Glycopolymer with Sulfated Fucose and 6'-Sialyllactose as a Dual-Targeted Inhibitor on Resistant Influenza A Virus Strains.

The frequent mutations of influenza A virus (IAV) have led to an urgent need for the development of innovative antiviral drugs. Glycopolymers offer significant advantages in biomedical applications owing to their biocompatibility and structural diversity. However, the primary challenge lies in the design and synthesis of well-defined glycopolymers to precisely control their biological functionalities. In this study, functional glycopolymers with sulfated fucose and 6'-sialyllactose were successfully synthesized through ring-opening metathesis polymerization and a postmodification strategy. The optimized heteropolymer exhibited simultaneous targeting of hemagglutinin and neuraminidase on the surface of IAV, as evidenced by MU-NANA assay and hemagglutination inhibition data. Antiviral experiments demonstrated that the glycopolymer displayed broad and efficient inhibitory activity against wild-type and mutant strains of H1N1 and H3N2 subtypes in vitro, thereby establishing its potential as a dual-targeted inhibitor for combating IAV resistance.

HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment.

Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.

NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.

The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here, we describe an upgraded genome polishing tool - NextPolish2, which can fix base errors remaining in those "highly accurate" genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors. We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere (T2T) genomes. NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.

Integrated multi-omics profiling reveals a clinically relevant molecular feature and potential therapeutic target on phyllodes tumors of breast.

Phyllodes tumors (PTs) has an increased risk of local relapse and distant metastases. Molecular features correlating to histologic grade and aggressive behavior of PTs are poorly characterized. Here, whole exome sequencing (WES) was performed to explore genetic mutations in 61 samples of fibroepithelial breast tumors, including 16 fibroadenomas (FAs), 18 benign PTs, 19 borderline PTs, and 8 malignant PTs. Our work clearly shows that FA, benign PT, borderline PT, and malignant PT are independent entities at the genomic level. They may exist as hidden sub-clones carrying specific genetic alterations. Malignant PT-specific mutations present a multi-gene co-mutational pattern suggesting a synergistic effect of co-mutated genes in processes associated with malignant behavior. Moreover, we made a combined genomic and transcriptomic analysis, which presented a mutated gene-based interaction with expression profiles. We found that EGFR mutations (c.710C > T, c.758A > G, c.1295A > G, and c.2156G > C) serve as a hub of interaction network in borderline PTs, which suggests EGFR tyrosine kinase inhibitors (EGFRi) might be effective for borderline PTs. We found TP53 mutations (c.730G > T, c.844C > T, and c.1019delA) serves as a hub event of molecular changes of malignant PTs. Thus, our study based on the omics platforms of genome and transcriptome provides a better understanding of relapse process and the potential targeted therapy in PTs, which is pivotal in improving molecular-guided patient selection and designing clinically relevant combination strategies.

Grain Boundary Defect Engineering in Rutile Iridium Oxide Boosts Efficient and Stable Acidic Water Oxidation.

Proton exchange membrane water electrolysis (PEMWE) is considered a promising technology for coupling with renewable energy sources to achieve clean hydrogen production. However, constrained by the sluggish kinetics of the anodic oxygen evolution reaction (OER) and the acidic abominable environment render the grand challenges in developing the active and stable OER electrocatalyst, leading to low efficiency of PEMWE. Herein, we develop the rutile-type IrO2 nanoparticles with abundant grain boundaries and the continuous nanostructure through the joule heating and sacrificial template method. The optimal candidate (350-IrO2) demonstrates remarkable electrocatalytic activity and stability during the OER, presenting a promising advancement for efficient PEMWE. DFT calculations verified that grain boundaries can modulate the electronic structure of Ir sites and optimize the adsorption of oxygen intermediates, resulting in the accelerated kinetics. 350-IrO2 affords a rapid OER process with 20 times higher mass activity (0.61 A mgIr -1) than the commercial IrO2 at 1.50 V vs. RHE. Benefiting from the reduced overpotential and the preservation of the stable rutile structure, 350-IrO2 exhibits the stability of 200 h test at 10 mA cm-2 with only trace decay of 11.8 mV. Moreover, the assembled PEMWE with anode 350-IrO2 catalyst outputs the current density up to 2 A cm-2 with only 1.84 V applied voltage, long-term operation for 100 h without obvious performance degradation at 1 A cm-2.

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.

Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. We apply NextDenovo to assemble 35 diverse human genomes from around the world using Nanopore long-read data. These genomes allow us to identify the landscape of segmental duplication and gene copy number variation in modern human populations. The use of NextDenovo should pave the way for population-scale long-read assembly using Nanopore long-read data.

Immune-enhancing activity of compound polysaccharide on the inactivated influenza vaccine.

Traditional Chinese medicine polysaccharides have numerous biological activities with broad applications in the biomedical industries. However, a clear understanding of the pharmacological activities of compound polysaccharides with multi-component structures remain challenging. This study aimed to investigate the immune boosting effect of compound polysaccharides on the influenza vaccine and assess the preliminary structure-activity relationship. The compound polysaccharide (CP) was isolated from the combined Chinese herbs lentinan, pachymaran and tremellan, and purified by gradient ethanol precipitation to obtain its subcomponents of CP-20, CP-40, CP-60, and CP-80 with decreasing molecular weights. These polysaccharides were mainly composed of glucans with different linkage patterns, including α-(1 â†’ 3)-glucan, α-(1 â†’ 4)-glucan and ß-(1 â†’ 6)-glucan. A significant improvement was observed in the survival of mice vaccinated with inactivated (IAV) vaccine and the isolated polysaccharides as adjuvants. A reduction in the pulmonary virus titer and weight loss were also observed. Moreover, CP-40 and CP-60, as well as the original CP, significantly enhanced the serum anti-IAV antibody titers and interleukin IL-2, IL-5, and IL-6 concentrations. These preliminary results indicate the immune boosting effect of the compound polysaccharides is highly relevant to the specific structural properties of the subcomponent, and CP-40 is worthy of further exploration as a glycan adjuvant for the IAV vaccine.

Chemical-toxicological insights and process comparison for estrogenic activity mitigation in municipal wastewater treatment plants.

Efforts in water ecosystem conservation require an understanding of causative factors and removal efficacies associated with mixture toxicity during wastewater treatment. This study conducts a comprehensive investigation into the interplay between wastewater estrogenic activity and 30 estrogen-like endocrine disrupting chemicals (EEDCs) across 12 municipal wastewater treatment plants (WWTPs) spanning four seasons in China. Results reveal substantial estrogenic activity in all WWTPs and potential endocrine-disrupting risks in over 37.5 % of final effluent samples, with heightened effects during colder seasons. While phthalates are the predominant EEDCs (concentrations ranging from 86.39 %) for both estrogenic activity and major EEDCs (phthalates and estrogens), with the secondary and tertiary treatment segments contributing 88.59 ± 8.12 % and 11.41 ± 8.12 %, respectively. Among various secondary treatment processes, the anaerobic/anoxic/oxic-membrane bioreactor (A/A/O-MBR) excels in removing both estrogenic activity and EEDCs. In tertiary treatment, removal efficiencies increase with the inclusion of components involving physical, chemical, and biological removal principles. Furthermore, correlation and multiple liner regression analysis establish a significant (p < 0.05) positive association between solid retention time (SRT) and removal efficiencies of estrogenic activity and EEDCs within WWTPs. This study provides valuable insights from the perspective of prioritizing key pollutants, the necessity of integrating more efficient secondary and tertiary treatment processes, along with adjustments to operational parameters like SRT, to mitigate estrogenic activity in municipal WWTPs. This contribution aids in managing endocrine-disrupting risks in wastewater as part of ecological conservation efforts.

Isotropic resolution plenoptic background oriented schlieren through dual-view acquisition.

The key to uncovering underlying fluid mechanisms lies in high-resolution and large-scale three-dimensional (3D) measurements of flow fields. Currently, the mainstream methods that are capable of volumetric measurements, such as tomographic background oriented schlieren and conventional plenoptic background oriented schlieren (plenoptic BOS), suffer system complexity and low axial resolution, respectively, prohibiting their application in high fidelity 3D flow measurement. This paper proposed an isotropic resolution plenoptic BOS (ISO plenoptic BOS) system that employed a mirror to create a second image view for the region of interest, thereby can achieve isotropic spatial resolution with only one camera. We comprehensively assessed the feasibility of the system by imaging the density field induced by candle flames, heat gun, and the Mach disk produced by the underexpanded jet through the high-pressure nozzle exit. All results proved that the dual-view plenoptic BOS system has higher axial resolution and can provide a more accurate 3D density field than the conventional system. As a BOS system that can achieve high-resolution volumetric imaging without the additional cost of cameras, data acquisition, hardware synchronization, and scanning, our ISO plenoptic BOS can expand the road to large-scale and high-resolution aerodynamic imaging.

Distinct microbial characteristics of the robust single-stage coupling system during the conversion from anammox-denitritation to anammox-denitratation patterns.

Simultaneous anammox-denitrification is effectively operated in two types, i.e., the anammox-denitritation (SAD pattern) and the anammox-denitratation (PDA pattern). The nitrate derived from inevitable nitrite oxidization likely determines the practical operational pattern of the coupling system, while little information is available regarding the microbial characteristics during the pattern conversion. Here, the single-stage bioreactor coupling anammox with denitrification was operated under conditions with a changed ratio of influent nitrite and nitrate. Results showed that the bioreactor exhibited a robust performance during the conversion from SAD to PDA patterns, corresponding with the total nitrogen removal efficiency ranging from 89.5% to 92.4%. Distinct community structures were observed in two patterns, while functional bacteria including the genera Denitratisoma, Thauera, Candidatus Brocadia, and Ca. Jettenia steadily co-existed. Meanwhile, the high transcription of hydrazine synthase genes demonstrated a stable anammox process, while the up-regulated transcription of nitrite and nitrous oxide reductase genes indicated that the complete denitrification process was enhanced for total nitrogen removal during the PDA pattern. Ecologically, stochastic processes dominantly governed the community assembly in two patterns. The PDA pattern improved the interconnectivity of communities, especially for the cooperative behaviors between dominant denitrifying bacteria and low-abundant species. These findings deepen our understanding of the microbial mechanism underlying the different patterns of the coupling system and potentially expand its engineering application.

Dynamics of bacterioplankton communities in the estuary areas of the Taihu Lake: Distinct ecological mechanisms of abundant and rare communities.

As the crucial confluences of rivers and lakes, the estuary areas with varied hydrodynamic exchanges intensively affect the bacterioplankton communities, whereas the ecological characteristics of the bacterioplankton in the areas have not been well understood. Here, the distribution patterns and assembly mechanisms of bacterioplankton communities in the estuary areas of the Taihu Lake were investigated using high-throughput sequencing and multivariate statistical analyses. Our results showed obvious seasonal variations in bacterioplankton diversity and community composition, which had significant correlations with water temperature. Neutral and null models together revealed that stochastic processes (especially dispersal limitation) were the major processes in shaping the communities across different seasons. By contrast, heterogeneous selection in deterministic processes exhibited increased impacts on community assembly during summer and autumn, which was significantly related to the comprehensive water quality index (WQI) rather than any single factor. In this study, rare communities displayed more pronounced seasonal dynamics compared to abundant communities, likely due to their sensitivity towards environmental factors. Accordingly, the heterogeneous selection of deterministic processes largely shaped the rare communities. These results enriched our understanding of the assembly mechanisms of bacterioplankton communities in estuary areas and emphasized the specific co-occurrence patterns of abundant and rare communities.

Highly efficient electrochemical ammonia synthesis via nitrate reduction over metallic Cu phase coupling sulfion oxidation.

Electrochemical nitrate reduction reaction (NO3RR) is a promising technology for ammonia production and denitrification of wastewater. Its application is seriously restricted by the development of the highly active and selective electrocatalyst and a rational electrolysis system. Here, we constructed an efficient electrochemical ammonia production process via nitrate reduction on the metallic Cu electrocatalyst when coupled with anodic sulfion oxidation reaction (SOR). The synthesized Cu catalyst delivers an excellent NH3 Faradaic efficiency of 96.0 % and a NH3 yield of 0.391 mmol h-1 cm-2 at -0.2 V vs. reversible hydrogen electrode, which mainly stem from the more favorable conversion of NO2 - to NH3 on Cu0. Importantly, the well-designed electrolysis system with cathodic NO3RR and anodic SOR achieves a dramatically reduced cell voltage of 0.8 V at 50 mA cm-2 in comparison with the one with anodic oxygen evolution reaction (OER) of 1.9 V. This work presents an effective strategy for the energy-saving ammonia production via constructing effective nitrate reduction catalyst and replacing the OER with SOR while removing the pollutants including nitrate and sulfion.

Temporal differentiation in the adaptation of functional bacteria to low-temperature stress in partial denitrification and anammox system.

Despite reliable nitrite supply through partial denitrification, the adaptation of denitrifying bacteria to low temperatures remains elusive in partial denitrification and anammox (PDA) systems. Here, temporal differentiations of the structure, activity, and relevant cold-adaptation mechanism of functional bacteria were investigated in a lab-scale PDA bioreactor at decreased temperature. Although distinct denitrifying bacteria dominated after low-temperature stress, both short- and long-term stresses exerted differential selectivity towards the species with close phylogenetic distance. Species Azonexus sp.149 showed high superiority over Azonexus sp.384 under short-term stress, and long-term stress improved the adaptation of Aquabacterium sp.93 instead of Aquabacterium sp.184. The elevated transcription of nitrite reductase genes suggested that several denitrifying bacteria (e.g., Azonexus sp.149) could compete with anammox bacteria for nitrite. Species Rivicola pingtungensis and Azonexus sp.149 could adapt through various adaptation pathways, such as the two-component system, cold shock protein (CSP), membrane alternation, and electron transport chain. By contrast, species Zoogloea sp.273 and Aquabacterium sp.93 mainly depended on the CSP and oxidative stress response. This study largely deepens our understanding of the performance deterioration in PDA systems during cold shock and provides several references for efficient adaptation to seasonal temperature fluctuation.

Uncovering the true features of dystrophin gene rearrangement and improving the molecular diagnosis of Duchenne and Becker muscular dystrophies.

Duchenne and Becker muscular dystrophies (DMD/BMD) are caused by complex mutations in the dystrophin gene (DMD). Currently, there is no integrative method for the precise detection of all potential DMD variants, a gap which we aimed to address using long-read sequencing. The captured long-read sequencing panel developed in this study was applied to 129 subjects, including 11 who had previously unsolved cases. The results showed that this method accurately detected DMD mutations, ranging from single-nucleotide variations to structural variations. Furthermore, our findings revealed that continuous exon duplication/deletion in the DMD/BMD cohort may be attributed to complex segmental rearrangements and that noncontiguous duplication/deletion is generally attributed to intragenic inversion or interchromosome translocation. Mutations in the deep introns were confirmed to produce a pseudoexon. Moreover, variations in female carriers were precisely identified. The integrated and precise DMD gene screening method proposed in this study could improve the molecular diagnosis of DMD/BMD.

Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing.

Structural variants (SVs), accounting for a larger fraction of the genome than SNPs/InDels, are an important pool of genetic variation, enabling environmental adaptations. Here, we perform long-read sequencing data of 320 Tibetan and Han samples and show that SVs are highly involved in high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict enhancers, target genes and biological functions. We reveal diverse Tibetan-specific SVs affecting the regulatory circuitry of biological functions, including the hypoxia response, energy metabolism and pulmonary function. We find a Tibetan-specific deletion disrupts a super-enhancer and downregulates EPAS1 using enhancer reporter, cellular knock-out and DNA pull-down assays. Our study expands the global SV landscape, reveals the role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles of SVs in human biology.

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.

BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome. RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data. CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.

A large pedigree study confirmed the CGG repeat expansion of RILPL1 Is associated with oculopharyngodistal myopathy.

BACKGROUND: Oculopharyngodistal myopathy (OPDM) is an autosomal dominant adult-onset degenerative muscle disorder characterized by ptosis, ophthalmoplegia and weakness of the facial, pharyngeal and limb muscles. Trinucleotide repeat expansions in non-coding regions of LRP12, G1PC1, NOTCH2NLC and RILPL1 were reported to be the etiologies for OPDM. RESULTS: In this study, we performed long-read whole-genome sequencing in a large five-generation family of 156 individuals, including 21 patients diagnosed with typical OPDM. We identified CGG repeat expansions in 5'UTR of RILPL1 gene in all patients we tested while no CGG expansion in unaffected family members. Repeat-primed PCR and fluorescence amplicon length analysis PCR were further confirmed the segregation of CGG expansions in other family members and 1000 normal Chinese controls. Methylation analysis indicated that methylation levels of the RILPL1 gene were unaltered in OPDM patients, which was consistent with previous studies. Our findings provide evidence that RILPL1 is associated OPDM in this large pedigree. CONCLUSIONS: Our results identified RILPL1 is the associated the disease in this large pedigree.

Combination of Sequencing Batch Operation and A/O Process to Achieve Partial Mainstream Anammox: Pilot-Scale Demonstration and Microbial Ecological Mechanism.

In this study, sequencing batch operation was successfully combined with a pilot-scale anaerobic biofilm-modified anaerobic/aerobic membrane bioreactor to achieve anaerobic ammonium oxidation (anammox) without inoculation of anammox aggregates for municipal wastewater treatment. Both total nitrogen and phosphorus removal efficiencies of the reactor reached up to 80% in the 250-day operation, with effluent concentrations of 4.95 mg-N/L and 0.48 mg-P/L. In situ enrichment of anammox bacteria with a maximum relative abundance of 7.86% was observed in the anaerobic biofilm, contributing to 18.81% of nitrogen removal, with denitrification being the primary removal pathway (38.41%). Denitrifying phosphorus removal (DPR) (40.54%) and aerobic phosphorus uptake (48.40%) played comparable roles in phosphorus removal. Metagenomic sequencing results showed that the biofilm contained significantly lower abundances of NO-reducing functional genes than the bulk sludge (p < 0.01), favoring anammox catabolism in the former. Interactions between the anammox bacteria and flanking community were dominated by cooperation behaviors (e.g., nitrite supply, amino acids/vitamins exchange) in the anaerobic biofilm community network. Moreover, the hydrolytic/fermentative bacteria and endogenous heterotrophic bacteria (Dechloromonas, Candidatus competibacter) were substantially enriched under sequencing batch operation, which could alleviate the inhibition of anammox bacteria by complex organics. Overall, this study provides a feasible and promising strategy for substantially enriching anammox bacteria and achieving partial mainstream anammox as well as DPR.

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.

Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.

Phylogenomic analyses provide insights into primate evolution.

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.