Chromosome-level Haploid Assembly of Cannabis sativa L. cv. Pink Pepper.

As molecular research on hemp (Cannabis sativa L.) continues to advance, there is a growing need for the accumulation of more diverse genome data and more accurate genome assemblies. In this study, we report the three-way assembly data of a cannabidiol (CBD)-rich cannabis variety, 'Pink Pepper' cultivar using sequencing technology: PacBio Single Molecule Real-Time (SMRT) technology, Illumina sequencing technology, and Oxford Nanopore Technology (ONT).

Exploring Gene Expression and Alternative Splicing in Duck Embryonic Myoblasts via Full-Length Transcriptome Sequencing.

The duck industry is vital for supplying high-quality protein, making research into the development of duck skeletal muscle critical for improving meat and egg production. In this study, we leveraged Oxford Nanopore Technologies (ONT) sequencing to perform full-length transcriptome sequencing of myoblasts harvested from the leg muscles of duck embryos at embryonic day 13 (E13), specifically examining both the proliferative (GM) and differentiation (DM) phases. Our analysis identified a total of 5797 novel transcripts along with 2332 long non-coding RNAs (lncRNAs), revealing substantial changes in gene expression linked to muscle development.

Nanopore Data-Driven T2T Genome Assemblies of Strains.

is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent strains using the Oxford Nanopore Technologies (ONT, R10.4.

[Coconstruire autrement avec des personnes aînées grâce à la science-fiction: nouveaux regards sur la recherche en robotique d'assistance sociale].

Cette note de recherche vise à présenter comment la science-fiction fut utilisée dans un projet de recherche pour coconstruire une vision commune de la robotique sociale favorisant la participation sociale des personnes aînées. Une recherche-action a été réalisée à l'aide de deux forums d'informateurs-clés regroupant des personnes aînées animés à partir d'extraits d'œuvres cinématographiques de science-fiction dans le but de stimuler leur réflexion. Une analyse de contenu thématique de ces forums a permis de mettre en évidence la contribution de l'usage de la science-fiction dans le cadre de cette démarche de recherche.

Rapid whole genome characterization of antimicrobial-resistant pathogens using long-read sequencing to identify potential healthcare transmission.

Objective: Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions.

Third generation sequencing transforming plant genome research: Current trends and challenges.

In recent years, third-generation sequencing (TGS) technologies have transformed genomics and transcriptomics research, providing novel opportunities for significant discoveries. The long-read sequencing platforms, with their unique advantages over next-generation sequencing (NGS), including a definitive protocol, reduced operational time, and real-time sequencing, possess the potential to transform plant genomics. TGS optimizes and enhances the efficiency of data analysis by removing the necessity for time-consuming assembly tools.

Comparison of direct RNA sequencing of Orthoavulavirus javaense using two different chemistries on the MinION platform.

Rapidly identifying and sequencing viral pathogens in poultry flocks can substantially reduce economic loss especially during disease outbreaks. Current next generation sequencing technologies require multi-step laboratory-intensive workflows to generate sequence data which precludes field adaptation. In this study, we hypothesized that direct RNA sequencing (DRS) using an Oxford Nanopore Technology (ONT) MinION device would enable sequencing of the full-length viral RNA genome of Orthoavulavirus javaense (OAVJ), the causative of Newcastle disease, a major poultry challenge.

Global Health and Peace: The Elusive Path with a Focus on Palestine, Ukraine, and Venezuela.

The interrelationality of health and peace is complex, multifactorial, and imbued with political and economic challenges. Peace and health outcomes reflect shared fundamental values related to the achievement of a balanced holistic condition on the individual and collective level. This causal relationship between social inequity and health requires special attention be paid to the impact of political instability and structural violence on undermining health systems in conflict zones.

Development and Comprehensive Evaluation of Culture-Independent, Long Amplicon-Based Targeted Next-Generation Sequencing Methods for Predicting Antimicrobial Resistance in Tuberculosis.

The great variety of antimicrobial resistance (AMR) profiles among tuberculosis (TB) patients necessitates a comprehensive detection method. This study developed culture-independent, long amplicon-based targeted next-generation sequencing (tNGS) methods for predicting AMR across 16 drugs within the complex (MTBC). Multiplex PCR amplification was employed to enrich 20 gene regions, with sequencing performed on either the Oxford Nanopore Technologies (ONT) or Illumina platforms.

Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus.

Introduction: Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.

Organelle genome assembly, annotation, and comparative analyses of two keystone species for wetlands worldwide.

is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving species evolutionary relationships.

The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease.

Objective: Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) long-read sequencing. This study aims to determine if ONT long-read sequencing can detect a second variant in other unresolved early-onset Parkinson's disease (EOPD) cases with 1 heterozygous PRKN or PINK1 variant.

Plasma-Based Comprehensive Genomic Profiling DNA Assays for Non-Small Cell Lung Cancer: A Health Technology Assessment.

Background: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, accounting for about 85% of all lung cancer cases. While some cases of NSCLC with actionable genomic alterations in the tumour cells may respond to standard therapies, they often show greater improvement with targeted therapies. The current standard of care in Ontario involves testing for actionable genomic alterations using both DNA and RNA panels via tissue testing alone.

Single-Exposure, Dual-Energy Subtraction Flat Panel X-Ray Detectors: A Health Technology Assessment.

Background: In medicine, x-rays are used to generate images of tissues and structures inside the body. X-rays are emitted by a source device and, after passing through the body, strike a detector, which forms an image of the tissues and structures the x-rays passed through. Dual-energy subtraction (DES) x-ray systems use radiation of different energy spectra (energy levels) and the principle of differential absorption characteristics of bone and soft tissue to produce separate bone and soft tissue x-ray images, in addition to a conventional x-ray image.

[Foot and ankle pathologies: how to prescribe the right imaging].

Musculoskeletal diseases of the foot and ankle are common reasons for primary care consultations. The purpose of this article, which focuses on the seven most common foot and ankle pathologies seen in general practice, is to help general practitioners perform an initial radiological assessment that allows for a correct diagnosis and can then be used by the specialist without the need for repeat imaging. This approach optimizes collaboration between the general practitioner and the specialist, reduces costs, and avoids unnecessary patient radiation.

[Review of common shoulder and elbow pathologies in athletes].

Sport participation in Switzerland is steadily growing, with 8% sustaining injuries while practicing. Most popular sports include hiking, cycling, swimming, alpine skiing, and fitness. Thirty percent of shoulder injuries in urban areas are sport-related, mainly from football, cycling, and alpine skiing.

[Removal of osteosynthesis material : a surgery not to be underestimated].

Hardware removal is one of the most commonly performed surgeries in orthopedic practice. It has a wide range of indications and is not limited to simple discomfort related to the hardware or pain. Contrary to popular belief, it is not always a simple surgery, free of complications.

[Septic pseudarthrosis of the long bones].

Septic pseudarthrosis of long bones presents a diagnostic challenge, both in recognizing the infection as the cause of nonunion and in achieving complete healing of both the infection and the bone. A multidisciplinary approach optimizes the diagnosis, surgical management, and antibiotic treatment. The objectif is to present the approaches for the diagnosis and treatment of this condition.

[When should a gluteus medius tendon rupture be operated on ?].

The gluteus medius allows hip abduction and stabilization of the pelvis when walking. A rupture of the gluteus medius tendon is associated with lateral hip pain, weakness, a positive Trendelenburg sign, and a limp. Diagnosis is confirmed by ultrasound or MRI.

[Concept of coronal alignment in total knee arthroplasty].

Total knee arthroplasty (TKA) is one of the most performed orthopedic surgeries worldwide. For many years, TKA implants were positioned according to a systematic approach known as mechanical alignment, which prioritized implant survival over the restoration of a more physiological knee. A high dissatisfaction rate of 20% after knee prosthesis has led to a rethinking of coronal alignment and a move towards a more personalized approach.

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.

Background: Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity.

Patterns of genomic instability in > 2000 patients with ovarian cancer across six clinical trials evaluating olaparib.

Background: The introduction of poly(ADP-ribose) polymerase (PARP) inhibitors represented a paradigm shift in the treatment of ovarian cancer. Genomic data from patients with high-grade ovarian cancer in six phase II/III trials involving the PARP inhibitor olaparib were analyzed to better understand patterns and potential causes of genomic instability.

Patients And Methods: Homologous recombination deficiency (HRD) was assessed in 2147 tumor samples from SOLO1, PAOLA-1, Study 19, SOLO2, OPINION, and LIGHT using next-generation sequencing technology.

A nearly telomere-to-telomere diploid genome assembly of Firmiana kwangsiensis, a threatened species in China.

Firmiana kwangsiensis is a tree species of high ornamental value. The species is critically endangered in the wild, and is listed as a first-class national protected wild plant in China, and a Plant Species with Extremely Small Populations in need of urgent protection. We have assembled a chromosome-scale, haplotype-resolved genome for F.

Telomere-to-telomere gapless genome assembly of the giant grouper (Epinephelus lanceolatus).

The giant grouper (Epinephelus lanceolatus) is a large coral reef fish distributed in the Indian Ocean and the Pacific Ocean. With a high market value, this species can grow up to approximately 2.7 meters in length and weigh 440 kilograms.

Saliva microbiome profiling by full-gene 16S rRNA Oxford Nanopore Technology versus Illumina MiSeq sequencing.

Molecular characterization of the oral microbiome is a crucial first step in experiments which aim to understand the complex dynamics of the oral microbiome or the interplay with host health and disease. Third-generation Oxford Nanopore Technology (ONT) offers advanced long-read sequencing capabilities, which hold promise for improved molecular characterization by distinguishing closely related microbial species within oral ecosystems in health and disease states. However, the performance of ONT sequencing of oral samples requires validation, and the consistency of this approach across different analytical and sampling conditions is not well understood.