Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.

Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.

Spatiotemporally Guided Single-Atom Bionanozyme for Targeted Antibiofilm Treatment.

The heterogeneous and dynamic microenvironment of biofilms complicates bacterial infection treatment. Nanozyme catalytic therapy has recently been promising in treating biofilm infections. However, active nanozymes designed with the required precision targeting the biofilm microenvironment are lacking. This work proposes a spatiotemporally guided single-atom bionanozyme (BioSAzyme) for targeted antibiofilm therapy based on protein engineering of copper single-atom nanozyme (Cu SAzyme). The Cu SAzyme, synthesized via a novel mechanochemistry-assisted method, features highly accessible Cu-N4 active sites exposed on 2D N-doped carbon, exhibiting excellent triple enzyme-like activities according to experimental results and density functional theory calculations. Inheriting biofunctionality from both glucose oxidase and concanavalin A, BioSAzyme can localize the biofilm glycocalyx and catalyze endogenous glucose into H2O2 and gluconic acid, thus triggering multiplex cascade reactions with pH self-adaption to consume glucose and glutathione and generate •OH radicals. This spatiotemporally guided bionanocatalytic agent effectively inhibits E. coli O157: H7 and methicillin-resistant S. aureus biofilms in vitro and in vivo. Taking together, this work opens up new avenues for the rational design of single-atom nanozymes for precise antibiofilm therapy.

Quality Evaluation of Guidelines for the Diagnosis and Treatment of Liver Failure.

OBJECTIVES: This study aimed to systematically assess the methodological quality and key recommendations of the guidelines for the diagnosis and treatment of liver failure (LF), furnishing constructive insights for guideline developers and equipping clinicians with evidence-based information to facilitate informed decision-making. DATA SOURCES: Electronic databases and manual searches from January 2011 to August 2023. STUDY SELECTION: Two reviewers independently screened titles and abstracts, then full texts for eligibility. Fourteen guidelines were included. DATA EXTRACTION AND SYNTHESIS: Two reviewers extracted data and checked by two others. Methodological quality of the guidelines was appraised using the Appraisal of Guidelines for Research and Evaluation II tool. Of the 14 guidelines, only the guidelines established by the Society of Critical Care Medicine and the American College of Gastroenterology (2023) achieved an aggregate quality score exceeding 60%, thereby meriting clinical recommendations. It emerged that there remains ample room for enhancement in the quality of the guidelines, particularly within the domains of stakeholder engagement, rigor, and applicability. Furthermore, an in-depth scrutiny of common recommendations and supporting evidence drawn from the 10 adult LF guidelines unveiled several key issues: controversy exists in the recommendation, the absence of supporting evidence and confusing use of evidence for recommendations, and a preference in evidence selection. CONCLUSIONS: There are high differences in methodological quality and recommendations among LF guidelines. Improving these existing problems and controversies will benefit existing clinical practice and will be an effective way for developers to upgrade the guidelines.

Assessment of the Efficacy of the Combination of RNAi of lncRNA DANCR with Chemotherapy to Treat Triple Negative Breast Cancer Using Magnetic Resonance Molecular Imaging.

Long noncoding RNA (lncRNA) differentiation antagonizing noncoding RNA (DANCR) is overexpressed in human triple-negative breast cancer (TNBC) and promotes cell migration and proliferation. TNBC is limited in treatment options relative to hormone-receptor-positive breast cancer and is commonly treated with chemotherapy, which is often compromised by acquired resistance. DANCR has been implicated in the development of chemoresistance across multiple cancer types. Here, we applied magnetic resonance molecular imaging (MRMI) with a targeted contrast agent, MT218, specific to extradomain-B fibronectin (EDB-FN), a marker for epithelial-to-mesenchymal transition, to assess the therapeutic efficacy of the combination of paclitaxel and ZD2-PEG-ECO/siDANCR nanoparticles (ZD2-siDANCR-ELNP) to treat TNBC. The treatment of orthotopic MDA-MB-231 TNBC in mice with paclitaxel significantly suppressed tumor growth but with a significant increase of EDB-FN in the tumor, as revealed by MRMI and immunohistochemistry. Combining ZD2-siDANCR-ELNP with paclitaxel further reduced tumor sizes, along with reduced EDB-FN expression. Interestingly, MT218-MRMI revealed a lower reduction of tumor signal enhancement with the combination treatment than that with the siDANCR treatment alone, which was supported by higher cell density in the tumors treated with the combination therapy, as shown by histochemical analysis. MT218-MRMI clearly revealed the changes of the tumor microenvironment in response to various therapies and is effective to noninvasively assess the response of TNBC tumors to the therapies. Regulating oncogenic lncRNA DANCR is an effective strategy for improving the outcomes of chemotherapy in TNBC.

Structure-activity relationships and activity enhancement techniques of marine bioactive peptides (MBPs).

Marine bioactive peptides (MBPs) are a type of natural compound with a variety of bioactivities, such as anticancer, antimicrobial, antioxidant, and antihypertensive. Due to a wide range of sources, low toxicity, and high specificity, MBPs have now received extensive attention in the fields of food, medicine, and cosmetics. The structure of MBPs determines their biological activities. Therefore, it is essential to analyze the relationship between the structure and bioactivity of MBPs. Because of the advantages of mild conditions, high specificity, safety, and environmental friendliness, enzymatic hydrolysis has become the most commonly used method to produce MBPs. However, the high cost and low yield of enzymatic methods have motivated researchers to search for alternative technologies. Novel pretreatments like ultrasound, microwave, high hydrostatic pressure, and pulsed electric fields have been employed in the production of MBPs. By inducing protein unfolding and increasing enzymatic cleavage sites, these techniques have been demonstrated to accelerate protein hydrolysis and enhance the biological activity of MBPs. This article reviews recent research advances on marine-derived protein hydrolysates and peptides, discusses the relationship between their biological activity and structure, and compares the mechanisms of action of different novel technologies used to promote protein hydrolysis and enhance the biological activity of MBPs. In addition, the current challenges facing the development and application of MBPs are outlined and possible future work in tackling these challenges is also suggested in the current review. It is hoped that this review can promote further development and application of marine active substances.

Regulating bacterial biofilms in food and biomedicine: unraveling mechanisms and Innovating strategies.

Bacterial biofilm has brought a lot of intractable problems in food and biomedicine areas. Conventional biofilm control mainly focuses on inactivation and removal of biofilm. However, with robust construction and enhanced resistance, the established biofilm is extremely difficult to eradicate. According to the mechanism of biofilm development, biofilm formation can be modulated by intervening in the key factors and regulatory systems. Therefore, regulation of biofilm formation has been proposed as an alternative way for effective biofilm control. This review aims to provide insights into the regulation of biofilm formation in food and biomedicine. The underlying mechanisms for early-stage biofilm establishment are summarized based on the key factors and correlated regulatory networks. Recent developments and applications of novel regulatory strategies such as anti/pro-biofilm agents, nanomaterials, functionalized surface materials and physical strategies are also discussed. The current review indicates that these innovative methods have contributed to effective biofilm control in a smart, safe and eco-friendly way. However, standard methodology for regulating biofilm formation in practical use is still missing. As biofilm formation in real-world systems could be far more complicated, further studies and interdisciplinary collaboration are still needed for simulation and experiments in the industry and other open systems.

Elevating nanomaterial optical sensor arrays through the integration of advanced machine learning techniques for enhancing visual inspection of food quality and safety.

Food quality and safety problems caused by inefficient control in the food chain have significant implications for human health, social stability, and economic progress and optical sensor arrays (OSAs) can effectively address these challenges. This review aims to summarize the recent applications of nanomaterials-based OSA for food quality and safety visual monitoring, including colourimetric sensor array (CSA) and fluorescent sensor array (FSA). First, the fundamental properties of various advanced nanomaterials, mainly including metal nanoparticles (MNPs) and nanoclusters (MNCs), quantum dots (QDs), upconversion nanoparticles (UCNPs), and others, were described. Besides, the diverse machine learning (ML) and deep learning (DL) methods of high-dimensional data obtained from the responses between different sensing elements and analytes were presented. Moreover, the recent and representative applications in pesticide residues, heavy metal ions, bacterial contamination, antioxidants, flavor matters, and food freshness detection were comprehensively summarized. Finally, the challenges and future perspectives for nanomaterials-based OSAs are discussed. It is believed that with the advancements in artificial intelligence (AI) techniques and integrated technology, nanomaterials-based OSAs are expected to be an intelligent, effective, and rapid tool for food quality assessment and safety control.

Valorization of potato by-products as a source of plant proteins: novel extraction techniques and potential applications.

The potential of potato by-products as a protein source presents an exciting opportunity to explore new methods and technologies to extract, enhance, and incorporate this valuable protein source into a variety of food products. This article reviews the progress in research related to potato and other tuber plant protein extraction technology. It also explores some conventional and novel techniques for plant protein extraction that may be applicable to tuber protein extraction. For extraction from solid matter, conventional methods such as acid-base extraction with heat assistance often mean a waste of energy, solvent, and destruction of protein structure. Enzyme-assisted, ultrasound-assisted, and pulsed electric field extraction have their own advantages as novel processing methods. For liquid by-products of tuber plants, precipitation, membrane filtration and chromatography are applied to extract proteins. By combining protein extraction with various biomass extraction methods, every part of the potatoes can be fully utilized, minimizing waste. This approach offers the opportunity to optimize the utilization of all potatoes components, reduce waste, generate additional revenue streams and ultimately increase the sustainability and effectiveness of the process.

Intravitreal Delivery of PEGylated-ECO Plasmid DNA Nanoparticles for Gene Therapy of Stargardt Disease.

OBJECTIVE: Current gene therapy of inherited retinal diseases is achieved mainly by subretinal injection, which is invasive with severe adverse effects. Intravitreal injection is a minimally invasive alternative for gene therapy of inherited retinal diseases. This work explores the efficacy of intravitreal delivery of PEGylated ECO (a multifunctional pH-sensitive amphiphilic amino lipid) plasmid DNA (pGRK1-ABCA4-S/MAR) nanoparticles (PEG-ELNP) for gene therapy of Stargardt disease. METHODS: Pigmented Abca4-/- knockout mice received 1 µL of PEG-ELNP solution (200 ng/uL, pDNA concentration) by intravitreal injections at an interval of 1.5 months. The expression of ABCA4 in the retina was determined by RT-PCR and immunohistochemistry at 6 months after the second injection. A2E levels in the treated eyes and untreated controls were determined by HPLC. The safety of treatment was monitored by scanning laser ophthalmoscopy and electroretinogram (ERG). RESULTS: PEG-ELNP resulted in significant ABCA4 expression at both mRNA level and protein level at]6 months after 2 intravitreal injections, and a 40% A2E accumulation reduction compared with non-treated controls. The PEG-ELNP also demonstrated excellent safety as shown by scanning laser ophthalmoscopy, and the eye function evaluation from electroretinogram. CONCLUSIONS: Intravitreal delivery of the PEG-ELNP of pGRK1-ABCA4-S/MAR is a promising approach for gene therapy of Stargardt Disease, which can also be a delivery platform for gene therapy of other inherited retinal diseases.

White rot fungi as a multifaceted biocontrol agent: Metabolic disruption and algal inhibition in Microcystis aeruginosa.

Microcystis aeruginosa is a prevalent cyanobacterium linked to water eutrophication and harmful algal blooms. While bacterial control strategies are well-studied, the effects of white rot fungi on Microcystis aeruginosa are less understood. This study examines the impact of whole fungal liquid, its centrifuged supernatant, and sterilized solutions on the algae's physiological and biochemical traits. Metabolomics and multivariate analysis identified significant changes in 47 metabolic markers, including carbohydrates, amino acids, and fatty acids, across treatments. The complete fungal liquid exhibited the strongest algicidal effect, likely due to synergistic solubilization mechanisms mediated by extracellular enzymes such as manganese peroxidase, catalase, and laccase. Notably, algicidal activity persisted even after sterilization, suggesting the presence of non-proteinaceous compounds like polysaccharides or lipids. The metabolic disturbances included downregulation of the TCA cycle and reduced fatty acid synthesis, leading to inhibited photosynthesis and compromised nucleic acid integrity in the algal cells. This research enhances our understanding of how white rot fungi disrupt Microcystis aeruginosa metabolism, providing a theoretical basis for their potential use in bioremediation of eutrophic aquatic environments.

Cystoderma yongpingense sp. nov. (Squamanitaceae, Agaricales) a new species from southwestern China.

The present study introduces a novel fungus, Cystoderma yongpingense, which was identified in the southwestern region of China. The new species is characterized by a pileus that ranges in color from light orange-red to orange-red; the pileus has a wrinkled surface and is accompanied by a persistent annulus that is membranous and floccose-scaly. Above the annulus, the color transitions from white to yellowish brown. This proposal is substantiated through analyses encompassing both morphological characteristics and phylogenetic relationships. The phylogenetic position of the newly discovered species has been further corroborated through comprehensive maximum likelihood and Bayesian sequence analyses of the ITS + nrLSU DNA regions. Additionally, the technical description of C. yongpingense is enhanced by detailed illustrations and comparative studies with species that are closely related.

[The role of seminal vesicles in male sexual function].

The seminal vesicle is an important accessory gland of the male reproductive system. In the past, some scholars focused more on its role in the fertilization process and neglected its relationship with male sexual function. Researches show that the seminal vesicle is involved in multiple processes such as sexual desire, penile erection, and ejaculation. Treatment of sexual dysfunction by medication targeting the seminal vesicle has achieved certain therapeutic effects. This article discusses the relationship between the seminal vesicle and sexual function in terms of physiopathology, clinical study and basic research, hoping to provide some new ideas on the clinical diagnosis and treatment of sexual dysfunction.

[Mechanisms of traditional Chinese medicine in the treatment of chronic nonbacterial prostatitis].

Chronic nonbacterial prostatitis (CNP) is one of the most common diseases in urology and andrology, with a complex etiology and a high incidence rate. Traditional Chinese medicine plays an important role in the treatment of CNP and can produce therapeutic effects through various action mechanisms. This article presents an overview of recent studies on the specific mechanisms of traditional Chinese medicine acting on CNP, including the mechanisms underlying its effects of anti-infection, anti-inflammation, immune regulation, improvement of urodynamics, endocrine regulation, improvement of microcirculation, and regulation of gut microbiota, aiming to provide some reference for the clinical application and basic studies of traditional Chinese medicine in the treatment of CNP.

[Ferroptosis in the testis: Progress in research].

Ferroptosis is a form of cell death resulting from the disruption of iron metabolism within cells and excessive accumulation of lipid peroxides. Research indicates that, under the influence of various pathogenic factors, ferroptosis impacts the male reproductive system and fertility by affecting the synthesis of testicular hormones and regulation of cellular functions through different pathways and numerators. This paper provides an overview of the action mechanisms of ferroptosis in the testis and its correlation with pathogenicity, offering some new insights into the treatment of male reproductive system diseases.

Serum thrombospondin-1 serves as a novel biomarker and agonist of gemcitabine-based chemotherapy in intrahepatic cholangiocarcinoma.

BACKGROUND: At present, the first-line treatment for advanced intrahepatic cholangiocarcinoma (ICC) is gemcitabine combined with cisplatin, but a considerable portion of ICC patients exhibit resistance to gemcitabine. Therefore, finding sensitisers for gemcitabine chemotherapy in ICC patients and predicting molecular markers for chemotherapy efficacy have become urgent needs. METHODS: In this study, PDX models were established to conduct gemcitabine susceptibility tests. The selected PDX tissues of the chemotherapy-sensitive group and drug-resistant group were subjected to transcriptome sequencing and protein chip technology to identify the key genes. Sixty-one ICC patients treated with gemcitabine chemotherapy were recruited for clinical follow-up validation. RESULTS: We found that thrombospondin-1 (TSP1) can predict gemcitabine chemosensitivity in ICC patients. The expression level of TSP1 could reflect the sensitivity of ICC patients to gemcitabine chemotherapy. Functional experiments further confirmed that TSP1 can increase the efficacy of gemcitabine chemotherapy for ICC. A mechanism study showed that TSP1 may affect the intake of oleic acid by binding to the CD36 receptor. CONCLUSIONS: In summary, we found a key molecule-TSP1-that can predict and improve the sensitivity of ICC patients to gemcitabine chemotherapy, which is of great significance for the treatment of advanced cholangiocarcinoma.

Amp-vortex edge-camera: a lensless multi-modality imaging system with edge enhancement.

We demonstrate a lensless imaging system with edge-enhanced imaging constructed with a Fresnel zone aperture (FZA) mask placed 3 mm away from a CMOS sensor. We propose vortex back-propagation (vortex-BP) and amplitude vortex-BP algorithms for the FZA-based lensless imaging system to remove the noise and achieve the fast reconstruction of high contrast edge enhancement. Directionally controlled anisotropic edge enhancement can be achieved with our proposed superimposed vortex-BP algorithm. With different reconstruction algorithms, the proposed amp-vortex edge-camera in this paper can achieve 2D bright filed imaging, isotropic, and directional controllable anisotropic edge-enhanced imaging with incoherent light illumination, by a single-shot captured hologram. The effect of edge detection is the same as optical edge detection, which is the re-distribution of light energy. Noise-free in-focus edge detection can be achieved by using back-propagation, without a de-noise algorithm, which is an advantage over other lensless imaging technologies. This is expected to be widely used in autonomous driving, artificial intelligence recognition in consumer electronics, etc.

Cystathionine gamma-lyase (Cth) induces efferocytosis in macrophages via ERK1/2 to modulate intestinal barrier repair.

BACKGROUND: The inflammatory response induced by intestinal ischaemia‒reperfusion injury (I/R) is closely associated with infectious complications and mortality in critically ill patients, and the timely and effective clearance of apoptotic cells is an important part of reducing the inflammatory response. Studies have shown that the efferocytosis by phagocytes plays an important role. Recently, studies using small intestine organoid models showed that macrophage efferocytosis could promote the repair capacity of the intestinal epithelium. However, no studies have reported efferocytosis in the repair of I/R in animal models. RESULTS: We used an in vivo efferocytosis assay and discovered that macrophage efferocytosis played an indispensable role in repairing and maintaining intestinal barrier function after I/R. In addition, the specific molecular mechanism that induced macrophage efferocytosis was Cth-ERK1/2 dependent. We found that Cth drove macrophage efferocytosis in vivo and in vitro. Overexpression/silencing Cth promoted/inhibited the ERK1/2 pathway, respectively, which in turn affected efferocytosis and mediated intestinal barrier recovery. In addition, we found that the levels of Cth and macrophage efferocytosis were positively correlated with the recovery of intestinal function in clinical patients. CONCLUSION: Cth can activate the ERK1/2 signalling pathway, induce macrophage efferocytosis, and thus promote intestinal barrier repair. Video Abstract.

Metformin modulates mitochondrial autophagy in renal tubular epithelial injury induced by high glucose via the Keap1/Nrf2 pathway.

The current study aimed to explore the role and underpinning molecular mechanisms of metformin in renal cellular injury induced by high glucose levels. Male C57BL/KsJ (db/db) and (db/m +) mice were utilized in this study. The experimental group was administered 1 mg/mL of metformin through drinking water. Renal tissues were harvested for hematoxylin and eosin (HE) staining, superoxide dismutase (SOD) activity detection, biochemical indices analysis, Western blotting, and qRT-PCR. HK-2 cells were utilized for Nrf2 siRNA transfection and to establish a high level of glucose-induced cell models. Metformin was administered at a concentration of 1 mmol/L in the experimental group. Cellular viability was assessed using CCK-8, whereas acridine orange (AO) staining and LC3-mitotracker co-localization staining were employed to evaluate autophagy. The expression of Nrf2, P21, LC3, PTEN-induced putative kinase 1 (PINK1), translocase of outer mitochondrial membrane 20 (TOMM20), and Kelch-like ECH-associated protein 1 (Keap1) were determined through Western blotting and qRT-PCR. Metformin mitigated renal tissue inflammatory damage in diabetic mice, as indicated by upregulated expression of Nrf2, PINK1, LC3, and TOMM20, and downregulated expression of Keap1 and P21. High level of glucose treatment in HK-2 cells resulted in decreased autophagy, and reduced expression of Nrf2, PINK1, LC3, and TOMM20 alongside elevated the expression of Keap1 and P21. Notably, metformin treatment partially counteracted these effects. Nrf2 knockdown intensified these phenomena in the high level of glucose-induced model. Protein-protein interaction network analysis indicated that Nrf2 could regulate the majority autophagy-related proteins via Keap1. Metformin modulates mitochondrial autophagy in high glucose-induced renal tubular epithelial senescence via the Keap1/Nrf2 pathway.

Recent advances in muscle food safety evaluation: Hyperspectral imaging analyses and applications.

As there is growing interest in process control for quality and safety in the meat industry, by integrating spectroscopy and imaging technologies into one system, hyperspectral imaging, or chemical or spectroscopic imaging has become an alternative analytical technique that can provide the spatial distribution of spectrum for fast and nondestructive detection of meat safety. This review addresses the configuration of the hyperspectral imaging system and safety indicators of muscle foods involving biological, chemical, and physical attributes and other associated hazards or poisons, which could cause safety problems. The emphasis focuses on applications of hyperspectral imaging techniques in the safety evaluation of muscle foods, including pork, beef, lamb, chicken, fish and other meat products. Although HSI can provide the spatial distribution of spectrum, characterized by overtones and combinations of the C-H, N-H, and O-H groups using different combinations of a light source, imaging spectrograph and camera, there still needs improvement to overcome the disadvantages of HSI technology for further applications at the industrial level.

Analysis and detection using novel terahertz spectroscopy technique in dietary carbohydrate-related research: Principles and application advances.

As one of the main functional substances, carbohydrates account for a large proportion of the human diet. Conventional analysis and detection methods of dietary carbohydrates and related products are destructive, time-consuming, and labor-intensive. In order to improve the efficiency of measurement and ensure food nutrition and consumer health, rapid and nondestructive quality evaluation techniques are needed. In recent years, terahertz (THz) spectroscopy, as a novel detection technology with dual characteristics of microwave and infrared, has shown great potential in dietary carbohydrate analysis. The current review aims to provide an up-to-date overview of research advances in using the THz spectroscopy technique in analysis and detection applications related to dietary carbohydrates. In the review, the principles of the THz spectroscopy technique are introduced. Advances in THz spectroscopy for quantitative and qualitative analysis and detection in dietary carbohydrate-related research studies from 2013 to 2022 are discussed, which include analysis of carbohydrate concentrations in liquid and powdery foods, detection of foreign body and chemical residues in carbohydrate food products, authentication of natural carbohydrate produce, monitoring of the fermentation process in carbohydrate food production and examination of crystallinity in carbohydrate polymers. In addition, applications in dietary carbohydrate-related detection research using other spectroscopic techniques are also briefed for comparison, and future development trends of THz spectroscopy in this field are finally highlighted.