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19 pages, 1062 KB  
Review
Calcium Signaling and Cardiac Adaptation to Stress: Focus on Pregnancy and Diabetes
by Sathya Velmurugan and Sanda Despa
Biomolecules 2025, 15(10), 1421; https://doi.org/10.3390/biom15101421 (registering DOI) - 7 Oct 2025
Abstract
Calcium (Ca2+) signaling regulates a wide range of processes in the heart, from contractility and excitability to energy supply and cell growth. Consequently, Ca2+ signaling plays a critical role in cardiac adaptation to both physiological and pathophysiological stress. This review [...] Read more.
Calcium (Ca2+) signaling regulates a wide range of processes in the heart, from contractility and excitability to energy supply and cell growth. Consequently, Ca2+ signaling plays a critical role in cardiac adaptation to both physiological and pathophysiological stress. This review examines the role of Ca2+ signaling in the heart’s physiological adaptation to pregnancy and its pathological maladaptation in diabetes. We focus on Ca2+-dependent mechanisms involved in hypertrophy, energy imbalance, and electrical remodeling in these two conditions, highlighting shared signaling pathways, functional outcomes, and key knowledge gaps. A deeper understanding of these mechanisms could reveal novel therapeutic targets to improve cardiac health in pregnancy and diabetes. Full article
(This article belongs to the Special Issue The Role of Calcium Signaling in Cardiac and Skeletal Muscle)
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19 pages, 3909 KB  
Article
The Effects of Long-Term Manure and Grass Mulching on Microbial Communities, Enzyme Activities, and Soil Organic Nitrogen Fractions in Orchard Soils of the Loess Plateau, China
by Qi Wang, Luxiao Guo, Xue Gao, Songling Chen, Xinxin Song, Fei Gao, Wei Liu, Hua Guo, Guoping Wang and Xinping Fan
Agriculture 2025, 15(19), 2084; https://doi.org/10.3390/agriculture15192084 - 6 Oct 2025
Abstract
Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of [...] Read more.
Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article
(This article belongs to the Section Agricultural Soils)
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25 pages, 988 KB  
Review
The NO Pathway as a Target in Patients with Stable and Advanced Heart Failure: An Additional Arrow in Our Quiver!
by Saverio D’Elia, Carmine Gentile, Achille Solimene, Rosa Franzese, Ettore Luisi, Antonio Caiazzo, Luigi Marotta, Simona Covino, Francesco Natale, Francesco S. Loffredo, Paolo Golino and Giovanni Cimmino
Biomolecules 2025, 15(10), 1420; https://doi.org/10.3390/biom15101420 - 6 Oct 2025
Abstract
The nitric oxide (NO) pathway is a fundamental regulator of vascular tone, myocardial function, and inflammation. In heart failure (HF), especially in advanced stages, dysregulation of NO–soluble guanylate cyclase (sGC)–cyclic guanosine monophosphate (cGMP) signaling contributes to endothelial dysfunction, increased vascular resistance, myocardial fibrosis, [...] Read more.
The nitric oxide (NO) pathway is a fundamental regulator of vascular tone, myocardial function, and inflammation. In heart failure (HF), especially in advanced stages, dysregulation of NO–soluble guanylate cyclase (sGC)–cyclic guanosine monophosphate (cGMP) signaling contributes to endothelial dysfunction, increased vascular resistance, myocardial fibrosis, and impaired cardiac performance. Chronic inflammation further reduces NO bioavailability, exacerbating HF progression This review synthesizes current knowledge on the role of the NO pathway in HF pathophysiology, with a focus on stable and advanced HF. Special attention is given to patient subgroups with comorbidities such as chronic kidney disease, where modulation of NO signaling may be particularly beneficial. We also evaluate therapeutic strategies targeting NO bioavailability and sGC stimulation. Evidence shows that impaired NO signaling promotes systemic and pulmonary vasoconstriction, elevates ventricular afterload, and worsens cardiac remodeling. Pharmacological agents that restore NO levels or activate downstream effectors such as sGC improve vasodilation, reduce fibrosis, and enhance myocardial relaxation. These effects are especially relevant in advanced HF patients and those with renal impairment, who often exhibit limited responses to conventional therapies. The NO pathway represents a promising therapeutic target in both stable and advanced HF. Modulating this pathway could improve outcomes, particularly in complex populations with multiple comorbidities, highlighting the need for further clinical research and tailored treatments. Full article
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19 pages, 916 KB  
Review
The Mechanisms of Sphagneticola trilobata Invasion as One of the Most Aggressive Invasive Plant Species
by Hisashi Kato-Noguchi and Midori Kato
Diversity 2025, 17(10), 698; https://doi.org/10.3390/d17100698 - 6 Oct 2025
Abstract
Sphagneticola trilobata (L.) Pruski has been introduced to many countries due to its ornamental and economic value. However, it has been listed in the world’s 100 worst alien invasive species due to its invasive nature. This species easily escapes cultivation and forms dense [...] Read more.
Sphagneticola trilobata (L.) Pruski has been introduced to many countries due to its ornamental and economic value. However, it has been listed in the world’s 100 worst alien invasive species due to its invasive nature. This species easily escapes cultivation and forms dense ground covers. It reproduces asexually through ramet formation from stem fragments. It also produces a large number of viable seeds that establish extensive seed banks. The movement of stem fragments and the dispersal of seeds, coupled with human activity, contribute to its short- and long-distance distribution. S. trilobata grows rapidly due to its high nutrient absorption and photosynthetic abilities. It exhibits high genetic and epigenetic variation. It can adapt to the different habitats and tolerate various adverse environmental conditions, including cold and high temperatures, low and high light irradiation, low nutrient levels, waterlogging, drought, salinity and global warming. S. trilobata has powerful defense systems against herbivory and pathogen infection. These systems activate the jasmonic acid signaling pathway, producing several defensive compounds. This species may also acquire more resources through allelopathy, which suppresses the germination and growth of neighboring plants. These life history traits and defensive abilities likely contribute to its invasive nature. This is the first review to focus on the mechanisms of its invasiveness in terms of growth, and reproduction, as well as its ability to adapt to different environmental conditions and defend itself. Full article
(This article belongs to the Special Issue Ecology, Distribution, Impacts, and Management of Invasive Plants)
22 pages, 2498 KB  
Article
Neuroprotective Effects of Betanin in a Mouse Model of Parkinson’s Disease: Behavioural and Neurotransmitter Pathway Insights
by Katarzyna Ziętal, Kamilla Blecharz-Klin, Ilona Joniec-Maciejak, Agnieszka Piechal, Justyna Pyrzanowska, Ewa Machaj, Dagmara Mirowska-Guzel and Ewa Widy-Tyszkiewicz
Int. J. Mol. Sci. 2025, 26(19), 9726; https://doi.org/10.3390/ijms26199726 - 6 Oct 2025
Abstract
The study aimed to evaluate the effect of betanin—a bioactive, natural pigment found in beetroot and prickly pear—on cognitive function, motor performance, and neurotransmission in a mouse model of Parkinson’s disease (PD). Aged mice with PD-like symptoms induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) were pretreated [...] Read more.
The study aimed to evaluate the effect of betanin—a bioactive, natural pigment found in beetroot and prickly pear—on cognitive function, motor performance, and neurotransmission in a mouse model of Parkinson’s disease (PD). Aged mice with PD-like symptoms induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) were pretreated with betanin (50 or 100 mg/kg b.w./day) via drinking water. Behavioural tests assessed motor skills, anxiety-related behaviour, and spatial memory. Biochemical analyses of central nervous system structures were conducted using high-performance liquid chromatography (HPLC) to determine neurotransmitter levels and metabolites. Betanin improved motor and cognitive functions in MPTP-treated mice. While learning ability remained unchanged, the 50 mg/kg dose alleviated spatial memory deficits. Biochemically, betanin moderately limited dopamine depletion and significantly influenced dopamine metabolism and serotonin levels. These findings suggest that betanin, as a functional food component, may exert neuroprotective effects and support cognitive and motor function in neurodegenerative conditions such as PD. Full article
(This article belongs to the Special Issue Drug Design and Development for Neurological Diseases)
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19 pages, 1201 KB  
Article
Sustainable Fashion in Slovenia: Circular Economy Strategies, Design Processes, and Regional Innovation
by Tanja Devetak and Alenka Pavko Čuden
Sustainability 2025, 17(19), 8890; https://doi.org/10.3390/su17198890 - 6 Oct 2025
Abstract
This study investigates sustainability-oriented design and production practices in Slovenia, focusing on brand-led approaches grounded in local innovation, cultural heritage and community engagement. Through mapping of Slovenian fashion enterprises, the research identifies and analyzes core sustainability and circularity strategies including zero- and low-waste [...] Read more.
This study investigates sustainability-oriented design and production practices in Slovenia, focusing on brand-led approaches grounded in local innovation, cultural heritage and community engagement. Through mapping of Slovenian fashion enterprises, the research identifies and analyzes core sustainability and circularity strategies including zero- and low-waste design, recycling, upcycling and the development of adaptable, long-lasting garments. Further attention is given to participatory design methods involving consumers, the strategic social media use for community building and service-based circular economy models such as lifetime garment repair. Technological and production innovations, localized supply chains and small-scale production models are assessed for their role in reducing environmental impact and advancing sustainable supply chain management. The study also analyzes initiatives to shorten the fashion loop, including dematerialization and production minimization, as pathways to reduce resource consumption. Methodologically, the study combines empirical fieldwork, participant observation and literature review to deliver a comprehensive analysis of Slovenia’s sustainable fashion sector. The findings contribute to the global discourse on regional and place-based sustainability in fashion demonstrating how design-driven, small- and medium-sized enterprises can integrate circular economy principles, cultural continuity and collaborative innovation to foster environmentally responsible and socially embedded fashion. Full article
(This article belongs to the Special Issue Sustainable Product Design, Manufacturing and Management)
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16 pages, 3325 KB  
Article
Synovial CXCL3+FOSL2+ Macrophages Mediate Inflammation via FOSL2/AP-1 in Rheumatoid Arthritis: A Single-Cell Transcriptome Analysis
by Yiwei Wu, Jinming Yang, Mengke Chen, Xiaoxiang Chen and Shan Cao
Int. J. Mol. Sci. 2025, 26(19), 9718; https://doi.org/10.3390/ijms26199718 - 6 Oct 2025
Abstract
Macrophages play a central role in joint inflammation and bone destruction in rheumatoid arthritis (RA). While activator protein-1 (AP-1) transcription factors have been implicated in RA pathogenesis, the specific roles of individual AP-1 members in regulating synovial macrophages remain unclear. To address this, [...] Read more.
Macrophages play a central role in joint inflammation and bone destruction in rheumatoid arthritis (RA). While activator protein-1 (AP-1) transcription factors have been implicated in RA pathogenesis, the specific roles of individual AP-1 members in regulating synovial macrophages remain unclear. To address this, two public single-cell transcriptomic datasets were first analyzed to profile synovial macrophages, and then to identify AP-1 family members and associated pathways via differential expression and gene set enrichment analyses. JUND, FOSL2, and FOSB were found to be highly enriched in the RA synovium, and a distinct CXCL3+FOSL2+ macrophage subset was identified, characterized by pro-inflammatory, metabolic, and differentiation-related pathways. Intercellular communication analysis further revealed that this CXCL3+FOSL2+ macrophage subset interacted with ACKR1+ endothelial cells within the synovial microenvironment. Validation in a large-cohort bulk transcriptomic dataset, together with functional assays using in vitro FOSL2 knockdown in U937 cell lines, further confirmed FOSL2’s role in promoting macrophage-driven inflammation. Collectively, these findings indicate that CXCL3+FOSL2+ macrophages drive RA synovitis via the FOSL2/AP-1 axis, highlighting a potential therapeutic target. Full article
(This article belongs to the Special Issue Macrophages in Human Diseases and Their Treatment)
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19 pages, 1740 KB  
Article
miR-10c Targets dgat2 and Affects the Expression of Genes Involved in Fatty Acid and Triglyceride Metabolism in Oreochromis niloticus Under Heat Stress
by Wen Wang, Wenjing Tao, Jixiang Hua, Siqi Lu, Yalun Dong, Jun Qiang and Yifan Tao
Int. J. Mol. Sci. 2025, 26(19), 9717; https://doi.org/10.3390/ijms26199717 - 6 Oct 2025
Abstract
Heat stress induces metabolic adaptations in fish, including the regulation of triglyceride (TG) synthesis/degradation to preserve cellular lipid balance and energy homeostasis. Diacylglycerol acyltransferase (DGAT) catalyzes the final step in TG synthesis. However, the molecular mechanisms by which DGAT regulates TG metabolism in [...] Read more.
Heat stress induces metabolic adaptations in fish, including the regulation of triglyceride (TG) synthesis/degradation to preserve cellular lipid balance and energy homeostasis. Diacylglycerol acyltransferase (DGAT) catalyzes the final step in TG synthesis. However, the molecular mechanisms by which DGAT regulates TG metabolism in heat-stressed fish remain unexplored. Our previous study suggested that miR-10c regulates dgat2 expression in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) under heat stress. Here, we characterized the GIFT miR-10c precursor as a 65-nucleotide transcript yielding a 22 nt mature miRNA (oni-miR-10c). A phylogenetic analysis revealed a high level of miR-10c sequence conservation across species. A dual-luciferase reporter assay confirmed dgat2 as a direct target of miR-10c. Overexpression of miR-10c in vivo down-regulated dgat2 transcripts and DGAT2 protein. SiRNA-knockdown of dgat2 resulted in upregulation of cpt1α, fas, and lpl and downregulation of hsl, thereby reprogramming lipid metabolism in GIFT hepatocytes. Thus, the miR-10c-dgat2 regulatory axis facilitates TG hydrolysis and promotes fatty acid metabolism under heat stress. Our findings highlight miR-10c’s potential as a dgat2 inhibitor and its function in regulating lipid metabolism in heat-stressed GIFT. Our study reveals a key molecular pathway mediating thermal adaptation of energy metabolism in fish, providing novel targets for preventing heat-induced metabolic disorders. Full article
(This article belongs to the Special Issue Latest Advances in Aquatic Genetic Improvement)
20 pages, 2510 KB  
Article
Effects of Arbuscular Mycorrhizal Fungi on the Physiological Responses and Root Organic Acid Secretion of Tomato (Solanum lycopersicum) Under Cadmium Stress
by Dejian Zhang, Xinyu Liu, Yuyang Zhang, Jie Ye and Qingping Yi
Horticulturae 2025, 11(10), 1204; https://doi.org/10.3390/horticulturae11101204 - 6 Oct 2025
Abstract
Arbuscular Mycorrhizal Fungi (AMF) can form symbiotic relationships with most plants. They can alleviate the toxic effects of heavy metals on plants. This study analyzed the effects of AMF (Diversispora versiformis, D.v.) on the physiological responses and root organic acid [...] Read more.
Arbuscular Mycorrhizal Fungi (AMF) can form symbiotic relationships with most plants. They can alleviate the toxic effects of heavy metals on plants. This study analyzed the effects of AMF (Diversispora versiformis, D.v.) on the physiological responses and root organic acid secretion of tomato (Solanum lycopersicum L.) under cadmium (Cd) stress, in order to elucidate how AMF enhance Cd tolerance. The results indicated that when the AMF inoculation rate of tomato seedlings ranged from 26.75% to 38.23%, the AMF treatment significantly promoted tomato growth. Cd significantly reduced the agronomic traits of tomato. However, AMF inoculation dramatically lowered the Cd level from 19.32 mg/kg to 11.54 mg/kg in tomato roots, and effectively reduced the negative effect of Cd toxicity on seedling growth. Cd stress also significantly reduced the chlorophyll fluorescence parameters, chlorophyll contents, and photosynthetic intensity parameters in seedling leaves, while the AMF treatment significantly increased these indicators. Under Cd stress, the AMF treatment significantly increased the activities of SOD, POD, and CAT, and reduced the levels of reactive oxygen species and the contents of osmotic regulatory substances in roots. Under Cd stress conditions, the AMF treatment also significantly increased the auxin level (57.24%) and reduced the abscisic acid level (18.19%), but had no significant effect on trans-zeatin riboside and gibberellin contents in roots. Cd stress markedly reduced the content of malic acid and succinic acid by 17.28% and 25.44%, respectively; however, after the AMF inoculation, these indicators only decreased by 2.47% and 2.63%, respectively. Under Cd stress, AMF could increase tomato roots’ antioxidant capacity to reduce ROS level, thereby alleviating the toxicity induced by ROS and maintaining reactive oxygen metabolism, enhancing the plant’s stress resistance. In summary, the AMF treatment enhances the osmotic regulation capacity and maintains the stability of cell membranes by reducing the levels of osmotic regulatory substances in roots. It also enhances the Cd tolerance of tomato plants by regulating the contents of root hormones and aerobic respiration metabolites, among other pathways. Therefore, inoculating plants with AMF is a prospective strategy for enhancing their adaptive capacity to Cd-polluted soils. Full article
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24 pages, 669 KB  
Review
Nutrient-Element-Mediated Alleviation of Cadmium Stress in Plants: Mechanistic Insights and Practical Implications
by Xichao Sun, Liwen Zhang, Yingchen Gu, Peng Wang, Haiwei Liu, Liwen Qiang and Qingqing Huang
Plants 2025, 14(19), 3081; https://doi.org/10.3390/plants14193081 - 6 Oct 2025
Abstract
Cadmium (Cd), a pervasive and highly phytotoxic metal pollutant, poses severe threats to agricultural productivity, ecosystem stability, and human health through its entry into the food chain. Plants have evolved intricate defense mechanisms, among which the strategic manipulation of nutrient elements emerges as [...] Read more.
Cadmium (Cd), a pervasive and highly phytotoxic metal pollutant, poses severe threats to agricultural productivity, ecosystem stability, and human health through its entry into the food chain. Plants have evolved intricate defense mechanisms, among which the strategic manipulation of nutrient elements emerges as a critical physiological and biochemical strategy for mitigating Cd stress. This comprehensive review delves deeply into the multifaceted roles of essential macronutrient elements (nitrogen, phosphorus, potassium, calcium, magnesium, sulfur), essential micronutrient elements (zinc, iron, manganese, copper) and non-essential beneficial elements (silicon, selenium) in modulating plant responses to Cd toxicity. We meticulously dissect the physiological, biochemical, and molecular underpinnings of how these nutrients influence Cd bioavailability in the rhizosphere, Cd uptake and translocation pathways, sequestration and compartmentalization within plant tissues, and the activation of antioxidant defense systems. Nutrient elements exert their influence through diverse mechanisms: competing with Cd for root uptake transporters, promoting the synthesis of complexes that reduce Cd mobility, stabilizing cell walls and plasma membranes to restrict apoplastic flow and symplastic influx, modulating redox homeostasis by enhancing antioxidant enzyme activities and non-enzymatic antioxidant pools, regulating signal transduction pathways, and influencing gene expression profiles related to metal transport, chelation, and detoxification. The complex interactions between nutrients themselves further shape the plant’s capacity to withstand Cd stress. Recent advances elucidating nutrient-mediated epigenetic regulation, microRNA involvement, and the role of nutrient-sensing signaling hubs in Cd responses are critically evaluated. Furthermore, we synthesize the practical implications of nutrient management strategies, including optimized fertilization regimes, selection of nutrient-efficient genotypes, and utilization of nutrient-enriched amendments, for enhancing phytoremediation efficiency and developing low-Cd-accumulating crops, thereby contributing to safer food production and environmental restoration in Cd-contaminated soils. The intricate interplay between plant nutritional status and Cd stress resilience underscores the necessity for a holistic, nutrient-centric approach in managing Cd toxicity in agroecosystems. Full article
(This article belongs to the Special Issue Plant Ecotoxicology and Remediation Under Heavy Metal Stress)
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22 pages, 6595 KB  
Article
Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection
by Zhixiu Wang, Tingting Zhou, Shaoxuan Gu, Jiaqi Yao, Suli Liu and Jiaming Mao
Microorganisms 2025, 13(10), 2310; https://doi.org/10.3390/microorganisms13102310 - 6 Oct 2025
Abstract
Citrobacter braakii is an emerging opportunistic pathogen of escalating clinical significance in animal hosts, though its pathogenic mechanisms remain poorly characterized. This study isolated a C. braakii strain (SCGY-1L) from diseased Siniperca chuatsi and confirmed its identity through integrated morphological, physiological, and molecular [...] Read more.
Citrobacter braakii is an emerging opportunistic pathogen of escalating clinical significance in animal hosts, though its pathogenic mechanisms remain poorly characterized. This study isolated a C. braakii strain (SCGY-1L) from diseased Siniperca chuatsi and confirmed its identity through integrated morphological, physiological, and molecular analyses. Comprehensive genomic sequencing revealed a 5.75 Mb genome comprising one circular chromosome and two plasmids. A Circos plot was constructed to visualize the genomic architecture of strain SCGY-1L, revealing 5482 protein-coding genes, 25 tRNA genes, and 86 rRNA genes. Additionally, 738 virulence-associated genes and 366 antibiotic resistance determinants were annotated, elucidating multidrug-resistant phenotypes including insensitivity to erythromycin and penicillin. Pathogenicity assessment established an LD50 of 1.28 × 106 CFU/mL in infected hosts, with histopathological analysis showing significant hemorrhage and necrosis in target organs (liver, spleen, kidney). Host transcriptome profiling generated 41.21 Gb of high-quality clean data, identifying 2201 differentially expressed genes post-infection (1568 up-regulated; 633 down-regulated). These were significantly enriched in phagocytosis, cytokine-mediated signaling, and inflammatory regulation pathways. These molecular insights establish C. braakii’s mechanistic framework for pathogenesis and host adaptation, providing critical targets for diagnostics and therapeutics against emerging Citrobacter infections. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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18 pages, 772 KB  
Article
A Pilot Epigenome-Wide Study of Posttraumatic Growth: Identifying Novel Candidates for Future Research
by Mackenzie Rubens, Paul Ruiz Pinto, Anita Sathyanarayanan, Olivia Miller, Amy B. Mullens, Dagmar Bruenig, Patricia Obst, Jane Shakespeare-Finch and Divya Mehta
Epigenomes 2025, 9(4), 39; https://doi.org/10.3390/epigenomes9040039 - 6 Oct 2025
Abstract
Background: Posttraumatic growth (PTG) refers to positive psychological change following trauma. While its psychological aspects are well-documented, the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may offer insight into PTG’s neurobiological basis. Aims: This study aimed to identify epigenetic [...] Read more.
Background: Posttraumatic growth (PTG) refers to positive psychological change following trauma. While its psychological aspects are well-documented, the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may offer insight into PTG’s neurobiological basis. Aims: This study aimed to identify epigenetic markers associated with PTG using an epigenome-wide association study (EWAS), the first of its kind in a trauma-exposed population. Methods: A longitudinal EWAS design was used to assess DNAm before and after trauma exposure in first-year paramedicine students (n = 39). Genome-wide methylation data were analyzed for associations with PTG, applying epigenome-wide and gene-wise statistical thresholds. Pathway enrichment analysis was also conducted. Results: The study identified two CpGs (cg09559117 and cg05351447) within the PCDHA1/PCDHA2 and PDZD genes significantly associated with PTG at the epigenome-wide threshold (p < 9.42 × 10–8); these were replicated in an independent sample. DNAm in 5 CpGs across known PTSD candidate genes ANK3, DICER1, SKA2, IL12B and TPH1 were significantly associated with PTG after gene-wise Bonferroni correction. Pathway analysis revealed that PTG-associated genes were overrepresented in the Adenosine triphosphate Binding Cassette (ABC) transporters pathway (p = 2.72 × 10−4). Conclusions: These results identify genes for PTG, improving our understanding of the neurobiological underpinnings of PTG. Full article
(This article belongs to the Special Issue DNA Methylation Markers in Health and Disease)
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15 pages, 2194 KB  
Article
Methylocystis hydrogenophila sp. nov.—A Type IIa Methanotrophic Bacterium Able to Utilize Hydrogen as an Alternative Energy Source
by Kangli Guo, Thomas Heimerl, Anna Hakobyan, Dongfei Han and Werner Liesack
Microorganisms 2025, 13(10), 2309; https://doi.org/10.3390/microorganisms13102309 - 5 Oct 2025
Abstract
A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2T represents a distinct species [...] Read more.
A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2T represents a distinct species within the genus, clearly separated from its closest relatives, namely Methylocystis suflitae NLS-7T, Methylocystis rosea SV97T, Methylocystis silviterrae FST, and Methylocystis hirsuta CSC1T. As is typical of the family Methylocystaceae, cells possess intracytoplasmic membranes arranged parallel to the cytoplasmic membrane, and the dominant fatty acids are C18:1ω8c and C18:1ω7c. The strain grows aerobically on methane as the primary carbon and energy source and expresses both low- and high-affinity particulate methane monooxygenase (pMMO), but lacks the soluble form. The species epithet reflects the strain’s ability to utilize hydrogen as an alternative energy source. A further feature is its use of asparagine as an osmoprotectant, enhancing salt tolerance. Genomic analysis reveals complete pathways for nitrogen fixation, denitrification, and hydrogen oxidation. These genetic and physiological characteristics support the designation of a novel species, for which the name Methylocystis hydrogenophila sp. nov. is proposed. The type strain is SC2T (=DSM 114506 = NCIMB 15437). Full article
(This article belongs to the Section Microbial Biotechnology)
19 pages, 2448 KB  
Article
Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia)
by Yoo-Shin Koh, Fanchao Zhu, Yoojeong Hwang and Mi-Jeong Yoo
Int. J. Mol. Sci. 2025, 26(19), 9704; https://doi.org/10.3390/ijms26199704 - 5 Oct 2025
Abstract
Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes [...] Read more.
Coptis trifolia (threeleaf goldthread) offers a valuable comparative system for investigating the evolution and regulation of benzylisoquinoline alkaloid (BIA) synthesis. In this study, we analyzed the leaf and root transcriptomes of C. trifolia using both long-read and short-read RNA-Sequencing. We assembled 41,926 unigenes (≥500 bp) and identified 37 genes related to BIA biosynthesis, including two transcription factors, bHLH1 and WRKY1. The number of BIA genes identified in C. trifolia was comparable to that in other Coptis species. Transcriptome analysis revealed that most of these genes were more highly expressed in roots than leaves. Consistent with previous studies, C. trifolia contained a single (S)-stylopine synthase (SPS) gene homolog, potentially multifunctional for (S)-canadine synthase (CAS), (S)-cheilanthifoline synthase (CFS), and SPS. Transcriptome and untargeted metabolomic data indicated greater variation in root samples than leaf samples, although slightly more differentially expressed transcripts and metabolites were observed in leaves. Targeted metabolite profiling showed higher BIA accumulation in roots, with epiberberine being the most abundant, followed by coptisine, berberine, and columbamine. These results provide essential genomic resources for comparative analysis of the BIA pathway across Ranunculaceae, targeted gene function studies for metabolic bioengineering, and conservation strategies for C. trifolia, a member of an early-diverging clade within the genus with limited genetic resources. Full article
(This article belongs to the Section Molecular Plant Sciences)
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23 pages, 4505 KB  
Article
Preparation and Performance Study of Uniform Silver–Graphene Composite Coatings via Zeta Potential Regulation and Electrodeposition Process Optimization
by Luyi Sun, Hongrui Zhang, Xiao Li, Dancong Zhang, Yuxin Chen, Taiyu Su and Ming Zhou
Nanomaterials 2025, 15(19), 1523; https://doi.org/10.3390/nano15191523 - 5 Oct 2025
Abstract
High-performance electrical contact materials are crucial for electric power systems, new energy vehicles, and rail transportation, as their properties directly impact the reliability and safety of electronic devices. Enhancing these materials not only improves energy efficiency but also offers notable environmental and economic [...] Read more.
High-performance electrical contact materials are crucial for electric power systems, new energy vehicles, and rail transportation, as their properties directly impact the reliability and safety of electronic devices. Enhancing these materials not only improves energy efficiency but also offers notable environmental and economic advantages. However, traditional composite contact materials often suffer from poor dispersion of the reinforcing phase, which restricts further performance improvement. Graphene (G), with its unique two-dimensional structure and exceptional electrical, mechanical, and tribological properties, is considered an ideal reinforcement for metal matrix composites. Yet, its tendency to agglomerate poses a significant challenge to achieving uniform dispersion. To overcome this, the study introduces a dual approach: modulation of the zeta potential (ζ) in the silver-plated liquid to enhance G’s dispersion stability, and concurrent optimization of the composite electrodeposition process. Experimental results demonstrate that this synergistic strategy enables the uniform distribution of G within the silver matrix. The resulting silver–graphene (Ag-G) composite coatings exhibit outstanding overall performance at both micro and macro levels. This work offers a novel and effective pathway for the design of advanced electrical contact materials with promising application potential. Full article
(This article belongs to the Section 2D and Carbon Nanomaterials)
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