Search Results (114)

Ligustrum japonicum Thunb. (Oleaceae) has long been valued for the medicinal properties. Its fruits are traditionally utilized, while the leaves and branches are generally discarded after fruit harvest. These aerial parts therefore represent underutilized by-products whose phytochemical profiles remain insufficiently characterized. To elucidate the organ-specific chemical diversity and assess the potential value of these underutilized parts, a comparative analysis of the fruits, leaves, and branches was performed using HPLC–MS/MS combined with GNPS-based molecular networking, with a particular focus on secoiridoids, the characteristic metabolites of the Oleaceae family. This approach revealed substantial overlap as well as distinct variations in secoiridoid profiles among the three plant organs. Chromatographic separation yielded 14 secoiridoid derivatives shared across all organs. In addition, four previously undescribed secoiridoids were isolated and identified through spectroscopic analyses: secoligunosides A (1) and B (2) from the leaves and secoligunosides C (3) and D (4) from the branches. Among the major identified secoiridoids, oleuropein (10), 8Z-nüezhenide (17), and GL-3 (18) exhibited weak proliferative activity, showing an approximately 10–20% increase compared to control, on human dermal papilla cells. Collectively, these findings demonstrate that the leaves and branches not only contain key secoiridoids found in the fruits but also harbor unique metabolites, highlighting their value as alternative or complementary medicinal resources. The underutilized parts of L. japonicum therefore represent promising sources of natural products and warrant further investigation for future therapeutic applications. Full article

The study investigated the diversity and ecology of Myxomycetes (Amoebozoa) along a vegetation gradient in the Cuzco department, Peru, spanning altitudes from 2500 to 4700 m. Field collections were carried out at six sites distributed across three distinct vegetation formations: non-Amazonian Forest, paramo, and high Andean zones with and without vegetation cover. The collected material was analyzed through direct observation, cultivation in moist chambers, and morphological identification, resulting in the record of 18 species, including three new records for Peru (Diderma circumdissilens, Licea tenera, and Perichaena luteola). Species richness was higher at lower altitudes and in environments with greater substrate availability, such as dead branches and mosses, but declined under extreme environmental conditions, particularly at high elevations. Principal component analysis revealed differences in community composition among the environments, associated with environmental variables and substrate types. The results highlight that the Peruvian Andes harbor a significant biodiversity of Myxomycetes, including species adapted to high-altitude conditions, reinforcing the importance of conservation and further study of these extreme ecosystems. We conclude that high mountain environments serve as biodiversity hotspots, and that future studies, including molecular techniques, are essential to understanding the distribution and adaptation of these organisms in the Andean environments. Full article

Triple-negative breast cancers (TNBC) lack estrogen, progesterone, and express little, if any, HER2 receptors on their surface. No targeted therapies exist for this aggressive form of breast cancer. A library of enriched fractions from marine organisms was screened in a multi-parametric cytotoxicity assay using MDA-MB-231 and MDA-MB-468 TNBC cells, grown as spheroids (3D cultures). Spheroids better resemble tumors and are considered more clinically predictive. The assay measures apoptosis via the cleavage of caspase 3/7, viability via DNA content, and loss of membrane integrity via 7AAD staining at 24 h of treatment. Fractions were also tested in a traditional 2D MTT assay at 72 h. A fraction from the sponge Aplysina was active in the 3D assay. Aplysinamisine I was identified as the compound responsible for the activity. Aplysinamisine I induces apoptosis in MDA-MB-268 spheroids with an IC₅₀ of 2.9 ± 0.28 µM at 24 h. This novel activity is the most potent for the compound to date. Its IC₅₀ in the MTT assay at 72 h is >80 µM. Striking synergy with Taxol™ is shown in both cell lines. Proteomic analysis led to a differential protein expression profile. Through bioinformatics, this profile led to the hypothesis that the inhibition of nucleophosmin is the potential mode of action of the compound. However, initial studies show only a modest decrease in nucleophosmin expression in spheroids treated with aplysinamisine I. Full article

The SNAC (Stress-responsive NAC) subfamily, a key branch of the conserved NAC transcription factor family, plays a central role in regulating plant stress response. However, systematic characterization of the SNAC family in cotton (Gossypium spp.) remains unclear. Employing a genome-wide screening approach, this study characterized 75 distinct SNAC transcription factor genes across ten Gossypium species, with tetraploid cottons harboring twice as many as their diploid progenitors. Phylogenetic analysis categorized the genes into three subgroups, with members of the same subgroup exhibiting conserved motif compositions and gene structures. Chromosomal localization revealed a conserved distribution pattern of SNAC genes between the Dt and At subgenomes in tetraploid cotton. Genomic collinearity analysis suggested that the primary driver of SNAC family expansion was segmental duplication. Promoter analysis predicted 2974 cis-regulatory elements, including cold- and hormone-responsive motifs, indicating their potential involvement in stress regulation. These GhSNAC genes indicated significant induced expressions under stress conditions, and GhSNAC3D exhibited the most significant up-regulated expression under low temperature stress. Genetic function studies displayed that VIGS-mediated GhSNAC3D-silencing significantly reduced the cold tolerance in cotton. This study systematically analyzed the genomic characteristics of the cotton SNAC family and functionally validated the molecular mechanism of GhSNAC3D-mediated cryogenic response, which lays a foundation for subsequent research on cold resistance in cotton and stress-resistant breeding. Full article

Yersinia pestis, the causative agent of plague, has triggered multiple pandemics throughout human history, yet its long-term evolutionary patterns and reservoir dynamics remain poorly understood. Here, we present a global phylogenomic analysis of ancient and modern Y. pestis strains spanning from the Neolithic and Bronze Age to the present day. We show that pandemic-causing lineages did not arise from a single ancestral strain but instead emerged independently along deep branches of the Y. pestis phylogeny. Pandemic-associated Y. pestis strains were recovered exclusively from human remains and display clear local temporal divergence, indicating evolution driven by human transmission during outbreaks. These findings support the hypothesis that plague emergence is driven by complex, regionally rooted reservoirs, with recurrent spillovers into human populations across millennia. Our work highlights the need to view plague not as a series of isolated outbreaks but as a long-standing zoonotic threat shaped by deep evolutionary history, host ecology, and human societal structures. Full article

Background/Objectives: The Plague of Justinian marked the beginning of the First Pandemic (541–750 CE), yet no genomic evidence of Yersinia pestis has previously been recovered from the Eastern Mediterranean, where the outbreak was first recorded. This study aimed to determine whether Y. pestis was present in a mid-6th to early 7th century mass grave in Jerash, Jordan, and to characterize its genome within the broader context of First Pandemic strains. Methods: We analyzed samples from multiple individuals recovered from the Jerash mass grave. Initial screening for potential pathogen presence was conducted using proteomics. Select samples were subjected to ancient DNA extraction and whole genome sequencing. Comparative genomic and phylogenetic analyses were conducted to assess strain identity and evolutionary placement. Results: Genomic sequencing recovered Y. pestis DNA from five individuals, revealing highly similar genomes. All strains clustered tightly with other First Pandemic lineages but were notably recovered from a region geographically close to the pandemic’s historical epicenter for the first time. The near-identical genomes across diverse individuals suggest an outbreak of a single circulating lineage at the time of this outbreak. Conclusions: This study provides the first genomic evidence of Y. pestis in the Eastern Mediterranean during the First Pandemic, linking archaeological findings with pathogen genomics near the origin point of the Plague of Justinian. Summary Sentence: Genomic evidence links Y. pestis to the First Pandemic in an ancient city. Full article

Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83–5.00 Mb and GC content of 37.15–37.35%. Genomic characterization identified conserved resistance genes (bla_IND-2, bla_CIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch. Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94–100 kb) carrying significant resistance genes (bla_OXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen. Full article

The Ma’anshan section of the lower Yangtze River features a complex multi-anabranching system, where the river divides into several branches around mid-channel sandbars, with distinct point bars alternately developing along both banks. Within this morphologically active system, Zhengpu Harbor suffered severe operational disruptions by accelerated siltation at its approach channel, primarily due to its vulnerable location downstream of the expanding Niutun River point-bar on the left bank. To systematically diagnose the mechanisms of siltation, this study integrates multi-method investigations: decadal-scale morphodynamic analysis using long-term bathymetric surveys, numerical modeling to quantify engineering impacts on flow dynamics, and multiple linear regression analysis for the contributions of key influencing factors. The result identifies three primary drivers of siltation, collectively responsible for 70% of the sediment accumulation, including the rightward shift of the thalweg in the Ma’anshan left branch, reduced flow diversion of the left Branch of Central bar, and the expansion of the Niutun River point bar. River engineering structures, such as bridges, contribute approximately 12%, while changes in upstream flow-sediment supply account for approximately 18%. To mitigate siltation at Zhengpu Harbor’s approach channel, this study proposes targeted engineering interventions to enhance local hydrodynamic conditions. The spur dikes were designed to enhance the morphological stabilization of the Central bar head to regulate flow distribution. A diversion channel could also be excavated at the tail of the Niutun River shoal, and emergency dredging was recommended at the harbor front. Numerical modeling indicates that these measures will increase flow velocity by over 0.1 m/s at the harbor front, mitigating the siltation situation. The study concludes that the proposed engineering measures can reduce annual siltation by approximately 30% under normal-year hydrological conditions, demonstrating their feasibility in mitigating siltation trends in multi-anabranching river systems. This research provides a reference for addressing siltation issues in harbors within complex anabranching river systems. Full article

Algal blooms produced by cyanobacteria liberate microcystins and other toxins that create a public health hazard. During the 2018 bloom of Microcystis aeruginosa in Florida, USA, residential and recreational exposures were associated with an increased risk of self-reporting respiratory, gastrointestinal, or ocular symptoms for 125 participants. Subsequently, 207 persons were interviewed between 2019 and 2024 in the absence of large-scale algal blooms and were considered non-exposed. Analyses of cyanotoxins and brevetoxins in water and air showed only intermittent, background levels of toxins during the non-bloom period. The purpose of this report was to compare symptom reporting between active bloom and non-bloom periods. The assessment of information bias from self-reported symptoms is an important issue in epidemiologic studies of harmful algal blooms. During the non-bloom period, no statistically significant associations with residential, recreational, or occupational exposures were found for any symptom group. Estimated risks for respiratory, gastrointestinal, and ocular symptoms, headache, and skin rash were significantly higher for persons sampled during the bloom than the non-bloom period with odds ratios (ORs) of 2.3 to 8.3. ORs for specific respiratory symptoms were also significantly elevated. After adjustment for confounders and multiple exposures in multivariable analyses, the differences in symptom reporting between bloom and non-bloom periods remained statistically significant. In summary, the use of self-reported symptoms in this epidemiologic study of exposure to a cyanobacterial algal bloom did not appear to introduce substantial information bias. Full article

Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. Understanding the dynamics of its spread is crucial for effective disease management. In this study, we investigated the involvement of asymptomatic carrier trees in the expansion of pine wilt disease through a series of experiments. Cage-releasing experiments revealed that sexually immature Japanese pine sawyer beetles, Monochamus alternatus, feeding on healthy pine branches drops only a minimal number of nematodes (primary infection). However, sexually mature beetles, still harboring numerous nematodes, fly to weakened trees for breeding and extend their feeding activities to healthy pines around weakened trees, infecting them with nematodes and thus spreading the disease further. Inoculation experiments on field-planted black pine seedlings demonstrated that even a small number of nematodes can lead to a high occurrence of asymptomatic carrier trees. Our findings suggest that nematode infections transmitted by sexually mature Monochamus beetles significantly contribute to the expansion of pine wilt damage and play a crucial role in the persistence of asymptomatic carrier trees. This conclusion is based on cage-release experiments demonstrating nematode transmission by mature beetles and inoculation experiments highlighting the conditions leading to asymptomatic carrier trees. Full article

Aegilops tauschii, a monocotyledonous annual grass, recognized as a pivotal progenitor of modern wheat (Triticum aestivum L.), serves as the D-genome donor in hexaploid wheat. This diploid species (2n = 2x = 14, DD) harbors a substantial reservoir of genetic diversity, particularly in terms of biotic and abiotic stress resistance traits. The extensive allelic variation present in its genome has been increasingly utilized for wheat genetic enhancement, particularly through introgression breeding programs aimed at improving yield potential and stress resilience. Heavy metal ATPases (HMAs), which belong to the P-type ATPase superfamily and are also known as P1B-type ATPases, play a crucial role in transporting heavy metals and maintaining metal ion homeostasis in plant cells. HMAs have been extensively studied in model plants like Arabidopsis thaliana and rice. However, this family has not been reported in A. tauschii. Here, we conducted the genome-wide identification and bioinformatics analysis of the AetHMA gene family in A. tauschii, resulting in the discovery of a total of nine AetHMA members. Among AetHMA genes, six pairs are large-block duplication genes, which mainly occur among the four genes of AetHMA2, AetHMA4, AetHMA8, and AetHMA9. Additionally, there is one pair that consists of tandem duplication genes (AetHMA6: AetHMA7). All AetHMAs can be classified into six groups (I–VI), which are further divided into two branches: the copper subclasses and the zinc subclasses. Initially, A. tauschii was grown in a 1/2 Hoagland nutrient solution and subsequently exposed to four heavy metals: zinc (Zn), copper (Cu), manganese (Mn), and cadmium (Cd). Following this treatment, the expression profiles of nine AetHMA genes were assessed. The results indicated that, under zinc and manganese stress, the HMA family members exhibited enhanced expression in the leaves, whereas the expression of most members in the roots was downregulated. In the roots, except for AetHMA2, AetHMA5, and AetHMA8, the expression levels of other members were upregulated in response to Cd exposure. Furthermore, AetHMA4 diminishes the tolerance of yeast to Mn by increasing the absorption of Mn, while AetHMA8 increases the tolerance of yeast to Cd by reducing the absorption of Cd. This study provides experimental data regarding the function of the AetHMA gene in the transport, regulation, and detoxification of heavy metal elements in A. tauschii. Full article

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses. Full article

Safflower (Carthamus tinctorius L.), a versatile medicinal and economic crop, harbors untapped genetic resources essential for stress resilience and metabolic regulation. The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors, exclusive to plants, are pivotal in orchestrating growth, development, and stress responses, yet their roles in safflower remain unexplored. Here, we report the comprehensive identification and characterization of 26 safflower TCP genes (CtTCPs), categorized into Class I (PROLIFERATING CELL FACTOR, PCF) and Class II (CINCINNATA and TEOSINTE BRANCHED1/CYCLOIDEA, CIN and CYC/TB1) subfamilies. Comparative phylogenetics, conserved motif, and gene structure analyses revealed a high degree of evolutionary conservation and functional divergence within the gene family. Promoter analyses uncovered light-, hormone-, and stress-responsive cis-elements, underscoring their regulatory potential. Functional insights from qRT-PCR analyses demonstrated dynamic CtTCP expression under abiotic stresses, including abscisic acid (ABA), Methyl Jasmonate (MeJA), Cold, and ultraviolet radiation b (UV-B) treatments. Notably, ABA stress triggered a significant increase in flavonoid accumulation, correlated with the upregulation of key flavonoid biosynthesis genes and select CtTCPs. These findings illuminate the complex regulatory networks underlying safflower’s abiotic stress responses and secondary metabolism, offering a molecular framework to enhance crop resilience and metabolic engineering for sustainable agriculture Full article

Microcystin (MC), a hepatotoxin produced by cyanobacteria, was introduced into the Indian River Lagoon (IRL), Florida, in 2005 through freshwater outflows. Since then, MC has been detected in humans, domestic animals, and wildlife in the lagoon. Potential public health effects associated with MC exposure along the IRL include an increased risk of non-alcoholic liver disease among area residents. Yet, there are limited studies characterizing liver disease, as well as the potential role of MC, in humans and animals in this region. Thus, histopathology reports (n = 133) were reviewed in the stranded common bottlenose dolphin (Tursiops truncatus truncatus) (n = 156, 2005–2024) to describe liver lesions in this important IRL sentinel. Liver and fecal samples (n = 161) from stranded individuals were screened for MC via an enzyme immunoassay (ELISA). These samples were then confirmed via the 2-methyl-3-methoxy-4-phenylbutyric acid technique (MMPB) to evaluate whether liver histopathologic lesions were linked to MC exposure. Minimally invasive MC screening methods were also assessed using respiratory swabs and vapor. Inflammation (24%, n = 32), fibrosis (23%, n = 31), lipidosis/vacuolation (11%, n = 15), and necrosis (11%, n = 14) were the most common liver anomalies observed. These non-specific lesions have been reported to be associated with MC exposure in numerous species in the peer-reviewed literature. Ten bottlenose dolphins tested positive for the toxin via ELISA, including two individuals with hepatic lipidosis, but none were confirmed by MMPB. Thus, this study did not provide evidence for MC-induced liver disease in IRL bottlenose dolphins. Other causes should be considered for the lesions observed (e.g., heavy metals, metabolic disease, and endoparasites). Respiratory swabs require further validation as a pre-mortem MC screening tool in free-ranging wildlife. Full article

Monitoring seaweed growth rates and biomass is crucial for optimizing harvest strategies in aquaculture systems. While such a task can be managed manually on a small farm with a few seaweed tanks, it is not feasible on a commercial farm with 1000s of tanks. To this end, an Internet of Things (IoT) based seaweed growth monitoring system is being developed at Harbor Branch Oceanographic Institute (HBOI) at Florida Atlantic University (FAU). Using the Integrated Multi-Trophic Aquaculture (IMTA) system at HBOI as the test site, the project aims to develop a solution that allows farm managers to monitor seaweed growth remotely using automated sensors. An important component of this IoT solution is the machine learning-based prediction model. This study introduces an advanced Long Short-Term Memory (LSTM)-based approach for forecasting seaweed growth and biomass. In particular, an algae growth mathematical model driven by readily available environmental and aquaculture conditions has been integrated as a physical constraint in the LSTM model. This design addresses a principal challenge in this study—the lack of continuous ground truth measurements, as the biomass is recorded only at discrete intervals (e.g., initial, weekly partial harvests, and final harvest). The LSTM models are trained and evaluated for their predictive performance using experimental and synthetic data. Compared with the LSTM models with MSE loss function alone, the results showed that the model with a loss function under physics constraint achieved a significantly lower error in predicting seaweed growth. The rationale behind choosing LSTM over other state-of-the-art models is presented in the paper. This study highlights the potential of integrating machine learning with physical models to optimize seaweed cultivation and support sustainable aquaculture practices. The proposed methodology can seamlessly extend to the remote sensing data in other aquaculture settings. Full article