Search Results (630)

Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance. Full article

Introduction: Scattering of kernels due to angular dehiscence is a key bottleneck in mechanized harvesting of oilseed rape. Materials and Methods: In this study, a dual-track “genotype–phenotype” screening strategy was established by innovatively integrating high-throughput KASP molecular marker technology and a standardized random collision phenotyping system for the complex quantitative trait of angular resistance. Results: Through the systematic evaluation of 634 oilseed rape hybrid progenies, it was found that the KASP marker S12.68, targeting the cleavage resistance locus (BnSHP1) on chromosome C9, achieved a 73.34% introgression rate (465/634), which was significantly higher than the traditional breeding efficiency (<40%). Phenotypic characterization screened seven excellent resources with cracking resistance index (SRI) > 0.6, of which four reached the high resistance standard (SRI > 0.8), including the core materials NR21/KL01 (SRI = 1.0) and YuYou342/KL01 (SRI = 0.97). Six breeding intermediate materials (44.7–48.7% oil content, mycosphaerella resistance MR grade or above) were created, combining high resistance to chipping and excellent agronomic traits. For the first time, it was found that local germplasm YuYou342 (non-KL01-derived line) was purely susceptible at the S12.68 locus (SRI = 0.86), but its angiosperm vascular bundles density was significantly increased by 37% compared with that of the susceptible material 0911 (p < 0.01); and the material 187308 (SRI = 0.78), although purely susceptible at S12.68, had a 2.8-fold downregulation in expression of the angiosperm-related gene, BnIND1, and a 2.8-fold downregulation of expression of the angiosperm-related gene, BnIND1. expression was significantly downregulated 2.8-fold (q < 0.05), indicating the existence of a novel resistance mechanism independent of the primary effector locus. Conclusions: The results of this research provide an efficient technical platform and breakthrough germplasm resources for oilseed rape crack angle resistance breeding, which is of great practical significance for promoting the whole mechanized production. Full article

Background: Many patients harbor minimal residual disease (MRD)—small clusters of residual tumor cells that survive therapy and evade conventional detection but drive recurrence. Although advances in molecular and computational methods have improved circulating tumor DNA (ctDNA)-based MRD detection, these approaches face challenges: ctDNA shedding fluctuates widely across tumor types, disease stages, and histological features. Additionally, low levels of driver mutations originating from healthy tissues can create background noise, complicating the accurate identification of bona fide tumor-specific signals. These limitations underscore the need for refined technologies to further enhance MRD detection beyond DNA sequences in solid malignancies. Methods: Profiling circulating cell-free mRNA (cfmRNA), which is hyperactive in tumor and non-tumor microenvironments, could address these limitations to inform postoperative surveillance and treatment strategies. This study reported the development of OncoMRD BREAST, a customized, gene signature-informed cfmRNA assay for residual disease monitoring in breast cancer. OncoMRD BREAST introduces several advanced technologies that distinguish it from the existing ctDNA-MRD tests. It builds on the patient-derived gene signature for capturing tumor activities while introducing significant upgrades to its liquid biopsy transcriptomic profiling, digital scoring systems, and tracking capabilities. Results: The OncoMRD BREAST test processes inputs from multiple cutting-edge biomarkers—tumor and non-tumor microenvironment—to provide enhanced awareness of tumor activities in real time. By fusing data from these diverse intra- and inter-cellular networks, OncoMRD BREAST significantly improves the sensitivity and reliability of MRD detection and prognosis analysis, even under challenging and complex conditions. In a proof-of-concept real-world pilot trial, OncoMRD BREAST’s rapid quantification of potential tumor activity helped reduce the risk of incorrect treatment strategies, while advanced predictive analytics contributed to the overall benefits and improved outcomes of patients. Conclusions: By tailoring the assay to individual tumor profiles, we aimed to enhance early identification of residual disease and optimize therapeutic decision-making. OncoMRD BREAST is the world’s first and only gene signature-powered test for monitoring residual disease in solid tumors. Full article

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat to global rice productivity. Although hybrid rice breeding has significantly enhanced yields, persistent genetic vulnerabilities within restorer lines continue to compromise BB resistance. This study addresses this challenge by implementing functional marker-assisted selection (FMAS) to pyramid two broad-spectrum resistance (R) genes, Xa21 and Xa23, into the elite, yet BB-susceptible, restorer line K608R. To enable precise Xa23 genotyping, we developed a novel three-primer functional marker (FM) system (IB23/CB23/IR23). This system complements the established U1/I2 markers used for Xa21. This recombination-independent FMAS platform facilitates simultaneous, high-precision tracking of both homozygous and heterozygous alleles, thereby effectively circumventing the linkage drag limitations typical of conventional markers. Through six generations of marker-assisted backcrossing followed by intercrossing, we generated K608R2123 pyramided lines harboring both R genes in homozygous states, achieving a recurrent parent genome recovery rate of 96.93%, as determined by single nucleotide polymorphism (SNP) chip analysis. The pyramided lines exhibited enhanced resistance against six virulent Xoo pathogenic races while retaining parental yield performance across key agronomic traits. Our FMAS strategy overcomes the historical trade-off between broad-spectrum resistance and the preservation of elite phenotypes, with the developed lines exhibiting resistance coverage complementary to that of both introgressed R genes. This integrated approach provides breeders with a reliable molecular tool to accelerate the development of high-yielding, disease-resistant varieties, demonstrating significant potential for practical deployment in rice improvement programs. The K608R2123 germplasm represents a dual-purpose resource suitable for both commercial hybrid seed production and marker-assisted breeding programs, and it confers synergistic resistance against diverse Xoo races, thereby providing a pivotal breeding resource for sustainable BB control in epidemic regions. Full article

Streptococcus pyogenes is a bacterial pathogen known to be the causative agent in many different illnesses, with Group A Streptococcus (GAS) pharyngitis (strep throat), being one of the more prevalent. The spread and severity of GAS pharyngitis can grow exponentially if individuals are not taking the proper precautions. Wastewater surveillance has been used to test for numerous different pathogens that humans spread throughout a community and in this study, we utilized wastewater surveillance to monitor GAS pharyngitis in a small city. Over a year, 57 wastewater influent samples were tested for S. pyogenes and three commonly tested respiratory viruses (Respiratory Syncytial Virus (RSV), SARS-CoV-2, Influenza A). Three microbial indicators and population normalizers (CrAssphage, Pepper mild mottle virus (PMMoV), and Mycobacterium) were tested as well to compare and contrast each indicator’s value and range over time. Wastewater data was then compared to publicly available search term data as clinical data was not readily available. There was a high correlation between the collected molecular data and the publicly available search term data for Streptococcus pyogenes. Additionally, this study provided more information about the seasonal trend of S. pyogenes throughout the year through molecular data and allowed for the ability to track peak infection months in this small city. Overall, these results highlight the substantial benefits of using wastewater surveillance for the monitoring of GAS pharyngitis. This study also provides helpful insights into future studies about the prevalence of respiratory bacteria and their seasonal trends in wastewater, allowing for public health systems to provide mitigation strategies. Full article

Polymer brushes (PBs) are transformative surface-modifying nanostructures, yet their synthesis via controlled methods like copper-mediated surface-initiated atom-transfer radical polymerization (Cu⁰-SI-ATRP) faces reproducibility challenges due to a lack of understanding of parameter interdependencies. This study systematically evaluates the Cu⁰-SI-ATRP process for polyacrylamide brushes (PAM-PBs), aiming to clarify key parameters that influence the synthesis process. This evaluation followed a step-by-step characterization that tracked molecular changes through infrared spectroscopy (IR) and surface development by contact angle (CA) through two different mixing methods: ultrasonic mixing and process simplification (Method A) and following literature-based parameters (Method B). Both methods, consisting of surface activation, 3-aminopropyltriethoxysilane (APTES) deposition, bromoisobutyryl bromide (BiBB) anchoring, and polymerization, were analyzed by varying parameters like concentration, temperature, and time. Results showed ultrasonication during surface activation enhanced siloxane (1139→1115 cm⁻¹) and amine (1531 cm⁻¹) group availability while reducing APTES concentration to 1 Vol% without drying sufficed for BiBB anchoring. BiBB exhibited insensitivity to concentration but benefited from premixing, evidenced by sharp C–Br (~1170 cm⁻¹) and methyl (3000–2800 cm⁻¹) bands. Additionally, it was observed that PAM-PBs improved with Method A, which had reduced variance in polymer fingerprint regions compared to Method B. Adding to the above, CA measurements gave complementary step-by-step information along the modifications of the surface, revealing distinct wettability behaviors between bulk PAM and synthesized PAM-PBs (from 51° to 37°). As such, this work identifies key parameter influence (e.g., mixing, BiBB concentration), simplifies steps (drying omission, lower APTES concentration), and demonstrates a step-by-step, systematic parameter decoupling that reduces variability. In essence, this detailed parameter analysis addresses the PAM-PBs synthesis process with better reproducibility than the previously reported synthesis method and achieves the identification of characteristic behaviors across the step-by-step process without the imperative need for higher-cost characterizations. Full article

The global prevalence of hepatocellular carcinoma (HCC) is getting worse, leading to an urgent need for improved diagnostic and prognostic strategies. Liquid biopsy, which analyzes circulating tumor cells (CTCs), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and extracellular vesicles (EVs), has emerged as a minimally invasive and promising alternative to traditional tissue biopsy. These biomarkers can be detected using sensitive molecular techniques such as digital PCR, quantitative PCR, methylation-specific assays, immunoaffinity-based CTC isolation, nanoparticle tracking analysis, ELISA, next-generation sequencing, whole-genome sequencing, and whole-exome sequencing. Despite several advantages, liquid biopsy still has challenges like sensitivity, cost-effectiveness, and clinical accessibility. Reports highlight the significance of multi-analyte liquid biopsy panels in enhancing diagnostic sensitivity and specificity. This approach offers a more comprehensive molecular profile of HCC, early detection, and tracking therapeutic treatment, particularly in those cases where single-analyte assays and imaging fail. The technological advancement in the isolation and analysis of CTC, cell-free nucleic acids, and EVs is increasing our understanding of extracting genetic information from HCC tumors and discovering mechanisms of therapeutic resistance. Furthermore, crucial information on tumor-specific transcriptomic and genomic changes can be obtained using cfRNA and cfDNA released into the peripheral blood by tumor cells. This review provides an overview of current liquid biopsy strategies in HCC and their use for early detection, prognosis, and monitoring the effectiveness of HCC therapy. Full article

This review aims to provide a comprehensive framework for implementing precision sports medicine, integrating genetics, pharmacogenomics, digital health solutions, and multi-omics data. Literature review was conducted using MEDLINE, EMBASE, Web of Science, and Cochrane Library databases (January 2018–April 2024), focusing on precision medicine applications in sports medicine, utilizing key terms including “precision medicine”, “sports medicine”, “genetics”, and “multi-omics”, with forward and backward citation tracking. The review identified key gene variants affecting athletic performance: endurance (AMPD1, PPARGC1A), power (ACTN3, NOS3), strength (PPARG), and injury susceptibility (COL5A1, MMP3), while also examining inherited conditions like cardiomyopathies (MYH7, MYBPC3). Pharmacogenomic guidelines were established for optimizing common sports medications, including NSAIDs (CYP2C9), opioids (CYP2D6), and cardiovascular drugs (SLCO1B1, CYP2C19). Digital health technologies, including wearables and predictive analytics, showed potential for enhanced athlete monitoring and injury prevention, while multi-omics approaches integrated various molecular data to understand exercise capacity and injury predisposition, enabling personalized assessments, training regimens, and therapeutic interventions based on individual biomolecular profiles. This review provides sports medicine professionals with a framework to deliver personalized care tailored to each athlete’s unique profile, promising optimized performance, reduced injury risks, and improved recovery outcomes. Full article

Background: Pancreatic adenocarcinoma (PAAD) is an aggressive subtype of pancreatic cancer that is estimated to have a 5-year overall survival rate of only 13%. Most patients present with advanced disease with unpredictable outcomes. The identification of prognostic biomarkers is important to accurately stratify these patients. Methods: We investigated the molecular and survival-related role of ENHO in PAAD by analyzing TGCA mRNA and miRNA data. Survival analysis was conducted using TIMER2.0, “survival”, and “survminer”. Gene set enrichment analysis was conducted using enrichr, while miRNA-mRNA interactions were identified using “multiMiR”. Immune infiltration was assessed using CIBERSORT ABS and ImmuCellAI. Results: We observed that ENHO was strikingly downregulated in PAAD tissues (p = 3.68 × 10⁻⁶⁸), and patients with higher ENHO levels enjoyed significantly better overall survival (HR = 0.597; 95% CI: 0.419–0.852; p < 0.01). Pathway analysis showed that genes co-upregulated with ENHO were enriched for insulin secretion and ion channel activity, whereas those co-downregulated were related to epithelial–mesenchymal transition and extracellular matrix remodeling. Higher ENHO also tracked with increased CD8⁺ T-cell infiltration and correlated positively with PDCD1 and LAG3 but negatively with B7-H3, CD70, and NT5E. Conclusions: Our results point to a protective role for ENHO in pancreatic adenocarcinoma. Full article

This study provides new insight into the mechanisms governing solid state dewetting (SSD) in SiGe alloys and underscores the potential of this bottom-up technique for fabricating self-organized defect-free nanostructures for CMOS-compatible photonic and nanoimprint applications. In particular, we investigate the SSD of Si_1−xGe_x thin films grown by molecular beam epitaxy on silicon-on-insulator (SOI) substrates, focusing on and clarifying the interplay of dewetting dynamics, strain elastic relaxation, and SiGe/SOI interdiffusion. Samples were annealed at 820 °C, and their morphological and compositional evolution was tracked using atomic force microscopy (AFM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and Raman spectroscopy, considering different annealing time steps. A sequential process typical of the SiGe alloy has been identified, involving void nucleation, short finger formation, and ruptures of the fingers to form nanoislands. XRD and Raman data reveal strain relaxation and significant Si-Ge interdiffusion over time, with the Ge content decreasing from 29% to 20% due to mixing with the underlying SOI layer. EDX mapping confirms a Ge concentration gradient within the islands, with higher Ge content near the top. Full article

African swine fever virus (ASFV), the causative agent of African swine fever (ASF), poses a catastrophic threat to global swine industries through its capacity for immune subversion and rapid evolution. Multigene family genes (MGFs)-encoded proteins serve as molecular hubs governing viral evolution, immune evasion, cell tropism, and disease pathogenesis. This review synthesizes structural and functional evidence demonstrating that MGFs-encoded proteins suppress both interferon signaling and inflammasome activation, while their genomic plasticity in variable terminal regions drives strain diversification and adaptation. Translationally, targeted deletion of immunomodulatory MGFs enables the rational design of live attenuated vaccines that improve protective efficacy while minimizing residual virulence. Moreover, hypervariable MGFs provide strain-specific signatures for PCR-based diagnostics and phylogeographic tracking, directly addressing outbreak surveillance challenges. By unifying virology with translational innovation, this review establishes MGFs as priority targets for next-generation ASF countermeasures. Full article

Vertebrate molecular genetic research methods typically employ single genetic loci (monolocus markers) and those involving a variable number of loci (multilocus markers). The former often employ microsatellites that ensure accuracy in establishing inbreeding, tracking pan-generational dynamics of genetic parameters, assessing genetic purity, and facilitating genotype/phenotype correlations. They also enable the determination and identification of unique alleles by studying and managing marker-assisted breeding regimes to control the artificial selection of agriculturally important traits. Microsatellites consist of 2–6 nucleotides that repeat numerous times and are widely distributed throughout genomes. Their main advantages lie in their ease of use for PCR amplification, their known genome localization, and their incredible polymorphism (variability) levels. Robust lab-based molecular technologies are supplemented by high-quality statistics and bioinformatics and have been widely employed, especially in those instances when more costly, high throughput techniques are not available. Here, we consider that human and livestock microsatellite studies have been a “roadmap” for the genetics, breeding, and conservation of wildlife and rare animal breeds. In this context, we examine humans and other primates, cattle and other artiodactyls, chickens and other birds, carnivores (cats and dogs), elephants, reptiles, amphibians, and fish. Studies originally designed for mass animal production have thus been adapted to save less abundant species, highlighting the need for molecular scientists to consider where research may be applied in different disciplines. Full article

Amphiphilic diblock copolymers comprising polyethylene glycol (PEG) and 1-vinyl imidazole (VIM) were synthesized using reversible addition–fragmentation chain transfer (RAFT) polymerization. The study focused on the synthesis of well-defined nanostructures with tunable composition and their functional modification for biomedical applications. The successful polymerization of PEG-b-PVIM diblock copolymers was confirmed via ¹H NMR spectroscopy, and their molecular weights were analyzed using gel permeation chromatography (GPC). The copolymers exhibited pH-responsive behavior, with effective pK values of approximately 4.2. To facilitate radiolabeling and in vivo tracking, a post-polymerization modification enabled the conjugation of a 1,4,7-Triazacyclononane-1,4,7-triacetic acid (NOTA) chelator via aminolysis. The final conjugates were purified and characterized, confirming successful functionalization. These findings highlight the potential of PEG_x-b-PVIM_y diblock copolymers for biomedical applications. Full article

(1) Background: Generation IV supercritical water-cooled reactors (SCWRs), including small modular reactor (SCW-SMR) variants, are pivotal in nuclear technology. Operating at 300–500 °C and 25 MPa, these reactors require detailed understanding of radiation chemistry and transient species to optimize water chemistry, reduce corrosion, and enhance safety. Boron, widely used as a neutron absorber, plays a significant role in reactor performance and safety. This study focuses on the yields of radiolytic species in subcritical and supercritical water exposed to ⁴He and ⁷Li recoil ions from the ¹⁰B(n,α)⁷Li fission reaction in SCWR/SCW-SMR environments. (2) Methods: We use Monte Carlo track chemistry simulations to calculate yields (G values) of primary radicals (e⁻_aq, H^•, and ^•OH) and molecular species (H₂ and H₂O₂) from water radiolysis by α-particles and Li³⁺ recoils across 1 picosecond to 0.1 millisecond timescales. (3) Results: Simulations show substantially lower radical yields, notably e⁻_aq and ^•OH, alongside higher molecular product yields compared to low linear energy transfer (LET) radiation, underscoring the high-LET nature of ¹⁰B(n,α)⁷Li recoil nuclei. Key changes include elevated G(^•OH) and G(H₂), and a decrease in G(H^•), primarily driven during the homogeneous chemical stage of radiolysis by the reaction H^• + H₂O → ^•OH + H₂. This reaction significantly contributes to H₂ production, potentially reducing the need for added hydrogen in coolant water to mitigate oxidizing species. In supercritical conditions, low G(H₂O₂) suggests that H₂O₂ is unlikely to be a major contributor to material oxidation. (4) Conclusions: The ¹⁰B(n,α)⁷Li reaction’s yield estimates could significantly impact coolant chemistry strategies in SCWRs and SCW-SMRs. Understanding radiolytic behavior in these conditions aids in refining reactor models and coolant chemistry to minimize corrosion and radiolytic damage. Future experiments are needed to validate these predictions. Full article

This study presents the development and validation of an elementary reaction pathway tracking algorithm based on reactive force field simulations, enabling the dynamic monitoring of cracking products at the 20,000-atom scale, the accurate identification of chain reaction pathways, and the comprehensive tracking of large carbon chain formation. The research demonstrates that the differences between methane and propylene cracking–polymerization reactions primarily stem from disparities in bond dissociation energies, radical stabilities, and molecular topologies, and the operation of molecular dynamics relies on LAMMPS 3 March 2020. The cracking pathway of methane is relatively straightforward, predominantly involving the homolytic cleavage of C–H bonds, followed by radical chain propagation leading to the formation of large carbonaceous species. In contrast, propylene, owing to its unsaturated structure and multiple reactive sites, exhibits more complex reaction networks and a wider diversity of products. Furthermore, the study elucidates the reaction pathways of intermediate species during methane and propylene cracking and investigates the effect of reaction temperature on carbon sheet development. In conclusion, the algorithm established in this work offers a detailed mechanistic insight into the gas-phase cracking of methane and propylene, providing a new theoretical basis for the optimization of gas-phase deposition processes and the rational design of carbon-based materials. Full article