Characterization of the ribosomal RNA methylase gene erm(A) and its promoter mutation in Campylobacter coli from chicken cecum.

Macrolide antibiotics are commonly used to treat campylobacteriosis in both clinical settings and animal husbandry. The emergence of macrolide-resistant Campylobacter poses public health risks. In this study, six Campylobacter coli strains carrying erm(A) gene were identified from chicken cecum samples, and the functionality and genetic environment of erm(A) were analyzed.

Contact Printing Based on Meniscus Vibration.

Utilizing the residual droplet produced from liquid bridge breakup for microdroplet deposition serves as an important supplementary method to conventional printing techniques. However, this approach typically relies on mechanical motion to form and break the liquid bridge between the liquid donor and acceptor surfaces, resulting in a relatively complex process and low printing efficiency (typically limited to several Hertz). Here, we propose a novel contact printing method based on the meniscus vibration (MVCP).

Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies.

Black carp (Mylopharyngodon piceus) is one of the "four famous domestic fishes" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies.

Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.

DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads.

Giraffe: A tool for comprehensive processing and visualization of multiple long-read sequencing data.

Third-generation sequencing techniques have become increasingly popular due to their capacity to produce long, high-quality reads. Effective comparative analysis across various samples and sequencing platforms is essential for understanding biological mechanisms and establishing benchmark baselines. However, existing tools for long-read sequencing predominantly focus on quality control (QC) and processing for individual samples, complicating the comparison of multiple datasets.

Dendritic polylysine co-delivery of paclitaxel and siAXL enhances the sensitivity of triple-negative breast cancer chemotherapy.

Drug resistance is common in triple-negative breast cancer (TNBC) therapy. To identify a method to overcome chemotherapy resistance in TNBC cells, an siRNA targeting the AXL gene (siAXL), which can overcome drug resistance, was used in this study. A nanodelivery system was constructed to co-deliver siAXL and paclitaxel (PTX).

Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.

Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping.

Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing.

Nanopore sequencing technologies have enabled the direct detection of base modifications in DNA or RNA molecules. Despite these advancements, the tools for visualizing electrical current, essential for analyzing base modifications, are often lacking in clarity and compatibility with diverse nanopore pipelines. Here, we present Nanopore Current Events Magnifier (nanoCEM, https://github.

Diesel exhaust particulate matter induces GC-1 spg cells oxidative stress by KEAP1-NRF2 pathway and inhibition of ATP5α1 S-sulfhydration.

Diesel exhaust particle (DEP) exposure induces a variety of toxicological effects through oxidative stress and inflammation responses. This research investigated the mechanisms underlying DEP-induced GC-1spg cells oxidative stress by examining ROS accumulation, antioxidant defense systems activation, mitochondrial dysfunction, and the Nrf2/Keap1/HO-1 pathway response. Subsequently, we further evaluated the ATP levels, ATP5α synthase activity and ATP5α synthase S-sulfhydrated modification in DEP-exposed GC-1 spg cells.

A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection.

Moritella viscosa (M. viscosa) and sea lice (Lepeophtheirus salmonis) are severe pathogens that primarily infect the skin of Atlantic salmon (Salmo salar), which cause significant economic losses in the farming industry. However, the pathogenesis and molecular mechanisms underlying the host's immune defence at the post-transcriptional level remain unclear.

Integrating metagenomic and isolation strategies revealed high contamination of pathogenies and resistome in market shrimps.

This study employs a comprehensive approach combining metagenomic analysis and bacterial isolation to elucidate the microbial composition, antibiotic resistance genes (ARGs), and virulence factors (VFGs) present in shrimps from market and supermarket. Metagenomic analysis of shrimps revealed a dominance of Proteobacteria and Bacteroidetes with Firmicutes notably enriched in some samples. On the other hand, the dominant bacteria isolated included Citrobacter portucalensis, Escherichia coli, Salmonella enterica, Vibrio species and Klebsiella pneumonaie.

Chromosome level genome assembly and transcriptome analysis of E11 cells infected by tilapia lake virus.

The E11 cell line, derived from striped snakehead fish (Channa striata), possesses a distinctive feature: it is persistently infected with a C-type retrovirus. Notably, it exhibits high permissiveness to piscine nodavirus and the emerging tilapia lake virus (TiLV). Despite its popularity in TiLV research, the absence of genome assembly for the E11 cell line and Channa striata has constrained research on host-virus interactions.

Sulforaphane inhibits the growth of prostate cancer by regulating the microRNA-3919/DJ-1 axis.

Background: Prostate cancer (PCa) is the second most common solid cancer among men worldwide and the fifth leading cause of cancer-related deaths in men. Sulforaphane (SFN), an isothiocyanate compound, has been shown to exert inhibitory effects on a variety of cancers. However, the biological function of SFN in PCa has not been fully elucidated.

Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing.

The escalating prevalence of multidrug-resistant (MDR) bacteria pose a significant public health threat. Understanding the genomic features and deciphering the antibiotic resistance profiles of these pathogens is crucial for development of effective surveillance and treatment strategies. In this study, we employed the R10.

Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications.

Modifications on viral RNAs (vRNAs), either genomic RNAs or RNA transcripts, have complex effects on the viral life cycle and cellular responses to viral infection. The advent of Oxford Nanopore Technologies Direct RNA Sequencing provides a new strategy for studying RNA modifications. To this end, multiple computational tools have been developed, but a systemic evaluation of their performance in mapping vRNA modifications is lacking.

Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing.

Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells.

Nanopore sequencing identifies differentially methylated genes in the central nervous system in experimental autoimmune encephalomyelitis.

Multiple Sclerosis (MS) is a chronic autoimmune-mediated demyelinating disease of the central nervous system (CNS) that might be triggered by aberrant epigenetic changes in the genome. DNA methylation is the most studied epigenetic mechanism that participates in MS pathogenesis. However, the overall methylation level in the CNS of MS patients remains elusive.

Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping.

Motivation: Primer design is a routine practice for modern molecular biology labs. Bioinformatics tools like primer3 and primer-blast have standardized the primer design for a specific region. However, large-scale primer design, especially for genome-wide screening, is still a labor-intensive job for most wet-lab researchers using these pipelines.

Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing.

Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies (ONT) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.

Transgenic IDH2 and IDH2 zebrafish models recapitulated features of human acute myeloid leukemia.

Isocitrate dehydrogenase 2 (IDH2) mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia (CN-AML) but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2 and IDH2 AML and reported their pathologic, functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co-expressing FLT3 and IDH2 mutations showed accentuation of myelopoiesis.

Insect-Specific Chimeric Viruses Potentiated Antiviral Responses and Inhibited Pathogenic Alphavirus Growth in Mosquito Cells.

Most alphaviruses are transmitted by mosquito vectors and infect a wide range of vertebrate hosts, with a few exceptions. Eilat virus (EILV) in this genus is characterized by a host range restricted to mosquitoes. Its chimeric viruses have been developed as safe and effective vaccine candidates and diagnostic tools.

Integrated Bioinformatics-Based Identification of Ferroptosis-Related Genes in Carotid Atherosclerosis.

Background: Ferroptosis, a type of cell death caused by phospholipid peroxidation, has lately been linked to the onset and development of numerous illnesses. Numerous investigations have demonstrated the close relationship between lipid peroxidation and carotid atherosclerosis. In order to get new knowledge for targeted therapy, bioinformatics analysis was employed in this study to discover the probable ferroptosis-related genes of carotid atherosclerosis.

Flurochloridone induced abnormal spermatogenesis by damaging testicular Sertoli cells in mice.

Background: Flurochloridone (FLC), a selective herbicide used on a global scale, has been reported to have male reproductive toxicity whose evidence is limited, but its mechanism remains unclear. The present study was conducted to systematically explore the male reproductive toxicity of FLC, including sperm quality, spermatogenesis, toxicity targets, and potential mechanisms.

Methods: Male C57BL/6 mice aged 6-7 weeks received gavage administration of FLC (365/730 mg/kg/day) for 28 consecutive days.