Search Results (7,168)

Fruit flies that belong to the genus Zeugodacus (Diptera: Tephritidae) pose significant threats as invasive pests of agricultural crops in Asia and sub-Saharan Africa. The intensification of transboundary trade in fresh horticultural produce has increased the risk of introducing invasive species such as fruit flies, more so through the inadvertent transport of their immature developmental stages. Such immature stages of fruit flies belonging to the Tephritidae family are frequently intercepted at the international borders worldwide and are unable to be identified to the species level using morphological characteristics. Molecular identification using mitochondrial Cytochrome Oxidase I (COI) gene has proven to be quite useful, as they are not constrained by developmental stages, sex, or colour morphs of the pest species in question. Also, real-time PCR-based species-specific assays offer quicker turnaround time since they do not require any post-PCR procedures. This study evaluated the utility of a real-time PCR assay based on the COI gene region to identify Zeugodacus cucurbitae from other Tephritid species. The developed real-time PCR assay provides a swift and precise way of discriminating between these highly invasive pest species during an interception event for rapid decision making. High specificity, having no cross-reactions with closely related Tephritids, and sensitivity of the developed assay will be extremely useful in discriminating Z. cucurbitae from other closely related fruit fly species. Z. cucurbitae-specific real-time PCR developed in this study is appropriate for organizations that carry out routine diagnostics to facilitate fresh produce imports and exports. Our assay is fully optimized for rapid deployment at international borders, offering reliable detection of the target species regardless of developmental stage, sex, or geographic origins. Full article

Protecting threatened elasmobranch species despite limited data on their distribution and abundance is a critical challenge, particularly in the context of increasing human impacts on marine ecosystems. In the northeastern Atlantic, species such as the leafscale gulper shark, Portuguese dogfish, spurdog, and spotted ray are facing pressures from overfishing, bycatch, habitat degradation, and climate change. The OSPAR Commission has listed these species as threatened and/or declining and aims to protect them by reliably identifying suitable habitats and integrating these areas into Marine Protected Areas (MPAs). In this study, we present a spatial modelling framework using regression-based approaches to identify suitable habitats for these four species. Results show that suitable habitats of the spotted ray (25.8%) and spurdog (18.8%) are relatively well represented within existing MPAs, while those of the deep-water sharks are underrepresented (6.0% for leafscale gulper shark, and 6.8% for Portuguese dogfish). Our findings highlight the need for additional MPAs in deep-sea continental slope areas, particularly west and northwest of Scotland and Ireland. Such expansions would support OSPAR’s goal to protect 30% of its maritime area by 2030 and could benefit broader deep-sea biodiversity, including other vulnerable demersal species and benthic communities. Full article

Atriplex hortensis var. rubra (red orache, RO) is a halotolerant species rich in nutraceutical compounds, which makes it a valuable crop for human nutrition. This plant could also be exploited for phytoremediation of contaminated soil and wastewater, and for saline aquaponics. A root rot disease was observed on hydroponically grown RO plants, caused by Pythium deliense and Pythium Cluster B2a sp. Identification was based on morphology, molecular analysis (ITS and COI), and phylogenetic analysis. We assessed disease severity in plants grown in a growth chamber with nutrient solutions containing different NaCl concentrations (0, 7, and 14 g L⁻¹ NaCl). In vitro growth at different salinity levels and temperatures was also evaluated. Both Pythium species were pathogenic but showed different responses. Pythium deliense was significantly more virulent than Pythium Cluster B2a sp., causing a steady reduction in root dry weight (RDW) of 70% across all salinity levels. Pythium Cluster B2a sp. reduced RDW by 50% at 0 and 7 g L⁻¹ NaCl while no symptoms were observed at 14 g L⁻¹ NaCl. Pythium deliense grew best at 7 and 14 g L⁻¹ NaCl, while Pythium Cluster B2a sp. growth was reduced at 14 g L⁻¹ NaCl. Both pathogens had an optimum temperature of 30 °C. This is the first report of Pythium spp. causing root rot on RO grown hydroponically. The effective use of halophytic crops must consider pathogen occurrence and fitness in saline conditions. Full article

Fructose-1,6-bisphosphatase (FBP) is a crucial regulatory enzyme in sucrose synthesis and photosynthetic carbon assimilation, functioning through two distinct isoforms: cytosolic FBP (cyFBP) and chloroplastic FBP (cpFBP). However, the identification and functional characterization of FBP genes in Saccharum remains limited. In this study, we conducted a systematic identification and comparative genomics analyses of FBPs in three Saccharum species. We further examined their expression patterns across leaf developmental zones, spatiotemporal profiles, and responses to diurnal rhythms and hormonal treatments. Our analysis identified 95 FBP genes, including 44 cyFBPs and 51 cpFBPs. Comparative analyses revealed significant divergence in physicochemical properties, gene structures, and motif compositions between the two isoforms. Expression profiling indicated that both cyFBPs and cpFBPs were predominantly expressed in leaves, particularly in maturing and mature zones. During diurnal cycles, their expression peaked around the night–day transition, with cpFBPs exhibiting earlier peaks than cyFBPs. FBP genes in Saccharum spontaneum displayed greater diurnal sensitivity than those in Saccharum officinarum. Hormonal treatments further revealed significant regulatory divergence in FBP genes, both between isoforms and across species. Notably, cyFBP_2 and cpFBP_2 members consistently exhibited higher expression levels across all datasets, suggesting their pivotal roles in sugarcane physiology. These findings not only identify potential target genes for enhancing sucrose accumulation, but also highlight the breeding value of S. spontaneum and S. officinarum in sugarcane breeding. Full article

Ongoing changes in the distribution and abundance of several tick species of medical relevance in Canada have prompted the development of the eTick platform—an image-based crowd-sourcing public surveillance tool for Canada enabling rapid tick species identification by trained personnel, and public health guidance based on tick species and province of residence of the submitter. Considering that more than 100,000 images from over 73,500 identified records representing 25 tick species have been submitted to eTick since the public launch in 2018, a partial automation of the image processing workflow could save substantial human resources, especially as submission numbers have been steadily increasing since 2021. In this study, we evaluate an end-to-end artificial intelligence (AI) pipeline to support tick identification from eTick user-submitted images, characterized by heterogeneous quality and uncontrolled acquisition conditions. Our framework integrates (i) tick localization using a fine-tuned YOLOv7 object detection model, (ii) resolution enhancement of cropped images via super-resolution Generative Adversarial Networks (RealESRGAN and SwinIR), and (iii) image classification using deep convolutional (ResNet-50) and transformer-based (ViT) architectures across three datasets (12, 6, and 3 classes) of decreasing granularities in terms of taxonomic resolution, tick life stage, and specimen viewing angle. ViT consistently outperformed ResNet-50, especially in complex classification settings. The configuration yielding the best performance—relying on object detection without incorporating super-resolution—achieved a macro-averaged F1-score exceeding 86% in the 3-class model (Dermacentor sp., other species, bad images), with minimal critical misclassifications (0.7% of “other species” misclassified as Dermacentor). Given that Dermacentor ticks represent more than 60% of tick volume submitted on the eTick platform, the integration of a low granularity model in the processing workflow could save significant time while maintaining very high standards of identification accuracy. Our findings highlight the potential of combining modern AI methods to facilitate efficient and accurate tick image processing in community science platforms, while emphasizing the need to adapt model complexity and class resolution to task-specific constraints. Full article

In this study, a Z-scheme Ho₂InSbO₇/Ag₃PO₄ (HAO) heterojunction photocatalyst was successfully fabricated for the first time by ultrasound-assisted solvothermal method. The structural features, compositional components and morphological characteristics of the synthesized materials were thoroughly characterized by a series of techniques, including X-ray diffraction, Fourier transform infrared spectroscopy, Raman spectrum, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy. A comprehensive array of analytical techniques, including ultraviolet-visible diffuse reflectance absorption spectra, photoluminescence spectroscopy, time-resolved photoluminescence spectroscopy, photocurrent testing, electrochemical impedance spectroscopy, electron paramagnetic resonance, and ultraviolet photoelectron spectroscopy, was employed to systematically investigate the optical, chemical, and photoelectronic properties of the materials. Using oxytetracycline (OTC), a representative tetracycline antibiotic, as the target substrate, the photocatalytic activity of the HAO composite was assessed under visible light irradiation. Comparative analyses demonstrated that the photocatalytic degradation capability of the HAO composite surpassed those of its individual components. Notably, during the degradation process, the application of the HAO composite resulted in an impressive removal efficiency of 99.89% for OTC within a span of 95 min, along with a total organic carbon mineralization rate of 98.35%. This outstanding photocatalytic performance could be ascribed to the efficient Z-scheme electron-hole separation system occurring between Ho₂InSbO₇ and Ag₃PO₄. Moreover, the adaptability and stability of the HAO heterojunction were thoroughly validated. Through experiments involving the capture of reactive species and electron paramagnetic resonance analysis, the active species generated by HAO were identified as hydroxyl radicals (•OH), superoxide anions (•O₂⁻), and holes (h⁺). This identification provides valuable insights into the mechanisms and pathways associated with the photodegradation of OTC. In conclusion, this research not only elucidates the potential of HAO as an efficient Z-scheme heterojunction photocatalyst but also marks a significant contribution to the advancement of sustainable remediation strategies for OTC contamination. Full article

In this work, the structures of the isolated anion and anhydrous and monohydrated sodium salts of alizarin red S (ARS) have been theoretically investigated within the density functional theory framework (B3LYP/6-311++G** calculations). The combination of calculations with the scaled quantum mechanics force field (SQMFF) methodology has allowed the assignment of the experimental infrared spectrum of ARS in the solid phase and the determination of the corresponding force constants. The structural analysis also included the investigation of the NMR and UV-visible spectra of the compound in solution in light of the undertaken quantum chemical calculations, the obtained theoretical data being in good agreement with the corresponding experimental ones. The impact of the presence of the Na⁺ counterion and hydration water on the properties of the organic ARS⁻ fragment was evaluated. Atoms in molecules theory (AIM) analysis was also undertaken to obtain further details on the electronic structure of the investigated species, and the HOMO-LUMO gap was determined to evaluate their relative reactivity. Globally, the results obtained in this work extend the available information on alizarin red S and may also be used for the fast identification of the three studied species of the compound investigated (anhydrous and monohydrated sodium salts and isolated anion). Full article

Background/Objectives: In recent years, lipids have emerged as critical regulators of different disease processes, being involved in cancer pathogenesis, progression, and outcome. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) has significantly expanded the technology’s reach, enabling spatially resolved profiling of lipids directly from tissue, including formalin-fixed paraffin-embedded (FFPE) specimens. In this context, MALDI matrix selection is crucial for lipid extraction and ionization, influencing key aspects such as molecular coverage and sensitivity, especially in such specimens with already depleted lipid content. Thus, in this work, we aim to explore the feasibility of mapping lipid species in FFPE clinical samples with MALDI-MSI using 6-aza-2-thiothymine (ATT) as a matrix of choice. Methods: To do so, ATT performances were first compared to those two other matrices commonly used for lipidomic analyses, 2′,5′-dihydroxybenzoic acid (DHB) and Norharmane (NOR), on lipid standards. Results: As a proof-of-concept, we then assessed ATT’s performance for the MALDI-MSI analysis of lipids in FFPE brain sections, both in positive and negative ion modes, comparing results with those obtained from other commonly used dual-polarity matrices. In this context, ATT enabled the putative annotation of 98 lipids while maintaining a well-balanced detection of glycerophospholipids (60.2%) and sphingolipids (32.7%) in positive ion mode. It outperformed both DHB and NOR in the identification of glycolipids (3%) and fatty acids (4%). Additionally, ATT exceeded DHB in terms of total lipid count (62 vs. 21) and class diversity and demonstrated performance comparable to NOR in negative ion mode. Moreover, ATT was applied to a FFPE glioblastoma tissue microarray (TMA) evaluating the ability of this matrix to reveal biologically relevant lipid features capable of distinguishing normal brain tissue from glioblastoma regions. Conclusions: Altogether, the results presented in this work suggest that ATT is a suitable matrix for pathology imaging applications, even at higher lateral resolutions of 20 μm, not only for proteomic but also for lipidomic analysis. This could enable the use of the same matrix type for the analysis of both lipids and peptides on the same tissue section, offering a unique strategic advantage for multi-omics studies, while also supporting acquisition in both positive and negative ionization modes. Full article

Background: The COVID-19 pandemic has profoundly altered the clinical and microbiological landscape of respiratory tract infections (RTIs), potentially reshaping pathogen distribution and antimicrobial resistance (AMR) profiles across care settings. Objectives: The objective of this study was to assess temporal trends in respiratory bacterial pathogens, antimicrobial resistance, and polymicrobial infections across three pandemic phases—pre-COVID (2018–2019), COVID (2020–2022), and post-COVID (2022–2024)—in hospitalized and ambulatory patients. Methods: We retrospectively analyzed 1827 respiratory bacterial isolates (hospitalized patients, n = 1032; ambulatory patients, n = 795) collected at a tertiary care center in Northern Italy. Data were stratified by care setting, anatomical site, and pandemic phase. Species identification and susceptibility testing followed EUCAST guidelines. Statistical analysis included chi-square and Fisher’s exact tests. Results: In hospitalized patients, a significant increase in Pseudomonas aeruginosa (from 45.5% pre-COVID to 58.6% post-COVID, p < 0.0001) and Acinetobacter baumannii (from 1.2% to 11.1% during COVID, p < 0.0001) was observed, with 100% extensively drug-resistant (XDR) rates for A. baumannii during the pandemic. Conversely, Staphylococcus aureus significantly declined from 23.6% pre-COVID to 13.7% post-COVID (p = 0.0012). In ambulatory patients, polymicrobial infections peaked at 41.2% during COVID, frequently involving co-isolation of Candida spp. Notably, resistance to benzylpenicillin in Streptococcus pneumoniae reached 80% (4/5 isolates) in hospitalized patients during COVID, and carbapenem-resistant P. aeruginosa (CRPA) significantly increased post-pandemic in ambulatory patients (0% pre-COVID vs. 23.5% post-COVID, p = 0.0014). Conclusions: The pandemic markedly shifted respiratory pathogen dynamics and resistance profiles, with distinct trends observed in hospital and community settings. Persistent resistance phenotypes and frequent polymicrobial infections, particularly involving Candida spp. in outpatients, underscore the need for targeted surveillance and antimicrobial stewardship strategies. Full article

Acinetobacter baumannii is one of the most challenging nosocomial pathogens associated with a variety of hospital infections, such as ventilator-associated pneumonia, wound and urinary tract infections, meningitis, and sepsis, primarily in patients treated in critical care settings. Its classification as a high-priority pathogen is due to the emergence of multidrug-resistant strains in healthcare environments and its tendency to spread clonally. A. baumannii belongs to the Acinetobacter calcoaceticus–Acinetobacter baumannii (Acb) complex, a group of genotypically and phenotypically similar species. Differentiating between the species is important because of their distinct clinical significance. However, conventional phenotypic methods, both manual and automated, often fail to provide accurate species-level identification. This review aims to summarize current phenotypic and genotypic methods for the identification of species within the Acb complex, evaluating their strengths and limitations to offer guidance for their appropriate application in diagnostic settings and epidemiological investigations. Full article

Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to comprehensively identify SiLEA genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. Methods: Genome-wide identification of SiLEA genes was conducted, followed by phylogenetic reconstruction, cis-acting element analysis of promoters, synteny analysis, and expression profiling. Results: Ninety-four SiLEA genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of SiLEA genes with sorghum and rice orthologs than with Arabidopsis thaliana AtLEA genes. Synteny analysis indicated the LEA gene family expansion through tandem and segmental duplication. Promoter cis-element analysis linked SiLEA genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among SiLEA members, while RT-qPCR verified ABA-induced transcriptional regulation of SiLEA genes. Conclusions: This study identified 94 SiLEA genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated SiASR-2, SiASR-5, and SiASR-6 in both shoots and roots. Full article

Effective species identification is crucial for the conservation and management of marine mammals, particularly in regions such as the Mediterranean Sea, where several cetacean populations are endangered or vulnerable. In this study, we developed and validated a High-Resolution Melting (HRM) analysis protocol for the rapid, cost-effective, and reliable identification of the four representative marine cetacean species that occur in the Mediterranean Sea: the bottlenose dolphin (Tursiops truncatus), the striped dolphin (Stenella coeruleoalba), the sperm whale (Physeter macrocephalus), and the fin whale (Balaenoptera physalus). Species-specific primers targeting mitochondrial DNA regions (cytochrome b and D-loop) were designed to generate distinct melting profiles. The protocol was tested on both tissue and fecal samples, demonstrating high sensitivity, reproducibility, and discrimination power. The results confirmed the robustness of the method, with melting curve profiles clearly distinguishing the target species and achieving a success rate > 95% in identifying unknown samples. The use of HRM offers several advantages over traditional sequencing methods, including reduced cost, speed, portability, and suitability for degraded samples, such as those from the stranded individuals. This approach provides a valuable tool for non-invasive genetic surveys and real-time species monitoring, contributing to more effective conservation strategies for cetaceans and enforcement of regulations against illegal trade. Full article

Urban wildlife conservation is emerging as a critical component of sustainable city ecosystems. Rather than simply increasing tree abundance or species richness, conservation management should focus on key species. In this research, Xishan Forest Park in Beijing was chosen as a case study. Our aim was to identify keystone taxa critical for avian foraging and nesting during the breeding season. We performed a network analysis linking bird species, their diets, and nest plants. Dietary components were detected using DNA metabarcoding conducted with avian fecal samples. Nest plants were identified via transect surveys. Two indices of the network, degree and weighted mean degree, were calculated to evaluate the importance of the dietary and nest plant species. We identified 13 bird host species from 107 fecal samples and 14 bird species from 107 nest observations. Based on the degree indices, fruit trees Morus and Prunus were detected as key food sources, exhibiting both the highest degree (degree = 9, 9) and weighted mean degree (lnwMD = 5.21, 4.63). Robinia pseudoacacia provided predominant nesting sites, with a predominant degree of 7. A few taxa, such as Styphnolobium japonicum and Rhamnus parvifolia, served dual ecological significance as both essential food sources and nesting substrates. Scrublands, as a unique habitat type, provided nesting sites and food for small-bodied birds. Therefore, targeted management interventions are recommended to sustain or enhance these keystone resource species and to maintain the multi-layered vertical vegetation structure to preserve the diverse habitats of birds. Full article

We report a case of catheter-associated bloodstream infection caused by a putative novel species in the genus Erwinia, identified using whole-genome sequencing (WGS). A female adolescent receiving long-term home parenteral nutrition via a central venous catheter (CVC) presented with a fever. Gram-negative rods were isolated from two CVC-derived blood culture sets, while peripheral cultures remained negative. Conventional identification methods, including VITEK 2, Phoenix M50, MALDI-TOF MS, and 16S rRNA and rpoB gene sequencing, failed to achieve species-level identification. WGS was performed on the isolate using Illumina MiSeq. Genomic analysis revealed a genome size of 5.39 Mb with 56.8% GC content and high assembly completeness. The highest average nucleotide identity (ANI) was 90.3% with Pantoea coffeiphila, and ≤85% with known Erwinia species, suggesting that it represents a distinct taxon. Phylogenetic analyses placed the isolate within the Erwinia clade but separate from any known species. Antimicrobial susceptibility testing showed broad susceptibility. This case highlights the utility of WGS for the identification of rare or novel organisms not captured by conventional methods and expands the clinical spectrum of Erwinia species. While the criteria for species delineation were met, the phenotypic characterization remains insufficient to formally propose a new species. Full article

Oxidative stress is a defining and pervasive driver of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS). As a molecular accelerant, reactive oxygen species (ROS) and reactive nitrogen species (RNS) compromise mitochondrial function, amplify lipid peroxidation, induce protein misfolding, and promote chronic neuroinflammation, creating a positive feedback loop of neuronal damage and cognitive decline. Despite its centrality in promoting disease progression, attempts to neutralize oxidative stress with monotherapeutic antioxidants have largely failed owing to the multifactorial redox imbalance affecting each patient and their corresponding variation. We are now at the threshold of precision redox medicine, driven by advances in syndromic multi-omics integration, Artificial Intelligence biomarker identification, and the precision of patient-specific therapeutic interventions. This paper will aim to reveal a mechanistically deep assessment of oxidative stress and its contribution to diseases of neurodegeneration, with an emphasis on oxidatively modified proteins (e.g., carbonylated tau, nitrated α-synuclein), lipid peroxidation biomarkers (F2-isoprostanes, 4-HNE), and DNA damage (8-OHdG) as significant biomarkers of disease progression. We will critically examine the majority of clinical trial studies investigating mitochondria-targeted antioxidants (e.g., MitoQ, SS-31), Nrf2 activators (e.g., dimethyl fumarate, sulforaphane), and epigenetic reprogramming schemes aiming to re-establish antioxidant defenses and repair redox damage at the molecular level of biology. Emerging solutions that involve nanoparticles (e.g., antioxidant delivery systems) and CRISPR (e.g., correction of mutations in SOD1 and GPx1) have the potential to transform therapeutic approaches to treatment for these diseases by cutting the time required to realize meaningful impacts and meaningful treatment. This paper will argue that with the connection between molecular biology and progress in clinical hyperbole, dynamic multi-targeted interventions will define the treatment of neurodegenerative diseases in the transition from disease amelioration to disease modification or perhaps reversal. With these innovations at our doorstep, the future offers remarkable possibilities in translating network-based biomarker discovery, AI-powered patient stratification, and adaptive combination therapies into individualized/long-lasting neuroprotection. The question is no longer if we will neutralize oxidative stress; it is how likely we will achieve success in the new frontier of neurodegenerative disease therapies. Full article