International Journal of Molecular Sciences

15 pages, 953 KB

Open AccessArticle

Biochemical Properties and Substrate Specificity of Two Acyl-CoA:Lysophosphatidic Acid Acyltransferases (PtATS2a and PtATS2b) from Diatom Phaeodactylum tricornutum

by Katarzyna Jasieniecka-Gazarkiewicz, Ada Połońska, Yangmin Gong and Antoni Banaś

Int. J. Mol. Sci. 2025, 26(20), 9936; https://doi.org/10.3390/ijms26209936 (registering DOI) - 12 Oct 2025

Abstract

Microsomal fractions from yeast Δale1 cells harbouring the empty plasmid pYES2/CT and from yeast cells overexpressing PtATS2a (Phatr3_J11916) or PtATS2b (Phatr3_J43099) were used in the studies. When sn-1-18:1-LPA and [¹⁴C]16:0-CoA were used as exogenous substrates, both Pt [...] Read more.

Microsomal fractions from yeast Δale1 cells harbouring the empty plasmid pYES2/CT and from yeast cells overexpressing PtATS2a (Phatr3_J11916) or PtATS2b (Phatr3_J43099) were used in the studies. When sn-1-18:1-LPA and [¹⁴C]16:0-CoA were used as exogenous substrates, both PtATS2a and PtATS2b showed the highest activity at 23 °C in the range of temperatures tested from 10 to 60 °C. Both enzymes showed the highest activity in alkaline pH. For PtATS2a, it was pH 10 while for PtATS2b, it was pH 11. At pH 6 and pH 12, the activities of both enzymes were very low. The calcium ions at concentrations of 0.05–1 mM drastically decreased the activity of both enzymes. The magnesium ions at a concentration of 0.05 mM had a little effect on the activity of both enzymes, while higher concentrations (0.5 mM and 1 mM) significantly inhibited their activity. To study the substrate specificity, seventeen different acyl-CoAs in combinations with sn-1-[¹⁴C]18:1-LPA were used. PtATS2a showed the highest preference for 18:4-CoA n-3 while PtATS2b for 18:1-CoA. The pattern of utilisation of other acyl-CoAs tested also differed between the two enzymes. The presented studies, for the first time, characterised LPAAT type enzymes from diatoms, organisms that naturally produced very-long-chain polyunsaturated fatty acids (VLC-PUFA). Full article

(This article belongs to the Section Biochemistry)

14 pages, 1310 KB

Open AccessArticle

Expected Mitochondrial Haplotype Richness in Remaining Populations of the Critically Endangered European Mink Mustela lutreola and Its Conservation Implications

by Jakub Skorupski, Przemysław Śmietana, Christian Seebass, Wolfgang Festl, Alexe Vasile, Natalia Kiseleva, Florian Brandes and Mihai Marinov

Int. J. Mol. Sci. 2025, 26(20), 9935; https://doi.org/10.3390/ijms26209935 (registering DOI) - 12 Oct 2025

Abstract

The European mink Mustela lutreola is one of the most threatened carnivores in Europe, having suffered dramatic range contractions and severe population fragmentation. Accurate knowledge of its genetic diversity is crucial for conservation planning, yet earlier studies based on partial mitochondrial markers offered [...] Read more.

The European mink Mustela lutreola is one of the most threatened carnivores in Europe, having suffered dramatic range contractions and severe population fragmentation. Accurate knowledge of its genetic diversity is crucial for conservation planning, yet earlier studies based on partial mitochondrial markers offered limited resolution and often underestimated haplotype richness. In this study, complete mitochondrial genomes from four extant populations (Russia, n = 11; Romania, n = 16; Germany, n = 24; France–Spain, n = 15) were analysed using a suite of non-parametric and asymptotic estimators (Fisher’s α, ACE, Jackknife1, Bootstrap, Chao1-based iNEXT) together with negative binomial modelling. A total of 41 haplotypes were detected, but extrapolated estimates indicated substantially higher richness, particularly in populations dominated by singletons. Rarefaction and extrapolation analyses revealed that sample sizes of 70–130 individuals per population are needed to approach complete haplotype detection. The France–Spain and Romania populations harboured the highest predicted richness, whereas Germany and Russia, both represented by ex situ stocks, showed lower diversity. These results refine earlier assumptions of extreme homogeneity in the Western population and demonstrate that significant mitochondrial variation persists at the continental scale. The study provides quantitative benchmarks for sampling design and genetic management, supporting preservation of evolutionary potential in this critically endangered species. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland: 3rd Edition)

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19 pages, 7284 KB

Open AccessArticle

Histological and Macromolecular Characterization of Folliculogenesis in Loggerhead Sea Turtles (Caretta caretta): Novel Insights into the Onset of Puberty

by Ludovica Di Renzo, Erica Trotta, Valentina Notarstefano, Laura Zonta, Elisabetta Giorgini, Luca Marisaldi, Giulia Mariani, Gabriella Di Francesco, Silva Rubini, Marco Matiddi, Cecilia Silvestri, Yakup Kaska, Giulia Chemello and Giorgia Gioacchini

Int. J. Mol. Sci. 2025, 26(20), 9934; https://doi.org/10.3390/ijms26209934 (registering DOI) - 12 Oct 2025

Abstract

The Adriatic Sea is a critical neritic habitat for juvenile and adult female loggerhead sea turtles (Caretta caretta), where intense anthropogenic pressures and environmental stressors may influence their reproductive biology. Knowledge on the onset of puberty in this population is limited [...] Read more.

The Adriatic Sea is a critical neritic habitat for juvenile and adult female loggerhead sea turtles (Caretta caretta), where intense anthropogenic pressures and environmental stressors may influence their reproductive biology. Knowledge on the onset of puberty in this population is limited by scarce information on the sub-adult stage, a transitional phase in which reproductive competence is acquired. This study integrated histological analysis and Fourier-transform infrared (FTIR) imaging spectroscopy to provide both structural and biochemical characterization of folliculogenesis, with emphasis on vitellogenesis, in C. caretta from the north-central Adriatic Sea. Histological analysis determined the progression of follicle development, while FTIR imaging, a label-free and spatially resolved technique, mapped the distribution of proteins, lipids, and nucleic acids across ovarian compartments. Logistic regression estimated the size at which 50% of females are sexually mature (L₅₀) at 58.54 cm Curved Carapace Length (CCL). Based on this value, 60% of sub-adult females were already mature, indicating earlier puberty than previously inferred from macroscopic criteria. These preliminary results, along with reports of sporadic nesting in the Adriatic, raise the question of whether this basin may host further nesting events in the future. FTIR imaging proved to be a powerful tool for reproductive biology in non-model marine vertebrates. Full article

(This article belongs to the Special Issue A Molecular Perspective on Reproductive Health, 2nd Edition)

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30 pages, 5106 KB

Open AccessArticle

From Transcription Factors Dysregulation to Malignancy: In Silico Reconstruction of Cancer’s Foundational Drivers—The Eternity Triangle

by Anna Lisa Cammarota, Albino Carrizzo, Margot De Marco, Nenad Bukvic, Francesco Jacopo Romano, Alessandra Rosati and Massimiliano Chetta

Int. J. Mol. Sci. 2025, 26(20), 9933; https://doi.org/10.3390/ijms26209933 (registering DOI) - 12 Oct 2025

Abstract

Cancer is a multifaceted disease characterized by uncontrolled cell division resulting from substantial disruptions of normal biological processes. Central to its development is cellular transformation, which involves a dynamic sequence of events including chromosomal translocations, genetic mutations, abnormal DNA methylation, post-translational protein modifications, [...] Read more.

Cancer is a multifaceted disease characterized by uncontrolled cell division resulting from substantial disruptions of normal biological processes. Central to its development is cellular transformation, which involves a dynamic sequence of events including chromosomal translocations, genetic mutations, abnormal DNA methylation, post-translational protein modifications, and other genetic and epigenetic alterations. These changes compromise physiological regulatory mechanisms and contribute to accelerated tumor growth. A critical factor in this process is the dysregulation of transcription factors (TFs) which regulate gene expression and DNA transcription. Dysregulation of TFs initiates a cascade of biochemical events, such as abnormal DNA replication, that further enhance cell proliferation and increase genomic instability. This microenvironment not only sustains tumor growth but also promotes the accumulation of somatic mutations, thereby fueling tumor evolution and heterogeneity. In this study, we employed an in silico approach to identify TFs regulating 622 key genes whose mutations are implicated in carcinogenesis. Transcriptional regulatory networks were analyzed through bioinformatics methods to elucidate molecular pathways involved in cancer development. A thorough understanding of these processes may help to clarify the function of dysregulated TFs and facilitate the development of novel therapeutic approaches designed to make cancer treatments personalized and efficacious. Full article

(This article belongs to the Special Issue Cell Proliferation and Differentiation in Cancer)

15 pages, 636 KB

Open AccessReview

Audiovestibular Dysfunction in Hyper-IgE Syndrome: A Systematic Review of Characteristics, Pathophysiology, Diagnosis, and Management

by Jiann-Jy Chen, Chih-Wei Hsu, Brendon Stubbs, Tien-Yu Chen, Chih-Sung Liang, Yen-Wen Chen, Bing-Yan Zeng and Ping-Tao Tseng

Int. J. Mol. Sci. 2025, 26(20), 9932; https://doi.org/10.3390/ijms26209932 (registering DOI) - 12 Oct 2025

Abstract

Hyper-IgE syndrome (HIES) is a rare genetic immunodeficiency characterized by elevated serum IgE levels and associated immune dysregulation, manifesting in recurrent infections, eczema, and skeletal abnormalities. Emerging evidence suggests a link between HIES and audiovestibular dysfunction, potentially mediated by IgE-driven inflammation in the [...] Read more.

Hyper-IgE syndrome (HIES) is a rare genetic immunodeficiency characterized by elevated serum IgE levels and associated immune dysregulation, manifesting in recurrent infections, eczema, and skeletal abnormalities. Emerging evidence suggests a link between HIES and audiovestibular dysfunction, potentially mediated by IgE-driven inflammation in the inner ear, which is not immunologically privileged. However, the nature of this association remains poorly understood. This systematic review synthesizes current evidence on the characteristics, pathophysiology, diagnostic approaches, and management of audiovestibular dysfunction in HIES patients. Literature searches across PubMed, Embase, ClinicalKey, Web of Science, and ScienceDirect (up to 6 August 2025) were conducted in accordance with PRISMA guidelines. Key findings indicate that HIES-related audiovestibular issues, including sensorineural hearing loss and vestibular impairment, may arise from IgE-mediated endolymphatic sac inflammation, leading to hydrops and hair cell damage. Diagnostic tools such as audiometry, electrocochleography, and allergen challenge tests show promise, with elevated IgE correlating with abnormal otoacoustic emissions and prolonged auditory brainstem response latencies. Treatment focuses on immunomodulation (e.g., corticosteroids, dupilumab) to mitigate IgE effects, though evidence is limited to case reports. A proposed schematic diagram illustrates pathophysiology, emphasizing IgE’s role in inner ear toxicity. Timely recognition and intervention may prevent progression to permanent hearing loss or vestibular disability, improving quality of life. Future research should explore genetic–immunologic mechanisms and prospective trials for targeted therapies. Trial registration: PROSPERO CRD420251120600. Full article

(This article belongs to the Special Issue Hearing Loss: Molecular Biological Insights, 2nd Edition)

44 pages, 2478 KB

Open AccessReview

Functional Roles of the Complement Immune System in Cardiac Inflammation and Hypertrophy

by Kathryn D. Hok, Haydn E. Rich, Anthony Shadid, Lavanya Gunamalai, Tingting Weng-Mills, Rajarajan A. Thandavarayan, Nirmal K. Banda, Marie-Francoise Doursout, Marcos I. Restrepo and Pooja Shivshankar

Int. J. Mol. Sci. 2025, 26(20), 9931; https://doi.org/10.3390/ijms26209931 (registering DOI) - 12 Oct 2025

Abstract

Cardiac inflammation and hypertrophy develop as a pathologic response to an array of insults, such as myocardial infarctions, chronic systemic hypertension, and valvular defects. Due to the high prevalence of such conditions, there is an increasing need to prevent and halt cardiac hypertrophy. [...] Read more.

Cardiac inflammation and hypertrophy develop as a pathologic response to an array of insults, such as myocardial infarctions, chronic systemic hypertension, and valvular defects. Due to the high prevalence of such conditions, there is an increasing need to prevent and halt cardiac hypertrophy. Because cardiac damage and subsequent remodeling can lead to arrhythmias, heart failure, and even sudden cardiac death, inhibition of cardiac hypertrophy is key to reducing cardiovascular-related mortality. The immune system is the driving force behind inflammatory reactions. All three pathways of complement system activation—classical, lectin, and alternative—are implicated in developing cardiac damage, inflammation, and hypertrophy due to infectious and non-infectious causes, autoimmune diseases, genetic polymorphisms, and forms of complement dysregulation. Of interest in this review is the role of the complement system, a collection of soluble and membrane-bound proteins that mediate inflammatory processes through interactions with signaling molecules and immune cells. This review comprehensively discusses the roles of these complement pathways in contagious, chronic inflammatory, genetic, and metabolic diseases. An overview of the completed and terminated clinical trials aimed at preventing cardiovascular mortality by targeting various aspects of the complement system and inflammatory reaction is included. Most current treatments for cardiac inflammation and remodeling primarily target the renin–angiotensin–aldosterone system (RAAS), which prevents further remodeling by reducing myocardial workload. However, moving forward, there may be a place for emerging anti-complement therapeutics, which impair the inflammatory response that generates hypertrophy itself. Full article

(This article belongs to the Special Issue Cardioimmunology: Inflammation and Immunity in Cardiovascular Disease)

13 pages, 1814 KB

Open AccessArticle

Gout Risk Allele Regulating IRF5 Expression Is Associated with Enhanced IL-1β Production in Response to Palmitate and Monosodium Urate Crystals

by Valentin Nica, Orsolya Gaal, Medeea Badii, Georgiana Cabău, Andreea-Manuela Mirea, Ioana Hotea, Cristina Pamfil, Simona Rednic, Radu A. Popp, Mihai G. Netea, Tania O. Crișan, Leo A. B. Joosten and HINT Consortium

Int. J. Mol. Sci. 2025, 26(20), 9930; https://doi.org/10.3390/ijms26209930 (registering DOI) - 12 Oct 2025

Abstract

Interferon Regulatory Factor 5 plays an important role in the regulation of innate immune responses by amplifying the Nuclear Factor κB response, which is critical in gout inflammation. Furthermore, the rs4728141 polymorphism C allele was associated with both increased IRF5 expression and susceptibility [...] Read more.

Interferon Regulatory Factor 5 plays an important role in the regulation of innate immune responses by amplifying the Nuclear Factor κB response, which is critical in gout inflammation. Furthermore, the rs4728141 polymorphism C allele was associated with both increased IRF5 expression and susceptibility to gout. We examine the association between rs4728141 and cytokine production in response to various Toll-Like Receptor ligands and describe the transcriptomic and proteomic changes observed in patients with gout and controls in relation to this polymorphism. We examine the transcriptome of freshly isolated peripheral blood mononuclear cells (PBMCs) from 93 normouricemic donors and 63 gout patients as well as serum inflammatory proteome in 197 control and 195 gout samples. Stimulation experiments of freshly isolated human PBMCs were performed over 24 h, followed by RNA-sequencing in gout patients and cytokine production measurement by ELISA in normouricemic donors and gout patients. The rs4728141 C allele was associated with increased IL-1β expression in unstimulated PBMCs of controls, but not in gout. No association between the polymorphism and serum inflammatory proteome was found. As expected, an increased IRF5 expression was observed in stimulated PBMCs of rs4728141 C allele carriers in response to several stimulations. Interestingly, IL-1β production was specifically enhanced in association to the rs4728141 C allele when cells were stimulated with palmitate with or without monosodium urate crystals. This pattern of cytokine production shows a functional impact of rs4728141 in gout through altered IL-1β production. Full article

(This article belongs to the Section Molecular Immunology)

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20 pages, 3797 KB

Open AccessArticle

Induced Mammary Epithelial Cell-Derived Extracellular Vesicles Promote the Repair of Skin Trauma

by Siyao Pan, Dandan Zhang, Guodong Wang, Longfei Sun, Mengzhen Wei, Shan Deng, Jianwei Chen, Prasanna Kallingappa, Xiang Yuan and Ben Huang

Int. J. Mol. Sci. 2025, 26(20), 9929; https://doi.org/10.3390/ijms26209929 (registering DOI) - 12 Oct 2025

Abstract

Although extracellular vesicles (EVs) from mesenchymal stem cells have shown potential in skin wound repair, the diversity of EV sources and the optimization of delivery systems still need further exploration. This study is the first to demonstrate that extracellular vesicles from chemically induced [...] Read more.

Although extracellular vesicles (EVs) from mesenchymal stem cells have shown potential in skin wound repair, the diversity of EV sources and the optimization of delivery systems still need further exploration. This study is the first to demonstrate that extracellular vesicles from chemically induced mammary epithelial cells (CiMECs-EVs) possess distinct skin wound repair activity. To enhance the therapeutic efficacy of CiMECs-EVs and optimize their delivery efficiency, we innovatively combined them with a chitosan hydrogel to construct a composite repair system (CiMECs-EVs-chitosan hydrogel, CMECG). This system was then applied to a rat skin wound model. The results showed that CMECG significantly promoted the proliferation and migration of fibroblasts and mammary epithelial cells (MECs). In animal experiments, the relative wound closure efficiency of the control group was approximately 70% on day 14, while that of the CMECG group (loaded with 200 μg CiMECs-Exo) was enhanced to 90%, markedly accelerating the wound healing process. Histological analysis indicated that this system could effectively restore the structural continuity of various skin layers and significantly promote the synthesis and remodeling of collagen at the wound site. Mechanistically, the wound healing effect of CiMECs-EVs is closely associated with the endogenous miRNAs they encapsulate. These miRNAs can coordinately regulate cell proliferation, migration, and angiogenesis, modulate the inflammatory microenvironment, and inhibit excessive scar formation—thus regulating the entire repair process. This process involves multiple wound healing-related signaling pathways, including MAPK, PI3K-Akt, FoxO, TGF-β, and JAK-STAT. In summary, this study successfully constructed a novel EV-chitosan hydrogel repair system. This system is expected to provide an effective and innovative EV-based therapeutic strategy for the clinical treatment of skin wound repair. Full article

(This article belongs to the Section Biochemistry)

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23 pages, 1951 KB

Open AccessArticle

Stabilization of G-Quadruplexes Modulates the Expression of DNA Damage and Unfolded Protein Response Genes in Canine Lymphoma/Leukemia Cells

by Beatriz Hernández-Suárez, David A. Gillespie, Ewa Dejnaka, Bożena Obmińska-Mrukowicz and Aleksandra Pawlak

Int. J. Mol. Sci. 2025, 26(20), 9928; https://doi.org/10.3390/ijms26209928 (registering DOI) - 12 Oct 2025

Abstract

G-quadruplexes have been identified as a promising anti-cancer target because of their ability to modulate the stability of mRNAs encoding oncogenes, tumor suppressor genes, and other potential therapeutic targets. Deregulation of DNA damage and Unfolded Protein Response pathways in cancer cells may create [...] Read more.

G-quadruplexes have been identified as a promising anti-cancer target because of their ability to modulate the stability of mRNAs encoding oncogenes, tumor suppressor genes, and other potential therapeutic targets. Deregulation of DNA damage and Unfolded Protein Response pathways in cancer cells may create vulnerabilities that can be exploited therapeutically. Previous studies have shown variations in the relative expression of DDR and UPR components in canine lymphoma and leukemia cell lines CLBL-1, CLB70, and GL-1. In the present study, we report the presence of G-quadruplex structures in these canine cell lines. Downregulation of the expression of DDR and UPR components at the mRNA level was observed in the CLBL-1 and CLB70 cell lines after stabilization of G4 structures using the ligand PhenDC3. In contrast, in GL-1 cells, important components of the DDR pathway, such as PARP1, GADD45A, and PIK3CB were upregulated in response to PhenDC3 treatment. Downregulation of DDIT4 mRNA expression, which encodes an important UPR component, was detected in the CLBL-1 and GL-1 cell lines after PhenDC3 exposure. These results suggest that G4 structures can be used to manipulate the expression of potential targets to treat lymphoma in dogs. A substantial enrichment of DNA replication and pyrimidine metabolism pathways was found in the GL-1 cell line after G4 stabilization. This finding suggests that PhenDC3 may induce DNA replication stress in this cell line. Collectively, these results support the feasibility of employing canine cancer cells as a model system to investigate the role of G-quadruplex structures in cancer. Full article

(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)

27 pages, 1048 KB

Open AccessReview

Impact of Early Postnatal Maternal Separation Stress on Pancreatic Function in Rodents: A Systematic Review and Meta-Analysis

by Laura García-Orozco, Josue Rivadeneira and Bélgica Vásquez

Int. J. Mol. Sci. 2025, 26(20), 9927; https://doi.org/10.3390/ijms26209927 (registering DOI) - 12 Oct 2025

Abstract

Early postnatal stress is a critical factor in metabolic programming. Maternal separation (MS) in rodents, a widely validated model, has been linked to pancreatic alterations. This systematic review and meta-analysis aimed to evaluate the effect of MS on pancreatic morphology and function in [...] Read more.

Early postnatal stress is a critical factor in metabolic programming. Maternal separation (MS) in rodents, a widely validated model, has been linked to pancreatic alterations. This systematic review and meta-analysis aimed to evaluate the effect of MS on pancreatic morphology and function in rodents. This review followed the PRISMA and SYRCLE guidelines, with a protocol registered in PROSPERO (CRD420251004633). Experimental studies in rodents comparing MS with standard rearing, which reported pancreatic morphofunctional and metabolic parameters, were included. A comprehensive search was performed in the Web of Science, Embase, Medline, Scopus, BIREME-BVS, and SciELO databases until March 2025, without language restrictions. Extracted data included glucose, insulin, insulin sensitivity indices (QUICKI, HOMA), and glucose tolerance tests (GTTs). Meta-analyses were performed using random-effects models, and subgroup analyses were applied to explore sources of heterogeneity. Of 491 references, 25 studies were included in the meta-analysis, which showed that MS was associated with significantly higher glucose levels (SMD −0.41; 95% CI: −0.71 to −0.11) and worse GTT response (SMD −1.02; 95% CI: −1.23 to −0.82). Furthermore, the QUICKI index was significantly decreased (SMD 0.75; 95% CI: 0.14 to 1.35), indicating insulin resistance. MS in rodents induces pancreatic alterations associated with insulin resistance and glucose intolerance, suggesting that early stress could program long-term metabolic vulnerability. Full article

(This article belongs to the Special Issue Metabolic Syndrome: New Insights in Pathogenesis, Diagnosis, Prevention, and Management)

37 pages, 2123 KB

Open AccessReview

Molecular Impact of Metabolic and Endocrine Disturbance on Endometrial Function in Polycystic Ovary Syndrome

by Jim Parker, Claire O’Brien, Talat Uppal and Kelton Tremellen

Int. J. Mol. Sci. 2025, 26(20), 9926; https://doi.org/10.3390/ijms26209926 (registering DOI) - 12 Oct 2025

Abstract

Polycystic ovary syndrome (PCOS) is a systemic metabolic and endocrine disorder that significantly disrupts reproductive physiology and endometrial function. In this narrative review, we examine the molecular impact of metabolic and hormonal imbalances on the endometrium of women with PCOS. We investigate the [...] Read more.

Polycystic ovary syndrome (PCOS) is a systemic metabolic and endocrine disorder that significantly disrupts reproductive physiology and endometrial function. In this narrative review, we examine the molecular impact of metabolic and hormonal imbalances on the endometrium of women with PCOS. We investigate the specific mechanisms that delineate how hyperinsulinemia and insulin resistance, chronic low-grade inflammation, and estrogen/progesterone/androgen imbalance contribute to altered epigenetic, transcriptomic, metabolomic, and signaling profiles in a wide array of different cell types within endometrial tissues. The synergistic interplay between upregulated inflammatory cytokines (e.g., IL-1,2,6,8,17,18, and TNF-α), along with key changes in critical molecular pathways associated with hyperinsulinemia and insulin resistance (e.g., PI3K/AKT/MAPK, and Wnt/β-catenin), in addition to aberrant sex steroid hormone signaling (e.g., CYP19A1, COX-2, PGE₂, HOXA10, 11βHSD2), promotes deleterious changes within the endometrial microenvironment. These anomalies underpin a spectrum of clinical manifestations observed in women with PCOS at each stage of the life course, including abnormal uterine bleeding in reproductive-age women, impaired decidualization in pregnancy, and altered postmenopausal endometrial physiology. Clinically, these alterations are associated with abnormal uterine bleeding, subfertility, implantation failure, miscarriage, pregnancy complications, and postmenopausal endometrial hyperplasia and cancer. Overall, our review provides novel insights into the molecular mechanisms linking systemic metabolic and endocrine dysfunction with endometrial pathology in PCOS and has broader implications that apply to all women. Full article

(This article belongs to the Special Issue Focus on Metabolic Research Priorities in PCOS)

16 pages, 3101 KB

Open AccessArticle

Synaptic Plasticity-Enhancing and Cognitive-Improving Effects of Standardized Ethanol Extract of Perilla frutescens var. acuta in a Scopolamine-Induced Mouse Model

by Jihye Lee, Eunhong Lee, Hyeon Ji Kweon, Somin Moon, Ho Jung Bae, Joon-Ho Hwang, Gun Hee Cho, Haram Kong, Mi-Houn Park, Sung-Kyu Kim, Dong Hyun Kim and Ji Wook Jung

Int. J. Mol. Sci. 2025, 26(20), 9925; https://doi.org/10.3390/ijms26209925 (registering DOI) - 12 Oct 2025

Abstract

In our previous study, we demonstrated that a standardized ethanol extract of Perilla frutescens var. acuta (PE) alleviates memory deficits in an Alzheimer’s disease mouse model by inhibiting amyloid β (Aβ) aggregation and promoting its disaggregation. However, the extent to which PE exerts [...] Read more.

In our previous study, we demonstrated that a standardized ethanol extract of Perilla frutescens var. acuta (PE) alleviates memory deficits in an Alzheimer’s disease mouse model by inhibiting amyloid β (Aβ) aggregation and promoting its disaggregation. However, the extent to which PE exerts additional cognitive benefits independent of Aβ pathology remained unclear. Here, we aimed to evaluate the effects of PE on synaptic plasticity and learning and memory functions. Male ICR mice were used, and cognitive impairment was induced by scopolamine administration. PE was orally administered at doses determined from previous studies, and cognitive performance was assessed using the passive avoidance, Y-maze, and Morris water maze tests. In parallel, hippocampal slices were employed to examine the effects of PE on synaptic plasticity. PE (100 and 300 μg/mL) significantly enhanced long-term potentiation (LTP) in a concentration-dependent manner without altering basal synaptic transmission. This facilitation of LTP was blocked by scopolamine (1 μM), a muscarinic acetylcholine receptor (mAChR) antagonist, and IEM-1460 (50 μM), a calcium-permeable α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (CP-AMPAR) inhibitor, indicating the involvement of mAChR and CP-AMPAR pathways. In vivo, PE (100, 250, and 500 mg/kg) treatment improved memory performance across all behavioral tasks and upregulated hippocampal synaptic proteins including GluN2B, PSD-95, and CaMKII. Collectively, these results demonstrate that PE ameliorates scopolamine (1 mg/kg)-induced cognitive impairment by enhancing synaptic plasticity, likely through modulation of mAChR, CP-AMPAR, and NMDA receptor signaling. These findings highlight the therapeutic potential of PE for memory deficits associated with cholinergic dysfunction. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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13 pages, 758 KB

Open AccessReview

Roles of Deubiquitinases OTUD3 and OTUD5 in Inflammatory Bowel Diseases

by Tomohiro Watanabe and Masatoshi Kudo

Int. J. Mol. Sci. 2025, 26(20), 9924; https://doi.org/10.3390/ijms26209924 (registering DOI) - 12 Oct 2025

Abstract

Excessive production of type I interferons (IFNs) underlies the immunopathogenesis of autoimmune disorders, including systemic lupus erythematosus and autoimmune pancreatitis. Whether type I IFNs play pathogenic or protective roles in the development of inflammatory bowel diseases (IBD) has been a matter of debate. [...] Read more.

Excessive production of type I interferons (IFNs) underlies the immunopathogenesis of autoimmune disorders, including systemic lupus erythematosus and autoimmune pancreatitis. Whether type I IFNs play pathogenic or protective roles in the development of inflammatory bowel diseases (IBD) has been a matter of debate. The production of type I IFNs is tightly regulated by the conjugation and removal of polyubiquitin chains on or from intracellular signaling molecules. OTU deubiquitinases 3 (OTUD3) and 5 (OTUD5) are enzymes that cleave various polyubiquitin chains from target proteins. OTUD3 and OTUD5 deubiquitinate key critical intracellular molecules of the type I IFN signaling pathways, stimulator of interferon genes (STING), and TNF receptor-associated factor 3 (TRAF3), respectively, and thus regulate the production of type I IFNs by innate immune cells. Recent studies provided evidence that the impaired function of OTUD3 and OTUD5 increases susceptibility to human and experimental IBD owing to the excessive production of type I IFNs caused by the activation of STING and TRAF3, respectively. Collectively, OTUD3 and OTUD5 play protective rather than pathogenic roles in the development of IBD through the negative regulation of type I IFN-mediated signaling pathways. In this review article, we discuss the association between the development of IBD and impaired function of OTUD3 or OTUD5 by focusing on their deubiquitinase activity and type I IFN responses. Full article

(This article belongs to the Section Molecular Immunology)

18 pages, 1048 KB

Open AccessArticle

Genome-Wide Inference of Essential Genes in Dirofilaria immitis Using Machine Learning

by Tulio L. Campos, Pasi K. Korhonen, Neil D. Young, Sunita B. Sumanam, Whitney Bullard, John M. Harrington, Jiangning Song, Bill C. H. Chang, Richard J. Marhoefer, Paul M. Selzer and Robin Gasser

Int. J. Mol. Sci. 2025, 26(20), 9923; https://doi.org/10.3390/ijms26209923 (registering DOI) - 12 Oct 2025

Abstract

The filarioid nematode Dirofilaria immitis is the causative agent of heartworm disease, a major parasitic infection of canids, felids and occasionally humans. Current prevention relies on macrocyclic lactone-based chemoprophylaxis, but the emergence of drug resistance highlights the need for new intervention strategies. Here, [...] Read more.

The filarioid nematode Dirofilaria immitis is the causative agent of heartworm disease, a major parasitic infection of canids, felids and occasionally humans. Current prevention relies on macrocyclic lactone-based chemoprophylaxis, but the emergence of drug resistance highlights the need for new intervention strategies. Here, we applied a machine learning (ML)-based framework to predict and prioritise essential genes in D. immitis in silico, using genomic, transcriptomic and functional datasets from the model organisms Caenorhabditis elegans and Drosophila melanogaster. With a curated set of 26 predictive features, we trained and evaluated multiple ML models and, using a defined threshold, we predicted 406 ‘high-priority’ essential genes. These genes showed strong transcriptional activity across developmental stages and were inferred to be enriched in pathways related to ribosome biogenesis, translation, RNA processing and signalling, underscoring their potential as anthelmintic targets. Transcriptomic analyses suggested that these genes are associated with key reproductive and neural tissues, while chromosomal mapping revealed a relatively even genomic distribution, in contrast to patterns observed in C. elegans and Dr. melanogaster. In addition, initial evidence suggested structural variation in the X chromosome compared with a recently published D. immitis assembly, indicating the importance of integrating long-read sequencing with high-throughput chromosome conformation capture (Hi-C) mapping. Overall, this study reinforces the potential of ML-guided approaches for essential gene discovery in parasitic nematodes and provides a foundation for downstream validation and therapeutic target development. Full article

(This article belongs to the Special Issue Investigating Host-Parasite Interactions for the Discovery of Novel Therapies and Vaccine Targets)

20 pages, 1430 KB

Open AccessArticle

Graphene Nanoplatelet-Embedded Urinary Catheters for Enhanced Photothermal Sterilization Against Bacterial Infections

by Nivedita, Kai-Yi Tzou, Muhammad Saukani and Tsung-Rong Kuo

Int. J. Mol. Sci. 2025, 26(20), 9922; https://doi.org/10.3390/ijms26209922 (registering DOI) - 12 Oct 2025

Abstract

The escalating crisis of bacterial antimicrobial resistance poses a severe threat to global health, necessitating novel strategies beyond conventional antibiotics. Photothermal therapy (PTT) has emerged as a promising alternative that leverages heat generated by laser irradiation to induce localized cellular damage and eradicate [...] Read more.

The escalating crisis of bacterial antimicrobial resistance poses a severe threat to global health, necessitating novel strategies beyond conventional antibiotics. Photothermal therapy (PTT) has emerged as a promising alternative that leverages heat generated by laser irradiation to induce localized cellular damage and eradicate bacteria. Among various photothermal agents, carbon-based nanomaterials like graphene nanoplatelets (GNPs) offer exceptional properties for PTT applications. This study introduces a novel urinary catheter (UC) embedded with GNPs (GNPUC), specifically designed for photothermal sterilization to combat catheter-associated bacterial infections. GNPs were systematically incorporated into polydimethylsiloxane (PDMS) catheters at varying weight percentages (1% to 10%). The fabricated GNPUCs exhibited low wettability, hydrophobic characteristics, and low adhesiveness, properties that are crucial for minimizing bacterial interactions and initial adhesion. Upon exposure to near-infrared (NIR) laser irradiation (808 nm, 1.5 W/cm²), the UC containing 10 weight percent of GNPs (10GNPUC) achieved a significant temperature of 68.8 °C, demonstrating its potent photothermal conversion capability. Quantitative agar plate tests confirmed the enhanced, concentration-dependent photothermal antibacterial activity of GNPUCs against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus). Notably, 5% and higher GNP concentrations achieved 100% mortality of S. aureus, while 1% and higher concentrations achieved 100% mortality of E. coli. These findings underscore the significant potential of GNP-embedded catheters as a highly effective photothermal antibacterial platform for future clinical applications in combating catheter-associated infections. Full article

(This article belongs to the Section Materials Science)

30 pages, 1356 KB

Open AccessReview

Immunology of Hypertension: Pathophysiological and Therapeutic Aspects

by Alexander Manzano, Heliana Parra, Daniela Ariza, Maria Marquina, Pablo Duran, María J. Calvo, Manuel Nava, Omar Ross, Julio César Contreras-Velásquez, Diego Rivera-Porras and Valmore Bermúdez

Int. J. Mol. Sci. 2025, 26(20), 9921; https://doi.org/10.3390/ijms26209921 (registering DOI) - 12 Oct 2025

Abstract

Hypertension affects over 1.39 billion people globally, causing 9.4 million deaths annually. This paper examines the intricate relationship between the immune system and hypertension, highlighting the contributions of both innate and adaptive immune responses. The innate response, involving natural killer (NK) cells, macrophages, [...] Read more.

Hypertension affects over 1.39 billion people globally, causing 9.4 million deaths annually. This paper examines the intricate relationship between the immune system and hypertension, highlighting the contributions of both innate and adaptive immune responses. The innate response, involving natural killer (NK) cells, macrophages, toll-like receptors (TLRs), and dendritic cells, contributes to organ damage and inflammatory responses, exacerbating hypertension. Adaptive immunity, particularly T cells, further exacerbates vascular and renal dysfunction through the release of cytokines such as IFN-γ, IL-17A, and TNF-α, ultimately leading to multisystem damage. Therapeutic strategies targeting these immune responses are being explored, including immunosuppressants such as mycophenolate mofetil (MMF) and methotrexate (MTX), as well as monoclonal antibodies against IL-1β and TNF-α. While these strategies show promise, further research is needed to evaluate their efficacy and safety. Furthermore, this paper highlights the potential benefits of immunological approaches in managing the root causes of hypertension, offering an alternative to conventional therapies focused on the renin–angiotensin–aldosterone system. In conclusion, this work highlights the immune mechanisms in the hypertension pathogenesis, identifying them as potential therapeutic targets for enhanced management and improved patient outcomes. Full article

(This article belongs to the Section Molecular Immunology)

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30 pages, 17532 KB

Open AccessArticle

Multiomics Investigation of Exhausted T Cells in Glioblastoma Tumor Microenvironment: CCL5 as a Prognostic and Therapeutic Target

by Ruihao Qin, Menglei Hua, Yaru Wang, Qi Zhang, Yong Cao, Yanyan Dai, Chenjing Ma, Xiaohan Zheng, Kaiyuan Ge, Huimin Zhang, Shi Li, Yan Liu, Lei Cao and Liuying Wang

Int. J. Mol. Sci. 2025, 26(20), 9920; https://doi.org/10.3390/ijms26209920 (registering DOI) - 12 Oct 2025

Abstract

Glioblastoma multiforme (GBM) is a common malignancy with poor prognosis, and exhausted T (TEX) cells, a subset of T cells characterized by progressive loss of effector functions, play a critical role in its progression. This study aimed to investigate the impact of TEX-related [...] Read more.

Glioblastoma multiforme (GBM) is a common malignancy with poor prognosis, and exhausted T (TEX) cells, a subset of T cells characterized by progressive loss of effector functions, play a critical role in its progression. This study aimed to investigate the impact of TEX-related genes on immune function, prognosis, and drug sensitivity in GBM through multiomics analysis. Initially, we identified a novel set of TEX-related genes specific to GBM and screened hub genes (CCL5, IL18, CXCR6, FCER1G, TNFSF13B) using conventional statistical methods combined with machine learning. A prognostic risk model was subsequently constructed based on TCGA data and validated in the CGGA cohort. Single-cell and pharmacogenomic analyses revealed significant differences in tumor microenvironment composition and drug sensitivity between risk groups. Notably, Palbociclib emerged as a potential therapeutic agent targeting the novel discovered biomarker CCL5. RT-qPCR results showed that T cells with low CCL5 expression exhibited reduced expression of immune checkpoint-related genes (PD1, TIM3, LAG3) and increased expression of CD28, suggesting enhanced immune function. In conclusion, our findings highlight five hub genes as prognostic markers that could stratify GBM patients with different immune landscapes and levels of drug sensitivity. Furthermore, experimental results suggest that low CCL5 expression could alleviate T cell exhaustion and represent a promising therapeutic target, offering new strategies for improving GBM prognosis. Full article

(This article belongs to the Special Issue Updates and Advances in the Field of Glioblastomas: Mechanisms, Microenvironment and Treatments)

22 pages, 4157 KB

Open AccessArticle

Fabrication and Characterization of Electrospun Keratin Mats with Echinacea purpurea L. and Biosynthesized Silver Nanoparticles

by Akvilė Andziukevičiūtė-Jankūnienė, Erika Adomavičiūtė, Carmen Gaidau, Virgilijus Valeika, Aistė Balčiūnaitienė, Jonas Viškelis, Maria Rapa and Virginija Jankauskaitė

Int. J. Mol. Sci. 2025, 26(20), 9919; https://doi.org/10.3390/ijms26209919 (registering DOI) - 12 Oct 2025

Abstract

This study presents the development of antibacterial electrospun nanofibrous mats composed of keratin and polyethylene oxide, incorporating Echinacea purpurea L. (EchP) and green-synthesized silver nanoparticles (bioAgNPs) produced using EchP extract. The successful synthesis of bioAgNPs was confirmed by [...] Read more.

This study presents the development of antibacterial electrospun nanofibrous mats composed of keratin and polyethylene oxide, incorporating Echinacea purpurea L. (EchP) and green-synthesized silver nanoparticles (bioAgNPs) produced using EchP extract. The successful synthesis of bioAgNPs was confirmed by colorimetric analysis, FTIR, XRD, and TEM. In vitro assays demonstrated antibacterial activity against both Gram-positive and Gram-negative bacteria at ~0.6 µg/mL. Keratin, extracted from sheep wool, retained partial native structure, supporting biocompatibility and cellular regeneration. Incorporation of EchP or bioAgNPs reduced solution viscosity by 25–45%, significantly affecting mat morphology and shifting fiber diameters toward the 50–100 nm range. Quantitative phytochemical analysis, conducted via UV-Vis spectrophotometry, showed 2–3 times higher release of tannins and phenolic compounds compared to hydroxycinnamic acid derivatives and flavonoids. Keratin electrospun mats with bioAgNPs exhibited about 1.5-fold lower polyphenol release, confirming the dual role of polyphenols as electron donors in Ag⁺ bioreduction and as stabilizers. Full article

(This article belongs to the Special Issue Phyto-Functional Nanomaterials: Synthesis, Characterization and Application)

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18 pages, 1513 KB

Open AccessArticle

Role of Lipoprotein(a) and Blood Cells Ratios in Peripheral Artery Disease

by Alexandra V. Tyurina, Olga I. Afanasieva, Marat V. Ezhov, Narek A. Tmoyan, Tatiana V. Balakhonova and Sergei N. Pokrovsky

Int. J. Mol. Sci. 2025, 26(20), 9918; https://doi.org/10.3390/ijms26209918 (registering DOI) - 12 Oct 2025

Abstract

Peripheral artery disease (PAD) is a major global health issue. This study investigated the relationship between lipoprotein(a) [Lp(a)], high-density lipoprotein cholesterol (HDL-C) to blood cells ratios, and PAD development. The study included 361 patients categorized into groups based on the presence of stenotic [...] Read more.

Peripheral artery disease (PAD) is a major global health issue. This study investigated the relationship between lipoprotein(a) [Lp(a)], high-density lipoprotein cholesterol (HDL-C) to blood cells ratios, and PAD development. The study included 361 patients categorized into groups based on the presence of stenotic atherosclerosis in lower limb arteries (LLAs) diagnosed via duplex ultrasound. Group 1 (n = 238) had atherosclerosis at the first visit. A second visit involved 281 patients: 158 from Group 1, 32 new diagnoses (Group 2), and 91 with no atherosclerosis at either visit (Group 3). Laboratory analysis included lipid profiles, Lp(a), and complete blood counts, calculating ratios like Lp(a)/HDL-C and monocyte-to-HDL-C ratio (MHR). Showed patients with stenotic atherosclerosis had significantly higher Lp(a) (20.2 vs. 12.1 mg/dL, p < 0.01), MHR (0.54 vs. 0.39, p = 0.002), and Lp(a)/HDL-C ratios (20.9 vs. 8.8, p = 0.003). The combination of monocytes ≥ 0.55 × 10⁹/L and Lp(a) ≥ 30 mg/dL was present in 27% of PAD patients vs. 10% without (p < 0.01). Kaplan–Meier analysis indicated that high Lp(a) levels led to chronic limb ischemia 9.5 years earlier. Combined assessment of Lp(a) and monocyte-related ratios provides superior predictive value for PAD, suggesting clinical utility for risk stratification and early intervention. Full article

(This article belongs to the Special Issue Identification of Novel Biomarkers Towards Improved Diagnosis and Management of Peripheral Vascular Diseases)

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8 pages, 1353 KB

Open AccessCommunication

Plant Cuticles Exhibit Significant Mid-Infrared Emissivity in the Atmospheric Windows

by Antonio Heredia, Ana González-Moreno, José J. Benítez and Eva Domínguez

Int. J. Mol. Sci. 2025, 26(20), 9917; https://doi.org/10.3390/ijms26209917 (registering DOI) - 12 Oct 2025

Abstract

As sessile organisms, plants have developed strategies to cope with exposure to high radiation. The plant cuticle is located at the interface between the plant and the surrounding environment, thus acting as a first barrier that protects plants against environmental conditions, including solar [...] Read more.

As sessile organisms, plants have developed strategies to cope with exposure to high radiation. The plant cuticle is located at the interface between the plant and the surrounding environment, thus acting as a first barrier that protects plants against environmental conditions, including solar radiation. The isolated cuticles displayed notable absorptance in the infrared spectral range which, according to Kirchhoff’s law of thermal radiation, equals the emission dissipation ability. Comparison among the different cuticles showed that a significant range of their reflectance, transmittance, and absorbance spectra match the spectral regions known as atmospheric windows, between 3–4 and 8–13 microns, located within the mid-infrared region (MIR). They allow energy to pass through into the outer space. These optical parameters varied between cuticles from different plant species and they were not a simple function of the cuticle’s thickness but the product of its specific composition in combination with its molecular arrangement. Full article

(This article belongs to the Special Issue Advanced Spectroscopy Research: New Findings and Perspectives)

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17 pages, 2870 KB

Open AccessArticle

Nitrogen-Doped Carbon Dots Alleviate Pesticide Toxicity in Tomato by Regulating Antioxidant Systems

by Xu Zhang, Yu Xin, Hao Wang, Yuting Dang, Wenhui Wang, Yi Gao, Yu Han, Rongrui Kang, Qinghua Shi and Han Du

Int. J. Mol. Sci. 2025, 26(20), 9916; https://doi.org/10.3390/ijms26209916 (registering DOI) - 12 Oct 2025

Abstract

The overuse of pesticides has raised serious food-safety and environmental concerns. Carbon dots (CDs) can act as biostimulants by enhancing photosynthesis, thereby promoting plant growth and stress tolerance. However, their roles in plant pesticide detoxification remain unclear. This study synthesized nitrogen-doped carbon dots [...] Read more.

The overuse of pesticides has raised serious food-safety and environmental concerns. Carbon dots (CDs) can act as biostimulants by enhancing photosynthesis, thereby promoting plant growth and stress tolerance. However, their roles in plant pesticide detoxification remain unclear. This study synthesized nitrogen-doped carbon dots (N-CDs) with strong blue fluorescence, excellent biocompatibility, and no cytotoxicity observed in HEK 293T cells. The N-CDs were synthesized from 1.025 g citric acid and 0.379 g urea, producing particles with a size of around 2.42 nm and abundant hydrophilic groups. When applied to tomato plants, N-CDs (especially at 150 mg·L⁻¹) significantly reduced chlorothalonil (CHT) residues affecting tomato, by up to 66%. Importantly, N-CDs also improved tomato plant growth, reversing the negative effects of CHT on key parameters such as height, leaf area, and biomass. Indeed, under CHT conditions, N-CDs significantly reduced the contents of malondialdehyde, superoxide, and hydrogen peroxide. In contrast, N-CDs significantly increased the activities of superoxide dismutase, peroxidases, catalase, and ascorbate peroxidase to 117.57%, 158.53%, 162.79%, and 152.23%, respectively. Notably, N-CDs dramatically changed the glutathione pool for tomato detoxification. Overall, this study synthesized the non-cytotoxic N-CDs that not only promote tomato growth but also alleviate CHT toxicity by strengthening the tomato’s antioxidant defense system. Full article

(This article belongs to the Special Issue Exploring Abiotic Stress in Plants: Mechanisms, Adaptations, and Mitigation Strategies)

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23 pages, 970 KB

Open AccessReview

bHLH Transcription Factors in Cereal Crops: Diverse Functions in Regulating Growth, Development and Stress Responses

by Song Song, Nannan Zhang, Xiaowei Fan and Guanfeng Wang

Int. J. Mol. Sci. 2025, 26(20), 9915; https://doi.org/10.3390/ijms26209915 (registering DOI) - 12 Oct 2025

Abstract

Basic helix-loop-helix (bHLH) transcription factors represent one of the largest transcriptional regulator families in cereal crops such as rice, maize, and wheat. They play crucial and diverse roles in regulating key agronomic traits and essential physiological processes. This review provides a systematic synthesis [...] Read more.

Basic helix-loop-helix (bHLH) transcription factors represent one of the largest transcriptional regulator families in cereal crops such as rice, maize, and wheat. They play crucial and diverse roles in regulating key agronomic traits and essential physiological processes. This review provides a systematic synthesis of the functionally characterized bHLH genes across the three major cereals, offering a comparative perspective on their roles in growth, development, and stress responses. We comprehensively summarize their documented functions, highlighting specific regulators such as TaPGS1 for grain size, rice ILI subfamily for leaf angle, OsbHLH004 for seed dormancy and maize “Ms23-Ms32-bHLH122-bHLH51” cascade for the anther development. Their conserved and species-specific functions in iron homeostasis (e.g., IRO2) and in responses to drought, cold, salinity, and pathogens are also detailed. Additionally, we discuss the underlying molecular mechanisms, including specific binding to E-box/G-box cis-elements, protein dimerization, and integration with hormone signaling pathways. By integrating the current knowledge, this review serves as a consolidated and up-to-date reference that highlights the strategic potential of bHLH transcription factors in molecular breeding programs for improving yield, quality, and stress tolerance in cereals. Full article

(This article belongs to the Special Issue Transcription Factors in Plant Gene Expression Regulation, 2nd Edition)

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11 pages, 1738 KB

Open AccessBrief Report

FLAG Immunoprecipitation-Based Mapping of the In Vivo Assembled Spliceosomal C* Complex

by Sweta Kumari and Kusum K. Singh

Int. J. Mol. Sci. 2025, 26(20), 9914; https://doi.org/10.3390/ijms26209914 (registering DOI) - 12 Oct 2025

Abstract

Pre-mRNA splicing is catalyzed by the ribonucleoprotein (RNP) complex known as the spliceosome. The spliceosomes are dynamic and undergo constant rearrangement, leading to the formation of the different spliceosomal complexes A, B, B^act, C, C*, and P. Isolation of the spliceosomal [...] Read more.

Pre-mRNA splicing is catalyzed by the ribonucleoprotein (RNP) complex known as the spliceosome. The spliceosomes are dynamic and undergo constant rearrangement, leading to the formation of the different spliceosomal complexes A, B, B^act, C, C*, and P. Isolation of the spliceosomal complex at a specific intermediate stage requires a means to enrich it. This study describes a strategy for studying intermediate spliceosomal complexes by combining BioID with splicing assays. The MINX splicing substrate with a mutation at the 3′ splice site was utilized to arrest and capture the spliceosomal C* complex before the second catalytic step of splicing. The splicing substrate also contains binding sites for the MS2 coat protein, which facilitates the pull-down of assembled complex by FLAG-MS2-tagged RNP immunoprecipitation and determines the captured proximal proteins by mass spectrometry. Full article

(This article belongs to the Section Molecular Biology)

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15 pages, 2956 KB

Open AccessArticle

Raman Scattering Analysis of High Explosives on Human Hair: From Aromatic (TNT) to Aliphatic (RDX and PETN)

by Francheska M. Colón-González, María A. Villarreal-Blanco, María P. García-Tovar, Priscilla D. Soler-Rodriguez, Tatiana P. Serrano-Zayas, Giancarlo L. Vargas-Alers, Emanuel Ocasio-Reyes, Luis. A. García-Cruz, John R. Castro-Suárez, Nataly J. Galán-Freyle, Leonardo C. Pacheco-Londoño, José A. Centeno-Ortiz and Samuel P. Hernández-Rivera

Int. J. Mol. Sci. 2025, 26(20), 9913; https://doi.org/10.3390/ijms26209913 (registering DOI) - 12 Oct 2025

Abstract

There is a need to develop rapid, in situ methods that require less sample preparation and lower limits of detection for the detection of High Explosives (HEs). Considering that human hair is one of the primary attributes of the human body, its presence [...] Read more.

There is a need to develop rapid, in situ methods that require less sample preparation and lower limits of detection for the detection of High Explosives (HEs). Considering that human hair is one of the primary attributes of the human body, its presence can be used to identify possible traces of hair evidence for forensic screenings. Using non-invasive in situ approaches coupled with multivariate analysis (MVA) can enable rapid detection, thereby decreasing analysis time and reducing the cognitive load on analysts, with response times as low as milliseconds or lower. This preliminary study demonstrates the detection of 2,4,6-trinitrotoluene (TNT), 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), and pentaerythritol tetranitrate (PETN) on black, bleached, and natural gray human hair coupled with principal component analysis (PCA). It was possible to discriminate the HE signals from those of the substrates (hair types) on black, gray, and bleached hair by monitoring characteristic peaks for the nitro group’s vibrations of the explosives. Gray hair presented good discrimination for the explosives due to the absence of melanin. The best modes for discriminating HEs from all three hair types were identified using PCA, with data pretreatment based on the first and second derivatives of the algorithms. The classifications were based on the more substantial variation in the NO₂ symmetric vibration for each HE. Full article

(This article belongs to the Special Issue Spectroscopic Techniques in Molecular Sciences)

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12 pages, 625 KB

Open AccessArticle

Magnesium Preserves Calcium Homeostasis and Contributes to Protect Myotubes from Inflammation-Induced Damage

by Giuseppe Pietropaolo, Sara Castiglioni, Jeanette A. Maier, Federica I. Wolf and Valentina Trapani

Int. J. Mol. Sci. 2025, 26(20), 9912; https://doi.org/10.3390/ijms26209912 (registering DOI) - 11 Oct 2025

Abstract

Magnesium (Mg²⁺) is a key regulator of cellular biochemical processes and an essential cofactor in skeletal muscle physiology. Although Mg²⁺ deficiency has been linked to reduced muscle strength, its role in the regulation of calcium (Ca²⁺) signaling and [...] Read more.

Magnesium (Mg²⁺) is a key regulator of cellular biochemical processes and an essential cofactor in skeletal muscle physiology. Although Mg²⁺ deficiency has been linked to reduced muscle strength, its role in the regulation of calcium (Ca²⁺) signaling and in inflammation remains incompletely understood. In this study, we examined the effects of Mg²⁺ availability using the murine myoblast cell line C2C12. Cells were differentiated under low, normal, or high Mg²⁺ conditions, and myotube formation, intracellular Ca²⁺ fluxes, and resistance to inflammatory stimuli were assessed. Mg²⁺ deficiency impaired myotube differentiation, while Mg²⁺ supplementation preserved Ca²⁺ response during stimulation and contributed to protect myotubes against inflammation-induced damage. Collectively, these findings highlight a dual role of Mg²⁺ in sustaining functional performance under repeated stress and protecting myotubes against inflammatory injury. This study supports the importance of adequate dietary Mg²⁺ intake as a potential strategy to mitigate muscle loss associated with aging and chronic inflammation. Full article

(This article belongs to the Section Molecular Immunology)

25 pages, 595 KB

Open AccessArticle

Analysis of the Phenolic Profile of Chelidonium majus L. and Its Combination with Sericin: Balancing Antimicrobial Activity and Cytocompatibility

by Ana Borges, José Luis Luis Ordóñez-Díaz, Yara Aquino, José Manuel Moreno-Rojas, María Luisa Martín Martín Calvo, Josiana A. A. Vaz and Ricardo C. Calhelha

Int. J. Mol. Sci. 2025, 26(20), 9911; https://doi.org/10.3390/ijms26209911 (registering DOI) - 11 Oct 2025

Abstract

The incorporation of bioactive natural compounds into biomedical applications offers a promising route to enhance therapeutic efficacy while supporting sustainability. In this study, we investigated the synergistic potential of Sericin, a silk-derived biopolymer, and Chelidonium majus L. (C. majus), a medicinal plant with [...] Read more.

The incorporation of bioactive natural compounds into biomedical applications offers a promising route to enhance therapeutic efficacy while supporting sustainability. In this study, we investigated the synergistic potential of Sericin, a silk-derived biopolymer, and Chelidonium majus L. (C. majus), a medicinal plant with a diverse phenolic profile, in relation to biological activities relevant for wound care and infection control. A combined experimental strategy was applied, integrating detailed chemical characterization of C. majus extracts with antimicrobial and cytocompatibility assays across different Sericin–plant extract ratios (1:1, 1:2, 2:2, and 2:1). Phytochemical analysis identified and quantified 57 phenolic compounds, including high levels of flavonoids (quercetin, kaempferol, isorhamnetin) and phenolic acids (caffeic and ferulic acid). Salicylic acid (123.6 µg/g), feruloyltyramine (111.8 µg/g), and pinocembrin (98.4 µg/g) were particularly abundant, compounds previously reported to disrupt microbial membranes and impair bacterial viability. These metabolites correlated with the strong antimicrobial activity of C. majus against Gram-positive strains (MIC = 5–10 mg/mL). In combination with Sericin, antimicrobial performance was ratio-dependent, with higher proportions of C. majus (2:1) retaining partial inhibitory effects. Cytocompatibility assays with HFF1 fibroblasts demonstrated low antiproliferative activity across most formulations (GI₅₀ > 400 µg/mL), supporting their potential safety in topical applications. Collectively, the results indicate a concentration-dependent interaction between C. majus phenolics and the Sericin protein matrix, reinforcing their suitability as candidates for natural-based wound healing materials. Importantly, the valorization of Sericin, an underutilized byproduct of the silk industry, together with a widely accessible medicinal plant, underscores the ecological and economic sustainability of this approach. Overall, this work supports the exploration of the development of biomaterials with potential for advancing tissue repair and wound management. Full article

(This article belongs to the Special Issue Novel Natural Compound for Wound and Tissue Repair and Regeneration: 4th Edition)

49 pages, 10722 KB

Open AccessReview

Triglycerides, Glucose Metabolism, and Type 2 Diabetes

by Yutang Wang

Int. J. Mol. Sci. 2025, 26(20), 9910; https://doi.org/10.3390/ijms26209910 (registering DOI) - 11 Oct 2025

Abstract

Type 2 diabetes is a major global health burden, causing approximately 2 million deaths annually. Recent studies have revealed a strong positive correlation between elevated triglyceride levels and plasma glucose, as well as increased prevalence, incidence, and mortality of type 2 diabetes, suggesting [...] Read more.

Type 2 diabetes is a major global health burden, causing approximately 2 million deaths annually. Recent studies have revealed a strong positive correlation between elevated triglyceride levels and plasma glucose, as well as increased prevalence, incidence, and mortality of type 2 diabetes, suggesting a potential causal link. This review explores the metabolic interconversion between triglycerides and glucose, emphasizing how excess carbohydrate intake leads to ectopic triglyceride accumulation, which in turn enhances hepatic gluconeogenesis. It highlights key signaling pathways through which ectopic triglyceride deposition drives insulin resistance, hyperinsulinemia, β-cell dysfunction and apoptosis, and increased glucose production—central mechanisms in diabetes pathogenesis. Evidence from clinical interventions, such as the reversal of type 2 diabetes through bariatric surgery and dietary energy restriction, supports the hypothesis that ectopic triglyceride accumulation is a driving factor. Furthermore, this review explains why omega-3 fatty acids and niacin, in contrast to fibrates, do not protect against type 2 diabetes, despite lowering triglycerides. Overall, this review emphasizes the contribution of ectopic triglyceride accumulation—driven by obesity, hypertriglyceridemia, excessive consumption of carbohydrates and fats, and physical inactivity—to the onset and progression of type 2 diabetes, offering valuable insights into potential therapeutic strategies. Full article

(This article belongs to the Special Issue The Role of Lipids in Health and Diseases)

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37 pages, 3801 KB

Open AccessReview

Molecular Signature in Focal Cortical Dysplasia: A Systematic Review of RNA and Protein Data

by Jalleh Shakerzadeh, Radim Jaroušek, Zita Goliášová and Milan Brázdil

Int. J. Mol. Sci. 2025, 26(20), 9909; https://doi.org/10.3390/ijms26209909 (registering DOI) - 11 Oct 2025

Abstract

Focal cortical dysplasia (FCD) is a major cause of drug-resistant epilepsy, yet its molecular basis remains poorly understood. Numerous studies have analyzed RNA, protein, and microRNA alterations, but results are often inconsistent across subtypes and methodologies. To address this gap, we conducted a [...] Read more.

Focal cortical dysplasia (FCD) is a major cause of drug-resistant epilepsy, yet its molecular basis remains poorly understood. Numerous studies have analyzed RNA, protein, and microRNA alterations, but results are often inconsistent across subtypes and methodologies. To address this gap, we conducted a systematic review integrating transcriptomic, proteomic, and microRNA data from 117 human studies of FCD subtypes I–III. Differentially expressed factors were extracted, categorized by subtype, and analyzed using pathway enrichment and network approaches. Our integrative analysis revealed convergent dysregulation of neuroinflammatory, synaptic, cytoskeletal, and metabolic pathways across FCD subtypes. Consistently altered genes, including IL1B, TLR4, BDNF, HMGCR, and ROCK2, together with dysregulated microRNAs such as hsa-miR-21-5p, hsa-miR-155-5p, and hsa-miR-132-3p, were linked to PI3K–Akt–mTOR, Toll-like receptor, and GABAergic signaling, emphasizing shared pathogenic mechanisms. Importantly, we identified overlapping transcript–protein patterns and subtype-specific molecular profiles that may refine diagnosis and inform therapeutic strategies. This review provides the first cross-omics molecular framework of FCD, demonstrating how convergent pathways unify heterogeneous findings and offering a roadmap for biomarker discovery and targeted interventions. Full article

(This article belongs to the Section Macromolecules)

13 pages, 6985 KB

Open AccessArticle

Investigation of the Role of miR-1236-3p in Heat Tolerance of American Shad (Alosa sapidissima) by Targeted Regulation of hsp90b1

by Mingkun Luo, Ying Liu, Wenbin Zhu, Bingbing Feng, Wei Xu and Zaijie Dong

Int. J. Mol. Sci. 2025, 26(20), 9908; https://doi.org/10.3390/ijms26209908 (registering DOI) - 11 Oct 2025

Abstract

High temperatures are one of the most important abiotic stressors affecting the survival and growth of American shad (Alosa sapidissima). Building on previous omics sequencing studies of A. sapidissima liver and gills under high temperature stress, this study focused on investigating [...] Read more.

High temperatures are one of the most important abiotic stressors affecting the survival and growth of American shad (Alosa sapidissima). Building on previous omics sequencing studies of A. sapidissima liver and gills under high temperature stress, this study focused on investigating the regulatory role of miR-1236-3p and its target gene hsp90b1. The results indicate that the full-length cDNA of the hsp90b1 gene is 2023 bp and comprises a 5’ end of 58 bp, a 3’ end of 84 bp, and a coding region of 1881 bp, encoding 626 amino acids. Sequence alignment and phylogenetic tree analysis reveal that the hsp90b1 sequence is highly conserved across species. In situ hybridization showed that hsp90b1 is mainly localized in the cytoplasm. Software prediction identified a potential binding site between miR-1236-3p and hsp90b1. Through the construction of wild-type and mutant 3’UTR hsp90b1 dual luciferase reporter plasmids, the targeted relationship between the two was confirmed. In addition, the spatiotemporal expression levels of the hsp90b1 was found to be highest in the multicellular stage and liver tissue at a cultivation temperature of 27 °C; miR-1236-3P was highly expressed in the hatching stage and heart tissue at 30 °C. These findings provide a theoretical foundation for further investigating the regulatory role of non-coding RNA in A. sapidissima heat stress and offer data for subsequent molecular breeding studies. Full article

(This article belongs to the Special Issue Harnessing Bioinformatics for miRNA Research: Methods, Insights and Applications)

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44 pages, 1366 KB

Open AccessReview

Scorpion Venom as a Source of Cancer Drugs: A Comprehensive Proteomic Analysis and Therapeutic Potential

by Stephanie Santos Suehiro Arcos, Mariana Ramos da Cunha Aguiar, Júlia de Oliveira, Matheus Ramos da Silva, Isabela de Oliveira Cavalcante Pimentel, Nicolas Gamboa dos Anjos, Gustavo Henrique Rohr Souza Machado, Kimberly Borges Evangelista, Fernanda Calheta Vieira Portaro and Leo Kei Iwai

Int. J. Mol. Sci. 2025, 26(20), 9907; https://doi.org/10.3390/ijms26209907 (registering DOI) - 11 Oct 2025

Abstract

Scorpion venom is a rich source of bioactive compounds with significant potential for anticancer drug development. Its diverse molecular composition, including neurotoxins, antimicrobial peptides, and enzymes, provides a vast library for therapeutic innovation. Proteomic analyses have characterized venom composition in several species, while [...] Read more.

Scorpion venom is a rich source of bioactive compounds with significant potential for anticancer drug development. Its diverse molecular composition, including neurotoxins, antimicrobial peptides, and enzymes, provides a vast library for therapeutic innovation. Proteomic analyses have characterized venom composition in several species, while further functional assays have clarified their anticancer mechanisms. This review synthesizes current knowledge on scorpion venom-derived peptides with demonstrated anticancer activity, which selectively target ion channels, induce apoptosis, or disrupt tumor microenvironments. Where available, we highlight proteomic studies that have identified these components and discuss their structural features relevant to drug design. We also examine clinical applications and the challenges in translating venom peptides into therapies. The crucial and growing role of proteomics in this field, particularly for venom fractionation, component identification, and structural characterization, is critically evaluated. Full article

(This article belongs to the Special Issue Advances in Proteomics in Cancer)

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