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Structural Plasticity of Flavin-Dependent Thymidylate Synthase Controlled by the Enzyme Redox State
Unraveling the Extra Virgin Olive Oil Effect on Inflammation and on Gut and Saliva Microbiota
Possible Anti-Aging and Anti-Stress Effects of Long-Term Transcendental Meditation Practice: Differences in Gene Expression, EEG Correlates of Cognitive Function, and Hair Steroids
Molecular Biomarkers for Timely and Personalized Prediction of Maternal-Fetal Health Risk
The Functional and Imaging Implications of Left Bundle Branch Pacing in Ischemic Cardiomyopathy

Journal Description

Biomolecules

Biomolecules is a peer-reviewed, open access journal on structures and functions of bioactive and biogenic substances, molecular mechanisms with biological and medical implications as well as biomaterials and their applications. Biomolecules is published monthly online by MDPI.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, CAPlus / SciFinder, and other databases.
Journal Rank: JCR - Q1 (Biochemistry and Molecular Biology) / CiteScore - Q1 (Biochemistry)
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 19.4 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Sections: published in 15 topical sections.
Testimonials: See what our editors and authors say about Biomolecules.
Companion journal: Receptors.

Impact Factor: 4.8 (2024); 5-Year Impact Factor: 5.6 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2218-273X

Latest Articles

24 pages, 2145 KiB

Open AccessReview

A New Perspective on Regenerative Medicine: Plant-Derived Extracellular Vesicles

by Yuan Zuo, Jinying Zhang, Bo Sun, Xinxing Wang, Ruiying Wang, Shuo Tian and Mingsan Miao

Biomolecules 2025, 15(8), 1095; https://doi.org/10.3390/biom15081095 - 28 Jul 2025

Plant-derived extracellular vesicles (PDEVs) are nanoscale, phospholipid bilayer-enclosed vesicles secreted by living cells through cytokinesis under physiological and pathological conditions. Owing to their high biocompatibility and stability, PDEVs have attracted considerable interest in regenerative medicine applications. They can exhibit the capacity to enhance [...] Read more.

Plant-derived extracellular vesicles (PDEVs) are nanoscale, phospholipid bilayer-enclosed vesicles secreted by living cells through cytokinesis under physiological and pathological conditions. Owing to their high biocompatibility and stability, PDEVs have attracted considerable interest in regenerative medicine applications. They can exhibit the capacity to enhance cellular proliferation, migration, and multi-lineage differentiation through immunomodulation, anti-inflammation effects, antioxidative protection, and tissue regeneration mechanisms. Given their abundant availability, favorable safety profile, and low immunogenicity risks, PDEVs have been successfully employed in therapeutic interventions for skeletal muscle disorders, cardiovascular diseases, neurodegenerative conditions, and tissue regeneration applications. This review mainly provides a comprehensive overview of PDEVs, systematically examining their biological properties, standardized isolation and characterization methodologies, preservation techniques, and current applications in regenerative medicine. Furthermore, we critically discuss future research directions and clinical translation potential, aiming to facilitate the advancement of PDEV-based therapeutic strategies. Full article

(This article belongs to the Section Molecular Medicine)

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33 pages, 1667 KiB

Open AccessSystematic Review

Vitamin D as a Modifiable Risk Factor in Schizophrenia a Systematic Review

by Jadwiga Mosiołek, Bartosz Mosiołek and Agata Szulc

Biomolecules 2025, 15(8), 1094; https://doi.org/10.3390/biom15081094 - 28 Jul 2025

The etiology of schizophrenia remains poorly understood. Although certain risk factors have been identified, effective preventive measures are still lacking. This study investigates potential preventive methods while focusing on the role of vitamin D and its status. The role of malnutrition in schizophrenia [...] Read more.

The etiology of schizophrenia remains poorly understood. Although certain risk factors have been identified, effective preventive measures are still lacking. This study investigates potential preventive methods while focusing on the role of vitamin D and its status. The role of malnutrition in schizophrenia risk was first identified in studies on the Dutch Hunger Winter. Vitamin D deficiency was hypothesized as a contributing factor shortly thereafter. This review aims to explore the correlations between vitamin D deficiency at various life stages (maternal, neonatal, adult) and schizophrenia risk, as well as its effects on pharmacokinetics, neurobiology, bone health, and metabolic syndrome. The studies were retrieved from two indexed databases, PubMed and Web of Science, following PRISMA guidelines and included studies published between 2000 and 2024. No correlation was found between maternal vitamin D levels and schizophrenia in offspring while a positive correlation was observed between low neonatal vitamin D levels and schizophrenia in later life. Approximately half of the studies on adults reported mean vitamin D concentrations of below 20 ng/mL which were negatively correlated with gray matter volume and bone health while positively correlated with the prevalence of metabolic syndrome. Additionally, vitamin D levels were also found to correlate with antipsychotic drug concentrations. Full article

(This article belongs to the Special Issue Biomarkers and Molecular Basis of Psychiatry)

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15 pages, 1507 KiB

Open AccessSystematic Review

Adenosine as an Active Ingredient in Topical Preparations Against Hair Loss: A Systematic Review and Meta-Analysis of Published Clinical Trials

by Ewelina Szendzielorz and Radoslaw Spiewak

Biomolecules 2025, 15(8), 1093; https://doi.org/10.3390/biom15081093 - 28 Jul 2025

Research results suggest the potential of topical adenosine as a hair-promoting agent. The aim of this study was to examine the available clinical evidence of the efficacy of topical adenosine products in hair loss. This systematic review was conducted in accordance with PRISMA [...] Read more.

Research results suggest the potential of topical adenosine as a hair-promoting agent. The aim of this study was to examine the available clinical evidence of the efficacy of topical adenosine products in hair loss. This systematic review was conducted in accordance with PRISMA and PICO guidelines and included articles indexed in PubMed, Scopus, and Web of Science. The strength of evidence was assessed according to the GRADE system. Wherever feasible, data were extracted for a meta-analysis. Among 8625 articles returned by the query, 7 clinical trials were identified of topical adenosine (lotion, shampoo) in hair loss. They unanimously reported on a reduction in hair loss and increase in hair density (strength of evidence very low to moderate). A meta-analysis of three eligible trials showed a tendency to increased hair density (OR = 1.03, 95% CI: 0.89–1.20, p = 0.68), an increase in thick hair (OR = 1.4, 95% CI: 0.82–2.38, p = 0.21) and a decrease in thin hairs (OR = 0.93, 95% CI: 0.61–1.43, p = 0.75) after 6 months of alopecia treatment with a 0.75% adenosine lotion. The results from clinical trials published until now suggest that topical adenosine increases hair thickness, reduces excessive hair loss, stimulates hair regrowth, and increases hair density. The overall strength of evidence remains low due to flawed design and small sample sizes in most trials. Nevertheless, topical adenosine products seem worth trying, especially in the case of contraindications or adverse effects to approved medicinal products for hair loss. Further, better designed trials of adenosine in hair loss are warranted. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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21 pages, 1855 KiB

Open AccessReview

Crosstalk Between N6-Methyladenosine and Other Epigenetic Mechanisms in Central Nervous System Development and Disorders

by Cuiping Qi, Xiuping Jin, Hui Wang and Dan Xu

Biomolecules 2025, 15(8), 1092; https://doi.org/10.3390/biom15081092 - 28 Jul 2025

A variety of epigenetic mechanisms—such as DNA methylation, histone alterations, RNA chemical modifications, and regulatory non-coding RNAs—collectively influence gene regulation and cellular processes. Among these, N6-methyladenosine (m⁶A) represents the most widespread internal modification in eukaryotic mRNA, exerting significant influence on RNA [...] Read more.

A variety of epigenetic mechanisms—such as DNA methylation, histone alterations, RNA chemical modifications, and regulatory non-coding RNAs—collectively influence gene regulation and cellular processes. Among these, N6-methyladenosine (m⁶A) represents the most widespread internal modification in eukaryotic mRNA, exerting significant influence on RNA metabolic pathways and modulating mRNA function at multiple levels. Studies have shown that m⁶A modification is highly enriched in the brain and regulates central nervous system development and various physiological functions. Recent studies have demonstrated that m⁶A interacts with other epigenetic regulators and triggers epigenetic remodeling, which further affects the development and occurrence of central nervous system diseases. In this review, we provide an up-to-date overview of this emerging research hotspot in biology, with a focus on the interplay between m⁶A and other epigenetic regulators. We highlight their potential roles and regulatory mechanisms in epigenetic reprogramming during central nervous system development and disease, offering insights into potential novel targets and therapeutic strategies for CNS disorders. Full article

(This article belongs to the Special Issue Identifying New Therapeutic Targets for Psychiatric Disease Using Transcriptomics and Epigenomics)

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23 pages, 4653 KiB

Open AccessArticle

Zinc-Induced Folding and Solution Structure of the Eponymous Novel Zinc Finger from the ZC4H2 Protein

by Rilee E. Harris, Antonio J. Rua and Andrei T. Alexandrescu

Biomolecules 2025, 15(8), 1091; https://doi.org/10.3390/biom15081091 - 28 Jul 2025

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein [...] Read more.

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein obtains its name. Alpha Fold 3 confidently predicts a structure for the zinc finger but also for similarly sized random sequences, providing equivocal information on its folding status. We show using synthetic peptide fragments that the zinc finger of ZC4H2 is genuine and folds upon binding a zinc ion with picomolar affinity. NMR pH titration of histidines and UV–Vis of a cobalt complex of the peptide indicate its four cysteines coordinate zinc, while two histidines do not participate in binding. The experimental NMR structure of the zinc finger has a novel structural motif similar to RANBP2 zinc fingers, in which two orthogonal hairpins each contribute two cysteines to coordinate zinc. Most of the nine ZARD mutations that occur in the ZC4H2 zinc finger are likely to perturb this structure. While the ZC4H2 zinc finger shares the folding motif and cysteine-ligand spacing of the RANBP2 family, it is missing key substrate-binding residues. Unlike the NZF branch of the RANBP2 family, the ZC4H2 zinc finger does not bind ubiquitin. Since the ZC4H2 zinc finger occurs in a single copy, it is also unlikely to bind DNA. Based on sequence homology to the VAB-23 protein, the ZC4H2 zinc finger may bind RNA of a currently undetermined sequence or have alternative functions. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions (3rd Edition))

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21 pages, 1019 KiB

Open AccessReview

Macrophage Reprogramming: Emerging Molecular Therapeutic Strategies for Nephrolithiasis

by Meng Shu, Yiying Jia, Shuwei Zhang, Bangyu Zou, Zhaoxin Ying, Xu Gao, Ziyu Fang and Xiaofeng Gao

Biomolecules 2025, 15(8), 1090; https://doi.org/10.3390/biom15081090 - 28 Jul 2025

Nephrolithiasis, predominantly driven by calcium oxalate (CaOx) crystal deposition, poses a significant global health burden due to its high prevalence and recurrence rates and limited preventive/therapeutic options. Recent research has underscored a pivotal role for macrophage polarization in nephrolithiasis pathogenesis. Pro-inflammatory phenotype macrophages [...] Read more.

Nephrolithiasis, predominantly driven by calcium oxalate (CaOx) crystal deposition, poses a significant global health burden due to its high prevalence and recurrence rates and limited preventive/therapeutic options. Recent research has underscored a pivotal role for macrophage polarization in nephrolithiasis pathogenesis. Pro-inflammatory phenotype macrophages exacerbate crystal-induced injury and foster stone formation by amplifying crystal adhesion via an NF-κB–IL-1β positive-feedback axis that sustains ROS generation and NLRP3 inflammasome activation, whereas anti-inflammatory phenotype macrophages facilitate crystal clearance and tissue repair. We have summarized the research on treating nephrolithiasis and related renal injury by targeting macrophage polarization in recent years, including therapeutic approaches through pharmacological methods, epigenetic regulation, and advanced biomaterials. At the same time, we have critically evaluated the novel therapeutic strategies for macrophage reprogramming and explored the future development directions of targeting macrophage reprogramming for nephrolithiasis treatment, such as using single-cell/spatial omics to reveal the heterogeneity of macrophages in the stone microenvironment, chimeric antigen receptor macrophages (CAR-Ms) as a potential therapy for specific crystal phagocytosis in certain areas, and multi-omics integration to address inter-patient immune differences. This review highlights that macrophage reprogramming is a transformative frontier in nephrolithiasis management and underscores the need for further research to translate these molecular insights into effective clinical applications. Full article

(This article belongs to the Section Molecular Medicine)

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12 pages, 432 KiB

Open AccessReview

Adventitious Root Formation in Cuttings: Insights from Arabidopsis and Prospects for Woody Plants

by Peipei Liu, Shili Zhang, Xinying Wang, Yuxuan Du, Qizhouhong He, Yingying Zhang, Lisha Shen, Hongfei Hu, Guifang Zhang and Xiaojuan Li

Biomolecules 2025, 15(8), 1089; https://doi.org/10.3390/biom15081089 - 28 Jul 2025

Cutting propagation is a commonly employed technology for vegetative reproduction in agricultural, forestry, and horticultural practice. The success of cutting propagation depends on adventitious root (AR) formation—a process whereby roots regenerate from stem cuttings or leaf cuttings. In this review, we summarize the [...] Read more.

Cutting propagation is a commonly employed technology for vegetative reproduction in agricultural, forestry, and horticultural practice. The success of cutting propagation depends on adventitious root (AR) formation—a process whereby roots regenerate from stem cuttings or leaf cuttings. In this review, we summarize the distinct stages of cutting-induced AR formation and highlight the pivotal roles of plant hormones and age in this process. Jasmonic acid (JA) acts as a master trigger for promoting AR formation, while auxin serves as the core regulator, driving AR formation. Furthermore, plant age is a crucial factor determining the regenerative competence of cuttings. Notably, age and JA collaboratively modulate auxin synthesis in cutting-induced AR formation. Overall, this review not only elucidates the molecular mechanisms underlying AR formation but also provides valuable insights for improving efficiency of cutting propagation in various plant species. Full article

(This article belongs to the Section Biological Factors)

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39 pages, 4911 KiB

Open AccessReview

The Multifaceted Role of p53 in Cancer Molecular Biology: Insights for Precision Diagnosis and Therapeutic Breakthroughs

by Bolong Xu, Ayitila Maimaitijiang, Dawuti Nuerbiyamu, Zhengding Su and Wenfang Li

Biomolecules 2025, 15(8), 1088; https://doi.org/10.3390/biom15081088 - 27 Jul 2025

The protein p53, often referred to as the “guardian of the genome,” is essential for preserving cellular balance and preventing cancerous transformations. As one of the most commonly altered genes in human cancers, its impaired function is associated with tumor initiation, development, and [...] Read more.

The protein p53, often referred to as the “guardian of the genome,” is essential for preserving cellular balance and preventing cancerous transformations. As one of the most commonly altered genes in human cancers, its impaired function is associated with tumor initiation, development, and resistance to treatment. Exploring the diverse roles of p53, which include regulating the cell cycle, repairing DNA, inducing apoptosis, reprogramming metabolism, and modulating immunity, provides valuable insights into cancer mechanisms and potential treatments. This review integrates recent findings on p53′s dual nature, functioning as both a tumor suppressor and an oncogenic promoter, depending on the context. Wild-type p53 suppresses tumors by inducing cell cycle arrest or apoptosis in response to genotoxic stress, while mutated variants often lose these functions or gain novel pro-oncogenic activities. Emerging evidence highlights p53′s involvement in non-canonical pathways, such as regulating tumor microenvironment interactions, metabolic flexibility, and immune evasion mechanisms. For instance, p53 modulates immune checkpoint expression and influences the efficacy of immunotherapies, including PD-1/PD-L1 blockade. Furthermore, advancements in precision diagnostics, such as liquid biopsy-based detection of p53 mutations and AI-driven bioinformatics tools, enable early cancer identification and stratification of patients likely to benefit from targeted therapies. Therapeutic strategies targeting p53 pathways are rapidly evolving. Small molecules restoring wild-type p53 activity or disrupting mutant p53 interactions, such as APR-246 and MDM2 inhibitors, show promise in clinical trials. Combination approaches integrating gene editing with synthetic lethal strategies aim to exploit p53-dependent vulnerabilities. Additionally, leveraging p53′s immunomodulatory effects through vaccine development or adjuvants may enhance immunotherapy responses. In conclusion, deciphering p53′s complex biology underscores its unparalleled potential as a biomarker and therapeutic target. Integrating multi-omics analyses, functional genomic screens, and real-world clinical data will accelerate the translation of p53-focused research into precision oncology breakthroughs, ultimately improving patient outcomes. Full article

(This article belongs to the Special Issue DNA Damage and Repair in Cancer Treatment)

19 pages, 8295 KiB

Open AccessArticle

Melatonin as an Alleviator in Decabromodiphenyl Ether-Induced Aberrant Hippocampal Neurogenesis and Synaptogenesis: The Role of Wnt7a

by Jinghua Shen, Lu Gao, Jingjing Gao, Licong Wang, Dongying Yan, Ying Wang, Jia Meng, Hong Li, Dawei Chen and Jie Wu

Biomolecules 2025, 15(8), 1087; https://doi.org/10.3390/biom15081087 - 27 Jul 2025

Developmental exposure to polybrominated diphenyl ethers (PBDEs), which are commonly used as flame retardants, results in irreversible cognitive impairments. Postnatal hippocampal neurogenesis, which occurs in the subgranular zone (SGZ) of the dentate gyrus, is critical for neuronal circuits and plasticity. Wnt7a-Frizzled5 (FZD5) is [...] Read more.

Developmental exposure to polybrominated diphenyl ethers (PBDEs), which are commonly used as flame retardants, results in irreversible cognitive impairments. Postnatal hippocampal neurogenesis, which occurs in the subgranular zone (SGZ) of the dentate gyrus, is critical for neuronal circuits and plasticity. Wnt7a-Frizzled5 (FZD5) is essential for both neurogenesis and synapse formation; moreover, Wnt signaling participates in PBDE neurotoxicity and also contributes to the neuroprotective effects of melatonin. Therefore, we investigated the impacts of perinatal decabromodiphenyl ether (BDE-209) exposure on hippocampal neurogenesis and synaptogenesis in juvenile rats through BrdU injection and Golgi staining, as well as the alleviation of melatonin pretreatment. Additionally, we identified the structural basis of Wnt7a and two compounds via molecular docking. The hippocampal neural progenitor pool (Sox2+BrdU+ and Sox2+GFAP+cells), immature neurons (DCX+) differentiated from neuroblasts, and the survival of mature neurons (NeuN+) in the dentate gyrus were inhibited. Moreover, in BDE-209-exposed offspring rats, it was observed that dendritic branching and spine density were reduced, alongside the long-lasting suppression of the Wnt7a-FZD5/β-catenin pathway and targeted genes (Prox1, Neurod1, Neurogin2, Dlg4, and Netrin1) expression. Melatonin alleviated BDE-209-disrupted memory, along with hippocampal neurogenesis and dendritogenesis, for which the restoration of Wnt7a-FZD5 signaling may be beneficial. This study suggested that melatonin could represent a potential intervention for the cognitive deficits induced by PBDEs. Full article

(This article belongs to the Section Molecular Biology)

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25 pages, 2594 KiB

Open AccessArticle

A Natural Polyphenol, Chlorogenic Acid, Attenuates Obesity-Related Metabolic Disorders in Male Rats via miR-146a-IRAK1-TRAF6 and NRF2-Mediated Antioxidant Pathways

by Rashid Fahed Alenezi, Adel Abdelkhalek, Gehad El-Sayed, Ioan Pet, Mirela Ahmadi, El Said El Sherbini, Daniela Pușcașiu and Ahmed Hamed Arisha

Biomolecules 2025, 15(8), 1086; https://doi.org/10.3390/biom15081086 - 27 Jul 2025

Chronic high-fat diet (HFD) feeding in male rats causes significant metabolic as well as inflammatory disturbances, including obesity, insulin resistance, dyslipidemia, liver and kidney dysfunction, oxidative stress, and hypothalamic dysregulation. This study assessed the therapeutic effects of chlorogenic acid (CGA), a natural polyphenol, [...] Read more.

Chronic high-fat diet (HFD) feeding in male rats causes significant metabolic as well as inflammatory disturbances, including obesity, insulin resistance, dyslipidemia, liver and kidney dysfunction, oxidative stress, and hypothalamic dysregulation. This study assessed the therapeutic effects of chlorogenic acid (CGA), a natural polyphenol, administered at 10 mg and 100 mg/kg/day for the last 4 weeks of a 12-week HFD protocol. Both CGA doses reduced body weight gain, abdominal circumference, and visceral fat accumulation, with the higher dose showing greater efficacy. CGA improved metabolic parameters by lowering fasting glucose and insulin and enhancing lipid profiles. CGA suppressed orexigenic genes (Agrp, NPY) and upregulated anorexigenic genes (POMC, CARTPT), suggesting appetite regulation in the hypothalamus. In abdominal white adipose tissue (WAT), CGA boosted antioxidant defenses (SOD, CAT, GPx, HO-1), reduced lipid peroxidation (MDA), and suppressed pro-inflammatory cytokines including TNF-α, IFN-γ, and IL-1β, while increasing the anti-inflammatory cytokine IL-10. CGA modulated inflammatory signaling via upregulation of miR-146a and inhibition of IRAK1, TRAF6, and NF-κB. It also reduced apoptosis by downregulating p53, Bax, and Caspase-3, and restoring Bcl-2. These findings demonstrate that short-term CGA administration effectively reverses multiple HFD-induced impairments, highlighting its potential as an effective therapeutic for obesity-related metabolic disorders. Full article

(This article belongs to the Special Issue Antioxidant and Anti-Inflammatory Activities of Phytochemicals)

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22 pages, 1822 KiB

Open AccessArticle

Increased Concentration of Anti-Egg Albumin Antibodies in Cerebrospinal Fluid and Serum of Patients with Alzheimer’s Disease—Discussion on Human Serpins’ Similarity and Probable Involvement in the Disease Mechanism

by Dionysia Amanatidou, Magdalini Tsolaki, Vasileios Fouskas, Ioannis Gavriilidis, Maria Myriouni, Anna Anastasiou, Athanasia Papageorgiou, Diona Porfyriadou, Zoi Parcharidi, Eleftheria Papasavva, Maria Fili and Phaedra Eleftheriou

Biomolecules 2025, 15(8), 1085; https://doi.org/10.3390/biom15081085 - 27 Jul 2025

Alzheimer’s Disease (AD) is a multifactorial process. Amyloid plaque formation constitutes the main characteristic of the disease. Despite the identification of numerous factors associated with AD, the mechanism remains unclear in several aspects. Disturbances in intestinal and blood–brain barrier (BBB) penetration, observed in [...] Read more.

Alzheimer’s Disease (AD) is a multifactorial process. Amyloid plaque formation constitutes the main characteristic of the disease. Despite the identification of numerous factors associated with AD, the mechanism remains unclear in several aspects. Disturbances in intestinal and blood–brain barrier (BBB) penetration, observed in AD, may facilitate immunologic response to food-derived antigens. In the present study, antibodies against egg albumin, bovine-casein, and N-Glycolyl-Neuraminic acid (Neu5Gc) were measured in the cerebrospinal fluid (CSF) and serum of the patients using an enzyme-linked immunosorbent assay (ELISA). Zero anti-Neu5Gc and low concentrations of anti-casein antibodies were detected. Increased anti-native egg albumin antibodies were present in the serum of patients of all stages with 65% positivity (p < 0.001) in mild disease and a higher percentage in females (81.9%, p < 0.001). Lower serum positivity to anti-denatured egg albumin antibodies was observed, showing a gradual increase with severity and higher prevalence also in females. In the CSF, anti-native and anti-denatured egg albumin antibodies were mainly observed in severely ill patients with accumulative positivity to either antigen, reaching 61.8% in severe vs. 15% in mild disease (p < 0.001). Increased values were mainly observed in males. Anti-egg albumin antibodies may be implicated in the disease mechanism through sequence/structural similarity with human proteins, mainly serpins, and it would be worth consideration in further investigations and therapeutic strategies. Full article

(This article belongs to the Special Issue Food, Microbe, Viral and Parasite-Derived Antibodies in Autoimmune and Chronic Diseases)

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17 pages, 13173 KiB

Open AccessArticle

High-Resolution Imaging and Interpretation of Three-Dimensional RPE Sheet Structure

by Kevin J. Donaldson, Micah A. Chrenek, Jeffrey H. Boatright and John M. Nickerson

Biomolecules 2025, 15(8), 1084; https://doi.org/10.3390/biom15081084 - 26 Jul 2025

The retinal pigment epithelium (RPE), a monolayer of pigmented cells, is critical for visual function through its interaction with the neural retina. In healthy eyes, RPE cells exhibit a uniform hexagonal arrangement, but under stress or disease, such as age-related macular degeneration (AMD), [...] Read more.

The retinal pigment epithelium (RPE), a monolayer of pigmented cells, is critical for visual function through its interaction with the neural retina. In healthy eyes, RPE cells exhibit a uniform hexagonal arrangement, but under stress or disease, such as age-related macular degeneration (AMD), dysmorphic traits like cell enlargement and apparent multinucleation emerge. Multinucleation has been hypothesized to result from cellular fusion, a compensatory mechanism to maintain cell-to-cell contact and barrier function, as well as conserve resources in unhealthy tissue. However, traditional two-dimensional (2D) imaging using apical border markers alone may misrepresent multinucleation due to the lack of lateral markers. We present high-resolution confocal images enabling three-dimensional (3D) visualization of apical (ZO-1) and lateral (α-catenin) markers alongside nuclei. In two RPE damage models, we find that seemingly multinucleated cells are often single cells with displaced neighboring nuclei and lateral membranes. This emphasizes the need for 3D analyses to avoid misidentifying multinucleation and underlying fusion mechanisms. Lastly, images from the NaIO₃ oxidative damage model reveal variability in RPE damage, with elongated, dysmorphic cells showing increased ZsGreen reporter protein expression driven by EMT-linked CAG promoter activity, while more regular RPE cells displayed somewhat reduced green signal more typical of epithelial phenotypes. Full article

(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)

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19 pages, 1330 KiB

Open AccessReview

Metallothionein and Other Factors Influencing Cadmium-Induced Kidney Dysfunction: Review and Commentary

by Gunnar F. Nordberg and Monica Nordberg

Biomolecules 2025, 15(8), 1083; https://doi.org/10.3390/biom15081083 - 26 Jul 2025

Cadmium is widely recognized as an important environmental toxicant that may give rise to kidney dysfunction, bone disease, and cancer in humans and animals. Kidney dysfunction occurs at very low exposures and is often considered as the most sensitive or critical effect. Cadmium [...] Read more.

Cadmium is widely recognized as an important environmental toxicant that may give rise to kidney dysfunction, bone disease, and cancer in humans and animals. Kidney dysfunction occurs at very low exposures and is often considered as the most sensitive or critical effect. Cadmium exposures of concern occur in many countries. In low- and middle-income countries with small-scale mining, excessive exposure to cadmium and other metals occurs in occupational and environmental settings. This is of particular importance in view of the growing demand for metals in global climate change mitigation. Since the 1970s, the present authors have contributed evidence concerning the role of metallothionein and other factors in influencing the toxicokinetics and toxicity of cadmium, particularly as it relates to the development of adverse effects on kidneys in humans and animals. The findings gave a background to the development of biomarkers employed in epidemiological studies, demonstrating the important role of metallothionein in protection against cadmium-induced kidney dysfunction in humans. Studies in cadmium-exposed population groups demonstrated how biomarkers of kidney dysfunction changed during 8 years after drastic lowering of environmental cadmium exposure. Other epidemiological studies showed the impact of a good zinc status in lowering the prevalence of cadmium-related kidney dysfunction. Increased susceptibility to Cd-induced kidney dysfunction was shown in a population with high exposure to inorganic arsenic when compared with a group with low such exposure. Several national and international organizations have used part of the reviewed information, but the metallothionein-related biomarkers and the interaction effects have not been fully considered. We hope that these data sets will also be included and improve risk assessments and preventive measures. Full article

(This article belongs to the Special Issue Current Advances of Metal Complexes for Biomedical Applications)

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20 pages, 17373 KiB

Open AccessArticle

The Memory Gene, Murashka, Is a Regulator of Notch Signalling and Controls the Size of the Drosophila Germline Stem Cell Niche

by Thifeen Deen, Hideyuki Shimizu, Marian B. Wilkin and Martin Baron

Biomolecules 2025, 15(8), 1082; https://doi.org/10.3390/biom15081082 - 26 Jul 2025

We identified Murashka, a RING finger protein, in an oogenesis screen as a regulator of Drosophila ovary germline stem cell niche development. Mutant alleles of murashka exhibited an enlarged niche phenotype reminiscent of increased Notch signalling and displayed genetic interactions with Notch alleles, [...] Read more.

We identified Murashka, a RING finger protein, in an oogenesis screen as a regulator of Drosophila ovary germline stem cell niche development. Mutant alleles of murashka exhibited an enlarged niche phenotype reminiscent of increased Notch signalling and displayed genetic interactions with Notch alleles, and with polychaetoid, a regulator of Notch during niche development. These interactions uncovered both positive and negative impacts on Notch in different genetic backgrounds. In S2 cells, Murashka formed a complex with Notch and colocalised with Notch in the secretory pathway. Murashka expression in S2 cells down-regulated Notch signalling levels but could result in increased fold induction due to the proportionally greater decrease in basal ligand-independent activity. In vivo Murashka expression had different outcomes on different Notch target genes. We observed a decrease in the expression of vestigial along the anterior/posterior boundary of the wing imaginal disc, but not of wingless at the dorsal/ventral boundary. Instead, weak ectopic wingless was observed, which was synergistically increased by the coexpression of Deltex, a positive regulator of ligand-independent signalling. Our results identify a novel developmental role for murashka, a gene previously only associated with a function in long-term memory, and indicate a regulatory role for Murashka through a physical interaction with Notch that has context-dependent outcomes. Murashka adds to a growing number of ubiquitin ligase regulators which interact with Notch at different locations within its secretory and endocytic trafficking pathways. Full article

(This article belongs to the Special Issue Notch and Its Regulation in Health and Disease)

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20 pages, 5937 KiB

Open AccessArticle

Development of a Serum Proteomic-Based Diagnostic Model for Lung Cancer Using Machine Learning Algorithms and Unveiling the Role of SLC16A4 in Tumor Progression and Immune Response

by Hanqin Hu, Jiaxin Zhang, Lisha Zhang, Tiancan Li, Miaomiao Li, Jianxiang Li and Jin Wang

Biomolecules 2025, 15(8), 1081; https://doi.org/10.3390/biom15081081 - 26 Jul 2025

Early diagnosis of lung cancer is crucial for improving patient prognosis. In this study, we developed a diagnostic model for lung cancer based on serum proteomic data from the GSE168198 dataset using four machine learning algorithms (nnet, glmnet, svm, and XGBoost). The model’s [...] Read more.

Early diagnosis of lung cancer is crucial for improving patient prognosis. In this study, we developed a diagnostic model for lung cancer based on serum proteomic data from the GSE168198 dataset using four machine learning algorithms (nnet, glmnet, svm, and XGBoost). The model’s performance was validated on datasets that included normal controls, disease controls, and lung cancer data containing both. Furthermore, the model’s diagnostic capability was further validated on an independent external dataset. Our analysis identified SLC16A4 as a key protein in the model, which was significantly downregulated in lung cancer serum samples compared to normal controls. The expression of SLC16A4 was closely associated with clinical pathological features such as gender, tumor stage, lymph node metastasis, and smoking history. Functional assays revealed that overexpression of SLC16A4 significantly inhibited lung cancer cell proliferation and induced cellular senescence, suggesting its potential role in lung cancer development. Additionally, correlation analyses showed that SLC16A4 expression was linked to immune cell infiltration and the expression of immune checkpoint genes, indicating its potential involvement in immune escape mechanisms. Based on multi-omics data from the TCGA database, we further discovered that the low expression of SLC16A4 in lung cancer may be regulated by DNA copy number variations and DNA methylation. In conclusion, this study not only established an efficient diagnostic model for lung cancer but also identified SLC16A4 as a promising biomarker with potential applications in early diagnosis and immunotherapy. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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18 pages, 3682 KiB

Open AccessArticle

Comparative Analysis of Testicular Transcriptional and Translational Landscapes in Yak and Cattle–Yak: Implications for Hybrid Male Sterility

by Mengli Cao, Shaoke Guo, Ziqiang Ding, Liyan Hu, Lin Xiong, Qianyun Ge, Jie Pei and Xian Guo

Biomolecules 2025, 15(8), 1080; https://doi.org/10.3390/biom15081080 - 25 Jul 2025

Cattle–yak, a hybrid of yak and cattle, exhibits significant heterosis but male infertility, hindering heterosis fixation. Although extensive research has been conducted on transcriptional mechanisms in the testes of cattle–yak, the understanding of their translational landscape remains limited. In this study, we characterized [...] Read more.

Cattle–yak, a hybrid of yak and cattle, exhibits significant heterosis but male infertility, hindering heterosis fixation. Although extensive research has been conducted on transcriptional mechanisms in the testes of cattle–yak, the understanding of their translational landscape remains limited. In this study, we characterized the translational landscape of yak and cattle–yak based on Ribo-seq technology integrated with RNA-seq data. The results revealed that gene expression was not fully concordant between transcriptional and translational levels, whereas cattle–yak testes exhibited a stronger correlation across these two regulatory layers. Notably, genes that were differentially expressed at the translational level only (MEIOB, MEI1, and SMC1B) were mainly involved in meiosis. A total of 4,236 genes with different translation efficiencies (TEs) were identified, and the TEs of most of the genes gradually decreased as the mRNA expression level increased. Further research revealed that genes with higher TE had a shorter coding sequence (CDS) length, lower GC content, and higher normalized minimum free energy in the testes of yaks, but this characteristic was not found in cattle–yaks. We also identified upstream open reading frames (uORFs) in yak and cattle–yak testes, and the sequence characteristics of translated uORFs and untranslated uORFs were markedly different. In addition, we identified several short polypeptides that may play potential roles in spermatogenesis. In summary, our study uncovers distinct translational dysregulations in cattle–yak testes, particularly affecting meiosis, which provides novel insights into the mechanisms of spermatogenesis and male infertility in hybrids. Full article

(This article belongs to the Section Molecular Biology)

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20 pages, 547 KiB

Open AccessArticle

Empirical Assessment of Sequence-Based Predictions of Intrinsically Disordered Regions Involved in Phase Separation

by Xuantai Wu, Kui Wang, Gang Hu and Lukasz Kurgan

Biomolecules 2025, 15(8), 1079; https://doi.org/10.3390/biom15081079 - 25 Jul 2025

Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the [...] Read more.

Phase separation processes facilitate the formation of membrane-less organelles and involve interactions within structured domains and intrinsically disordered regions (IDRs) in protein sequences. The literature suggests that the involvement of proteins in phase separation can be predicted from their sequences, leading to the development of over 30 computational predictors. We focused on intrinsic disorder due to its fundamental role in related diseases, and because recent analysis has shown that phase separation can be accurately predicted for structured proteins. We evaluated eight representative amino acid-level predictors of phase separation, capable of identifying phase-separating IDRs, using a well-annotated, low-similarity test dataset under two complementary evaluation scenarios. Several methods generate accurate predictions in the easier scenario that includes both structured and disordered sequences. However, we demonstrate that modern disorder predictors perform equally well in this scenario by effectively differentiating phase-separating IDRs from structured regions. In the second, more challenging scenario—considering only predictions in disordered regions—disorder predictors underperform, and most phase separation predictors produce only modestly accurate results. Moreover, some predictors are broadly biased to classify disordered residues as phase-separating, which results in low predictive performance in this scenario. Finally, we recommend PSPHunter as the most accurate tool for identifying phase-separating IDRs in both scenarios. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics and Systems Biology Section)

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25 pages, 11171 KiB

Open AccessArticle

Artesunate Ameliorates SLE Atherosclerosis Through PPARγ-Driven Cholesterol Efflux Restoration and Disruption of Lipid Raft-Organized TLR9/MyD88 Signaling Pathway

by Miao Zhang, Xinyu Pan, Yuanfang He, Kairong Sun, Zhiyu Wang, Weiyu Tian, Haonan Qiu, Yiqi Wang, Chengping Wen and Juan Chen

Biomolecules 2025, 15(8), 1078; https://doi.org/10.3390/biom15081078 - 25 Jul 2025

Systemic lupus erythematosus (SLE) is characterized by autoimmune dysregulation, elevated autoantibody production, and persistent inflammation, predisposing patients to atherosclerosis (AS). Atherogenesis is dependent on lipid homeostasis and inflammatory processes, with the formation of lipid-laden, macrophage-derived foam cells (MDFC) essential for atherosclerotic lesion progression. [...] Read more.

Systemic lupus erythematosus (SLE) is characterized by autoimmune dysregulation, elevated autoantibody production, and persistent inflammation, predisposing patients to atherosclerosis (AS). Atherogenesis is dependent on lipid homeostasis and inflammatory processes, with the formation of lipid-laden, macrophage-derived foam cells (MDFC) essential for atherosclerotic lesion progression. Elevated cholesterol levels within lipid rafts trigger heightened pro-inflammatory responses in macrophages via Toll-like receptor 9 (TLR9). Artesunate (ART), an artemisinin derivative sourced from Artemisia annua, exhibits therapeutic potential in modulating inflammation and autoimmune conditions. Nonetheless, its impact and mechanisms in SLE-associated AS (SLE-AS) remain largely unexplored. Our investigation demonstrated that ART could effectively ameliorate lupus-like symptoms and atherosclerotic plaque development in SLE-AS mice. Moreover, ART enhanced cholesterol efflux from MDFC by upregulating ABCA1, ABCG1, and SR-B1 both in vivo and in vitro. Moreover, ART reduced cholesterol accumulation in bone marrow-derived macrophages (BMDMs), thereby diminishing TLR9 recruitment to lipid rafts. ART also suppressed TLR9 expression and its downstream effectors in the kidney and aorta of SLE-AS mice, attenuating the TLR9-mediated inflammatory cascade in CPG2395 (ODN2395)-stimulated macrophages. Through bioinformatics analysis and experimental validation, PPARγ was identified as a pivotal downstream mediator of ART in macrophages. Depleting PPARγ levels reduced the expression of ABCA1, ABCG1, and SR-B1 in macrophages, consequently impeding cholesterol efflux. In conclusion, these findings suggest that ART ameliorates SLE-AS by restoring cholesterol homeostasis through the PPARγ-ABCA1/ABCG1/SR-B1 pathway and suppressing lipid raft-driven TLR9/MyD88 inflammation. Full article

(This article belongs to the Section Lipids)

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16 pages, 1930 KiB

Open AccessArticle

A Microfluidic System for Real-Time Monitoring and In Situ Metabolite Detection of Plasma-Enhanced Wound Healing

by Zujie Gao, Jinlong Xu, Hengxin Zhao, Xiaobing Zheng, Zijian Lyu, Qiwei Liu, Hao Chen, Yu Zhang, He-Ping Li and Yongjian Li

Biomolecules 2025, 15(8), 1077; https://doi.org/10.3390/biom15081077 - 25 Jul 2025

Although cold atmospheric plasma (CAP) has shown promise in facilitating wound repair due to its non-thermal and non-invasive properties, its dynamic effects on cellular response and metabolic regulation remain poorly characterized, and the mechanism is still unclear. In this study, we developed a [...] Read more.

Although cold atmospheric plasma (CAP) has shown promise in facilitating wound repair due to its non-thermal and non-invasive properties, its dynamic effects on cellular response and metabolic regulation remain poorly characterized, and the mechanism is still unclear. In this study, we developed a microfluidic experimental system that integrates a CAP treatment module with multiparametric in situ sensing capabilities, along with precise environmental control of temperature, humidity, and CO₂ concentration. A stratified microfluidic chip was engineered to co-culture HaCaT keratinocytes and HSF fibroblasts. CAP treatment was applied within this platform, and the dynamic processes of cell migration, proliferation, and multiple metabolic markers were simultaneously monitored. The experimental results show that the system can not only achieve real-time observation in the healing process under plasma intervention, but also find that the healing process is closely related to the concentration of NO₂⁻. In addition, the study also found that keratin KRT14, which is thought to be closely related to wound healing, decreased significantly in the process of plasma-induced healing. The platform provides high-resolution experimental tools to elucidate the biological effects of CAP and has the potential for parameter optimization, material evaluation, and personalized therapeutic development to advance plasma research and clinical translational applications. Full article

(This article belongs to the Special Issue Advances in Plasma Bioscience and Medicine: 2nd Edition)

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15 pages, 8667 KiB

Open AccessArticle

A Novel Synthetic Tag Induces Palmitoylation and Directs the Subcellular Localization of Target Proteins

by Jun Ka, Gwanyeob Lee, Seunghyun Han, Haekwan Jeong and Suk-Won Jin

Biomolecules 2025, 15(8), 1076; https://doi.org/10.3390/biom15081076 - 25 Jul 2025

Proper subcellular localization is essential to exert the designated function of a protein, not only for endogenous proteins but also transgene-encoded proteins. Post-translational modification is a frequently used method to regulate the subcellular localization of a specific protein. While there are a number [...] Read more.

Proper subcellular localization is essential to exert the designated function of a protein, not only for endogenous proteins but also transgene-encoded proteins. Post-translational modification is a frequently used method to regulate the subcellular localization of a specific protein. While there are a number of tags that are widely used to direct the target protein to a specific location within a cell, these tags often fail to emulate the dynamics of protein trafficking, necessitating an alternative approach to the direct subcellular localization of transgene-encoded proteins. Here, we report the development of a new synthetic polypeptide protein tag comprised of ten amino acids, which promotes membrane localization of a target protein. This short synthetic peptide tag, named “Palmito-Tag”, induces ectopic palmitoylation on the cysteine residue within the tag, thereby promoting membrane localization of the target proteins without affecting their innate function. We show that the target proteins with the Palmito-Tag are incorporated into the membranous organelles within the cells, including the endosomes, as well as extracellular vesicles. Given the reversible nature of palmitoylation, the Palmito-Tag may allow us to shift the subcellular localization of the target protein in a context-dependent manner. With the advent of therapeutic applications of exosomes and other extracellular vesicles, we believe that the ability to reversibly modify a target protein and direct its deposition to the specific subcellular milieu will help us explore more effective venues to harness the potential of extracellular vesicle-based therapies. Full article

(This article belongs to the Special Issue Feature Papers in Cellular Biochemistry)

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