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Keywords = molecular communications

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32 pages, 5152 KiB  
Review
From Homeostasis to Neuroinflammation: Insights into Cellular and Molecular Interactions and Network Dynamics
by Ludmila Müller, Svetlana Di Benedetto and Viktor Müller
Cells 2025, 14(1), 54; https://doi.org/10.3390/cells14010054 (registering DOI) - 5 Jan 2025
Abstract
Neuroinflammation is a complex and multifaceted process that involves dynamic interactions among various cellular and molecular components. This sophisticated interplay supports both environmental adaptability and system resilience in the central nervous system (CNS) but may be disrupted during neuroinflammation. In this article, we [...] Read more.
Neuroinflammation is a complex and multifaceted process that involves dynamic interactions among various cellular and molecular components. This sophisticated interplay supports both environmental adaptability and system resilience in the central nervous system (CNS) but may be disrupted during neuroinflammation. In this article, we first characterize the key players in neuroimmune interactions, including microglia, astrocytes, neurons, immune cells, and essential signaling molecules such as cytokines, neurotransmitters, extracellular matrix (ECM) components, and neurotrophic factors. Under homeostatic conditions, these elements promote cellular cooperation and stability, whereas in neuroinflammatory states, they drive adaptive responses that may become pathological if dysregulated. We examine how neuroimmune interactions, mediated through these cellular actors and signaling pathways, create complex networks that regulate CNS functionality and respond to injury or inflammation. To further elucidate these dynamics, we provide insights using a multilayer network (MLN) approach, highlighting the interconnected nature of neuroimmune interactions under both inflammatory and homeostatic conditions. This perspective aims to enhance our understanding of neuroimmune communication and the mechanisms underlying shifts from homeostasis to neuroinflammation. Applying an MLN approach offers a more integrative view of CNS resilience and adaptability, helping to clarify inflammatory processes and identify novel intervention points within the layered landscape of neuroinflammatory responses. Full article
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10 pages, 2552 KiB  
Case Report
The Silent Threat of Human Metapneumovirus: Clinical Challenges and Diagnostic Insights from a Severe Pneumonia Case
by Rubens Carmo Costa-Filho, Felipe Saddy, João Luiz Ferreira Costa, Leandro Reis Tavares and Hugo Caire Castro Faria Neto
Viewed by 549
Abstract
Background: Human metapneumovirus (hMPV) is a respiratory pathogen that has gained increasing recognition due to advancements in molecular diagnostic tools, which have improved its detection and characterization. While severe disease manifestations are traditionally associated with pediatric, elderly, or immunocompromised patients, hMPV-related pneumonia in [...] Read more.
Background: Human metapneumovirus (hMPV) is a respiratory pathogen that has gained increasing recognition due to advancements in molecular diagnostic tools, which have improved its detection and characterization. While severe disease manifestations are traditionally associated with pediatric, elderly, or immunocompromised patients, hMPV-related pneumonia in immunocompetent adults remains underexplored. Methods: This case report describes a 68-year-old male who developed severe community-acquired pneumonia (CAP) caused by hMPV despite being immunocompetent and having no significant comorbidities. The diagnosis was confirmed via multiplex RT-PCR, excluding bacterial and viral coinfections. Laboratory and imaging findings supported a viral etiology, while empirical antibiotics were initially prescribed due to diagnostic uncertainty. Results: The patient presented with respiratory symptoms that progressed to hypoxia, productive cough, and fatigue, requiring hospitalization. Imaging revealed bilateral ground-glass opacities and consolidations typical of viral pneumonia. Molecular diagnostics enabled accurate pathogen identification and guiding appropriate management, and the patient fully recovered with supportive care. Conclusion: This case underscores the importance of rapid molecular diagnostics for hMPV, reducing unnecessary antibiotics and enhancing management. Routine incorporation of hMPV testing into clinical protocols could improve the diagnosis and resource use. The development of vaccines, such as the IVX-A12 in phase II trials, offers hope for targeted prevention, underscoring the need for further research and therapeutic innovations. Full article
(This article belongs to the Special Issue Viral Diseases: Current Research and Future Directions)
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12 pages, 3161 KiB  
Article
Surface Plasmon Mediated Angular and Wavelength Tunable Retroreflectors Using Parallel-Superimposed Surface Relief Bi-Gratings
by Maxwell Dollar, Yazan Bdour, Paul Rochon and Ribal Georges Sabat
Appl. Sci. 2025, 15(1), 339; https://doi.org/10.3390/app15010339 - 1 Jan 2025
Viewed by 410
Abstract
This study presents the design and fabrication of light retroreflectors utilizing surface plasmon resonance (SPR) in parallel-superimposed bi-grating structures. The bi-gratings were inscribed onto a thin azobenzene molecular glass film via photolithography and subsequently coated with a thin gold layer to support SPR. [...] Read more.
This study presents the design and fabrication of light retroreflectors utilizing surface plasmon resonance (SPR) in parallel-superimposed bi-grating structures. The bi-gratings were inscribed onto a thin azobenzene molecular glass film via photolithography and subsequently coated with a thin gold layer to support SPR. The two superimposed gratings operate in tandem, with one grating coupling incident light into the SPR mode and the other coupling it back out toward the light source, thereby achieving retroreflection. Monochromatic retroreflection is demonstrated for a target wavelength (785 nm) at angles from 5° to 10°, while multi-wavelength retroreflection is achieved for red, orange, and green wavelengths at corresponding angles. The findings highlight the potential of these bi-gratings for applications in optical sensing, communication, and advanced photonic systems, where compact, tunable, and angularly responsive designs are essential. Full article
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32 pages, 3920 KiB  
Review
Latin America’s Dengue Outbreak Poses a Global Health Threat
by Michelle Teixeira de Almeida, Davi Gabriel Salustiano Merighi, Aline Biazola Visnardi, Cauê Augusto Boneto Gonçalves, Vitor Martins de Freitas Amorim, Anielle Salviano de Almeida Ferrari, Anacleto Silva de Souza and Cristiane Rodrigues Guzzo
Viruses 2025, 17(1), 57; https://doi.org/10.3390/v17010057 - 1 Jan 2025
Viewed by 696
Abstract
Dengue fever, caused by the dengue virus (DENV), poses a significant global health challenge, particularly in tropical and subtropical regions. Recent increases in indigenous DENV cases in Europe are concerning, reflecting rising incidence linked to climate change and the spread of Aedes albopictus [...] Read more.
Dengue fever, caused by the dengue virus (DENV), poses a significant global health challenge, particularly in tropical and subtropical regions. Recent increases in indigenous DENV cases in Europe are concerning, reflecting rising incidence linked to climate change and the spread of Aedes albopictus mosquitoes. These vectors thrive under environmental conditions like temperature and humidity, which are increasingly influenced by climate change. Additionally, global travel accelerates the cross-border spread of mosquito-borne diseases. DENV manifests clinically in a spectrum from asymptomatic cases to severe conditions like dengue hemorrhagic fever and dengue shock syndrome, influenced by viral serotype and host factors. In 2024, Brazil experienced a fourfold increase in dengue cases compared to 2023, accompanied by higher mortality. Conventional control measures, such as vector control, community engagement, and vaccination, proved insufficient as climate change exacerbated mosquito proliferation, challenging containment efforts. In this regard, our review analyzes prevention measures and therapeutic protocols during the outbreak while addressing DENV transmission dynamics, clinical presentations, and epidemiological shifts. It also evaluates diagnostic strategies combining clinical assessment with serological and molecular testing, providing information to improve diagnostic and preventive measures. The global expansion of dengue-endemic regions, including outbreaks in Europe, highlights the urgent need for enhanced surveillance, proactive interventions, and international collaboration to mitigate the growing threat of Dengue and other arboviruses like West Nile, Zika, Chikungunya, Oropouche, and Yellow Fever viruses. Full article
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12 pages, 2494 KiB  
Article
Congenital Zika Syndrome: Insights from Integrated Proteomic and Metabolomic Analysis
by Leticia Gomes-de-Pontes, Lucila Akune Barreiros, Lillian Nunes Gomes, Ranieri Coelho Salgado, Sarah Maria da Silva Napoleão, Paulo V. Soeiro-Pereira, Saulo Duarte Passos and Antonio Condino-Neto
Biomolecules 2025, 15(1), 32; https://doi.org/10.3390/biom15010032 - 30 Dec 2024
Viewed by 285
Abstract
Background: In this study, we investigated the role of extracellular vesicles (EVs) in the pathogenesis of Congenital Zika Syndrome (CZS). Previous studies have highlighted the role of EVs in intercellular communication and the modulation of biological processes during viral infections, motivating our in-depth [...] Read more.
Background: In this study, we investigated the role of extracellular vesicles (EVs) in the pathogenesis of Congenital Zika Syndrome (CZS). Previous studies have highlighted the role of EVs in intercellular communication and the modulation of biological processes during viral infections, motivating our in-depth analysis. Our objective was to identify specific molecular signatures in the EVs of patients with CZS, focusing on their potential as biomarkers and on cellular pathways affected by the infection. Methods: We conducted advanced proteomic and metabolomic analyses using mass spectrometry for protein and metabolite identification. EVs were isolated from CZS patient samples and control groups using Izon qEV size-exclusion chromatography columns. Data analysis was performed using tools such as Cytoscape/String for protein interaction networks and MetaboAnalyst for metabolic patterns, highlighting differences between groups through PCA and volcano plots. Results: The analyzed EVs presented distinct molecular profiles in patients with CZS. Proteomic analysis revealed significant alterations in specific proteins, suggesting involvement in the PI3K-AKT-mTOR pathway, while metabolomics highlighted metabolites related to critical processes in Zika virus pathogenesis. These findings suggest a key role for the PI3K-AKT-mTOR pathway in regulating cellular processes during infection and indicate the involvement of EVs in intercellular communication. Additionally, the results identified potential biomarkers capable of aiding early diagnosis and assessing disease progression. Conclusions: This study demonstrates that EVs play a crucial role in intercellular communication during Zika virus infection. The identification of specific alterations in the PI3K-AKT-mTOR pathway highlights a possible therapeutic target, providing new opportunities for the development of more effective treatment strategies for CZS. Our findings significantly advance the understanding of CZS and underscore the need for further investigations using advanced techniques to validate and explore these potential molecular targets. Full article
(This article belongs to the Special Issue Extracellular Vesicles as Biomarkers of Diseases)
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28 pages, 2050 KiB  
Review
Molecular Mechanisms Linking Omega-3 Fatty Acids and the Gut–Brain Axis
by Anna Zinkow, Wojciech Grodzicki, Malwina Czerwińska and Katarzyna Dziendzikowska
Viewed by 783
Abstract
The gut–brain axis (GBA) is a complex communication network connecting the gastrointestinal tract (GIT) and the central nervous system (CNS) through neuronal, endocrine, metabolic, and immune pathways. Omega-3 (n-3) fatty acids, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are crucial food components [...] Read more.
The gut–brain axis (GBA) is a complex communication network connecting the gastrointestinal tract (GIT) and the central nervous system (CNS) through neuronal, endocrine, metabolic, and immune pathways. Omega-3 (n-3) fatty acids, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are crucial food components that may modulate the function of this axis through molecular mechanisms. Derived mainly from marine sources, these long-chain polyunsaturated fatty acids are integral to cell membrane structure, enhancing fluidity and influencing neurotransmitter function and signal transduction. Additionally, n-3 fatty acids modulate inflammation by altering eicosanoid production, reducing proinflammatory cytokines, and promoting anti-inflammatory mediators. These actions help preserve the integrity of cellular barriers like the intestinal and blood–brain barriers. In the CNS, EPA and DHA support neurogenesis, synaptic plasticity, and neurotransmission, improving cognitive functions. They also regulate the hypothalamic–pituitary–adrenal (HPA) axis by reducing excessive cortisol production, associated with stress responses and mental health disorders. Furthermore, n-3 fatty acids influence the composition and function of the gut microbiota, promoting beneficial bacterial populations abundance that contribute to gut health and improve systemic immunity. Their multifaceted roles within the GBA underscore their significance in maintaining homeostasis and supporting mental well-being. Full article
(This article belongs to the Special Issue Bioactive Compounds from Functional Foods, 2nd Edition)
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23 pages, 4348 KiB  
Article
Extracellular Vesicles and Tunnelling Nanotubes as Mediators of Prostate Cancer Intercellular Communication
by Jessica K. Heatlie, Joanna Lazniewska, Courtney R. Moore, Ian R. D. Johnson, Bukuru D. Nturubika, Ruth Williams, Mark P. Ward, John J. O’Leary, Lisa M. Butler and Doug A. Brooks
Biomolecules 2025, 15(1), 23; https://doi.org/10.3390/biom15010023 - 27 Dec 2024
Viewed by 326
Abstract
Prostate cancer (PCa) pathogenesis relies on intercellular communication, which can involve tunnelling nanotubes (TNTs) and extracellular vesicles (EVs). TNTs and EVs have been reported to transfer critical cargo involved in cellular functions and signalling, prompting us to investigate the extent of organelle and [...] Read more.
Prostate cancer (PCa) pathogenesis relies on intercellular communication, which can involve tunnelling nanotubes (TNTs) and extracellular vesicles (EVs). TNTs and EVs have been reported to transfer critical cargo involved in cellular functions and signalling, prompting us to investigate the extent of organelle and protein transfer in PCa cells and the potential involvement of the androgen receptor. Using live cell imaging microscopy, we observed extensive formation of TNTs and EVs operating between PCa, non-malignant, and immune cells. PCa cells were capable of transferring lysosomes, mitochondria, lipids, and endoplasmic reticulum, as well as syndecan-1, sortilin, Glut1, and Glut4. In mechanistic studies, androgen-sensitive PCa cells exhibited changes in cell morphology when stimulated by R1881 treatment. Overexpression assays of a newly designed androgen receptor (AR) plasmid revealed its novel localization in PCa cellular vesicles, which were also transferred to neighbouring cells. Selected molecular machinery, thought to be involved in intercellular communication, was investigated by knockdown studies and Western blotting/immunofluorescence/scanning electron microscopy (SEM). PCa TNTs and EVs transported proteins and organelles, which may contain specialist signalling, programming, and energy requirements that support cancer growth and progression. This makes these important intercellular communication systems ideal potential targets for therapeutic intervention. Full article
(This article belongs to the Special Issue Advances in the Pathology of Prostate Cancer)
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26 pages, 7731 KiB  
Review
Key Interleukins in Inflammatory Bowel Disease—A Review of Recent Studies
by David Aebisher, Dorota Bartusik-Aebisher, Agnieszka Przygórzewska, Piotr Oleś, Paweł Woźnicki and Aleksandra Kawczyk-Krupka
Int. J. Mol. Sci. 2025, 26(1), 121; https://doi.org/10.3390/ijms26010121 - 26 Dec 2024
Viewed by 458
Abstract
Inflammatory bowel disease (IBD) is an immune disorder of the gastrointestinal tract with a complex aetiopathogenesis, whose development is influenced by many factors. The prevalence of IBD is increasing worldwide, in both industrialized and developing countries, making IBD a global health problem that [...] Read more.
Inflammatory bowel disease (IBD) is an immune disorder of the gastrointestinal tract with a complex aetiopathogenesis, whose development is influenced by many factors. The prevalence of IBD is increasing worldwide, in both industrialized and developing countries, making IBD a global health problem that seriously affects quality of life. In 2019, there were approximately 4.9 million cases of IBD worldwide. Such a large number of patients entails significant healthcare costs. In the treatment of patients with IBD, the current therapeutic target is mucosal healing, as intestinal inflammation often persists despite resolution of abdominal symptoms. Treatment strategies include amino salicylates, corticosteroids, immunosuppressants, and biologic therapies that focus on reducing intestinal mucosal inflammation, inducing and prolonging disease remission, and treating complications. The American College of Gastroenterology (ACG) guidelines also indicate that nutritional therapies may be considered in addition to other therapies. However, current therapeutic approaches are not fully effective and are associated with various limitations, such as drug resistance, variable efficacy, and side effects. As the chronic inflammation that accompanies IBD is characterized by infiltration of a variety of immune cells and increased expression of a number of pro-inflammatory cytokines, including IL-6, TNF-α, IL-12, IL-23 and IFN-γ, new therapeutic approaches are mainly targeting immune pathways. Interleukins are one of the molecular targets in IBD therapy. Interleukins and related cytokines serve as a means of communication for innate and adaptive immune cells, as well as nonimmune cells and tissues. These cytokines play an important role in the pathogenesis and course of IBD, making them promising targets for current and future therapies. In our work, we review scientific studies published between January 2022 and November 2024 describing the most important interleukins involved in the pathogenesis of IBD. Some of the papers present new data on the precise role that individual interleukins play in IBD. New clinical data have also been provided, particularly on blocking interleukin 23 and interleukin 1beta. In addition, several new approaches to the use of different interleukins in the treatment of IBD have been described in recent years. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Advances in Biochemistry)
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21 pages, 5403 KiB  
Article
Integrated Analysis of Metatranscriptome and Amplicon Sequencing to Reveal Distinctive Rhizospheric Microorganisms of Salt-Tolerant Rice
by Wenna Meng, Zhenling Zhou, Mingpu Tan, Anqi Liu, Shuai Liu, Jiaxue Wang, Zhiguang Sun, Yiluo Tan, Yan Liu, Baoxiang Wang and Yanming Deng
Viewed by 263
Abstract
Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance [...] Read more.
Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including Hormiactis, Emericellopsis, Ceriosporopsis, Dirkmeia, and Moesziomyces predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as Desulfoprunum and Hydrogenophaga exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the “two-component system”, “sulfur metabolism”, and “microbial metabolism in diverse environments”. The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like Ceriosporopsis and Dirkmeria, along with bacteria such as Desulfoprunum, Rippkaea, and Bellilinea, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions. Full article
(This article belongs to the Special Issue Physiological and Molecular Responses for Stress Tolerance in Rice)
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20 pages, 747 KiB  
Review
Biogenesis of Extracellular Vesicles (EVs) and the Potential Use of Embryo-Derived EVs in Medically Assisted Reproduction
by Andreja Ovčar and Borut Kovačič
Int. J. Mol. Sci. 2025, 26(1), 42; https://doi.org/10.3390/ijms26010042 - 24 Dec 2024
Viewed by 297
Abstract
Extracellular vesicles (EVs) are lipid bilayer-bound particles released from cells that cannot replicate on their own, play a crucial role in intercellular communication, and are implicated in various physiological and pathological processes. Within the domain of embryo culture media research, extensive studies have [...] Read more.
Extracellular vesicles (EVs) are lipid bilayer-bound particles released from cells that cannot replicate on their own, play a crucial role in intercellular communication, and are implicated in various physiological and pathological processes. Within the domain of embryo culture media research, extensive studies have been conducted to evaluate embryo viability by analyzing spent culture medium. Advanced methodologies such as metabolomic profiling, proteomic and genomic analyses, transcriptomic profiling, non-coding RNA assessments, and oxidative status measurements have been employed to further understand the molecular characteristics of embryos and improve selection criteria for successful implantation. In the field of EVs, only a limited number of studies have been conducted on embryo-conditioned medium, indicating a significant gap in knowledge regarding the potential role of EVs in embryo development and implantation. Therefore, this review aims to evaluate current research findings on EVs enriched from animal and human embryo spent medium. By unraveling the potential link between embryo-derived EVs and embryo selection in clinical settings, such research might enhance embryo-selection methods in assisted reproductive technologies, eventually increasing the success rates of fertility treatments and advancing our understanding of mechanisms underlying successful embryo development and implantation in humans. Full article
(This article belongs to the Special Issue Molecular Biology and Hormonal Regulation in Reproductive Processes)
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13 pages, 1243 KiB  
Communication
Microbial Community, Fatty Acid Composition, and Health Potential of Horse Oil Fermented with Barley Nuruk
by Jeong-Ha Lee, Sung-Eun Bae, Ho-Min Kang, Yu-Jin Ha and Chang-Gu Hyun
Viewed by 400
Abstract
This study investigates the multifunctional potential of horse oil fermented with barley nuruk, a traditional fermentation starter, focusing on its α-glucosidase inhibitory activity and bioactive applicability. Gas chromatography–tandem mass spectrometry (GC-MS/MS) revealed significant changes in fatty acid composition during fermentation, with oleic acid [...] Read more.
This study investigates the multifunctional potential of horse oil fermented with barley nuruk, a traditional fermentation starter, focusing on its α-glucosidase inhibitory activity and bioactive applicability. Gas chromatography–tandem mass spectrometry (GC-MS/MS) revealed significant changes in fatty acid composition during fermentation, with oleic acid amide and palmitic acid amide remaining stable and stearic acid amide forming prominently by day 10. Molecular docking demonstrated that the amide structures play a key role in α-glucosidase inhibition through essential hydrogen bonding interactions. Next-generation sequencing (NGS) analysis showed a notable reduction in pathogenic bacteria, such as Salmonella enterica, and a dominance of Lactobacillus acidophilus (95.2%) by day 10. The α-glucosidase inhibitory activity increased progressively with fermentation, with the day 10 extract surpassing the synthetic inhibitor acarbose, highlighting its potential for diabetes management. A human skin primary irritation test confirmed the hypoallergenic nature of both hexane-extracted and fermented horse oil products, ensuring their safety for topical applications. In conclusion, fermented horse oil demonstrates significant α-glucosidase inhibitory activity and proven safety, positioning it as a promising natural resource for therapeutic and functional product development. Further studies are needed for clinical validation and commercialization in diabetes management and related applications. Full article
(This article belongs to the Section Microbial Metabolism, Physiology & Genetics)
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23 pages, 1915 KiB  
Review
Microplastic and Extracellular Vesicle Interactions: Recent Studies on Human Health and Environment Risks
by Eleonora Calzoni, Nicolò Montegiove, Alessio Cesaretti, Agnese Bertoldi, Gaia Cusumano, Giovanni Gigliotti and Carla Emiliani
Biophysica 2024, 4(4), 724-746; https://doi.org/10.3390/biophysica4040047 - 21 Dec 2024
Viewed by 404
Abstract
Microplastics (MPs) are widespread environmental pollutants that have drawn significant attention due to their possible health risks to humans and animals, as well as their extensive presence in ecosystems. Recent growing evidence highlights a remarkable relationship between MPs and extracellular vesicles (EVs), nanoscale [...] Read more.
Microplastics (MPs) are widespread environmental pollutants that have drawn significant attention due to their possible health risks to humans and animals, as well as their extensive presence in ecosystems. Recent growing evidence highlights a remarkable relationship between MPs and extracellular vesicles (EVs), nanoscale particles involved in intercellular communication. The purpose of this review was to investigate how the relationships between MPs and EVs can affect cellular functions and how this interaction could impact environmental conditions leading to broader ecological risks. The interaction patterns and bioactivity of both MPs and EVs are strongly influenced by biophysical characteristics such as hydrophobicity, surface charge, and particle size, which have received particular attention from the scientific community. Recent studies indicate that MPs affect EV distribution and their capacity to function appropriately in biological systems. Additionally, MPs can modify the molecular cargo of EVs, which may result in alterations of cell signaling pathways. Understanding the interactions between MPs and EVs could provide important opportunities to comprehend their potential effects on human health and environmental systems, especially when it comes to cancer development, endocrine, metabolic, and inflammatory disorders, and ecological disruptions. This review emphasizes the necessity of multidisciplinary research to clarify the molecular and biophysical mechanisms regulating the interaction between MPs and EVs. Full article
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17 pages, 2717 KiB  
Review
Enzymatic Regulation of the Gut Microbiota: Mechanisms and Implications for Host Health
by Zipeng Jiang, Liang Mei, Yuqi Li, Yuguang Guo, Bo Yang, Zhiyi Huang and Yangyuan Li
Biomolecules 2024, 14(12), 1638; https://doi.org/10.3390/biom14121638 - 20 Dec 2024
Viewed by 648
Abstract
The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical [...] Read more.
The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical reactions that have an impact on the gut microbial community, affecting both the microorganisms and the gut environment. Enzymes play an important role in the regulation of the intestinal microbiota, but the interactions between enzymes and microbial communities, as well as the precise mechanisms of enzymes, remain a challenge in scientific research. Enzymes serve both traditional nutritional functions, such as the breakdown of complex substrates into absorbable small molecules, and non-nutritional roles, which encompass antibacterial function, immunomodulation, intestinal health maintenance, and stress reduction, among others. This study categorizes enzymes according to their source and explores the mechanistic principles by which enzymes drive gut microbial activity, including the promotion of microbial proliferation, the direct elimination of harmful microbes, the modulation of bacterial interaction networks, and the reduction in immune stress. A systematic understanding of enzymes in regulating the gut microbiota and the study of their associated molecular mechanisms will facilitate the application of enzymes to precisely regulate the gut microbiota in the future and suggest new therapeutic strategies and dietary recommendations. In conclusion, this review provides a comprehensive overview of the role of enzymes in modulating the gut microbiota. It explores the underlying molecular and cellular mechanisms and discusses the potential applications of enzyme-mediated microbiota regulation for host gut health. Full article
(This article belongs to the Special Issue Novel Antimicrobial Strategies for Animal Health)
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47 pages, 2520 KiB  
Review
Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition
by Tomasz Grzyb and Justyna Szulc
Int. J. Mol. Sci. 2024, 25(24), 13601; https://doi.org/10.3390/ijms252413601 - 19 Dec 2024
Viewed by 400
Abstract
While gaining increasing attention, plant–microbiome–environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the [...] Read more.
While gaining increasing attention, plant–microbiome–environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron—elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology. Full article
(This article belongs to the Special Issue The Molecular Research of Plant and Microbial Communities)
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19 pages, 7471 KiB  
Article
Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of Senecio scandens Buch.-Ham in Hepatocellular Carcinoma Inhibition
by Jiayi Jiang, Haitao Wu, Xikun Jiang, Qing Ou, Zhanpeng Gan, Fangfang Han and Yongming Cai
Pharmaceuticals 2024, 17(12), 1707; https://doi.org/10.3390/ph17121707 - 18 Dec 2024
Viewed by 352
Abstract
Background: Hepatocellular carcinoma (HCC), a prevalent form of primary liver malignancy, arises from liver-specific hepatocytes. Senecio scandens Buch.-Ham(Climbing senecio) is a bitter-tasting plant of the Compositae family with anti-tumor properties. This study aims to identify the molecular targets and pathways through which Climbing [...] Read more.
Background: Hepatocellular carcinoma (HCC), a prevalent form of primary liver malignancy, arises from liver-specific hepatocytes. Senecio scandens Buch.-Ham(Climbing senecio) is a bitter-tasting plant of the Compositae family with anti-tumor properties. This study aims to identify the molecular targets and pathways through which Climbing senecio regulates HCC. Methods: Active ingredients of Climbing senecio were collected from four online databases and mapped to relevant target databases to obtain predicted targets. After recognizing the key pathways through which Climbing senecio acts in HCC. Gene expression data from GSE54238 Underwent differential expression and weighted gene correlation network analyses to identify HCC-related genes. The “Climbing senecio-Hepatocellular Carcinoma Targets” network was constructed using Cytoscape 3.10.1 software, followed by topology analysis to identify core genes. The expression and distribution of key targets were evaluated, and the differential expression of each key target between normal and diseased samples was calculated. Moreover, single-cell data from the Gene Expression Omnibus (GSE202642) were used to assess the distribution of Climbing senecio’s bioactive targets within major HCC clusters. An intersection analysis of these clusters with pharmacological targets and HCC-related genes identified Climbing senecio’s primary targets for this disease. Cell communication, receiver operating characteristic (ROC)analysis, survival analysis, immune filtration analysis, and molecular docking studies were conducted for detailed characterization. Results: Eleven components of Climbing senecio were identified, along with 520 relevant targets, 300 differentially expressed genes, and 3765 co-expression module genes associated with HCC. AKR1B1, CA2, FOS, CXCL2, SRC, ABCC1, and PLIN1 were identified within the intersection of HCC-related genes and Climbing senecio targets. TGFβ, IL-1, VEGF, and CXCL were identified as significant factors in the onset and progression of HCC. These findings underscore the anti-HCC potential and mode of action of Climbing senecio, providing insights into multi-targeted treatment approaches for HCC. Conclusions: This study revealed that Climbing senecio may target multiple pathways and genes in the process of regulating HCC and exert potential drug effects through a multi-target mechanism, which provides a new idea for the treatment of HCC. However, the research is predicated on network database analysis and bioinformatics, offering insights into HCC therapeutic potential while emphasizing the need for further validation. Full article
(This article belongs to the Section Pharmacology)
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