International Journal of Molecular Sciences

22 pages, 4995 KiB

Open AccessArticle

Comprehensive In Vitro and In Silico Analysis of Antimicrobial and Insecticidal Properties of Essential Oil of Myrtus communis L. from Algeria

by Ghozlane Barboucha, Noureddine Rahim, Amina Bramki, Houssem Boulebd, Anna Andolfi, Khaoula Boulacheb, Amina Boulacel, Maria Michela Salvatore and Marco Masi

Int. J. Mol. Sci. 2025, 26(10), 4754; https://doi.org/10.3390/ijms26104754 - 15 May 2025

Abstract

This study investigated the phytochemical composition and biological activities of Myrtus communis essential oil (EO) from Algeria, focusing on its antimicrobial, antifungal, and insecticidal properties using in vitro and in silico approaches. Gas chromatography–mass spectrometry (GC-MS) analysis identified myrtenyl acetate (57.58%), 1,8-cineole (17.82%), [...] Read more.

This study investigated the phytochemical composition and biological activities of Myrtus communis essential oil (EO) from Algeria, focusing on its antimicrobial, antifungal, and insecticidal properties using in vitro and in silico approaches. Gas chromatography–mass spectrometry (GC-MS) analysis identified myrtenyl acetate (57.58%), 1,8-cineole (17.82%), and α-terpineol (6.82%) as the major constituents. M. communis EO exhibited significant antibacterial activity, particularly against Staphylococcus aureus (13.00 ± 0.70 mm) and Salmonella typhimurium (13.00 ± 1.50 mm), with moderate inhibition of Bacillus subtilis (10 ± 1.00 mm) and Escherichia coli (9.00 ± 0.70 mm), while Pseudomonas aeruginosa showed resistance. The antifungal activity was notable against Fusarium oxysporum (16.50 ± 0.50 mm), Aspergillus fumigatus (11.00 ± 1.00 mm), and Penicillium sp. (9.00 ± 0.60 mm) but ineffective against Aspergillus niger. Insecticidal activity against Tribolium castaneum was evaluated using contact toxicity, fumigation toxicity, and repellent activity assays. The EO demonstrated potent insecticidal effects, with an LC₅₀ value of 0.029 µL/insect for contact toxicity and 162.85 µL/L air for fumigation after 96 h. Additionally, the EO exhibited strong repellent activity, achieving 99.44% repellency at a concentration of 0.23 mg/cm² after 24 h. Density functional theory (DFT) calculations provided insights into the molecular geometry and electronic properties of the key bioactive compounds. Molecular docking studies evaluated their binding affinities to bacterial enzymes (DNA gyrase, dihydrofolate reductase6, and Gyrase B) and insecticidal targets (acetylcholinesterase), revealing strong interactions, particularly for geranyl acetate and methyleugenol. These findings highlight M. communis EO as a promising natural antimicrobial and insecticidal agent, with potential applications in plant protection and biopesticide development. Full article

(This article belongs to the Special Issue The Advances in Antimicrobial Biomaterials)

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30 pages, 3721 KiB

Open AccessReview

Systematic Review: Does Exercise Training Influence Ghrelin Levels?

by Wissal Abassi, Nejmeddine Ouerghi, Antonella Muscella, Santo Marsigliante, Moncef Feki and Anissa Bouassida

Int. J. Mol. Sci. 2025, 26(10), 4753; https://doi.org/10.3390/ijms26104753 - 15 May 2025

Abstract

Ghrelin, a gastric-derived peptide, regulates appetite, food intake, and energy homeostasis. Body weight plays a crucial role in modulating circulating ghrelin levels. Since exercise training is one of the most valuable tools for controlling body weight, it is relevant to consider whether exercise [...] Read more.

Ghrelin, a gastric-derived peptide, regulates appetite, food intake, and energy homeostasis. Body weight plays a crucial role in modulating circulating ghrelin levels. Since exercise training is one of the most valuable tools for controlling body weight, it is relevant to consider whether exercise can influence total ghrelin secretion. This study aims to perform a systematic review of the effect of acute/chronic exercise on plasma ghrelin levels. An extensive literature search was carried out on various databases, including PubMed, ScienceDirect, and Google Scholar. The search was conducted using English keywords such as acute-exercise, transient-exercise, exercise, chronic-exercise, training, physical-activity, physical-training, exercise training, and total-ghrelin, ghrelin, appetite-related-peptides, gastrointestinal-peptides, gastrointestinal-hormones, and appetite-regulating-hormone. Initially, 2104 studies were identified. After evaluating study quality, data from 61 relevant studies were extracted for inclusion in this review. Most studies indicated that short-term acute aerobic exercise did not affect total ghrelin levels regardless of exercise intensity, characteristics, or growth hormone (GH) secretion. However, long and very-long aerobic/chronic exercise increased total ghrelin levels, mainly in overweight/obese individuals. Acute/chronic exercise may differentially influence total ghrelin secretion. Short-term acute aerobic exercise induces stable plasma ghrelin concentrations, independent of GH secretion. Long-term aerobic training increased its levels mainly in overweight/obese individuals through body composition and oxidative stress reduction. Additionally, total ghrelin secretion is more sensitive to exercise/training duration than exercise/training intensity. Full article

(This article belongs to the Special Issue Hormone Signaling in Human Health and Diseases, 2nd Edition)

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19 pages, 4154 KiB

Open AccessArticle

Estradiol Promotes Myelin Repair in the Spinal Cord of Female Mice in a CXCR4 Chemokine Receptor-Independent Manner

by Marianne Bardy-Lagarde, Narimene Asbelaoui, Michael Schumacher and Abdel Mouman Ghoumari

Int. J. Mol. Sci. 2025, 26(10), 4752; https://doi.org/10.3390/ijms26104752 - 15 May 2025

Abstract

In the adult central nervous system (CNS), myelin regeneration primarily occurs through the differentiation of oligodendrocyte progenitor cells into mature oligodendrocytes. In men, declining testosterone levels accelerate the progression of multiple sclerosis (MS), while in women, menopause worsens MS-related disability. We previously demonstrated [...] Read more.

In the adult central nervous system (CNS), myelin regeneration primarily occurs through the differentiation of oligodendrocyte progenitor cells into mature oligodendrocytes. In men, declining testosterone levels accelerate the progression of multiple sclerosis (MS), while in women, menopause worsens MS-related disability. We previously demonstrated that functional testes and testosterone are required for the spontaneous remyelination of a focal lysolecithin (LPC)-induced demyelinating lesion in the spinal cords of male mice. Testosterone-dependent myelin repair was dependent on the induction of the chemokine receptor CXCR4 in astrocytes that repopulated the lesion and on cooperation between androgen-receptor signaling and CXCR4 signaling. In the present study, we investigated whether ovaries and estradiol have a comparable key role in female mice. Ovariectomy prevents, the appearance of astrocytes, while treatment with estradiol enhances astrocyte numbers and promotes remyelination by oligodendrocytes within the LPC-demyelinated lesion. Unlike testosterone, estradiol did not induce CXCR4 expression, and its effects remained unaffected by the CXCR4 inhibitor AMD3100. As was seen with testosterone treatment, the presence of astrocytes and myelinating oligodendrocytes within the LPC lesion of estradiol-treated females prevented the incursion of Schwann cells. These findings highlight estradiol’s crucial role in CNS remyelination in females, providing a strong rationale for estrogen-replacement therapy in estrogen-deficient and menopausal women with MS. Full article

(This article belongs to the Special Issue Demyelinating Diseases: From Molecular Mechanisms to, Therapeutic Strategies—3rd Edition)

15 pages, 2645 KiB

Open AccessArticle

Modeling the Copy Number of HSATII Repeats in Human Pericentromere

by Puranjan Ghimire and Richard I. Joh

Int. J. Mol. Sci. 2025, 26(10), 4751; https://doi.org/10.3390/ijms26104751 - 15 May 2025

Abstract

Tandemly repeated DNA fragments are major components of centromeres and pericentromeric heterochromatin, which is responsible for chromosomal stability and segregation. Recent evidence suggests that transcripts from these repeats play a key role in heterochromatin maintenance, and these repeats can be highly dynamic with [...] Read more.

Tandemly repeated DNA fragments are major components of centromeres and pericentromeric heterochromatin, which is responsible for chromosomal stability and segregation. Recent evidence suggests that transcripts from these repeats play a key role in heterochromatin maintenance, and these repeats can be highly dynamic with various copy numbers. Here, we developed a mathematical model for human satellite repeats, which tracks the silenced and desilenced repeats, lncRNA, and copy number. Our model shows that chromatin factors for silencing and RNA stability can facilitate copy gain in satellites. Also, the system can be bistable, and cells with different copy numbers, silenced repeats with a small copy number, and desilenced repeats with a large copy number may coexist. To incorporate the cooperative methylation by neighboring repeats and the local chromatin environment, we also developed a spatial model where the local chromatin environment facilitates methylation locally. This model suggests that a local domain of silenced repeats may be an important feature of copy number regulation. Our models suggest that pericentromeric repeats are highly dynamic, and small changes in chromatin regulation can lead to large changes in satellite copy numbers. Full article

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

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16 pages, 517 KiB

Open AccessReview

The Role of microRNAs in Inflammatory Bowel Disease

by Aneta Sokal-Dembowska, Sara Jarmakiewicz-Czaja, Kacper Helma and Rafał Filip

Int. J. Mol. Sci. 2025, 26(10), 4750; https://doi.org/10.3390/ijms26104750 - 15 May 2025

Abstract

Deregulation of microRNAs (miRNAs) has been implicated in the development of inflammatory bowel disease (IBD). Specific miRNAs are differentially expressed in patients with IBD compared to healthy individuals. Regulation of their expression can modulate the inflammatory response, the composition of the intestinal microbiota, [...] Read more.

Deregulation of microRNAs (miRNAs) has been implicated in the development of inflammatory bowel disease (IBD). Specific miRNAs are differentially expressed in patients with IBD compared to healthy individuals. Regulation of their expression can modulate the inflammatory response, the composition of the intestinal microbiota, and intestinal barrier function. miRNAs can regulate the immune and inflammatory response via multiple mechanisms, from Th1/Th17 regulation and ferroptosis to modulation of NLRP3 (NOD-like receptor family, pyrin domain-containing 3) and control of the NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) pathway. The use of miRNAs as biomarkers and therapeutic targets may help monitor IBD treatment and support the development of new, more individualized therapies that minimize common side effects. Full article

(This article belongs to the Special Issue Inflammatory Bowel Disease: Molecular Advances in Pathogenesis and Therapies)

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30 pages, 2663 KiB

Open AccessReview

IGFBP-2 and IGF-II: Key Components of the Neural Stem Cell Niche? Implications for Glioblastoma Pathogenesis

by Abigail J. Harland and Claire M. Perks

Int. J. Mol. Sci. 2025, 26(10), 4749; https://doi.org/10.3390/ijms26104749 - 15 May 2025

Abstract

Glioblastoma is a fatal and aggressive cancer with no cure. It is becoming increasingly clear that glioblastoma initiation is a result of adult neural stem cell (NSC) transformation—most likely those within the subventricular zone (SVZ). Indeed, transcriptomic analysis indicates that glioblastomas are reminiscent [...] Read more.

Glioblastoma is a fatal and aggressive cancer with no cure. It is becoming increasingly clear that glioblastoma initiation is a result of adult neural stem cell (NSC) transformation—most likely those within the subventricular zone (SVZ). Indeed, transcriptomic analysis indicates that glioblastomas are reminiscent of a neurodevelopmental hierarchy, in which neural stem and progenitor markers are widely expressed by tumour stem-like cells. However, NSC fates and the cues that drive them are poorly understood. Studying the crosstalk within NSC niches may better inform our understanding of glioblastoma initiation and development. Insulin-like growth factor binding protein 2 (IGFBP-2) has a well-established prognostic role in glioblastoma, and cell-based mechanistic studies show the independent activation of downstream oncogenic pathways. However, IGFBP-2 is more commonly recognised as a modulator of insulin-like growth factors (IGFs) for receptor tyrosine kinase signal propagation or attenuation. In the adult human brain, both IGFBP-2 and IGF-II expression are retained in the choroid plexus (ChP) and secreted into the cerebral spinal fluid (CSF). Moreover, secretion by closely associated cells and NSCs themselves position IGFBP-2 and IGF-II as interesting factors within the NSC niche. In this review, we will highlight the experimental findings that show IGFBP-2 and IGF-II influence NSC behaviour. Moreover, we will link this to glioblastoma biology and demonstrate the requirement for further analysis of these factors in glioma stem cells (GSCs). Full article

(This article belongs to the Special Issue The Role of the IGF Axis in Disease, 4th Edition)

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20 pages, 692 KiB

Open AccessPerspective

Next-Level Prediction of Structural Progression in Knee Osteoarthritis: A Perspective

by Johanne Martel-Pelletier and Jean-Pierre Pelletier

Int. J. Mol. Sci. 2025, 26(10), 4748; https://doi.org/10.3390/ijms26104748 - 15 May 2025

Abstract

Osteoarthritis (OA) is a prevalent and disabling chronic disease, with knee OA being the most common form, affecting approximately 73% of individuals over 55 years. Traditional clinical assessments often fail to predict knee structural progression accurately, highlighting the need for improved prognostic methods. [...] Read more.

Osteoarthritis (OA) is a prevalent and disabling chronic disease, with knee OA being the most common form, affecting approximately 73% of individuals over 55 years. Traditional clinical assessments often fail to predict knee structural progression accurately, highlighting the need for improved prognostic methods. This perspective explores the complexity of stratifying knee OA patients based on rapid structural progression. It underscores the importance of such early identification to enable timely and personalized intervention and optimize disease-modifying OA drug clinical trial design, as many trial participants show minimal progression, complicating the assessment of treatment efficacy. We highlight the potential of machine learning (ML) and deep learning (DL) in overcoming this prognostic challenge, as these methodologies enhance classification/stratification capabilities by leveraging multidimensional data and capturing the intricate relationships between diverse features. These include panels of biochemical markers and imaging markers, such as those from magnetic resonance imaging (MRI), as integrating MRI data into ML/DL prognostic models enhances such prediction performance. These automated ML/DL models will offer a transformative approach to stratifying knee OA patients and represent a paradigm shift in disease management. Ultimately, ML/DL applications will not only improve patient outcomes but will also promote innovation in OA research, clinical practice, and therapeutics. Full article

(This article belongs to the Special Issue Osteoarthritis: From Molecular Mechanism to Novel Therapy)

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15 pages, 2090 KiB

Open AccessArticle

Assessment of the Curative Anti-Glycation Properties of a Novel Injectable Formulation Combining Dual-Weight Hyaluronic Acid (Low- and Mid/High-Molecular Weight) with Trehalose on Human Skin Ex Vivo

by Robert Chmielewski, Agata Lebiedowska and Wioletta Barańska-Rybak

Int. J. Mol. Sci. 2025, 26(10), 4747; https://doi.org/10.3390/ijms26104747 - 15 May 2025

Abstract

Glycation influences skin aging through non-enzymatic reactions between reducing sugars and proteins, forming advanced glycation end-products (AGEs) that accelerate skin deterioration. This study evaluates the curative anti-glycation effects of an injectable formulation combining dual-molecular-weight hyaluronic acid (low and mid/high) with trehalose in methylglyoxal-induced [...] Read more.

Glycation influences skin aging through non-enzymatic reactions between reducing sugars and proteins, forming advanced glycation end-products (AGEs) that accelerate skin deterioration. This study evaluates the curative anti-glycation effects of an injectable formulation combining dual-molecular-weight hyaluronic acid (low and mid/high) with trehalose in methylglyoxal-induced glycation in human skin explants. Thirty-six human skin explants were allocated across five experimental groups in a 12-day study. Glycation was induced using methylglyoxal (500 μM) on days 1 and 4, followed by curative product administration on day 5. CML (Nε-(carboxymethyl)lysine) immunohistochemistry was performed to assess glycation levels in the reticular dermis at days 6, 8, and 12, with quantitative analysis conducted through standardized image analysis. The formulation significantly reduced CML formation by 60% on day 6 compared to untreated controls (p < 0.001). Under methylglyoxal-induced glycation stress the product showed sustained curative effects, with CML reductions of 69% on day 6 (p = 0.008), 68% on day 8 (p = 0.012), and 61% on day 12 (p = 0.033) compared to methylglyoxal treatment alone. Cell viability remained unaffected throughout the study period across all experimental conditions. The tested injectable formulation exhibits significant and sustained curative anti-glycation properties in human skin explants for 12 days, effectively counteracting methylglyoxal-induced glycation damage without affecting cell viability. These findings advance anti-aging skin interventions, offering a novel approach to address glycation-induced skin damage with potential applications in clinical dermatology and aesthetic medicine. Full article

(This article belongs to the Special Issue Molecular Mechanisms for Skin Protection and Aging)

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23 pages, 23247 KiB

Open AccessArticle

The Alpha/Beta-Hydrolase Fold Superfamily in Brassica napus: Expression Profiles and Functional Implications of Clade-3 BnABH Proteins in Response to Abiotic Stress

by Yahui Ding, Lianqiang Feng, Pu Li, Xindeng Yang, Muzi Li, Hanxuan Liu, Jiamin Xu, Jitong Zhang, Shouwu Sun, Xiaona Zhou, Wenfang Hao, Yanfeng Zhang and Chang-Gen Xie

Int. J. Mol. Sci. 2025, 26(10), 4746; https://doi.org/10.3390/ijms26104746 - 15 May 2025

Abstract

Alpha/beta hydrolase (ABHs) fold esterase/lipase proteins represent a prominent family within the serine hydrolase (SH) superfamily that includes esterases and lipases and other catalytic and non-catalytic proteins. ABHs play crucial roles in both the fundamental and secondary metabolic pathways, including the synthesis and [...] Read more.

Alpha/beta hydrolase (ABHs) fold esterase/lipase proteins represent a prominent family within the serine hydrolase (SH) superfamily that includes esterases and lipases and other catalytic and non-catalytic proteins. ABHs play crucial roles in both the fundamental and secondary metabolic pathways, including the synthesis and degradation of triacylglycerols (TAGs), key components of plant oils. Despite their importance in oil production, the ABH gene family in the oil crop Brassica napus has not been comprehensively analyzed. In the present study, we identified 777 BnABH genes in the B. napus cultivar ‘Zhongshuang 11’ (ZS11). Phylogenetic analysis categorized these BnABH genes into 10 distinct groups. Twenty-four BnABHs were identified through esterase activity staining and mass spectrometry, 11 of which were classified into clade C3. Examination of the gene and protein structures, expression patterns, and cis-elements of the BnABHs in clade C3 suggested diverse functional roles across different tissues and in response to various environmental stresses. In particular, BnABH205 was highly induced by high temperatures. Subcellular localization analysis revealed that the BnABH205 protein was localized to the plastid. Further analysis revealed five haplotypes within the coding and 3′ untranslated regions of BnABH205 that were significantly associated with seed oil content (SOC). Overall, this study provides a comprehensive understanding of BnABHs and introduces a robust methodology for identifying potential esterase/lipase genes that regulate seed oil content (SOC) in response to environmental hazards, especially heat waves during seed maturation. Full article

(This article belongs to the Special Issue Plant and Environmental Interactions (Abiotic Stress))

19 pages, 1840 KiB

Open AccessArticle

Involvement of lncRNAs NEAT1 and ZBTB11-AS1 in Active and Persistent HIV-1 Infection in C20 Human Microglial Cell Line

by Camila Pereira-Montecinos, Isidora Pittet-Díaz, Isidora Morales-Vejar, Catalina Millan-Hidalgo, Victoria Rojas-Celis, Eva Vallejos-Vidal, Felipe E. Reyes-López, Loreto F. Fuenzalida, Sebastián Reyes-Cerpa and Daniela Toro-Ascuy

Int. J. Mol. Sci. 2025, 26(10), 4745; https://doi.org/10.3390/ijms26104745 - 15 May 2025

Abstract

HIV-1 infection in microglia induces HIV-associated neurocognitive disorder (HAND). Recent evidence suggests that microglia can be infected with HIV-1 in the active, persistent, or latent replication stages. The molecular mechanisms governing these stages of infection are still the subject of continuous study. In [...] Read more.

HIV-1 infection in microglia induces HIV-associated neurocognitive disorder (HAND). Recent evidence suggests that microglia can be infected with HIV-1 in the active, persistent, or latent replication stages. The molecular mechanisms governing these stages of infection are still the subject of continuous study. In this study, we analyzed the relationship between HIV-1 infection and two lncRNAs, NEAT1 and ZBTB11-AS1, on different days post-infection. We found that on days 1 and 4 post-infection, HIV-1 was actively replicating; meanwhile, by day 21, HIV-1 had entered a persistent stage. We also noted that the expression levels of NEAT1 and ZBTB11-AS1 varied during these different stages of HIV-1 infection in microglia, as did their subcellular localization. We performed an interaction network analysis and identified DDX3X and ZC3HAV1 as hypothetically related to NEAT1 and ZBTB11-AS1 in the C20 human microglial cell line. Additionally, we determined that IL-6, a cytokine regulated by DDX3X and ZC3HAV1, exhibits changes in protein expression levels during both active and persistent HIV-1 infection. Full article

(This article belongs to the Special Issue Beyond Silos: A Comprehensive Understanding of HIV Functional Cure and NeuroHIV)

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35 pages, 1150 KiB

Open AccessArticle

Optimized and Validated Stability-Indicating RP-HPLC Method for Comprehensive Profiling of Process-Related Impurities and Stress-Induced Degradation Products in Rivaroxaban (XARELTO)^®

by Aktham H. Mestareehi

Int. J. Mol. Sci. 2025, 26(10), 4744; https://doi.org/10.3390/ijms26104744 - 15 May 2025

Abstract

An isocratic reverse-phase high-performance liquid chromatography (RP-HPLC) method, coupled with photodiode array detection (PDA), was developed for the identification and characterization of stress degradation products and an unknown process-related impurity of rivaroxaban in bulk drug form. Rivaroxaban, a selective and direct Factor Xa [...] Read more.

An isocratic reverse-phase high-performance liquid chromatography (RP-HPLC) method, coupled with photodiode array detection (PDA), was developed for the identification and characterization of stress degradation products and an unknown process-related impurity of rivaroxaban in bulk drug form. Rivaroxaban, a selective and direct Factor Xa inhibitor, underwent forced degradation under hydrolytic (acidic, alkaline, and neutral), photolytic, thermal, and oxidative stress conditions, following the ICH’s guidelines. The drug displayed significant susceptibility to acid, base, and oxidative environments leading to the formation of eleven degradation products. All degradation products, along with process impurities and Rivaroxaban, were effectively separated using a (4.6 × 250 mm, 5 µm) C18 Thermo ODS Hypersil column at ambient temperature. The mobile phase composed of acetonitrile and monobasic potassium phosphate (pH 2.9) in a 30:70 (v/v) ratio, with a flow rate of 1.0 mL/min, and detection was carried out at 249 nm. The LC-PDA method was validated in accordance with the ICH’s guidelines and USP38-NF33, demonstrating specificity, linearity, accuracy, precision, and robustness. Recovery studies showed results within the range of 98.6–103.4%, with a % RSD LT 2%. The limits of detection (LOD) and quantitation (LOQ) for rivaroxaban were determined to be 0.30 ppm and 1.0 ppm, respectively. Stress studies confirmed that the degradation products did not interfere with rivaroxaban detection, establishing the method as stability-indicating. Specific impurities were identified, including impurity G at 2.79 min, impurity D at 3.50 min, impurity H at 5.32 min, impurity C at 6.14 min, impurity E at 8.36 min, impurity A at 9.03 min, and impurity F at 9.49 min. Additionally, several unknown impurities were observed at 3.20, 4.00, 4.59, and 4.77 min. Statistical evaluation confirmed the method’s reliability, making it suitable for routine analysis, quality control of raw materials, formulations of varying strengths, dissolution studies, and bioequivalence assessments of rivaroxaban formulations. Full article

(This article belongs to the Section Biochemistry)

24 pages, 1583 KiB

Open AccessArticle

MixOmics Integration of Biological Datasets Identifies Highly Correlated Variables of COVID-19 Severity

by Noa C. Harriott, Michael S. Chimenti, Gregory Bonde and Amy L. Ryan

Int. J. Mol. Sci. 2025, 26(10), 4743; https://doi.org/10.3390/ijms26104743 - 15 May 2025

Abstract

Despite several years passing since the COVID-19 pandemic was declared, challenges remain in understanding the factors that can predict the severity of COVID-19 disease and complications of SARS-CoV-2 infection. While many large-scale multi-omic datasets have been published, integration of these datasets has the [...] Read more.

Despite several years passing since the COVID-19 pandemic was declared, challenges remain in understanding the factors that can predict the severity of COVID-19 disease and complications of SARS-CoV-2 infection. While many large-scale multi-omic datasets have been published, integration of these datasets has the potential to substantially increase the biological insight gained, allowing a more complex comprehension of the disease pathogenesis. Such insight may improve our ability to predict disease progression, detect severe cases more rapidly and develop effective therapeutics. In this study, we have applied an innovative machine learning algorithm to delineate COVID severity based on the integration of paired samples of proteomic and transcriptomic data from a small cohort of patients testing positive for SARS-CoV-2 infection with differential disease severity. Targeted plasma proteomics and an onco-immune targeted transcriptomic panel were performed on sequential samples from a cohort of 23 severe, 21 moderate and 10 mild COVID-19 patients. We applied DIABLO, a new integrative method, to identify multi-omics biomarker panels that can discriminate between multiple phenotypic groups, such as the varied severity of disease in COVID-19 patients. As COVID-19 severity is known among our sample group, we can train models using this as the outcome variable and calculate features that are important predictors of severe disease. In this study, we detect highly correlated key variables of severe COVID-19 using transcriptomic discriminant analysis and multi-omics integration methods. This approach highlights the power of data integration from a small cohort of patients, offering a better biological understanding of the molecular mechanisms driving COVID-19 severity and an opportunity to improve the prediction of disease trajectories and targeted therapeutics. Full article

(This article belongs to the Special Issue Proteomics and Its Applications in Disease 3.0)

18 pages, 1200 KiB

Open AccessReview

The Role of Intermittent Fasting in the Activation of Autophagy Processes in the Context of Cancer Diseases

by Waleria Wolska, Izabela Gutowska, Agata Wszołek and Wojciech Żwierełło

Int. J. Mol. Sci. 2025, 26(10), 4742; https://doi.org/10.3390/ijms26104742 - 15 May 2025

Abstract

Intermittent fasting (IF) is a dietary approach that influences key metabolic pathways, including autophagy—a crucial mechanism in maintaining cellular homeostasis. Autophagy plays a dual role in oncogenesis, acting both as a tumor suppressor and a survival mechanism under metabolic stress. IF has shown [...] Read more.

Intermittent fasting (IF) is a dietary approach that influences key metabolic pathways, including autophagy—a crucial mechanism in maintaining cellular homeostasis. Autophagy plays a dual role in oncogenesis, acting both as a tumor suppressor and a survival mechanism under metabolic stress. IF has shown potential for reducing cancer risk and enhancing therapeutic efficacy by sensitizing tumor cells to chemotherapy and radiotherapy. However, its effects depend heavily on the type and stage of cancer. Potential risks, such as excessive weight loss and malnutrition, require careful evaluation. Further clinical studies are needed to optimize IF protocols as adjuncts to cancer therapy. This review discusses autophagy mechanisms induced by IF, their therapeutic implications in oncology, and the limitations of this dietary strategy. Full article

(This article belongs to the Section Molecular Oncology)

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16 pages, 2200 KiB

Open AccessBrief Report

Efficient Searches in Protein Sequence Space Through AI-Driven Iterative Learning

by Ignacio Suárez-Martín, Valeria A. Risso, Rocío Romero-Zaliz and Jose M. Sanchez-Ruiz

Int. J. Mol. Sci. 2025, 26(10), 4741; https://doi.org/10.3390/ijms26104741 - 15 May 2025

Abstract

The protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers the engineering of novel enzymes through library screening and is a major obstacle to any attempt to predict natural protein evolution. Recently, specialized methodologies have been used to [...] Read more.

The protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers the engineering of novel enzymes through library screening and is a major obstacle to any attempt to predict natural protein evolution. Recently, specialized methodologies have been used to determine fitness data on ~260,000 sequences for the gene of the enzyme dihydrofolate reductase and antibody affinity data for all combinations of the mutations present in the receptor-binding domain (RBD) of the Omicron strain of SARS-CoV-2 (~30,000 variants). We show that upon iterative training on a total of just a few hundred variants, various state-of-the-art AI tools (multi-layer perceptron, random forest, and XGBoost algorithms) find very high fitness variants of the enzyme and predict the antibody evasion patterns of the RBD. This work provides a basis for efficient, widely applicable, low-throughput experimental approaches to assess viral protein evolution and to engineer enzymes for biotechnological applications. Full article

(This article belongs to the Section Molecular Biophysics)

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14 pages, 777 KiB

Open AccessArticle

CD133 Expression in Circulating Tumor Cells as a Prognostic Marker in Colorectal Cancer

by Katsuji Sawai, Kenji Koneri, Youhei Kimura and Takanori Goi

Int. J. Mol. Sci. 2025, 26(10), 4740; https://doi.org/10.3390/ijms26104740 - 15 May 2025

Abstract

Identifying prognostic markers in colorectal cancer (CRC) is crucial for improving treatment outcomes. Although carcinoembryonic antigen (CEA) is recommended in the guidelines of the National Comprehensive Cancer Network, its sensitivity and specificity are inconsistent, limiting its utility in patients with normal CEA levels. [...] Read more.

Identifying prognostic markers in colorectal cancer (CRC) is crucial for improving treatment outcomes. Although carcinoembryonic antigen (CEA) is recommended in the guidelines of the National Comprehensive Cancer Network, its sensitivity and specificity are inconsistent, limiting its utility in patients with normal CEA levels. Circulating tumor cells (CTCs), including those expressing CD133—a cancer stem cell marker involved in tumor progression and therapy resistance—are associated with metastasis and survival outcomes. This study evaluated the prognostic significance of CD133-positive CTCs, and their combined effect with CEA, in patients with CRC. Peripheral blood samples from 195 patients with CRC (stages I–IV) were analyzed. CTCs were isolated using OncoQuick tubes and CD133 mRNA expression was detected by reverse transcription polymerase chain reaction. In clinicopathological analysis, CD133-positive CTCs were detected in 27.2% of cases, correlating with serosal invasion (p = 0.016). Multivariate Cox analysis showed that CD133-positive CTCs were associated with worse disease-specific survival (p = 0.001). Patients with CD133-positive CTCs and CEA ≥ 5 ng/mL (high CEA) had a significantly poorer prognosis (p < 0.001), whereas those with CD133-negative CTCs and CEA < 5 ng/mL (low CEA) had a better prognosis (p = 0.039). CD133 expression in CTCs, especially in combination with CEA, may serve as a valuable prognostic marker in CRC. Full article

(This article belongs to the Section Molecular Oncology)

15 pages, 3343 KiB

Open AccessArticle

Green Synthesis of Zinc Oxide Nanoparticles Using Aqueous Extract of Pavonia zeylanica to Mediate Photocatalytic Degradation of Methylene Blue: Studies on Reaction Kinetics, Reusability and Mineralization

by Dhananjay Purushotham, Abhilash Mavinakere Ramesh, Divakara Shetty Thimmappa, Nataraj Kalegowda, Gowtham Hittanahallikoppal Gajendramurthy, Shiva Prasad Kollur and Murali Mahadevamurthy

Int. J. Mol. Sci. 2025, 26(10), 4739; https://doi.org/10.3390/ijms26104739 - 15 May 2025

Abstract

Nanoparticles (especially zinc and titanium oxide) have been found to be effective in photodegrading pollutants (organic/inorganic) from industrial wastewater. Presently, this study aimed at biosynthesizing zinc oxide nanoparticles (ZnO-NPs) from the leaf extract of Pavonia zeylanica, a plant with significant medical value, [...] Read more.

Nanoparticles (especially zinc and titanium oxide) have been found to be effective in photodegrading pollutants (organic/inorganic) from industrial wastewater. Presently, this study aimed at biosynthesizing zinc oxide nanoparticles (ZnO-NPs) from the leaf extract of Pavonia zeylanica, a plant with significant medical value, and evaluating their photocatalytic properties against methylene blue (MB), an azo dye (100 mg L⁻¹, pH 7), using solar irradiation, along with the measurement of their reusability and mineralization efficiency. The characterization of the Pz-ZnO-NPs showed an absorbance peak at 313 nm, with a bandgap value of 3.04 eV and a size of 19.58 nm. This study’s results show that the synthesized Pz-ZnO-NPs, upon treatment with MB dye after 2 h of solar irradiation, showed an 89.32% degradation, which was concentration-dependent and followed pseudo-first-order kinetics. The reusability studies indicated that the Pz-ZnO-NPs were able to degrade MB dye after five repeated cycles of its usage. The structural composition of the Pz-ZnO-NPs evaluated by XRD showed that the peak position stayed constant. Nevertheless, the peak intensity dropped, indicating that the ZnO-NPs’ crystal structure was unaffected. Furthermore, advanced oxidation process studies, which included an evaluation of COD and TOC, revealed that both the contents decreased significantly during the photocatalysis process, wherein the electron-rich organic dyes were converted to nontoxic products through mineralization. Full article

(This article belongs to the Special Issue Synthesis, Characterization and Phyto-Function of Nanophotocatalysts)

13 pages, 2037 KiB

Open AccessArticle

Excessive Existence of Positively Charged Amino Acids Caused Off-Target Recognition in the Seed Region of Clostridium butyricum Argonaute

by Wenzhuo Ma, Wenping Lyu and Lizhe Zhu

Int. J. Mol. Sci. 2025, 26(10), 4738; https://doi.org/10.3390/ijms26104738 - 15 May 2025

Abstract

Clostridium butyricum Argonaute (CbAgo) can achieve DNA-guided DNA recognition and cleavage at physiological temperatures (~37 °C), making it a promising tool for gene editing. However, its significant off-target effects, particularly associated with the seed region (sites 2–8), pose challenges for precise [...] Read more.

Clostridium butyricum Argonaute (CbAgo) can achieve DNA-guided DNA recognition and cleavage at physiological temperatures (~37 °C), making it a promising tool for gene editing. However, its significant off-target effects, particularly associated with the seed region (sites 2–8), pose challenges for precise gene therapy. This study focuses on enhancing the specificity of the seed region recognition to mitigate these off-target effects. We investigated the molecular recognition process between the CbAgo-gDNA complex and the seed region of the target DNA using molecular dynamics simulations and automated path searching. Our findings reveal that positively charged residues located in an α-helix domain at the DNA–protein interface (R279, H285, K287, K288, K291, K298) facilitate rapid binding to the DNA phosphate backbone. Such interaction enhances the pre-formation of the DNA double helix, reducing the reliance on base complementarity during duplex pairing. Further simulations showed that alanine replacement of these positively charged residues led to significantly improved sequence specificity for the target DNA seed region. Collectively, these results offered critical insights into the origin of off-target recognition by CbAgo in its seed region, shedding lights on its fidelity enhancement. Full article

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

18 pages, 1852 KiB

Open AccessArticle

Evaluating the Chemical Composition and Antitumor Activity of Origanum vulgare ssp. hirtum Essential Oil in a Preclinical Colon Cancer Model

by Georgios Aindelis, Katerina Spyridopoulou, Sotiris Kyriakou, Angeliki Tiptiri-Kourpeti, Mihalis I. Panayiotidis, Aglaia Pappa and Katerina Chlichlia

Int. J. Mol. Sci. 2025, 26(10), 4737; https://doi.org/10.3390/ijms26104737 - 15 May 2025

Abstract

Origanum vulgare ssp. hirtum is an aromatic plant native to various Mediterranean regions and has been traditionally used in folk medicine. This study investigates the chemical composition and the potential antitumor activity of its essential oil in a preclinical model of CT26 colorectal [...] Read more.

Origanum vulgare ssp. hirtum is an aromatic plant native to various Mediterranean regions and has been traditionally used in folk medicine. This study investigates the chemical composition and the potential antitumor activity of its essential oil in a preclinical model of CT26 colorectal cancer in BALB/c mice. Mice received prophylactic oral administration of the essential oil, and tumor progression, immune modulation, and apoptosis were evaluated. Even treatment with low doses (350 parts per million, ppm in 100 μL final volume) of the essential oil significantly suppressed tumor growth by approximately 44%. This effect correlated with the enhanced expression of antitumorigenic cytokines, including a 2.7-fold increase in type I interferons (IFN), IFN-γ (from 46.5 to 111.9 pg/μL per mg of protein) and tumor necrosis factor alpha (TNF-α) (from 34.5 to 103 pg/μL per mg of protein). Furthermore, the production of granzyme B, a key mediator of cytotoxic immune cell function, was notably increased from 96.1 to 319.6 pg/μL per mg of protein. An elevated activation of caspase 3, a central effector caspase of all apoptotic cascades, was also observed in tumors from oregano-treated mice. These findings suggest that O. vulgare ssp. hirtum essential oil exhibits promising antitumor properties through immune modulation and immunity-mediated apoptosis induction, supporting its potential development as a bioactive compound for cancer prevention or therapy. Full article

(This article belongs to the Special Issue The Roles of Phytochemicals and Antioxidants in Colon Cancers)

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37 pages, 2709 KiB

Open AccessReview

Different Mechanisms in Doxorubicin-Induced Neurotoxicity: Impact of BRCA Mutations

by Kriti S. Bhatt, Aman Singh, Gursharan S. Marwaha, Naresh Ravendranathan, Inderbir S. Sandhu, Kristen Kim, Eesha Singh, Jefferson C. Frisbee and Krishna K. Singh

Int. J. Mol. Sci. 2025, 26(10), 4736; https://doi.org/10.3390/ijms26104736 - 15 May 2025

Abstract

The genotoxic drug doxorubicin (Dox) remains one of the most powerful chemotherapeutic options available for a wide range of cancers including breast, ovarian, and other cancers. However, emerging evidence links Dox treatment with chemotherapy-induced cognitive impairment, a condition that is popularly referred to [...] Read more.

The genotoxic drug doxorubicin (Dox) remains one of the most powerful chemotherapeutic options available for a wide range of cancers including breast, ovarian, and other cancers. However, emerging evidence links Dox treatment with chemotherapy-induced cognitive impairment, a condition that is popularly referred to as Dox-induced neurotoxicity or “chemobrain”, which limits the use of the drug. There are no specific treatments for Dox-induced neurotoxicity, only interventions to mitigate the neurotoxic effects of the drug. Accumulating evidence indicates that DNA damage, oxidative stress, dysregulation of autophagy and neurogenesis, inflammation, and apoptosis play central roles in Dox-induced neurotoxicity. Additionally, germline mutations in the tumour suppressor genes breast cancer susceptibility genes 1 and 2 (BRCA1 and BRCA2) increase the risk of breast, ovarian, and related cancers. BRCA1 and BRCA2 are distinct proteins that play crucial, unique roles in homologous recombination-mediated double-stranded break repair. Furthermore, BRCA1 and 2 mitigate oxidative stress in both neural cells and brain microvascular endothelial cells, which suggests that they have a critical role as regulators of pathways central to the development of Dox-induced neurotoxicity. Despite research on the effects of Dox on cognitive function, there is a gap in knowledge about the role of BRCA1 and BRCA2 in Dox-induced neurotoxicity. In this review, we discuss existing findings about the role of different mechanisms and the role of BRCA1 and BRCA2 in Dox-induced neurotoxicity, along with future perspectives. Full article

(This article belongs to the Collection Feature Papers in Molecular Toxicology)

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16 pages, 705 KiB

Open AccessArticle

Prognostic Value of a Multivariate Gut Microbiome Model for Progression from Normal Cognition to Mild Cognitive Impairment Within 4 Years

by Anne Bauch, Julia Baur, Iris Honold, Matthias Willmann, Greta Louise Weber, Stephan Müller, Sebastian Sodenkamp, Silke Peter, Ulrich Schoppmeier and Christoph Laske

Int. J. Mol. Sci. 2025, 26(10), 4735; https://doi.org/10.3390/ijms26104735 - 15 May 2025

Abstract

Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer’s disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in [...] Read more.

Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer’s disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in the scope of research in MCI. Therefore, we investigated the ability of longitudinal taxonomic and functional gut microbiome data from 100 healthy controls (HC) to predict the progression from normal cognition to MCI over a 4-year follow-up period (4yFU). Logistic regression models were built with baseline features that best discriminated between the two groups using an ANOVA-type statistical analysis. The best model for the discrimination of MCI converters was based on functional data using Gene Ontology (GO), which included 14 features. This model achieved an area under the receiver operating characteristic curve (AUROC) of 0.84 at baseline, 0.78 at the 1-year follow-up (1yFU), and 0.75 at 4yFU. This functional model outperformed the taxonomic model, which included 38 genera features, in terms of descriptive performance and showed comparable efficacy to combined analyses integrating functional, taxonomic, and clinical characteristics. Thus, gut microbiome algorithms have the potential to predict MCI conversion in HCs over a 4-year period, offering a promising innovative supplement for early AD identification. Full article

(This article belongs to the Special Issue Molecular Research in Human Microbiome 2.0)

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13 pages, 2577 KiB

Open AccessArticle

Anti-IL-4, Anti-IL-17, and Anti-IFN-Gamma Activity in the Saliva of Amblyomma sculptum Ticks

by Helioswilton Sales-Campos, Chamberttan Souza Desidério, Rafael Obata Trevisan, Rodolfo Pessato Timóteo, Victor Hugo Palhares Flávio-Reis, Yago Marcos Pessoa-Gonçalves, Marcos Vinicius da Silva, Eliane Esteves, Thiago de Jesus Oliveira, Pedro Ismael da Silva Junior and Carlo José Freire Oliveira

Int. J. Mol. Sci. 2025, 26(10), 4734; https://doi.org/10.3390/ijms26104734 - 15 May 2025

Abstract

The saliva of hematophagous arthropods, such as ticks and triatomines, contains bioactive ligands capable of modulating immune molecules, including cytokines. Cytokines play a critical role in immune regulation and have therapeutic relevance in inflammatory and immune-mediated diseases. Despite recent advances, identifying cytokine-binding molecules [...] Read more.

The saliva of hematophagous arthropods, such as ticks and triatomines, contains bioactive ligands capable of modulating immune molecules, including cytokines. Cytokines play a critical role in immune regulation and have therapeutic relevance in inflammatory and immune-mediated diseases. Despite recent advances, identifying cytokine-binding molecules remains a significant challenge. Interferon-gamma (IFN-γ), interleukin-4 (IL-4), and interleukin-17 (IL-17) are key cytokines involved in inflammation, adaptive immunity, and host defense. This study evaluated the ability of salivary components from Amblyomma sculptum and compared the results to the triatomine Rhodnius neglectus (used as control) to bind to IL-2, IL-4, IL-6, IL-10, IL-17, IFN-γ, and TNF-α using ELISA assays with human cytokines. Saliva samples were tested at dilutions of 1:25, 1:50, and 1:100. Saliva from A. sculptum, which demonstrated significant anti-cytokine activity, was fractionated via HPLC to identify the active components. The results confirmed the inhibitory capacity of A. sculptum saliva on IFN-γ, IL-4, and IL-17, with inhibition rates ranging from 30% to 70%, depending on the cytokine and dilution. No inhibitory activity was observed against IL-2, IL-6, IL-10, or TNF-α. These findings underscore the immunomodulatory role of A. sculptum saliva during tick feeding and suggest its potential for the development of novel immunobiologics to treat inflammatory and immune-mediated diseases. Full article

(This article belongs to the Special Issue Advances in Pro-Inflammatory and Anti-Inflammatory Cytokines)

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27 pages, 8052 KiB

Open AccessArticle

The RNA Chaperone Hfq and Small Non-Coding RNAs Modulate the Biofilm Formation of the Fish Pathogen Yersinia ruckeri

by María J. Barros, Lillian G. Acuña, Felipe Hernández-Vera, Pía Vásquez-Arriagada, Diego Peñaloza, Ana Moya-Beltrán, Fausto Cabezas-Mera, Francisco Parra, Fernando Gil, Juan A. Fuentes and Iván L. Calderón

Int. J. Mol. Sci. 2025, 26(10), 4733; https://doi.org/10.3390/ijms26104733 - 15 May 2025

Abstract

The fish pathogen Yersinia ruckeri forms biofilms on abiotic surfaces, contributing to recurrent infections in aquaculture. Increasing evidence suggests that the RNA chaperone Hfq and small non-coding RNAs (sRNAs) are key regulators of bacterial biofilm formation. However, the regulatory mechanisms mediated by these [...] Read more.

The fish pathogen Yersinia ruckeri forms biofilms on abiotic surfaces, contributing to recurrent infections in aquaculture. Increasing evidence suggests that the RNA chaperone Hfq and small non-coding RNAs (sRNAs) are key regulators of bacterial biofilm formation. However, the regulatory mechanisms mediated by these factors remain largely unexplored in Y. ruckeri. In this study, we investigated the roles of Hfq and the Hfq-dependent sRNAs RprA, ArcZ, and RybB in the biofilm formation of Y. ruckeri. We first characterized the sRNAome of biofilm-forming cells, identifying the conserved RprA, ArcZ, and RybB, among the upregulated sRNAs. We then evaluated motility, biofilm formation, and architecture in strains lacking either hfq (Δhfq) or these sRNAs (ΔsRNA). Our results reveal that both Δhfq and ΔsRNA strains exhibit significant alterations in biofilm and motility phenotypes, including changes in bacterial morphology and extracellular matrix. Furthermore, expression analyses indicate that these sRNAs modulate the transcription of key regulatory factors, flagellar and phosphodiesterase genes, ultimately influencing intracellular cyclic di-GMP levels, a key second messenger in biofilm formation. Together, our findings demonstrate that Hfq and its associated sRNAs play critical regulatory roles in Y. ruckeri biofilm formation by controlling the expression of genes involved in motility, bacterial envelope proteins, and c-di-GMP metabolism. Full article

(This article belongs to the Collection Feature Papers in Molecular Microbiology)

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16 pages, 3484 KiB

Open AccessReview

Mitochondrial Calcium Uniporter (MCU)-Mediated Calcium Overload in Psychoactive Drug Neurotoxicity: From Pathogenesis to Therapeutic Targets

by Xinyan Yang, Yinyu Chen, Gaolin Zheng, Qianyun Nie and Peng Zhang

Int. J. Mol. Sci. 2025, 26(10), 4732; https://doi.org/10.3390/ijms26104732 - 15 May 2025

Abstract

With rapid societal changes and increasing stress levels, the abuse of psychoactive substances has emerged as a global health crisis. Studies indicate that the mitochondrial calcium uniporter (MCU) plays a pivotal role in neurotoxic damage induced by psychoactive substances. As the primary channel [...] Read more.

With rapid societal changes and increasing stress levels, the abuse of psychoactive substances has emerged as a global health crisis. Studies indicate that the mitochondrial calcium uniporter (MCU) plays a pivotal role in neurotoxic damage induced by psychoactive substances. As the primary channel for mitochondrial Ca²⁺ uptake, MCU dysfunction can lead to Ca²⁺ overload, oxidative stress, and apoptosis, representing a crucial mechanism underlying neurotoxic damage. Psychoactive substances such as 3,4-Methylenedioxymethamphetamine (MDMA), cocaine, and morphine influence MCU function through multiple pathways, resulting in excessive Ca²⁺ accumulation and mitochondrial dysfunction, ultimately leading to neuronal injury. Although MCU inhibitors have demonstrated potential in alleviating Ca²⁺ overload and improving neural function in preliminary studies, their selectivity and long-term safety require further evaluation. Future research should explore the precise regulatory mechanisms of MCU in neurotoxic damage induced by psychoactive substances and develop more effective targeted therapeutic strategies. Full article

(This article belongs to the Special Issue Toxicology of Psychoactive Drugs)

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13 pages, 904 KiB

Open AccessArticle

by Adam Płoński, Anna Krupa, Adam Filip Płoński, Dariusz Pawlak, Marcin Gabriel, Beata Sieklucka, Jerzy Głowiński and Krystyna Pawlak

Int. J. Mol. Sci. 2025, 26(10), 4731; https://doi.org/10.3390/ijms26104731 - 15 May 2025

Abstract

Atherosclerosis is a major contributor to ischemic stroke. Carotid plaque instability is a critical determinant of cerebrovascular events, yet its identification remains challenging. One chemokine with well-documented proatherogenic properties is MCP-1, whose levels are elevated in patients with conditions such as hypertension, obesity, [...] Read more.

Atherosclerosis is a major contributor to ischemic stroke. Carotid plaque instability is a critical determinant of cerebrovascular events, yet its identification remains challenging. One chemokine with well-documented proatherogenic properties is MCP-1, whose levels are elevated in patients with conditions such as hypertension, obesity, and atherosclerosis. This study evaluated the association between obesity, serum MCP-1 levels, and carotid plaque instability as determined by ultrasound gray-scale median (GSM) analysis in 77 patients who underwent carotid endarterectomy. Patients were classified by body mass index. Serum MCP-1 concentrations were measured using the enzyme-linked immunosorbent assay technique. Analyses were performed to explore relationships between clinical parameters, biochemical markers, and plaque stability. Increasing body weight was paralleled by higher MCP-1 levels and lower GSM values, indicative of unstable plaques. Moreover, logistic regression analysis identified MCP-1 as one of the independent predictors of plaque instability, particularly in overweight and hypertensive patients. These results indicate the potential usefulness of MCP-1 as a biomarker of carotid plaque instability, confirming the negative effect of obesity in promoting other known cardiovascular risk factors causing plaque instability in patients with carotid atherosclerosis. Full article

(This article belongs to the Special Issue Atherosclerosis: From Molecular Biology to Therapeutic Perspective: 6th Edition)

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20 pages, 4815 KiB

Open AccessArticle

Spinach Extract Reduces Kidney Damage in Diabetic Rats by Impairing the AGEs/RAGE Axis

by Javier Flores-Estrada, Agustina Cano-Martínez, Luz Ibarra-Lara, Adriana Jiménez, Carmen Palacios-Reyes, Luis J. Pinto García, María G. Ortiz-López, Olga Nelly Rodríguez-Peña and Luis Barbo Hernández-Portilla

Int. J. Mol. Sci. 2025, 26(10), 4730; https://doi.org/10.3390/ijms26104730 - 15 May 2025

Abstract

The interaction between advanced glycation end products (AGEs) and their RAGE receptor (AGEs/RAGE axis) triggers several signaling pathways that lead to the development of diabetic nephropathy (DN). One of the most studied AGEs is Nε-(1-Carboxymethyl)-L-lysine (CML). Spinacia oleracea is an edible plant with [...] Read more.

The interaction between advanced glycation end products (AGEs) and their RAGE receptor (AGEs/RAGE axis) triggers several signaling pathways that lead to the development of diabetic nephropathy (DN). One of the most studied AGEs is Nε-(1-Carboxymethyl)-L-lysine (CML). Spinacia oleracea is an edible plant with beneficial health properties, but its effect on the AGE/RAGE axis in kidney damage is unknown. Objective: We aimed to investigate the functional role of spinach methanolic extract (SME) on kidney damage in diabetic rats associated with the CML/RAGE axis. Methods: Forty adult male Wistar rats were used in this study and divided into four groups: control rats (CTRL), SME-administered CTRL (400 mg/kg; SME), streptozotocin-induced diabetic nephropathy rats (STZ), and SME-treated STZ (STZ-SME); treatments were administered daily. After 12 weeks, serum AGEs, creatinine in urine, and lipid peroxidation in kidneys were measured. The distribution and expression levels of inflammatory and fibrotic mediators and RAGE signaling were evaluated through immunohistochemistry (NOX4, CML, RAGE, nuclear NF-κB, TNF-α, IL-1β, TGF-β1, SMAD2/3, CTGF, and a-SMA) and immunolocalization of CML/RAGE. Results: Glycoside flavonoid derivatives, such as patuletin and spinacetin, were primarily identified in the extract. Kidneys from the STZ group showed altered morphology, dead cells in the proximal tubules, and increased oxidative stress markers; notably, these effects were improved by SME treatment (STZ-SME). The STZ-SME group showed a lower staining intensity for CML and RAGE, which was associated with a decrease in the expression of inflammatory and fibrotic factors compared with the STZ group. In all groups, the distribution of these markers varied among proximal tubule, glomerular, and interstitial cells. Conclusions: SME treatment may help to prevent or delay kidney damage in diabetic rats by regulating inflammatory and fibrotic processes associated with the AGEs/RAGE pathway, a mechanism involved in the development of nephropathy. Full article

(This article belongs to the Special Issue Dietary Antioxidants in Human Health)

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13 pages, 1677 KiB

Open AccessArticle

INO10, a Chaga Mushroom Extract, Alleviates Alzheimer’s Disease-Related Pathology and Cognitive Deficits in 3xTg-AD Mice

by Soyoung Ban, Thuong Thi Do, Jang-Won Pyo, Minho Moon and Jong-Tae Park

Int. J. Mol. Sci. 2025, 26(10), 4729; https://doi.org/10.3390/ijms26104729 - 15 May 2025

Abstract

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by cognitive impairment with amyloid-β (Aβ) accumulation, tau hyperphosphorylation, and neuroinflammation. Among these pathological features, microglial activation is hallmark of neuroinflammation. Chaga (Inonotus obliquus) extract has been traditionally used for its diverse [...] Read more.

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by cognitive impairment with amyloid-β (Aβ) accumulation, tau hyperphosphorylation, and neuroinflammation. Among these pathological features, microglial activation is hallmark of neuroinflammation. Chaga (Inonotus obliquus) extract has been traditionally used for its diverse pharmacological properties, including anti-inflammatory and neuroprotective effects. This study aimed to evaluate the therapeutic potential of INO10, an inotodiol-rich chaga extract, in murine BV2 microglial cells and a 3xTg-AD mouse model. In BV2 cells, INO10 significantly reduced LPS-induced expression of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α), indicating its potent anti-inflammatory effects. Oral administration of INO10 significantly improved spatial memory in 3xTg-AD mice, as evidenced by increased spontaneous alternation in the Y-maze test. Furthermore, INO10 treatment attenuated neuroinflammation, as indicated by reduced microglial activation and downregulated expression of pro-inflammatory cytokines. In addition, immunohistochemical analysis confirmed that INO10 exhibited favorable bioavailability, supporting its potential as a neuroprotective agent. Histological analysis further revealed a reduction in Ab accumulation and tau phosphorylation in the hippocampus, accompanied by a marked decrease in neuroinflammatory markers. These findings suggest that INO10 effectively mitigates AD-related pathology by reducing Aβ deposition, tau hyperphosphorylation, and neuroinflammation, ultimately leading to cognitive enhancement. Given its multi-target neuroprotective properties, INO10 may serve as a promising natural compound for AD treatment. Further investigations are warranted to elucidate its precise mechanisms and clinical applicability. Full article

(This article belongs to the Section Molecular Neurobiology)

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18 pages, 3645 KiB

Open AccessArticle

Effects of Graphene Derivatives and Near-Infrared Laser Irradiation on E. coli Biofilms and Stress Response Gene Expression

by Yuliya Maksimova, Ekaterina Pyankova, Larisa Nesterova and Aleksandr Maksimov

Int. J. Mol. Sci. 2025, 26(10), 4728; https://doi.org/10.3390/ijms26104728 - 15 May 2025

Abstract

Photothermal therapy combines the effects of near-infrared laser (NIR laser) and strong light-absorbing materials to combat pathogens and unwanted biofilms. Graphene derivatives have a negative effect on microorganisms, and the combination of NIR laser irradiation and carbon nanomaterials (CNMs) can enhance their antibacterial [...] Read more.

Photothermal therapy combines the effects of near-infrared laser (NIR laser) and strong light-absorbing materials to combat pathogens and unwanted biofilms. Graphene derivatives have a negative effect on microorganisms, and the combination of NIR laser irradiation and carbon nanomaterials (CNMs) can enhance their antibacterial effect. This investigation is devoted to the determination of the expression level of bacterial stress response genes (soxS and rpoS) under graphene oxide (GO), reduced graphene oxide (rGO), and NIR laser irradiation (1270 nm). GO, rGO and NIR laser irradiation separately and irradiation in the presence of graphene derivatives cause an increase in the expression level of rpoS associated with the general stress response of bacteria. GO and rGO do not change the expression level of soxS associated with the cell response to oxidative stress, and decrease it in the presence of a strong oxidizing agent paraquat (PQ). The expression of soxS increases under laser irradiation, but decreases under NIR laser irradiation in combination with graphene derivatives. The effect of GO, rGO, and NIR laser irradiation on the formation and eradication of E. coli biofilms was studied. NIR laser with GO and rGO suppresses the metabolic rate and decreases the intracellular ATP content by 94 and 99.6%, respectively. CNMs are shown to reduce biofilm biomass and the content of extracellular polymeric substances (EPSs), both exopolysaccharides and protein in the biofilm matrix. Graphene derivatives in combination with NIR laser irradiation may be an effective means of combating emerging and mature biofilms of Gram-negative bacteria. Full article

(This article belongs to the Section Molecular Microbiology)

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13 pages, 3295 KiB

Open AccessArticle

Structure of K102 Capsular Polysaccharide from Acinetobacter baumannii KZ-1102 and Its Cleavage by Phage Cato Depolymerase

by Anastasia A. Kasimova, Nikolay P. Arbatsky, Ekaterina A. Gornostal, Mikhail M. Shneider, Eugene A. Sheck, Alexander S. Shashkov, Andrey A. Shelenkov, Yulia V. Mikhailova, Ilya S. Azizov, Mikhail V. Edelstein, Andrey V. Perepelov, Anna M. Shpirt, Konstantin A. Miroshnikov, Anastasia V. Popova and Yuriy A. Knirel

Int. J. Mol. Sci. 2025, 26(10), 4727; https://doi.org/10.3390/ijms26104727 - 15 May 2025

Abstract

Acinetobacter baumannii is a significant nosocomial pathogen characterized by the ability to produce a wide variety of capsular polysaccharides (CPSs). The structures of a K102-type CPS isolated from A. baumannii KZ-1102 and its Smith degradation product were determined by sugar analysis, 1D and [...] Read more.

Acinetobacter baumannii is a significant nosocomial pathogen characterized by the ability to produce a wide variety of capsular polysaccharides (CPSs). The structures of a K102-type CPS isolated from A. baumannii KZ-1102 and its Smith degradation product were determined by sugar analysis, 1D and 2D ¹H NMR spectroscopy, and ¹³C NMR spectroscopy. The K102 CPS biosynthesis gene cluster (KL102) contains genes for common sugar synthesis, K unit processing, capsule export, glycosyl transfer, initiating sugar phosphate transfer, and genes that encode d-GlcpNAc/d-GalpNAc dehydrogenase and phosphoglycerol transferase. The CPS is composed of a pentasaccharide repeating unit (K unit) consisting of a tetrasaccharide backbone including one α-d-Galp, three α-d-GlcpNAc residues, and one residue of a β-d-Glcp as a side chain. The tailspike depolymerase of the specific Obolenskvirus phage Cato was found to cleave the α-d-GlcpNAc-(1→6)-α-d-GlcpNAc linkage in the K102 CPS to give the monomer and dimer of the K repeating unit, which were characterized by high-resolution electrospray ionization mass spectrometry as well as ¹H and ¹³C NMR spectroscopy. Full article

(This article belongs to the Collection State-of-the-Art Macromolecules in Russia)

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13 pages, 1395 KiB

Open AccessArticle

Serum Antibody Titres Against Porphyromonas gingivalis Fim A in Patients with Periodontitis with and Without Diabetes Mellitus Type 2

by Sabine Groeger, Nathalie Mueller, Jens Martin Herrmann and Joerg Meyle

Int. J. Mol. Sci. 2025, 26(10), 4726; https://doi.org/10.3390/ijms26104726 - 15 May 2025

Abstract

Periodontitis and type 2 diabetes mellitus are interconnected in a bidirectional relationship, yet the underlying mechanisms remain poorly understood. Porphyromonas gingivalis (P. gingivalis), a key periodontal pathogen, has been implicated in both conditions. This study investigates the association between antibody responses [...] Read more.

Periodontitis and type 2 diabetes mellitus are interconnected in a bidirectional relationship, yet the underlying mechanisms remain poorly understood. Porphyromonas gingivalis (P. gingivalis), a key periodontal pathogen, has been implicated in both conditions. This study investigates the association between antibody responses to P. gingivalis and the coexistence of periodontitis and diabetes, aiming to explore its potential as a biomarker for early screening. The developed enzyme linked immunosorbent assay (ELISA) was used to analyse in a pilot study the serum of subjects with periodontitis (n = 26), subjects with periodontitis and type 2 diabetes mellitus (n = 15), and healthy individuals (n = 13) for immunoglobulin (Ig)G- and IgM-antibody titres against FimA. A statistically significant difference (p < 0.001) between the IgG titres of the three study groups was observed. Patients with periodontitis and type 2 diabetes mellitus showed the highest IgG titres and thus the highest level of IgG antibodies, followed by periodontitis patients and finally the orally healthy subjects. This study demonstrated the establishment of a reliable and reproducible ELISA for the detection of antibodies against FimA from P. gingivalis W83. In addition, the outcomes of this study can be used to develop a screening assay that can indicate existing periodontitis and type 2 diabetes mellitus based on IgG antibody titres against FimA from P. gingivalis. Full article

(This article belongs to the Special Issue The Impact of Biomolecules on the Pathogenesis of Oral and Periodontal Diseases)

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19 pages, 2845 KiB

Open AccessArticle

Accelerated Biological Aging in Exfoliation Glaucoma Assessed by Fundus-Derived Predicted Age and Advanced Glycation End Products

by Masaki Tanito and Makoto Koyama

Int. J. Mol. Sci. 2025, 26(10), 4725; https://doi.org/10.3390/ijms26104725 - 15 May 2025

Abstract

Glaucoma is an age-related neurodegenerative disease characterized by progressive optic nerve damage. Accelerated biological aging, assessed using predicted age derived from fundus images, may serve as a biomarker for glaucoma progression. This study aimed to examine fundus-derived age acceleration among patients with primary [...] Read more.

Glaucoma is an age-related neurodegenerative disease characterized by progressive optic nerve damage. Accelerated biological aging, assessed using predicted age derived from fundus images, may serve as a biomarker for glaucoma progression. This study aimed to examine fundus-derived age acceleration among patients with primary open-angle glaucoma (POAG), exfoliation glaucoma (EXG), and controls, and to explore its biochemical basis through advanced glycation end products (AGEs). Fundus photographs from 237 participants (79 POAG, 79 EXG, and 79 age- and sex-matched controls) were analyzed using a deep learning model (EfficientNet) previously trained to predict biological age. AGE accumulation was assessed by measuring skin autofluorescence (sAF). Multivariate regression analyses were conducted to identify factors influencing predicted age acceleration, with stratification into age tertiles to control for age-related effects. EXG patients demonstrated significant accelerated biological aging compared to controls (p = 0.006), particularly evident in younger and middle-aged tertiles. AGE scores were significantly elevated in EXG relative to both POAG (p = 0.009) and control groups (p = 0.003). Predicted age and AGE scores were more strongly correlated than chronological age and AGEs, especially in the middle tertile (p = 0.002). Accelerated biological aging detected via fundus images occurs prominently in EXG, potentially reflecting underlying AGE accumulation. Fundus-derived predicted age could serve as a non-invasive biomarker for assessing glaucoma progression risk and warrants further exploration in clinical applications. Full article

(This article belongs to the Special Issue Advances In and Insights into the Treatment of Glaucoma)

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Int. J. Mol. Sci., Volume 26, Issue 10 (May-2 2025) – 289 articles

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