic pairs enable HO activation for sensitive immunoassays.

Regulating the performance of peroxidase (POD)-like nanozymes is a prerequisite for achieving highly sensitive and accurate immunoassays. Inspired by natural enzyme catalysis, we design a highly active and selective nanozyme by loading atomically dispersed tungsten (W) sites on Pd metallene (W-O-Pdene) to construct an artificial three-dimensional (3D) catalytic center. The 3D asymmetric W-O-Pd atomic pairs can effectively stretch the O-O bonds in HO and further promote the desorption of HO to enhance POD-like activity.

Biomimetic Electronic Communication of Iodine Doped Single-Atom Fe Site for Highly Active and Stable Dopamine Oxidation.

Rational design of highly active and stable catalysts for dopamine oxidation is still a great challenge. Herein, inspired by the catalytic pocket of natural enzymes, an iodine (I)-doped single Fe-site catalyst (I/FeNC) is synthesized to mimic the catalytic center of heme enzymes in both geometrical and electronic structures, aiming to enhance dopamine (DA) oxidation. Experimental studies and theoretical calculations show that electronic communication between I and FeN effectively modulates the electronic structure of the active site, greatly optimizing the overlap of Fe 3d and O 2p orbitals, thereby enhancing OH adsorption.