International Journal of Molecular Sciences

14 pages, 4690 KiB

Open AccessArticle

Systematic Analysis of Dof Gene Family in Prunus persica Unveils Candidate Regulators for Enhancing Cold Tolerance

by Zheng Chen, Xiaojun Wang, Juan Yan, Zhixiang Cai, Binbin Zhang, Jianlan Xu, Ruijuan Ma, Mingliang Yu and Zhijun Shen

Int. J. Mol. Sci. 2025, 26(15), 7509; https://doi.org/10.3390/ijms26157509 (registering DOI) - 4 Aug 2025

Abstract

Late-spring frost events severely damage low-chill peach blossoms, causing significant yield losses. Although 5-aminolevulinic acid (ALA) enhances cold tolerance through the PpC3H37-PpWRKY18 module, the regulatory mechanism of ALA on PpC3H37 remains to be elucidated. Using yeast one-hybrid screening with the PpC3H37 promoter as [...] Read more.

Late-spring frost events severely damage low-chill peach blossoms, causing significant yield losses. Although 5-aminolevulinic acid (ALA) enhances cold tolerance through the PpC3H37-PpWRKY18 module, the regulatory mechanism of ALA on PpC3H37 remains to be elucidated. Using yeast one-hybrid screening with the PpC3H37 promoter as bait, we identified PpDof9 as a key interacting transcription factor. A genome-wide analysis revealed 25 PpDof genes in peaches (Prunus persica). These genes exhibited variable physicochemical properties, with most proteins predicted as nuclear-localized. Subcellular localization experiments in tobacco revealed that PpDof9 was localized to the nucleus, consistent with predictions. A synteny analysis indicated nine segmental duplication pairs and tandem duplications on chromosomes 5 and 6, suggesting duplication events drove family expansion. A conserved motif analysis confirmed universal presence of the Dof domain (Motif 1). Promoter cis-element screening identified low-temperature responsive (LTR) elements in 12 PpDofs, including PpDof1, PpDof8, PpDof9, and PpDof25. The quantitative real-time PCR (qRT-PCR) results showed that PpDof1, PpDof8, PpDof9, PpDof15, PpDof16, and PpDof25 were significantly upregulated under low-temperature stress, and this upregulation was further enhanced by ALA pretreatment. Our findings demonstrate ALA-mediated modulation of specific PpDof TFs in cold response and provide candidates (PpDof1, PpDof9, PpDof8, PpDof25) for enhancing floral frost tolerance in peaches. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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26 pages, 1034 KiB

Open AccessReview

Metabolic Interactions in the Tumor Microenvironment of Classical Hodgkin Lymphoma: Implications for Targeted Therapy

by Michał Kurlapski, Alicja Braczko, Paweł Dubiela, Iga Walczak, Barbara Kutryb-Zając and Jan Maciej Zaucha

Int. J. Mol. Sci. 2025, 26(15), 7508; https://doi.org/10.3390/ijms26157508 (registering DOI) - 4 Aug 2025

Abstract

Classical Hodgkin lymphoma (cHL) is a biologically and clinically unique malignancy characterized by rare Hodgkin and Reed–Sternberg (HRS) cells surrounded by a dense and diverse inflammatory infiltrate. These malignant cells actively reshape the tumor microenvironment (TME) through metabolic reprogramming and immune evasion strategies. [...] Read more.

Classical Hodgkin lymphoma (cHL) is a biologically and clinically unique malignancy characterized by rare Hodgkin and Reed–Sternberg (HRS) cells surrounded by a dense and diverse inflammatory infiltrate. These malignant cells actively reshape the tumor microenvironment (TME) through metabolic reprogramming and immune evasion strategies. This review synthesizes current knowledge on how metabolic alterations contribute to tumor survival, immune dysfunction, and therapeutic resistance in cHL. We discuss novel therapeutic approaches aimed at disrupting these processes and examine the potential of combining metabolic interventions with immune-based strategies—such as immune checkpoint inhibitors (CPIs), epigenetic modulators, bispecific antibodies, and CAR-T/CAR-NK cell therapies—which may help overcome resistance and enhance anti-tumor responses. Several agents are currently under investigation for their ability to modulate immune cell metabolism and restore effective immune surveillance. Altogether, targeting metabolic vulnerabilities within both tumor and immune compartments offers a promising, multifaceted strategy to improve clinical outcomes in patients with relapsed or refractory cHL. Full article

(This article belongs to the Special Issue Lymphoma: Molecular Pathologies and Therapeutic Strategies)

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21 pages, 632 KiB

Open AccessReview

DNA Methylation in Bladder Cancer: Diagnostic and Therapeutic Perspectives—A Narrative Review

by Dragoş Puia, Marius Ivănuță and Cătălin Pricop

Int. J. Mol. Sci. 2025, 26(15), 7507; https://doi.org/10.3390/ijms26157507 (registering DOI) - 3 Aug 2025

Abstract

Bladder cancer pathogenesis is closely linked to epigenetic alterations, particularly DNA methylation and demethylation processes. Environmental carcinogens and persistent inflammatory stimuli—such as recurrent urinary tract infections—can induce aberrant DNA methylation, altering gene expression profiles and contributing to malignant transformation. This review synthesizes current [...] Read more.

Bladder cancer pathogenesis is closely linked to epigenetic alterations, particularly DNA methylation and demethylation processes. Environmental carcinogens and persistent inflammatory stimuli—such as recurrent urinary tract infections—can induce aberrant DNA methylation, altering gene expression profiles and contributing to malignant transformation. This review synthesizes current evidence on the role of DNA methyltransferases (DNMT1, DNMT3a, DNMT3b) and the hypermethylation of key tumour suppressor genes, including A2BP1, NPTX2, SOX11, PENK, NKX6-2, DBC1, MYO3A, and CA10, in bladder cancer. It also evaluates the therapeutic application of DNA-demethylating agents such as 5-azacytidine and highlights the impact of chronic inflammation on epigenetic regulation. Promoter hypermethylation of tumour suppressor genes leads to transcriptional silencing and unchecked cell proliferation. Urine-based DNA methylation assays provide a sensitive and specific method for non-invasive early detection, with single-target approaches offering high diagnostic precision. Animal models are increasingly employed to validate these findings, allowing the study of methylation dynamics and gene–environment interactions in vivo. DNA methylation represents a key epigenetic mechanism in bladder cancer, with significant diagnostic, prognostic, and therapeutic implications. Integration of human and experimental data supports the use of methylation-based biomarkers for early detection and targeted treatment, paving the way for personalized approaches in bladder cancer management. Full article

(This article belongs to the Section Molecular Oncology)

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16 pages, 823 KiB

Open AccessArticle

Biomarker Correlations in PTSD: IL-18, IRE1, pERK, and ATF6 via Courtauld Emotional Control Scale (CECS)

by Izabela Woźny-Rasała and Ewa Alicja Ogłodek

Int. J. Mol. Sci. 2025, 26(15), 7506; https://doi.org/10.3390/ijms26157506 (registering DOI) - 3 Aug 2025

Abstract

Post-traumatic stress disorder (PTSD) is a chronic mental health condition resulting from exposure to traumatic events. It is associated with long-term neurobiological changes and disturbances in emotional regulation. Understanding the sociodemographic profiles, biomarkers, and emotional control in patients with PTSD helps to better [...] Read more.

Post-traumatic stress disorder (PTSD) is a chronic mental health condition resulting from exposure to traumatic events. It is associated with long-term neurobiological changes and disturbances in emotional regulation. Understanding the sociodemographic profiles, biomarkers, and emotional control in patients with PTSD helps to better comprehend the impact of the disorder on the body and its clinical course. An analysis of biomarkers such as Interleukin-18 (IL-18), Inositol-Requiring Enzyme 1 (IRE1), Phosphorylated Extracellular Signal-Regulated Kinase (pERK), and Activating Transcription Factor–6 (ATF-6) in PTSD patients with varying durations of illness (≤5 years and >5 years) and a control group without PTSD revealed significant differences. Patients with recently diagnosed PTSD (≤5 years) showed markedly elevated levels of inflammatory and cellular stress markers, indicating an intense neuroinflammatory response during the acute phase of the disorder. In the chronic PTSD group (>5 years), the levels of these biomarkers were lower than in the recently diagnosed group, but still significantly higher than in the control group. An opposite trend was observed regarding the suppression of negative emotions, as measured by the Courtauld Emotional Control Scale (CECS): individuals with chronic PTSD exhibited a significantly greater suppression of anger, depression, and anxiety than those with recent PTSD or healthy controls. Correlations between biomarkers were strongest in individuals with chronic PTSD, suggesting a persistent neuroinflammatory dysfunction. However, the relationships between biomarkers and emotional suppression varied depending on the stage of PTSD. These findings highlight the critical role of PTSD duration in shaping the neurobiological and emotional mechanisms of the disorder, which may have important implications for therapeutic strategies and patient monitoring. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

19 pages, 1016 KiB

Open AccessArticle

Genetic Associations of ITGB3, FGG, GP1BA, PECAM1, and PEAR1 Polymorphisms and the Platelet Activation Pathway with Recurrent Pregnancy Loss in the Korean Population

by Eun Ju Ko, Eun Hee Ahn, Hyeon Woo Park, Jae Hyun Lee, Da Hwan Kim, Young Ran Kim, Ji Hyang Kim and Nam Keun Kim

Int. J. Mol. Sci. 2025, 26(15), 7505; https://doi.org/10.3390/ijms26157505 (registering DOI) - 3 Aug 2025

Abstract

Recurrent pregnancy loss (RPL) is defined as the occurrence of two or more pregnancy losses before 20 weeks of gestation. RPL is a common medical condition among reproductive-age women, with approximately 23 million cases reported annually worldwide. Up to 5% of pregnant women [...] Read more.

Recurrent pregnancy loss (RPL) is defined as the occurrence of two or more pregnancy losses before 20 weeks of gestation. RPL is a common medical condition among reproductive-age women, with approximately 23 million cases reported annually worldwide. Up to 5% of pregnant women may experience two or more consecutive pregnancy losses. Previous studies have investigated risk factors for RPL, including maternal age, uterine pathology, genetic anomalies, infectious agents, endocrine disorders, thrombophilia, and immune dysfunction. However, RPL is a disease caused by a complex interaction of genetic factors, environmental factors (e.g., diet, lifestyle, and stress), epigenetic factors, and the immune system. In addition, due to the lack of research on genetics research related to RPL, the etiology remains unclear in up to 50% of cases. Platelets play a critical role in pregnancy maintenance. This study examined the associations of platelet receptor and ligand gene variants, including integrin subunit beta 3 (ITGB3) rs2317676 A > G, rs3809865 A > T; fibrinogen gamma chain (FGG) rs1049636 T > C, rs2066865 T > C; glycoprotein 1b subunit alpha (GP1BA) rs2243093 T > C, rs6065 C > T; platelet endothelial cell adhesion molecule 1 (PECAM1) rs2812 C > T; and platelet endothelial aggregation receptor 1 (PEAR1) rs822442 C > A, rs12137505 G > A, with RPL prevalence. In total, 389 RPL patients and 375 healthy controls (all Korean women) were enrolled. Genotyping of each single nucleotide polymorphism was performed using polymerase chain reaction–restriction fragment length polymorphism and the TaqMan genotyping assay. All samples were collected with approval from the Institutional Review Board at Bundang CHA Medical Center. The ITGB3 rs3809865 A > T genotype was strongly associated with RPL prevalence (pregnancy loss [PL] ≥ 2: adjusted odds ratio [AOR] = 2.505, 95% confidence interval [CI] = 1.262–4.969, p = 0.009; PL ≥ 3: AOR = 3.255, 95% CI = 1.551–6.830, p = 0.002; PL ≥ 4: AOR = 3.613, 95% CI = 1.403–9.307, p = 0.008). The FGG rs1049636 T > C polymorphism was associated with a decreased risk in women who had three or more pregnancy losses (PL ≥ 3: AOR = 0.673, 95% CI = 0.460–0.987, p = 0.043; PL ≥ 4: AOR = 0.556, 95% CI = 0.310–0.997, p = 0.049). These findings indicate significant associations of the ITGB3 rs3809865 A > T and FGG rs1049636 T > C polymorphisms with RPL, suggesting that platelet function influences RPL in Korean women. Full article

(This article belongs to the Special Issue Molecular Research in Gynecological Diseases—2nd Edition)

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21 pages, 3334 KiB

Open AccessArticle

Protective Efficacy of Lactobacillus plantarum Postbiotic beLP-K in a Dexamethasone-Induced Sarcopenia Model

by Juyeong Moon, Jin-Ho Lee, Eunwoo Jeong, Harang Park, Hye-Yeong Song, Jinsu Choi, Min-ah Kim, Kwon-Il Han, Doyong Kim, Han Sung Kim and Tack-Joong Kim

Int. J. Mol. Sci. 2025, 26(15), 7504; https://doi.org/10.3390/ijms26157504 (registering DOI) - 3 Aug 2025

Abstract

Sarcopenia is characterized by a reduction in muscle function and skeletal muscle mass relative to that of healthy individuals. In older adults and those who are less resistant to sarcopenia, glucocorticoid secretion or accumulation during treatment exacerbates muscle protein degradation, potentially causing sarcopenia. [...] Read more.

Sarcopenia is characterized by a reduction in muscle function and skeletal muscle mass relative to that of healthy individuals. In older adults and those who are less resistant to sarcopenia, glucocorticoid secretion or accumulation during treatment exacerbates muscle protein degradation, potentially causing sarcopenia. This study assessed the preventive effects and mechanisms of heat-killed Lactobacillus plantarum postbiotic beLP-K (beLP-K) against dexamethasone (DEX)-induced sarcopenia in C2C12 myotubes and Sprague-Dawley rats. The administration of beLP-K did not induce cytotoxicity and mitigated cell damage caused by DEX. Furthermore, beLP-K significantly reduced the expression of forkhead box O3 α (FoxO3α), muscle atrophy f-box (MAFbx)/atrogin-1, and muscle RING-finger protein-1 (MuRF1), which are associated with muscle protein degradation. DEX induced weight loss in rats; however, in the beLP-K group, weight gain was observed. Micro-computed tomography analysis revealed that beLP-K increased muscle mass, correlating with weight and grip strength. beLP-K alleviated the DEX-induced reduction in grip strength and increased the mass of hind leg muscles. The correlation between beLP-K administration and increased muscle mass was associated with decreased expression levels of muscle degradation-related proteins such as MAFbx/atrogin-1 and MuRF1. Therefore, beLP-K may serve as a treatment for sarcopenia or as functional food material. Full article

(This article belongs to the Section Molecular Biology)

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24 pages, 1912 KiB

Open AccessReview

Utility of Multicellular Spheroids for Investigating Mechanisms of Chemoresistance in Triple-Negative Breast Cancer

by Keith N. Ncube, Iman van den Bout, Clarissa Willers, Chrisna Gouws and Werner Cordier

Int. J. Mol. Sci. 2025, 26(15), 7503; https://doi.org/10.3390/ijms26157503 (registering DOI) - 3 Aug 2025

Abstract

Chemoresistance is a major challenge in the treatment of triple-negative breast cancer (TNBC). Multicellular spheroids are an attractive platform for investigating chemoresistance in TNBC, as they replicate the cues of the tumour microenvironment in vivo. We conducted a comprehensive literature search to summarise [...] Read more.

Chemoresistance is a major challenge in the treatment of triple-negative breast cancer (TNBC). Multicellular spheroids are an attractive platform for investigating chemoresistance in TNBC, as they replicate the cues of the tumour microenvironment in vivo. We conducted a comprehensive literature search to summarise the multifactorial and interlinked mechanisms driving chemoresistance in TNBC spheroids. These mechanisms include spatial heterogeneity, hypoxia, extracellular matrix remodelling, tumour–stroma crosstalk, drug efflux, apoptotic resistance, and cancer stem cell signalling. Strategies for overcoming chemoresistance in TNBC spheroids include nanocarrier systems to overcome spatial diffusion limitations, pathway inhibition, and targeting tumour–microenvironment interactions. Despite their advantages, some spheroid models face challenges such as low reproducibility, a lack of heterogeneity, variability in size and shape, limited vascularisation, and constraints in long-term culture. Advanced culturing platforms such as clinostat bioreactors allow for extended culture periods, enabling mature spheroid drug testing. Furthermore, advanced analytical techniques provide spatially resolved spheroid data. These multifactorial and interlinked mechanisms reflect the tumour microenvironment in vivo that spheroids recapitulate, rendering them valuable models for studying chemoresistance. The incorporation of stromal components and advanced analytical workflows will enhance the utility and translational relevance of spheroids as reliable preclinical models for drug discovery in TNBC. Full article

(This article belongs to the Special Issue Recent Advances in 3D Tumor Models for Cancer Research)

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Graphical abstract

33 pages, 1280 KiB

Open AccessReview

Pathophysiology of Status Epilepticus Revisited

by Rawiah S. Alshehri, Moafaq S. Alrawaili, Basma M. H. Zawawi, Majed Alzahrany and Alaa H Habib

Int. J. Mol. Sci. 2025, 26(15), 7502; https://doi.org/10.3390/ijms26157502 (registering DOI) - 3 Aug 2025

Abstract

Status epilepticus occurs when a seizure lasts more than five minutes or when multiple seizures occur with incomplete return to baseline. SE induces a myriad of pathological changes involving synaptic and extra-synaptic factors. The transition from a self-limiting seizure to a self-sustaining one [...] Read more.

Status epilepticus occurs when a seizure lasts more than five minutes or when multiple seizures occur with incomplete return to baseline. SE induces a myriad of pathological changes involving synaptic and extra-synaptic factors. The transition from a self-limiting seizure to a self-sustaining one is established by maladaptive receptor trafficking, whereby GABA_A receptors are progressively endocytosed while glutamatergic receptors (NMDA and AMPA) are transported to the synaptic membrane, causing excitotoxicity and alteration in glutamate-dependent downstream signaling. The subsequent influx of Ca²⁺ exposes neurons to increased levels of [Ca²⁺]i, which overwhelms mitochondrial buffering, resulting in irreversible mitochondrial membrane depolarization and mitochondrial injury. Oxidative stress resulting from mitochondrial leakage and increased production of reactive oxygen species activates the inflammasome and induces a damage-associated molecular pattern. Neuroinflammation perpetuates oxidative stress and exacerbates mitochondrial injury, thereby jeopardizing mitochondrial energy supply in a state of accelerated ATP consumption. Additionally, Ca²⁺ overload can directly damage neurons by activating enzymes involved in the breakdown of proteins, phospholipids, and nucleic acids. The cumulative effect of these effector pathways is neuronal injury and neuronal death. Surviving neurons undergo long-term alterations that serve as a substrate for epileptogenesis. This review highlights the multifaceted mechanisms underlying SE self-sustainability, pharmacoresistance, and subsequent epileptogenesis. Full article

(This article belongs to the Special Issue From Molecular Insights to Novel Therapies: Neurological Diseases)

25 pages, 900 KiB

Open AccessReview

Stem Cell-Derived Corneal Epithelium: Engineering Barrier Function for Ocular Surface Repair

by Emily Elizabeth Fresenko, Jian-Xing Ma, Matthew Giegengack, Atalie Carina Thompson, Anthony Atala, Andrew J. W. Huang and Yuanyuan Zhang

Int. J. Mol. Sci. 2025, 26(15), 7501; https://doi.org/10.3390/ijms26157501 (registering DOI) - 3 Aug 2025

Abstract

The cornea, the transparent anterior window of the eye, critically refracts light and protects intraocular structures. Corneal pathologies, including trauma, infection, chemical injury, metabolic diseases, genetic conditions, and age-related degeneration, can lead to significant visual impairment. While penetrating keratoplasty or full-thickness corneal transplantation [...] Read more.

The cornea, the transparent anterior window of the eye, critically refracts light and protects intraocular structures. Corneal pathologies, including trauma, infection, chemical injury, metabolic diseases, genetic conditions, and age-related degeneration, can lead to significant visual impairment. While penetrating keratoplasty or full-thickness corneal transplantation remains a standard and effective intervention for severe corneal dysfunction, limitations in donor tissue availability and the risk of immunogenic graft rejection necessitate alternative therapeutic strategies. Furthermore, for cases of isolated epithelial disfunction, a full-thickness cornea graft may not be required or effective. This review examines the potential of corneal epithelial constructs derived from autologous stem cells with functional barrier properties for corneal reconstruction and in vitro pharmacotoxicity testing. In this review, we delineate the current limitations of corneal transplantation, the advantages of stem cell-based approaches, and recent advances in generating engineered corneal epithelium. Finally, we address remaining technical challenges and propose future research directions aimed at clinical translation. Full article

(This article belongs to the Special Issue Enhancing Stem Cell Grafting in Tissue Regeneration and Repair)

17 pages, 3172 KiB

Open AccessArticle

The Effect of Ketamine on the Immune System in Patients with Treatment-Resistant Depression

by Łukasz P. Szałach, Klaudia Ciesielska-Figlon, Agnieszka Daca, Wiesław J. Cubała and Katarzyna A. Lisowska

Int. J. Mol. Sci. 2025, 26(15), 7500; https://doi.org/10.3390/ijms26157500 (registering DOI) - 3 Aug 2025

Abstract

Treatment-resistant depression (TRD) is associated with immune dysregulation. Ketamine, a rapid-acting antidepressant, may exert effects via immunomodulation. The aim was to examine ketamine’s impact on immune markers in TRD, including T-cell subsets, cytokines, and in vitro T-cell responses. Eighteen TRD inpatients received 0.5 [...] Read more.

Treatment-resistant depression (TRD) is associated with immune dysregulation. Ketamine, a rapid-acting antidepressant, may exert effects via immunomodulation. The aim was to examine ketamine’s impact on immune markers in TRD, including T-cell subsets, cytokines, and in vitro T-cell responses. Eighteen TRD inpatients received 0.5 mg/kg iv ketamine. Blood was sampled at baseline, 4 h, and 24 h to analyze T-cell phenotypes (CD28, CD69, CD25, CD95, HLA-DR) and serum cytokines (IL-6, IL-8, IL-10, TNF-α, IL-1β, IL-12p70). In vitro, PBMCs from TRD patients and controls were exposed to low (185 ng/mL) and high (300 ng/mL) ketamine doses. Ketamine induced a transient increase in total T cells and CD4⁺CD25⁺ and CD4⁺CD28⁺ subsets at 4 h, followed by a reduction in CD4⁺ and an increase in CD8⁺ T cells at 24 h, decreasing the CD4⁺/CD8⁺ ratio. Activation markers (CD4⁺CD69⁺, CD4⁺HLA-DR⁺, CD8⁺CD25⁺, CD8⁺HLA-DR⁺) declined at 24 h. Serum IL-10 increased, IL-6 decreased, and IL-8 levels—initially elevated—showed a sustained reduction. In vitro, high-dose ketamine enhanced the proliferation of TRD CD4⁺ T cells and dose-dependent IL-8 and IL-6 secretion from activated cells. Ketamine induces rapid, transient immune changes in TRD, including reduced T-cell activation and cytokine modulation. A sustained IL-8 decrease suggests anti-inflammatory effects and potential as a treatment-response biomarker. Full article

(This article belongs to the Special Issue Molecular Insights into Anxiety and Depression: Pathomechanisms and Therapeutic Strategies)

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18 pages, 57416 KiB

Open AccessArticle

Green Synthesis and Characterization of Silver Nanoparticles Using Artemisia terrae-albae Extracts and Evaluation of Their Cytogenotoxic Effects

by Moldyr Dyusebaeva, Dmitriy Berillo, Zhansaya Yesbussinova, Nailya Ibragimova, Daniil Shepilov, Sandugash Sydykbayeva, Almagul Almabekova, Nurzhan Chinibayeva, Adewale Olufunsho Adeloye and Gulzat Berganayeva

Int. J. Mol. Sci. 2025, 26(15), 7499; https://doi.org/10.3390/ijms26157499 (registering DOI) - 3 Aug 2025

Abstract

The development of non-toxic silver nanoparticles (AgNPs) for medical and other diverse applications is steadily increasing. However, this study specifically aims to determine the cytotoxic effects of AgNPs synthesized via a green chemistry approach using aqueous-ethanol and ethyl acetate extracts of Artemisia terrae-albae [...] Read more.

The development of non-toxic silver nanoparticles (AgNPs) for medical and other diverse applications is steadily increasing. However, this study specifically aims to determine the cytotoxic effects of AgNPs synthesized via a green chemistry approach using aqueous-ethanol and ethyl acetate extracts of Artemisia terrae-albae. The photophysical, morphological, and size distribution characteristics of the synthesized AgNPs are analyzed using UV-Vis spectroscopy and transmission electron microscopy (TEM). A modified Allium cepa assay is employed to evaluate biological responses, including root growth, root number, and mitotic index. In this assay, the cell cycles of onion bulbs are synchronized and pre-incubated at 4 °C for 72 h prior to treatment. This study reveals that the AgNPs synthesized from the ethanol extract exhibit notable stability and higher cytotoxicity activity, with a root length of 0.6 ± 0.13 cm, root number of 16 ± 6.88, and mitotic index of 25.0 ± 2.6. These values are significantly more cytogenotoxic than those observed for the ethyl-acetate-derived nanoparticles, which show a root length of 0.8 ± 0.17 cm, root number of 18 ± 6.27, and mitotic index of 36 ± 3.6. These findings highlight the potential of green-synthesized AgNPs as effective cytotoxic agents, especially those obtained from ethanol extract, possibly due to a greater influence of the quantity of diverse phenolic compounds present in the complex mixtures than in the ethyl acetate extract, which otherwise enhanced their morphology, shape, and size. These, overall, contributed to the biological activity. Full article

(This article belongs to the Special Issue Latest Advances in Nanoparticles for Modern Biomedicine (2nd Edition))

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60 pages, 1110 KiB

Open AccessReview

The Redox Revolution in Brain Medicine: Targeting Oxidative Stress with AI, Multi-Omics and Mitochondrial Therapies for the Precision Eradication of Neurodegeneration

by Matei Șerban, Corneliu Toader and Răzvan-Adrian Covache-Busuioc

Int. J. Mol. Sci. 2025, 26(15), 7498; https://doi.org/10.3390/ijms26157498 (registering DOI) - 3 Aug 2025

Abstract

Oxidative stress is a defining and pervasive driver of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS). As a molecular accelerant, reactive oxygen species (ROS) and reactive nitrogen species (RNS) compromise mitochondrial function, amplify lipid peroxidation, induce [...] Read more.

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

(This article belongs to the Special Issue Neurodegenerative Disease: Looking for Oxidative Stress and Inflammation Mechanisms)

27 pages, 1413 KiB

Open AccessArticle

Effects of ε-Poly-L-Lysine/Chitosan Composite Coating on the Storage Quality, Reactive Oxygen Species Metabolism, and Membrane Lipid Metabolism of Tremella fuciformis

by Junzheng Sun, Yingying Wei, Longxiang Li, Mengjie Yang, Yusha Liu, Qiting Li, Shaoxiong Zhou, Chunmei Lai, Junchen Chen and Pufu Lai

Int. J. Mol. Sci. 2025, 26(15), 7497; https://doi.org/10.3390/ijms26157497 (registering DOI) - 3 Aug 2025

Abstract

This study aimed to investigate the efficacy of a composite coating composed of 150 mg/L ε-Poly-L-lysine (ε-PL) and 5 g/L chitosan (CTS) in extending the shelf life and maintaining the postharvest quality of fresh Tremella fuciformis. Freshly harvested T. fuciformis were treated [...] Read more.

This study aimed to investigate the efficacy of a composite coating composed of 150 mg/L ε-Poly-L-lysine (ε-PL) and 5 g/L chitosan (CTS) in extending the shelf life and maintaining the postharvest quality of fresh Tremella fuciformis. Freshly harvested T. fuciformis were treated by surface spraying, with distilled water serving as the control. The effects of the coating on storage quality, physicochemical properties, reactive oxygen species (ROS) metabolism, and membrane lipid metabolism were evaluated during storage at (25 ± 1) °C. The results showed that the ε-PL/CTS composite coating significantly retarded quality deterioration, as evidenced by reduced weight loss, maintained whiteness and color, and higher retention of soluble sugars, soluble solids, and soluble proteins. The coating also effectively limited water migration and loss. Mechanistically, the coated T. fuciformis exhibited enhanced antioxidant capacity, characterized by increased superoxide anion (O₂⁻) resistance capacity, higher activities of antioxidant enzymes (SOD, CAT, APX), and elevated levels of non-enzymatic antioxidants (AsA, GSH). This led to a significant reduction in malondialdehyde (MDA) accumulation, alongside improved DPPH radical scavenging activity and reducing power. Furthermore, the ε-PL/CTS coating preserved cell membrane integrity by inhibiting the activities of lipid-degrading enzymes (lipase, LOX, PLD), maintaining higher levels of key phospholipids (phosphatidylinositol and phosphatidylcholine), delaying phosphatidic acid accumulation, and consequently reducing cell membrane permeability. In conclusion, the ε-PL/CTS composite coating effectively extends the shelf life and maintains the quality of postharvest T. fuciformis by modulating ROS metabolism and preserving membrane lipid homeostasis. This study provides a theoretical basis and a practical approach for the quality control of fresh T. fuciformis. Full article

(This article belongs to the Section Biochemistry)

36 pages, 3231 KiB

Open AccessReview

CRISPR-Cas Gene Editing Technology in Potato

by Zagipa Sapakhova, Rakhim Kanat, Khanylbek Choi, Dias Daurov, Ainash Daurova, Kabyl Zhambakin and Malika Shamekova

Int. J. Mol. Sci. 2025, 26(15), 7496; https://doi.org/10.3390/ijms26157496 (registering DOI) - 3 Aug 2025

Abstract

Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food [...] Read more.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food security threats in many countries. Traditional potato breeding faces several challenges, primarily due to its genetic complexity and the time-consuming nature of the process. Therefore, gene editing—CRISPR-Cas technology—allows for more precise and rapid changes to the potato genome, which can speed up the breeding process and lead to more effective varieties. In this review, we consider CRISPR-Cas technology as a potential tool for plant breeding strategies to ensure global food security. This review summarizes in detail current and potential technological breakthroughs that open new opportunities for the use of CRISPR-Cas technology for potato breeding, as well as for increasing resistance to abiotic and biotic stresses, and improving potato tuber quality. In addition, the review discusses the challenges and future perspectives of the CRISPR-Cas system in the prospects of the development of potato production and the regulation of gene-edited crops in different countries around the world. Full article

(This article belongs to the Section Molecular Plant Sciences)

20 pages, 3151 KiB

Open AccessArticle

Intermittent Hypoxia Induces Cognitive Dysfunction and Hippocampal Gene Expression Changes in a Mouse Model of Obstructive Sleep Apnea

by Kenta Miyo, Yuki Uchida, Ryota Nakano, Shotaro Kamijo, Masahiro Hosonuma, Yoshitaka Yamazaki, Hikaru Isobe, Fumihiro Ishikawa, Hiroshi Onimaru, Akira Yoshikawa, Shin-Ichi Sakakibara, Tatsunori Oguchi, Takuya Yokoe and Masahiko Izumizaki

Int. J. Mol. Sci. 2025, 26(15), 7495; https://doi.org/10.3390/ijms26157495 (registering DOI) - 3 Aug 2025

Abstract

Obstructive sleep apnea syndrome (OSAS) is characterized by cycles of decreased blood oxygen saturation followed by reoxygenation due to transient apnea. Cognitive dysfunction is a complication of OSAS, but its mechanisms remain unclear. Eight-week-old C57BL/6J mice were exposed to intermittent hypoxia (IH) to [...] Read more.

Obstructive sleep apnea syndrome (OSAS) is characterized by cycles of decreased blood oxygen saturation followed by reoxygenation due to transient apnea. Cognitive dysfunction is a complication of OSAS, but its mechanisms remain unclear. Eight-week-old C57BL/6J mice were exposed to intermittent hypoxia (IH) to model OSAS, and cognitive function and hippocampal gene expression were analyzed. Three groups were maintained for 28 days: an IH group (oxygen alternating between 10 and 21% in 2 min cycles, 8 h/day), sustained hypoxia group (SH) (10% oxygen, 8 h/day), and control group (21% oxygen). Behavioral tests and RNA sequencing (RNA-seq) analysis were performed. While Y-maze test results showed no differences, the IH group demonstrated impaired memory and learning in passive avoidance tests compared to control and SH groups. RNA-seq revealed coordinated suppression of mitochondrial function genes and oxidative stress response pathways, specifically in the IH group. RT-qPCR showed decreased Lars2, Hmcn1, and Vstm2l expression in the IH group. Pathway analysis showed the suppression of the KEAP1-NFE2L2 antioxidant pathway in the IH group vs. the SH group. Our findings demonstrate that IH induces cognitive dysfunction through suppression of the KEAP1-NFE2L2 antioxidant pathway and downregulation of mitochondrial genes (Lars2, Vstm2l), leading to oxidative stress and mitochondrial dysfunction. These findings advance our understanding of the molecular basis underlying OSAS-related cognitive impairment. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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26 pages, 1260 KiB

Open AccessArticle

Osteogenic Differentiation of Mesenchymal Stem Cells Induced by Geometric Mechanotransductive 3D-Printed Poly-(L)-Lactic Acid Matrices

by Harrison P. Ryan, Bruce K. Milthorpe and Jerran Santos

Int. J. Mol. Sci. 2025, 26(15), 7494; https://doi.org/10.3390/ijms26157494 (registering DOI) - 2 Aug 2025

Abstract

Bone-related defects present a key challenge in orthopaedics. The current gold standard, autografts, poses significant limitations, such as donor site morbidity, limited supply, and poor morphological adaptability. This study investigates the potential of scaffold geometry to induce osteogenic differentiation of human adipose-derived stem [...] Read more.

Bone-related defects present a key challenge in orthopaedics. The current gold standard, autografts, poses significant limitations, such as donor site morbidity, limited supply, and poor morphological adaptability. This study investigates the potential of scaffold geometry to induce osteogenic differentiation of human adipose-derived stem cells (hADSCs) through mechanotransduction, without the use of chemical inducers. Four distinct poly-(L)-lactic acid (PLA) scaffold architectures—Traditional Cross (Tc), Triangle (T), Diamond (D), and Gyroid (G)—were fabricated using fused filament fabrication (FFF) 3D printing. hADSCs were cultured on these scaffolds, and their response was evaluated utilising an alkaline phosphatase (ALP) assay, immunofluorescence, and extensive proteomic analyses. The results showed the D scaffold to have the highest ALP activity, followed by Tc. Proteomics results showed that more than 1200 proteins were identified in each scaffold with unique proteins expressed in each scaffold, respectively Tc—204, T—194, D—244, and G—216. Bioinformatics analysis revealed structures with complex curvature to have an increased expression of proteins involved in mid- to late-stage osteogenesis signalling and differentiation pathways, while the Tc scaffold induced an increased expression of signalling and differentiation pathways pertaining to angiogenesis and early osteogenesis. Full article

(This article belongs to the Special Issue Novel Approaches for Tissue Repair and Tissue Regeneration)

56 pages, 1035 KiB

Open AccessReview

Trace Elements—Role in Joint Function and Impact on Joint Diseases

by Łukasz Bryliński, Katarzyna Brylińska, Filip Woliński, Jolanta Sado, Miłosz Smyk, Olga Komar, Robert Karpiński, Marcin Prządka and Jacek Baj

Int. J. Mol. Sci. 2025, 26(15), 7493; https://doi.org/10.3390/ijms26157493 (registering DOI) - 2 Aug 2025

Abstract

Proper joint function has a significant impact on people’s quality of life. Joints are the point of connection between two or more bones and consist of at least three elements: joint surfaces, the joint capsule, and the joint cavity. Joint diseases are a [...] Read more.

Proper joint function has a significant impact on people’s quality of life. Joints are the point of connection between two or more bones and consist of at least three elements: joint surfaces, the joint capsule, and the joint cavity. Joint diseases are a serious social problem. Risk factors for the development of these diseases include overweight and obesity, gender, and intestinal microbiome disorders. Another factor that is considered to influence joint diseases is trace elements. Under normal conditions, elements such as iron (Fe), copper (Cu), cobalt (Co), iodine (I), manganese (Mn), zinc (Zn), silver (Ag), cadmium (Cd), mercury (Hg), lead (Pb), nickel (Ni) selenium (Se), boron (B), and silicon (Si) are part of enzymes involved in reactions that determine the proper functioning of cells, regulate redox metabolism, and determine the maturation of cells that build joint components. However, when the normal concentration of the above-mentioned elements is disturbed and toxic elements are present, dangerous joint diseases can develop. In this article, we focus on the role of trace elements in joint function. We describe the molecular mechanisms that explain their interaction with chondrocytes, osteocytes, osteoblasts, osteoclasts, and synoviocytes, as well as their proliferation, apoptosis, and extracellular matrix synthesis. We also focus on the role of these trace elements in the pathogenesis of joint diseases: rheumatoid arthritis (RA), osteoarthritis (OA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), and systemic lupus erythematosus (SLE). We describe the roles of increased or decreased concentrations of individual elements in the pathogenesis and development of joint diseases and their impact on inflammation and disease progression, referring to molecular mechanisms. We also discuss their potential application in the treatment of joint diseases. Full article

(This article belongs to the Special Issue Musculoskeletal Disorders: From Molecular Pathology to Novel Therapeutic Approach)

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17 pages, 2547 KiB

Open AccessArticle

A Host Cell Vector Model for Analyzing Viral Protective Antigens and Host Immunity

by Sun-Min Ahn, Jin-Ha Song, Seung-Eun Son, Ho-Won Kim, Gun Kim, Seung-Min Hong, Kang-Seuk Choi and Hyuk-Joon Kwon

Int. J. Mol. Sci. 2025, 26(15), 7492; https://doi.org/10.3390/ijms26157492 (registering DOI) - 2 Aug 2025

Abstract

Avian influenza A viruses (IAVs) pose a persistent threat to the poultry industry, causing substantial economic losses. Although traditional vaccines have helped reduce the disease burden, they typically rely on multivalent antigens, emphasize humoral immunity, and require intensive production. This study aimed to [...] Read more.

Avian influenza A viruses (IAVs) pose a persistent threat to the poultry industry, causing substantial economic losses. Although traditional vaccines have helped reduce the disease burden, they typically rely on multivalent antigens, emphasize humoral immunity, and require intensive production. This study aimed to establish a genetically matched host–cell system to evaluate antigen-specific immune responses and identify conserved CD8+ T cell epitopes in avian influenza viruses. To this end, we developed an MHC class I genotype (B21)-matched host (Lohmann VALO SPF chicken) and cell vector (DF-1 cell line) model. DF-1 cells were engineered to express the hemagglutinin (HA) gene of clade 2.3.4.4b H5N1 either transiently or stably, and to stably express the matrix 1 (M1) and nucleoprotein (NP) genes of A/chicken/South Korea/SL20/2020 (H9N2, Y280-lineage). Following prime-boost immunization with HA-expressing DF-1 cells, only live cells induced strong hemagglutination inhibition (HI) and virus-neutralizing (VN) antibody titers in haplotype-matched chickens. Importantly, immunization with DF-1 cells transiently expressing NP induced stronger IFN-γ production than those expressing M1, demonstrating the platform’s potential for differentiating antigen-specific cellular responses. CD8+ T cell epitope mapping by mass spectrometry identified one distinct MHC class I-bound peptide from each of the HA-, M1-, and NP-expressing DF-1 cell lines. Notably, the identified HA epitope was conserved in 97.6% of H5-subtype IAVs, and the NP epitope in 98.5% of pan-subtype IAVs. These findings highlight the platform’s utility for antigen dissection and rational vaccine design. While limited by MHC compatibility, this approach enables identification of naturally presented epitopes and provides insight into conserved, functionally constrained viral targets. Full article

(This article belongs to the Special Issue Molecular Research on Immune Response to Virus Infection and Vaccines)

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15 pages, 1899 KiB

Open AccessArticle

Lipidomic Profile of Individuals Infected by Schistosoma mansoni

by Thainá Rodrigues de Souza Fialho, Ronald Alves dos Santos, Yuri Tabajara, Ane Caroline Casaes, Michael Nascimento Macedo, Bruna Oliveira Lopes Souza, Kelvin Edson Marques de Jesus, Leonardo Paiva Farias, Camilla Almeida Menezes, Isadora Cristina de Siqueira, Carlos Arterio Sorgi, Adriano Queiroz and Ricardo Riccio Oliveira

Int. J. Mol. Sci. 2025, 26(15), 7491; https://doi.org/10.3390/ijms26157491 (registering DOI) - 2 Aug 2025

Abstract

Schistosoma mansoni infection is associated with hepatic inflammation and fibrosis, but its systemic metabolic effects remain poorly understood. This study aimed to investigate changes in the serum lipidomic profile associated with S. mansoni infection and parasite load in individuals from an endemic area. [...] Read more.

Schistosoma mansoni infection is associated with hepatic inflammation and fibrosis, but its systemic metabolic effects remain poorly understood. This study aimed to investigate changes in the serum lipidomic profile associated with S. mansoni infection and parasite load in individuals from an endemic area. This cross-sectional analysis was nested within a longitudinal cohort study conducted in northeastern Brazil. Parasitological diagnosis and quantification were performed using the Kato–Katz technique. A total of 45 individuals were selected and divided into three groups: high parasite load (HL), low parasite load (LL), and uninfected controls (NegE). Serum samples were analyzed using mass-spectrometry-based lipidomics. The most abundant lipid subclasses across all groups were phosphatidylcholines (PC), triacylglycerols (TAG), and phosphatidylethanolamines (PE). However, individuals in the HL group exhibited distinct lipidomic profiles, with increased levels of specific phosphatidylinositols (PI) and reduced levels of certain TAG species compared to the NegE group. These changes may reflect host–parasite interactions and immune–metabolic alterations driven by intense infection. Our findings suggest that S. mansoni infection, particularly at higher parasite burdens, can influence the host’s serum lipid profile and may contribute to metabolic disturbances in endemic populations. Full article

(This article belongs to the Special Issue Omics Science and Research in Human Health and Disease)

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16 pages, 8522 KiB

Open AccessArticle

Plant Extracts as Modulators of the Wound Healing Process—Preliminary Study

by Anna Herman, Aleksandra Leska, Patrycja Wińska and Andrzej Przemysław Herman

Int. J. Mol. Sci. 2025, 26(15), 7490; https://doi.org/10.3390/ijms26157490 (registering DOI) - 2 Aug 2025

Abstract

The treatment of chronic wounds is one of the most complex therapeutic problems of modern medicine. It leads to patients’ protracted recovery, generating high treatment costs. Herbal products may be useful in the treatment of chronic wounds via a wide range of pharmacological [...] Read more.

The treatment of chronic wounds is one of the most complex therapeutic problems of modern medicine. It leads to patients’ protracted recovery, generating high treatment costs. Herbal products may be useful in the treatment of chronic wounds via a wide range of pharmacological properties and multidirectional effects on the wound healing phases. The study aims to determine the ability of selected plant extracts to modulate the processes involved in wound healing. The antimicrobial (MIC, MBC, MFC) and antioxidant (ABTS, DPPH) activities, cytotoxicity (MTT test), scratch wound test, and collagen assay were tested. R. canina (MBC 0.39 mg/mL) and V. venifera (MBC 3.13 mg/mL) extracts had bactericidal activities against P. aeruginosa and S. aureus, respectively. The V. vinifera extract showed the highest antioxidant activity in both ABTS (EC50 0.078 mg/mL) and DPPH (EC50 0.005 mg/mL) methods. The percentage of wound closure observed for C. cardunculus, R. rosea, and R. canina extracts with HaCaT, and V. vinifera extract with Hs27 cells was set as 100%. V. vinifera extract (50 μg/mL) stimulated collagen synthesis 5.16 times more strongly than ascorbic acid. Our preliminary study showed that some plant extracts may be promising modulators of the wound healing process, although further in-depth studies are necessary to determine their effectiveness in the in vivo model. Full article

(This article belongs to the Special Issue Novel Natural Compound for Wound and Tissue Repair and Regeneration: 3rd Edition)

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23 pages, 8591 KiB

Open AccessArticle

Targeting Cellular Senescence with Liposome-Encapsulated Fisetin: Evidence of Senomorphic Effect

by Agata Henschke, Bartosz Grześkowiak, Olena Ivashchenko, María Celina Sánchez-Cerviño, Emerson Coy and Sergio Moya

Int. J. Mol. Sci. 2025, 26(15), 7489; https://doi.org/10.3390/ijms26157489 (registering DOI) - 2 Aug 2025

Abstract

Cellular senescence is closely connected with cancer progression, recurrence, and metastasis. Senotherapy aims to soothe the harmful effects of senescent cells either by inducing their apoptosis (senolytic) or by suppressing the senescence-associated secretory phenotype (SASP) (senomorphic). Fisetin, a well-studied senotherapeutic drug, was selected [...] Read more.

Cellular senescence is closely connected with cancer progression, recurrence, and metastasis. Senotherapy aims to soothe the harmful effects of senescent cells either by inducing their apoptosis (senolytic) or by suppressing the senescence-associated secretory phenotype (SASP) (senomorphic). Fisetin, a well-studied senotherapeutic drug, was selected for this study to evaluate its efficiency when delivered in a liposomal formulation. The experiment evaluated the impact of liposome-encapsulated fisetin on senescent cells induced by doxorubicin (DOX) from two cell lines: WI-38 (normal lung fibroblasts) and A549 (lung carcinoma). Senescence was characterized by SA-β-galactosidase (SA-β-gal) activity, proliferation, morphology, and secretion of pro-inflammatory interleukin 6 (IL-6) and interleukin 8 (IL-8). Due to fisetin’s hydrophobic nature, it was encapsulated in liposomes to enhance cellular delivery. Cellular uptake studies confirmed that the liposomes were effectively internalized by both senescent cell types. Treatment with fisetin-loaded liposomes revealed a lack of senolytic effects but showed senomorphic activity, as evidenced by a significant reduction in IL-6 and IL-8 secretion in senescent cells. The liposomal formulation enhanced fisetin’s therapeutic efficacy, showing comparable results even at the lowest tested concentration. Full article

(This article belongs to the Section Molecular Pharmacology)

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13 pages, 2812 KiB

Open AccessArticle

Fungal Laccases with High and Medium Redox Potential: Is the T1 Center Potential a Key Characteristic of Catalytic Efficiency in Heterogeneous and Homogeneous Reactions?

by Olga Morozova, Maria Khlupova, Irina Vasil’eva, Alexander Yaropolov and Tatyana Fedorova

Int. J. Mol. Sci. 2025, 26(15), 7488; https://doi.org/10.3390/ijms26157488 (registering DOI) - 2 Aug 2025

Abstract

Catalytic and bioelectrocatalytic properties of four white rot fungal laccases (Trametes hirsuta, ThL; Coriolopsis caperata, CcL; Steccherinum murashkinskyi, SmL; and Antrodiella faginea, AfL) from different orthologous groups were comparatively studied in homogeneous reactions of electron donor substrate oxidation [...] Read more.

Catalytic and bioelectrocatalytic properties of four white rot fungal laccases (Trametes hirsuta, ThL; Coriolopsis caperata, CcL; Steccherinum murashkinskyi, SmL; and Antrodiella faginea, AfL) from different orthologous groups were comparatively studied in homogeneous reactions of electron donor substrate oxidation and in a heterogeneous reaction of dioxygen electroreduction. The ThL and CcL laccases belong to high-redox-potential enzymes (E⁰_T1 = 780 mV), while the AfL and SmL laccases are medium-redox-potential enzymes (E⁰_T1 = 620 and 650 mV). We evaluated the efficiency of laccases in mediatorless bioelectrocatalytic dioxygen reduction by the steady-state potential (E_ss), onset potential (E_onset), half-wave potential (E_1/2), and the slope of the linear segment of the polarization curve. A good correlation was observed between the T1 center potential of the laccases and their electrocatalytic characteristics; however, no correlation with the homogeneous reactions of electron donor substrates’ oxidation was detected. The results obtained are discussed in the light of the known data on the three-dimensional structures of the laccases studied. Full article

(This article belongs to the Special Issue Advanced Research on Enzymes in Biocatalysis)

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16 pages, 2407 KiB

Open AccessArticle

Transcriptional Analysis of Spodoptera frugiperda Sf9 Cells Infected with Daphnis nerii Cypovirus-23

by Wendong Kuang, Jian Yang, Jinchang Wang, Chenghua Yan, Junhui Chen, Xinsheng Liu, Chunhua Yang, Zhigao Zhan, Limei Guan, Jianghuai Li, Tao Deng, Feiying Yang, Guangqiang Ma and Liang Jin

Int. J. Mol. Sci. 2025, 26(15), 7487; https://doi.org/10.3390/ijms26157487 (registering DOI) - 2 Aug 2025

Abstract

Daphnis nerii cypovirus-23 (DnCPV-23) is a new type of cypovirus that has a lethal effect on many species of Sphingidae pests. DnCPV-23 can replicate in Spodoptera frugiperda Sf9 cells, but the replication characteristics of the virus in this cell line are still unclear. [...] Read more.

Daphnis nerii cypovirus-23 (DnCPV-23) is a new type of cypovirus that has a lethal effect on many species of Sphingidae pests. DnCPV-23 can replicate in Spodoptera frugiperda Sf9 cells, but the replication characteristics of the virus in this cell line are still unclear. To determine the replication characteristics of DnCPV-23 in Sf9 cells, uninfected Sf9 cells and Sf9 cells at 24 and 72 h after DnCPV-23 infection were collected for transcriptome analysis. Compared to uninfected Sf9 cells, a total of 188 and 595 differentially expressed genes (DEGs) were identified in Sf9 cells collected at 24 hpi and 72 h, respectively. KEGG analyses revealed that 139 common DEGs in two treatment groups were related to nutrition and energy metabolism-related processes, cell membrane integrity and function-related pathways, detoxification-related pathways, growth and development-related pathways, and so on. We speculated that these cellular processes might be manipulated by viruses to promote replication. This study provides an important basis for further in-depth research on the mechanism of interaction between viruses and hosts. It provides additional basic information for the future exploitation of DnCPV-23 as a biological insecticide. Full article

(This article belongs to the Special Issue Functional Genomics of Insects: Unraveling Genetic Mechanisms and Applications)

12 pages, 757 KiB

Open AccessBrief Report

DNA-Programmable Oligonucleotide Insecticide Eriola-11 Targets Mitochondrial 16S rRNA and Exhibits Strong Insecticidal Activity Against Woolly Apple Aphid (Eriosoma lanigerum) Hausmann

by Vol Oberemok, Kate Laikova, Oksana Andreeva, Anastasia Dmitrienko, Tatiana Rybareva, Jamin Ali and Nikita Gal’chinsky

Int. J. Mol. Sci. 2025, 26(15), 7486; https://doi.org/10.3390/ijms26157486 (registering DOI) - 2 Aug 2025

Abstract

The potent and selective ‘genetic zipper’ method for insect pest control consists of three essential components: an antisense DNA (the finder), its complementary mature rRNA or pre-rRNA of the pest (the target), and the host’s endogenous DNA-guided rRNase (the degrader). Although this approach [...] Read more.

The potent and selective ‘genetic zipper’ method for insect pest control consists of three essential components: an antisense DNA (the finder), its complementary mature rRNA or pre-rRNA of the pest (the target), and the host’s endogenous DNA-guided rRNase (the degrader). Although this approach has been validated, the spectrum of effective rRNA targets remains insufficiently explored. In this study, we report for the first time the insecticidal efficacy of a novel oligonucleotide insecticide, Eriola-11, which targets the mitochondrial 16S rRNA of the woolly apple aphid Eriosoma lanigerum Hausmann. We hypothesized that the antisense-mediated silencing of mitochondrial rRNA would impair aphid viability and lead to physiological disruptions associated with mitochondrial energy metabolism. Eriola-11 was applied either once or twice (with a 24 h interval) to aphid-infested plants, and aphid mortality was recorded over 14 days. Mitochondrial 16S rRNA expression levels were quantified using molecular assays, and the degradation kinetics of Eriola-11 were assessed in aphid tissue homogenates. Results showed significant insecticidal activity, with 67.55% mortality after a single treatment and 83.35% after two treatments. Treated aphids exhibited the loss of their characteristic white woolly wax covering, and mitochondrial 16S rRNA expression was reduced 0.66-fold relative to the control. Additionally, Eriola-11 was fully degraded by aphid DNases from tissue homogenates within 3 h, highlighting its rapid biodegradability. These findings establish mitochondrial 16S rRNA as a viable target for antisense insecticides and expand the catalogue of potential rRNA-based targets, offering a promising avenue for environmentally sustainable pest control strategies. Full article

(This article belongs to the Special Issue Antisense Oligonucleotides: Versatile Tools with Broad Applications)

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22 pages, 1496 KiB

Open AccessReview

Drosophila melanogaster: How and Why It Became a Model Organism

by Maria Grazia Giansanti, Anna Frappaolo and Roberto Piergentili

Int. J. Mol. Sci. 2025, 26(15), 7485; https://doi.org/10.3390/ijms26157485 (registering DOI) - 2 Aug 2025

Abstract

Drosophila melanogaster is one of the most known and used organisms worldwide, not just to study general biology problems but above all for modeling complex human diseases. During the decades, it has become a central tool to understand the genetics of human disease, [...] Read more.

Drosophila melanogaster is one of the most known and used organisms worldwide, not just to study general biology problems but above all for modeling complex human diseases. During the decades, it has become a central tool to understand the genetics of human disease, how mutations alter the behavior and health of cells, tissues, and organs, and more recently to test new compounds with a potential therapeutic use. But how did this small insect become so crucial in genetics? And how is it currently used in the study of human conditions affecting millions of people? In this review, we retrace the historical origins of its adoption in genetics laboratories and list all the advantages it provides to scientific research, both for its daily usage and for the fine tuning of gene regulation through genetic engineering approaches. We also provide some examples of how it is used to study human diseases such as cancer, neurological and infectious diseases, and its importance in drug discovery and testing. Full article

(This article belongs to the Special Issue Drosophila: A Versatile Model in Biology and Medicine—2nd Edition)

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36 pages, 8123 KiB

Open AccessArticle

Enhanced Methodology for Peptide Tertiary Structure Prediction Using GRSA and Bio-Inspired Algorithm

by Diego A. Soto-Monterrubio, Hernán Peraza-Vázquez, Adrián F. Peña-Delgado and José G. González-Hernández

Int. J. Mol. Sci. 2025, 26(15), 7484; https://doi.org/10.3390/ijms26157484 (registering DOI) - 2 Aug 2025

Abstract

Recent advancements have been made in the precise prediction of protein structures within the Protein Folding Problem (PFP), particularly in relation to minimizing the energy function to achieve stable and biologically relevant protein structures. This problem is classified as NP-hard within computational theory, [...] Read more.

Recent advancements have been made in the precise prediction of protein structures within the Protein Folding Problem (PFP), particularly in relation to minimizing the energy function to achieve stable and biologically relevant protein structures. This problem is classified as NP-hard within computational theory, necessitating the development of various techniques and algorithms. Bio-inspired algorithms have proven effective in addressing NP-hard challenges in practical applications. This study introduces a novel hybrid algorithm, termed GRSABio, which integrates the strategies of Jumping Spider Algorithm (JSOA) with the Golden Ratio Simulated Annealing (GRSA) for peptide prediction. Furthermore, the GRSABio algorithm incorporates a Convolutional Neural Network for fragment prediction (FCNN), forms an enhanced methodology called GRSABio-FCNN. This integrated framework achieves improved structure refinement based on energy for protein prediction. The proposed enhanced GRSABio-FCNN approach was applied to a dataset of 60 peptides. The Wilcoxon and Friedman statistics test were employed to compare the GRSABio-FCNN results against recent state-of-the-art-approaches. The results of these tests indicate that the GRSABio-FCNN approach is competitive with state-of-the-art methods for peptides up to 50 amino acids in length and surpasses leading PFP algorithms for peptides with up to 30 amino acids. Full article

(This article belongs to the Special Issue Advances in Biomathematics, Computational Biology, and Bioengineering)

25 pages, 1542 KiB

Open AccessReview

Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions

by Leonid A. Shaposhnikov, Aleksei S. Rozanov and Alexey E. Sazonov

Int. J. Mol. Sci. 2025, 26(15), 7483; https://doi.org/10.3390/ijms26157483 (registering DOI) - 2 Aug 2025

Abstract

Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous [...] Read more.

Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous recombination, transposon mutagenesis, and phage-derived recombineering opened the door to targeted gene disruption, but low efficiencies and marker footprints limited throughput. Recent phage RecT/RecE-mediated recombineering and CRISPR/Cas counter-selection now enable scar-less point edits, seamless deletions, and multi-kilobase insertions at efficiencies approaching model organisms. Endogenous Cas9 systems, dCas-based CRISPR interference, and CRISPR-guided transposases further extend the toolbox, allowing multiplex knockouts, precise single-base mutations, conditional knockdowns, and payloads up to 10 kb. The remaining hurdles include strain-specific barriers, reliance on selection markers for large edits, and the limited host-range of recombinases. Nevertheless, convergence of phage enzymes, CRISPR counter-selection and high-throughput oligo recombineering is rapidly transforming LAB into versatile chassis for cell-factory and therapeutic applications. Full article

(This article belongs to the Special Issue Probiotics in Health and Disease)

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19 pages, 2574 KiB

Open AccessArticle

The Neuroregenerative Effects of IncobotulinumtoxinA (Inco/A) in a Nerve Lesion Model of the Rat

by Oscar Sánchez-Carranza, Wojciech Danysz, Klaus Fink, Maarten Ruitenberg, Andreas Gravius and Jens Nagel

Int. J. Mol. Sci. 2025, 26(15), 7482; https://doi.org/10.3390/ijms26157482 (registering DOI) - 2 Aug 2025

Abstract

The use of Botulinum Neurotoxin A (BoNT/A) to treat peripheral neuropathic pain from nerve injury has garnered interest for its long-lasting effects and safety. This study examined the effects of IncobotulinumtoxinA (Inco/A), a BoNT/A variant without accessory proteins, on nerve regeneration in rats [...] Read more.

The use of Botulinum Neurotoxin A (BoNT/A) to treat peripheral neuropathic pain from nerve injury has garnered interest for its long-lasting effects and safety. This study examined the effects of IncobotulinumtoxinA (Inco/A), a BoNT/A variant without accessory proteins, on nerve regeneration in rats using the chronic constriction injury (CCI) model. Inco/A was administered perineurally at two time points: on days 0 and 21 post CCI. Functional and histological assessments were conducted to evaluate the effect of Inco/A on nerve regeneration. Sciatic Functional Index (SFI) measurements and Compound Muscle Action Potential (CMAP) recordings were conducted at different time points following CCI. Inco/A-treated animals exhibited a 65% improved SFI and 22% reduction in CMAP onset latencies compared to the vehicle-treated group, suggesting accelerated functional nerve recovery. Tissue analysis revealed enhanced remyelination in Inco/A-treated animals and 60% reduction in CGRP and double S100β signal expression compared to controls. Strikingly, 30% reduced immune cell influx into the injury site was observed following Inco/A treatment, suggesting that its anti-inflammatory effect contributes to nerve regeneration. These findings show that two injections of Inco/A promote functional recovery by enhancing neuroregeneration and modulating inflammatory processes, supporting the hypothesis that Inco/A has a neuroprotective and restorative role in nerve injury conditions. Full article

(This article belongs to the Section Molecular Neurobiology)

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18 pages, 2432 KiB

Open AccessArticle

Alkali Lignin-Based Biopolymer Formulations for Electro-Assisted Drug Delivery of Natural Antioxidants in Breast Cancer Cells—A Preliminary Study

by Severina Semkova, Radina Deneva, Georgi Antov, Donika Ivanova and Biliana Nikolova

Int. J. Mol. Sci. 2025, 26(15), 7481; https://doi.org/10.3390/ijms26157481 (registering DOI) - 2 Aug 2025

Abstract

Recently, a number of natural biologically active substances have been proven to be attractive alternatives to conventional anticancer medicine or as adjuvants in contemporary combination therapies. Although lignin-based materials were previously accepted as waste materials with limited usefulness, recent studies increasingly report the [...] Read more.

Recently, a number of natural biologically active substances have been proven to be attractive alternatives to conventional anticancer medicine or as adjuvants in contemporary combination therapies. Although lignin-based materials were previously accepted as waste materials with limited usefulness, recent studies increasingly report the possibility of their use for novel applications in various industrial branches, including biomedicine. In this regard, the safety, efficiency, advantages and limitations of lignin compounds for in vitro/in vivo applications remain poorly studied and described. This study was carried out to investigate the possibility of using newly synthesized, alkali lignin-based micro-/nano-biopolymer formulations (Lignin@Formulations/L@F) as carriers for substances with antioxidant and/or anticancer effectiveness. Moreover, we tried to assess the opportunity for using an electro-assisted approach for achieving improved intracellular internalization. An investigation was conducted on an in vitro panel of breast cell lines, namely two breast cancer lines with different metastatic potentials and one non-tumorigenic line as a control. The characterization of all tested formulations was performed via DLS (dynamic light scattering) analysis. We developed an improved separation procedure via size/charge unification for all types of Lignin@Formulations. Moreover, in vitro applications were investigated. The results demonstrate that compared to healthy breast cells, both tested cancer lines exhibited slight sensitivity after treatment with different formulations (empty or loaded with antioxidant substances). This effect was also enhanced after applying electric pulses. L@F loaded with Quercetin was also explored only on the highly metastatic cancer cell line as a model for the breast cancer type most aggressive and non-responsive to traditional treatments. All obtained data suggest that the tested formulations have potential as carriers for the electro-assisted delivery of natural antioxidants such as Quercetin. Full article

(This article belongs to the Special Issue Natural Products in Cancer Prevention and Treatment)

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23 pages, 4116 KiB

Open AccessArticle

A Naturally Occurring Urinary Collagen Type I Alpha 1-Derived Peptide Inhibits Collagen Type I-Induced Endothelial Cell Migration at Physiological Concentrations

by Hanne Devos, Ioanna K. Mina, Foteini Paradeisi, Manousos Makridakis, Aggeliki Tserga, Marika Mokou, Jerome Zoidakis, Harald Mischak, Antonia Vlahou, Agnieszka Latosinska and Maria G. Roubelakis

Int. J. Mol. Sci. 2025, 26(15), 7480; https://doi.org/10.3390/ijms26157480 (registering DOI) - 2 Aug 2025

Abstract

Collagen type I (COL(I)) is a key component of the extracellular matrix (ECM) and is involved in cell signaling and migration through cell receptors. Collagen degradation produces bioactive peptides (matrikines), which influence cellular processes. In this study, we investigated the biological effects of [...] Read more.

Collagen type I (COL(I)) is a key component of the extracellular matrix (ECM) and is involved in cell signaling and migration through cell receptors. Collagen degradation produces bioactive peptides (matrikines), which influence cellular processes. In this study, we investigated the biological effects of nine most abundant, naturally occurring urinary COL(I)-derived peptides on human endothelial cells at physiological concentrations, using cell migration assays, mass spectrometry-based proteomics, flow cytometry, and AlphaFold 3. While none of the peptides significantly altered endothelial migration by themselves at physiological concentrations, full-length COL(I) increased cell migration, which was inhibited by Peptide 1 (²²⁹NGDDGEAGKPGRPGERGPpGp²⁴⁹). This peptide uniquely contains the DGEA and GRPGER motifs, interacting with integrin α2β1. Flow cytometry confirmed the presence of integrin α2β1 on human endothelial cells, and AlphaFold 3 modeling predicted an interaction between Peptide 1 and integrin α2. Mass spectrometry-based proteomics investigating signaling pathways revealed that COL(I) triggered phosphorylation events linked to integrin α2β1 activation and cell migration, which were absent in COL(I) plus peptide 1-treated cells. These findings identify Peptide 1 as a biologically active COL(I)-derived peptide at a physiological concentration capable of modulating collagen-induced cell migration, and provide a foundation for further investigation into its mechanisms of action and role in urine excretion. Full article

(This article belongs to the Special Issue The Role of Extracellular Matrix Proteins in Pathogenesis: 2nd Edition)

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Int. J. Mol. Sci., Volume 26, Issue 15 (August-1 2025) – 482 articles

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