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Search Results (295)

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18 pages, 2121 KB  
Article
Gender- and Grade-Dependent Activation of Androgen Receptor Signaling in Adult-Type Diffuse Gliomas: Epigenetic Insights from a Retrospective Cohort Study
by Lidia Gatto, Sofia Asioli, Luca Morandi, Enrico Di Oto, Vincenzo Di Nunno, Alicia Tosoni, Marta Aprile, Stefania Bartolini, Lucia Griva, Sofia Melotti, Francesca Gentilini, Giuseppe Pinto, Francesco Casadei, Maria Pia Foschini, Caterina Tonon, Raffaele Lodi and Enrico Franceschi
Biomedicines 2025, 13(10), 2379; https://doi.org/10.3390/biomedicines13102379 - 28 Sep 2025
Viewed by 302
Abstract
Background: The androgen receptor (AR) is a ligand-dependent transcription factor of the nuclear steroid receptor superfamily, implicated in the pathogenesis of various solid tumors. The AR gene, located on chromosome Xq11–12, is accompanied by several X-linked genes that modulate AR expression and [...] Read more.
Background: The androgen receptor (AR) is a ligand-dependent transcription factor of the nuclear steroid receptor superfamily, implicated in the pathogenesis of various solid tumors. The AR gene, located on chromosome Xq11–12, is accompanied by several X-linked genes that modulate AR expression and function, including FLNA, UXT, and members of the melanoma antigen gene (MAGE) family (MAGEA1, MAGEA11, MAGEC1, MAGEC2). While the AR has been investigated in multiple tumor types, its role in adult-type diffuse gliomas remains largely unexplored. Here, we characterized AR protein expression and the promoter methylation status of the AR and associated regulatory genes in adult-type diffuse gliomas. Methods: A retrospective analysis was conducted on 50 patients with adult-type diffuse gliomas, including IDH-mutant gliomas (grades 2–4) and IDH-wildtype glioblastomas (GBMs), classified according to the 2021 WHO criteria. AR nuclear expression was assessed by immunohistochemistry (IHC). Methylation-specific PCR and quantitative DNA methylation analyses were employed to evaluate promoter methylation of the AR and selected co-regulatory genes. Results: AR nuclear positivity correlated significantly with male sex (p = 0.04) and higher tumor grade, with the highest expression in IDH-wildtype GBMs (p = 0.04). In IDH-mutant gliomas, AR immunoreactivity was more prevalent in astrocytomas than in 1p/19q codeleted oligodendrogliomas (p = 0.02). AR expression was associated with unmethylated MGMT promoter status (p = 0.02). DNA methylation analysis revealed AR gene hypomethylation in tumors displaying nuclear AR positivity and in IDH-wildtype GBMs (Kruskal–Wallis p < 0.05). Additionally, methylation patterns of AR co-regulators located on the X chromosome suggest epigenetic regulation of AR signaling in gliomas. Conclusions: The findings reveal distinct AR pathway activation patterns in adult-type diffuse gliomas, particularly IDH-wildtype GBMs, suggesting that further exploration of antiandrogen therapies is warranted. Full article
(This article belongs to the Special Issue Mechanisms and Novel Therapeutic Approaches for Gliomas)
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8 pages, 191 KB  
Article
Assessment of Cervical Genotoxicity in Infertile Women Receiving IVF Therapy Using Micronucleus Test
by Fatma Kılıç Hamzaoğlu, Feyza Özçelik, Kaddafi Özçelik, Ayşe Gül Zamani and Kazım Gezginç
J. Clin. Med. 2025, 14(19), 6837; https://doi.org/10.3390/jcm14196837 - 26 Sep 2025
Viewed by 220
Abstract
Background: In vitro fertilization (IVF) has become a widely used method of assisted reproduction. However, concerns remain regarding the potential genotoxic effects of ovarian stimulation protocols used during IVF, especially in relation to cervical epithelial cells. The micronucleus (MN) assay is a validated [...] Read more.
Background: In vitro fertilization (IVF) has become a widely used method of assisted reproduction. However, concerns remain regarding the potential genotoxic effects of ovarian stimulation protocols used during IVF, especially in relation to cervical epithelial cells. The micronucleus (MN) assay is a validated cytogenetic biomarker of chromosomal damage and genome instability, increasingly utilized in cancer risk assessment. This study aimed to evaluate the genotoxic effect of IVF treatment on cervical epithelial cells in infertile women by comparing MN frequency before and after IVF cycles and with matched healthy controls. Methods: This prospective observational study included 15 women undergoing IVF and 15 age-matched healthy controls. All IVF participants had primary infertility and were undergoing their first IVF/ICSI cycle. Cervical smear samples were collected from the IVF group before and three months after treatment failure. MN assay was applied, and cytogenetic parameters (MN, binucleated cells, broken egg cells, and budding cells) were evaluated under light microscopy. Non-parametric statistical tests were used for analysis. Results: A statistically significant increase in MN frequency was found in the IVF group following treatment compared to pre-treatment samples and the control group (p = 0.001). HPV status was not assessed during the study period and is acknowledged as a key limitation. However, no significant differences were observed in other nuclear anomalies. Pre-treatment MN frequencies were not significantly different from those in controls. Conclusions: The findings suggest a potential cytogenetic impact of IVF-related hormonal stimulation on cervical epithelial cells, as evidenced by increased MN frequency. While no direct clinical implications were identified, these changes warrant further investigation into the long-term genomic safety of assisted reproductive technologies. Full article
(This article belongs to the Section Obstetrics & Gynecology)
15 pages, 2435 KB  
Case Report
Balanced Translocations Involving the DMD Gene as a Cause of Muscular Dystrophy in Female Children: A Description of Three Cases
by Ekaterina O. Vorontsova, Aysylu Murtazina, Elena Zinina, Alexander V. Polyakov, Maria Sumina, Olga A. Rybakova, Dmitry Vlodavets, Dmitry Kazakov, Yulia Suvorova, Inna V. Sharkova, Nina A. Demina, Svetlana A. Repina, Vera A. Bulanova, Maria Antonova, Elena Dadali, Andrey V. Marakhonov, Nadezhda V. Shilova, Sergey I. Kutsev and Olga A. Shchagina
Int. J. Mol. Sci. 2025, 26(19), 9389; https://doi.org/10.3390/ijms26199389 - 25 Sep 2025
Viewed by 280
Abstract
Duchenne muscular dystrophy (DMD) is typically described in boys with a pathogenic variant in the DMD. However, in certain cases, females may also exhibit symptoms of this X-linked disorder. In the present study, the cause of Duchenne muscular dystrophy in three girls [...] Read more.
Duchenne muscular dystrophy (DMD) is typically described in boys with a pathogenic variant in the DMD. However, in certain cases, females may also exhibit symptoms of this X-linked disorder. In the present study, the cause of Duchenne muscular dystrophy in three girls was reciprocal translocations t(X;2), t(X;12), and t(X;16), with breakpoints located within the DMD gene sequence. All patients had global development delay, predominantly proximal muscle weakness, calf muscle hypertrophy, and elevated creatine kinase levels up to 100 times the normal range (16,000–26,694 U/L). All underwent cardiac ultrasound and electromyography, and two of the girls also had muscle MRI data. After receiving negative results of MLPA aimed at the detection of DMD deletions and duplications, as well as the limb-girdle muscular dystrophy gene panel sequencing, the patients were referred to whole genome sequencing, which allowed to detect a translocation involving the short arm of the X chromosome and with breakpoints in the DMD. Karyotyping confirmed reciprocal translocations in all patients, with de novo status established in all three cases. The results of this study contribute to the understanding of clinical polymorphism and genetic heterogeneity of the disease, highlighting the importance of a comprehensive approach to genetic diagnostics in atypical cases. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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11 pages, 1321 KB  
Article
Beyond Spherical: Unveiling the Significance of Oval Blastocyst Morphology on Euploidy and Implantation Success
by Jakub Wyroba, Agnieszka Kuczyńska, Klaudia Kasperkowicz, Katarzyna Kostarczyk, Pawel Kordowitzki and Joanna Kochan
Cells 2025, 14(18), 1468; https://doi.org/10.3390/cells14181468 - 19 Sep 2025
Viewed by 373
Abstract
The selection of the most suitable embryo, based on the morphology and shape, for embryo transfer is a critical aspect of the in vitro fertilization (IVF) process, as its precision can significantly enhance the overall effectiveness of IVF and contribute to a healthy [...] Read more.
The selection of the most suitable embryo, based on the morphology and shape, for embryo transfer is a critical aspect of the in vitro fertilization (IVF) process, as its precision can significantly enhance the overall effectiveness of IVF and contribute to a healthy birth. This study aimed to compare the chromosomal status and implantation potential of oval-shaped blastocysts versus normal-shaped blastocysts on day 5 post-ICSI (intracytoplasmic sperm injection). Initially, the frequency of oval blastocysts was assessed by analyzing 1328 embryos from 610 ICSI cycles. Subsequently, 80 patients undergoing ICSI and PGT-A (preimplantation genetic testing for aneuploidy), who had both normal and oval blastocysts in the same cycle, were selected to evaluate the euploid rate relative to blastocyst morphology. Finally, the implantation outcomes of fresh embryo transfers involving oval and normal-shaped blastocysts, neither of which had undergone PGT-A, were analyzed. Half of the blastocysts from each group were transferred after assisted hatching (AH), and the other half were transferred without AH. Blastocyst shape does not appear to correlate with an increased risk of aneuploidy but does influence hatching ability. Following AH, the implantation potential of elongated blastocysts is equivalent to that of normally shaped blastocysts, suggesting AH is beneficial for oval embryos. Consequently, the transfer of oval blastocysts is considered as safe and effective as the transfer of normally shaped embryos. Full article
(This article belongs to the Section Tissues and Organs)
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20 pages, 8840 KB  
Article
Characterization of the Soybean GPAT Gene Family Identifies GmGPAT1 as a Key Protein in Salt Stress Tolerance
by Xin Li, Yunlong Li, Yan Sun, Sinan Li, Quan Cai, Shujun Li, Minghao Sun, Tao Yu, Xianglong Meng and Jianguo Zhang
Plants 2025, 14(18), 2862; https://doi.org/10.3390/plants14182862 - 13 Sep 2025
Viewed by 608
Abstract
Glycerol-3-phosphate acyltransferases (GPATs) catalyze the initial and rate-limiting step of glycerolipid biosynthesis, yet their contribution to salt tolerance in the soybean (Glycine max (L.) Merr.) plants remains largely uncharacterized. In this study, a total of 27 GmGPAT genes were identified, and their [...] Read more.
Glycerol-3-phosphate acyltransferases (GPATs) catalyze the initial and rate-limiting step of glycerolipid biosynthesis, yet their contribution to salt tolerance in the soybean (Glycine max (L.) Merr.) plants remains largely uncharacterized. In this study, a total of 27 GmGPAT genes were identified, and their evolutionary relationships, chromosomal distribution, conserved motifs, and cis-regulatory elements were comprehensively analyzed. Through transcriptomic and qPCR analyses, many GmGPATs were found to be predominantly expressed in roots, with GmGPAT1, a plastid-targeted isoform, displaying the most rapid and pronounced transcriptional activation under salt stress. GFP-fusion experiments in transient expression assays confirmed plastid localization of GmGPAT1. Heterologous expression in Escherichia coli together with enzyme kinetics analyses validated its enzymatic function as a GPAT family member. The soybean hairy-root lines overexpressing GmGPAT1 exhibited enhanced root elongation, increased biomass, and improved photosynthetic efficiency under 120 mM NaCl stress, while CRISPR/Cas9 knockout mutants showed pronounced growth inhibition. Physiological assays demonstrated that GmGPAT1 overexpression mitigated oxidative damage by limiting reactive oxygen species (ROS) accumulation and lipid peroxidation, increasing antioxidant enzyme activities (CAT, SOD, POD), and elevating the ratios of AsA/DHA and GSH/GSSG. These changes contributed to redox homeostasis and improved Na+ extrusion capacity. A genome-wide association study (GWAS) involving 288 soybean accessions identified a single nucleotide polymorphism in the GmGPAT1 promoter that was significantly correlated with salt tolerance, and the beneficial Hap1 allele emerged as a promising molecular marker for breeding. Together, these analyses emphasize the status of GmGPAT1 as a major regulator of salt stress adaptation through the coordinated modulation of lipid metabolism and redox balance, extend the functional annotation of the soybean GPAT family, and highlight new genetic resources that can be leveraged to enhance tolerance to salt stress in soybean cultivars. Full article
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17 pages, 1935 KB  
Article
Chromosomal Instability and Periodontal Disease in Idiopathic Infertility: Evidence of a Possible Association
by Cristina-Crenguţa Albu, Ştefan-Dimitrie Albu, Claudia Florina Bogdan-Andreescu, Cristian-Viorel Poalelungi, Constantin Marian Damian, Alexandru Burcea, Andreea-Mariana Bănățeanu, Emin Cadar, Dan Alexandru Slăvescu and Anca Daniela Brăila
Biology 2025, 14(9), 1256; https://doi.org/10.3390/biology14091256 - 12 Sep 2025
Viewed by 424
Abstract
Background: Chromosomal instability (CIN) may underlie a subset of idiopathic infertility, and chronic periodontitis could contribute to genomic fragility. We tested whether periodontal status is associated with cytogenetic instability in adults with idiopathic infertility. Methods: This was a cross-sectional study of 60 adults [...] Read more.
Background: Chromosomal instability (CIN) may underlie a subset of idiopathic infertility, and chronic periodontitis could contribute to genomic fragility. We tested whether periodontal status is associated with cytogenetic instability in adults with idiopathic infertility. Methods: This was a cross-sectional study of 60 adults aged 20–40 years, comprising idiopathic infertility (n = 30) and fertile controls (n = 30), each with 18 women and 12 men. Significant exclusions included systemic inflammatory disease, pregnancy/lactation, recent antibiotics/NSAIDs, and periodontal therapy within 6 months. Periodontal examination recorded probing depth (PD), clinical attachment loss (CAL), and bleeding on probing (BOP). Cytogenetic testing used mitomycin C-induced chromosomal breakage to derive the Breakage Index (BI); CIN was defined as BI ≥ 4.0. Analyses compared infertile with CIN (n = 19), infertile without CIN (n = 11), and controls (n = 30). Results: Infertile participants with CIN had a higher periodontitis burden compared to infertile participants without CIN and to controls (moderate–severe: 89.5% vs. 54.5% vs. 26.7%); mean BI also differed (5.2 ± 0.9 vs. 1.3 ± 0.5 vs. 0.4 ± 0.2). Periodontal measures followed the same gradient, with greater CAL and PD in CIN-positive infertility. Conclusions: In idiopathic infertility, CIN was cross-sectionally associated with more severe periodontitis, and the BI correlated with CAL, PD, and BOP. Causality cannot be inferred and residual confounding cannot be excluded. Periodontal screening is a feasible adjunct that may help identify a modifiable inflammatory burden; prospective and interventional studies are warranted. Full article
(This article belongs to the Section Medical Biology)
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25 pages, 3945 KB  
Article
Synergistic MDM2-STAT3 Inhibition Demonstrates Strong Anti-Leukemic Efficacy in Acute Lymphoblastic Leukemia
by Erhan Aptullahoglu and Emrah Kaygusuz
Int. J. Mol. Sci. 2025, 26(17), 8648; https://doi.org/10.3390/ijms26178648 - 5 Sep 2025
Viewed by 1096
Abstract
Acute lymphoblastic leukemia (ALL) remains a formidable therapeutic challenge, particularly within high-risk cohorts. Advances in next-generation sequencing have elucidated critical mutations that significantly influence prognosis and therapeutic decision-making. Tyrosine kinase inhibitors (TKIs) have significantly improved treatment outcomes in Philadelphia chromosome-positive (Ph+) ALL. Meanwhile, [...] Read more.
Acute lymphoblastic leukemia (ALL) remains a formidable therapeutic challenge, particularly within high-risk cohorts. Advances in next-generation sequencing have elucidated critical mutations that significantly influence prognosis and therapeutic decision-making. Tyrosine kinase inhibitors (TKIs) have significantly improved treatment outcomes in Philadelphia chromosome-positive (Ph+) ALL. Meanwhile, emerging therapies such as monoclonal antibodies and chimeric antigen receptor (CAR) T-cell therapies show promise for B-cell ALL, although they are associated with considerable toxicities. These developments underscore the persistent need for alternative therapeutic strategies that can benefit a wider range of patients. In this study, human ALL cell lines—characterized by either wild-type or mutant tumor protein p53 (TP53) status—were treated with RG7388 (an MDM2 (mouse double minute 2 homolog) inhibitor) and BBI608 (a STAT3 (signal transducer and activator of transcription 3) inhibitor), both as single agents and in combination. Cell viability was quantified using XTT assays, while apoptosis was assessed via flow cytometry. Additionally, immunoblotting and qRT-PCR were employed to evaluate changes in protein and gene expression, respectively. RG7388 demonstrated potent growth inhibition in the majority of ALL cell lines, with p53-mutant cell lines exhibiting resistance. BBI608 reduced cell viability across all tested cell lines, though with variable sensitivity. Notably, the combination of RG7388 and BBI608 elicited synergistic anti-proliferative effects in p53 wild-type and partially functional p53-mutant cells, enhancing apoptosis and stabilizing p53 protein levels. In contrast, MOLT-4 cells, which harbor concurrent TP53 and STAT3 mutations, did not benefit from the combination treatment, indicating an inherent resistance phenotype within this subset. Collectively, these findings highlight the therapeutic potential of combined MDM2 and STAT3 inhibition in ALL, particularly in p53 wild-type and partially functional p53-mutant contexts. This combinatorial approach augments apoptosis and tumor growth suppression, offering a promising avenue for expanding treatment options for a broader patient population. Further investigation is warranted to validate these preclinical findings and to explore translational implications in genetically diverse ALL subsets. Full article
(This article belongs to the Special Issue Molecular Research in Hematologic Malignancies)
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18 pages, 5056 KB  
Article
The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01
by Yanming Qiao, Zhiyuan Jia, Yuying Liu, Na Zhang, Chun Luo, Lina Meng, Yajie Cheng, Minglei Li, Xiuchao Xie and Jianzhao Qi
J. Fungi 2025, 11(9), 647; https://doi.org/10.3390/jof11090647 - 1 Sep 2025
Viewed by 612
Abstract
Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the [...] Read more.
Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01, domesticated from the Qinling Mountains. A multi-platform sequencing strategy (Illumina and PacBio HiFi) yielded a high-quality 82.23 Mb assembly anchored to 11 chromosomes, exhibiting high completeness (98.4% BUSCO) and 46.03% GC content. Annotation predicted 15,847 protein-coding genes, with 81.12% functionally assigned. Genome-wide analysis identified 8.46 million high-confidence single-nucleotide polymorphisms (SNPs). Notably, methylation profiling revealed 3.25 million methylation events, with elevated densities on chromosomes 4, 9, and 10, suggesting roles in gene silencing and environmental adaptation. Phylogenomic analyses clarified the evolutionary status of G. lapidescens, whilst gene family evolution indicated moderate dynamics reflecting niche adaptation. Carbohydrate-Active enzymes (CAZymes) analysis identified 521 enzymes, including 211 Glycoside Hydrolases (GHs), consistent with organic matter degradation. Additionally, 3279 SSRs were catalogued as molecular markers. This foundational resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit, underpinning future research into medicinal compound biosynthesis, environmental adaptation, germplasm conservation, and sustainable cultivation. Full article
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24 pages, 2380 KB  
Article
Genomic Insights into the Probiotic Functionality and Safety of Lactiplantibacillus pentosus Strain TBRC 20328 for Future Food Innovation
by Tayvich Vorapreeda, Tanapawarin Rampai, Warinthon Chamkhuy, Rujirek Nopgasorn, Siwaporn Wannawilai and Kobkul Laoteng
Foods 2025, 14(17), 2973; https://doi.org/10.3390/foods14172973 - 26 Aug 2025
Viewed by 670
Abstract
Lactiplantibacillus species have been historically used for food applications. Although several species are regarded as safe according to their regulatory status, the safety issues and functional roles of these lactic acid bacteria have been given attention. A selected Lactiplantibacillus strain TBRC 20328, with [...] Read more.
Lactiplantibacillus species have been historically used for food applications. Although several species are regarded as safe according to their regulatory status, the safety issues and functional roles of these lactic acid bacteria have been given attention. A selected Lactiplantibacillus strain TBRC 20328, with probiotic properties isolated from fermented Isan-style pork sausage (Mam), was evaluated for its safety through whole-genome sequencing and analysis using integrative bioinformatics tools. The metabolic genes were assessed through comparative genome analysis among Lactiplantibacillus species. The genome of the strain TBRC 20328 consisted of one circular chromosome (3.49 Mb) and five plasmids (totaling 0.25 Mb), encoding 3056 and 284 protein-coding genes, respectively. It exhibited an average nucleotide identity (ANI) with other Lactiplantibacillus pentosus strains of over 95%. Whole-genome analysis confirmed the absence of virulence and antimicrobial resistance genes, supporting its safety for food applications. Functional annotation revealed clusters for bacteriocins (plantaricin EF and pediocin) and polyketides, indicating potential roles in biopreservation and host interactions. Genes involved in the biosynthesis of some short-chain fatty acids and exopolysaccharides were also identified. Comparative genomic analysis across 33 other Lactiplantibacillus strains identified 2380 orthogroups, with 94 unique to the Lp. pentosus group. These included gene clusters involved in malonate decarboxylation, leucine biosynthesis, and 5-oxoprolinase activity. Such distinct genomic features emphasize the sustainable biotechnological potential and safety of Lp. pentosus TBRC 23028. Together, the findings highlight its promise as a safe and functional probiotic candidate with broad applications in functional food development and precision fermentation technologies. Full article
(This article belongs to the Section Food Microbiology)
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9 pages, 469 KB  
Review
Deep Learning Models: Their Relationship with Embryonic Euploidies and Reproductive Outcomes
by Aikaterini Selntigia, Lucia Maresca, Diletta Montanino Oliva, Camilla Coianiz and Daniela Galliano
Genes 2025, 16(8), 981; https://doi.org/10.3390/genes16080981 - 20 Aug 2025
Viewed by 844
Abstract
Background: Embryo selection in in vitro fertilization (IVF) aims to prioritize embryos with the highest reproductive potential. While preimplantation genetic testing for aneuploidy (PGT-A) remains the gold standard for identifying euploid embryos, it is invasive and not universally applicable. Deep learning (DL)-based models, [...] Read more.
Background: Embryo selection in in vitro fertilization (IVF) aims to prioritize embryos with the highest reproductive potential. While preimplantation genetic testing for aneuploidy (PGT-A) remains the gold standard for identifying euploid embryos, it is invasive and not universally applicable. Deep learning (DL)-based models, such as the intelligent data analysis (iDA) score, have emerged as non-invasive alternatives for embryo assessment. This review critically evaluates the relationship between iDAScore (versions 1.0 and 2.0), embryo euploidy, and clinical outcomes, including live birth and miscarriage rates. Methods: A narrative review was performed using PubMed and Google Scholar, covering studies published from January 2020 to May 2025. The search included terms such as “iDAScore,” “deep learning,” “euploidy,” and “live birth.” Only English-language full-text studies assessing the predictive performance of iDAScore relative to chromosomal status or reproductive outcomes were included. Results: Six retrospective studies met the inclusion criteria. All reported a statistically significant association between higher iDAScore values and embryo euploidy. AUC values for euploidy prediction ranged from 0.60 to 0.68. In several studies, iDAScore was also positively associated with live birth rates and negatively with miscarriage rates. However, the predictive accuracy was moderate when restricted to euploid embryo cohorts, indicating that iDAScore may be more effective in broader populations where chromosomal status is unknown. Conclusions: iDAScore represents a promising adjunct to traditional embryo assessment. Although it cannot replace PGT-A, it may aid in embryo prioritization when genetic testing is not feasible. Larger prospective studies are warranted to further validate its clinical utility. Full article
(This article belongs to the Section Bioinformatics)
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34 pages, 448 KB  
Systematic Review
Evaluation of the Effectiveness and Accuracy of Non-Invasive Preimplantation Genetic Testing (niPGT) Compared to Invasive Embryo Biopsy
by Charalampos Voros, Menelaos Darlas, Diamantis Athanasiou, Antonia Athanasiou, Aikaterini Athanasiou, Kyriakos Bananis, Georgios Papadimas, Charalampos Tsimpoukelis, Athanasios Gkirgkinoudis, Ioakeim Sapantzoglou, Ioannis Papapanagiotou, Dimitrios Vaitsis, Aristotelis-Marios Koulakmanidis, Vasileios Topalis, Nikolaos Thomakos, Marianna Theodora, Panagiotis Antsaklis, Fotios Chatzinikolaou, Hans Atli Dahl, Georgios Daskalakis and Dimitrios Loutradisadd Show full author list remove Hide full author list
Biomedicines 2025, 13(8), 2010; https://doi.org/10.3390/biomedicines13082010 - 18 Aug 2025
Viewed by 1191
Abstract
Background: Preimplantation genetic testing for aneuploidy (PGT-A) is a popular approach in assisted reproductive technology that improves embryo selection and implantation rates. Traditional approaches rely on trophectoderm (TE) biopsy, which is an invasive procedure that might jeopardize embryo integrity and create technical constraints [...] Read more.
Background: Preimplantation genetic testing for aneuploidy (PGT-A) is a popular approach in assisted reproductive technology that improves embryo selection and implantation rates. Traditional approaches rely on trophectoderm (TE) biopsy, which is an invasive procedure that might jeopardize embryo integrity and create technical constraints such as mosaicism-related misclassification. Non-invasive preimplantation genetic testing (niPGT) has emerged as a possible alternative, using embryonic cell-free DNA (cfDNA) extracted from wasted culture media or blastocoel fluid to assess chromosomal status without requiring direct embryo manipulation. Methods: This systematic study investigates the molecular mechanisms behind cfDNA release, its biological properties, and the technological concerns that influence its utilization in niPGT. We look at recent advances in next-generation sequencing (NGS), whole-genome amplification (WGA), and bioinformatic techniques that improve cfDNA-based aneuploidy detection. In addition, we compare the sensitivity, specificity, and concordance rates of niPGT to conventional TE biopsy, highlighting the major aspects impacting its diagnostic performance. Results: The release of cfDNA from embryos is influenced by apoptotic and necrotic processes, active DNA shedding, and extracellular vesicle secretion, which results in fragmented chromosomal material of different qualities and quantities. While niPGT has shown promise as a noninvasive screening approach, significant variability in cfDNA yield, maternal DNA contamination, and sequencing biases all have an impact on test accuracy. Studies show that niPGT and TE biopsies have moderate-to-high concordance, although there are still issues in detecting mosaicism, segmental aneuploidies, and DNA degradation artifacts. Conclusions: NiPGT is a safer and less intrusive alternative to TE biopsy, with potential clinical benefits. However, technical advancements are required to improve cfDNA collecting procedures, reduce contamination, and improve sequencing accuracy. Additional large-scale validation studies are needed to create standardized methodologies and ensure that niPGT achieves the diagnostic reliability requirements required for widespread clinical deployment in IVF programs. Full article
(This article belongs to the Special Issue New Advances in Human Reproductive Biology)
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20 pages, 2276 KB  
Article
Post-Transcriptional Regulation of the MiaA Prenyl Transferase by CsrA and the Small RNA CsrB in Escherichia coli
by Joseph I. Aubee, Kinlyn Williams, Alexandria Adigun, Olufolakemi Olusanya, Jalisa Nurse and Karl M. Thompson
Int. J. Mol. Sci. 2025, 26(13), 6068; https://doi.org/10.3390/ijms26136068 - 24 Jun 2025
Viewed by 935
Abstract
MiaA is responsible for the addition of the isopentyl modification to adenine 37 in the anticodon stem loop of specific tRNAs in Escherichia coli. Mutants in miaA have pleotropic effects on the cell in E. coli and play a role in virulence [...] Read more.
MiaA is responsible for the addition of the isopentyl modification to adenine 37 in the anticodon stem loop of specific tRNAs in Escherichia coli. Mutants in miaA have pleotropic effects on the cell in E. coli and play a role in virulence gene regulation. In addition, MiaA is necessary for stress response gene expression by promoting efficient decoding of UUX-leucine codons, and genes with elevated UUX-leucine codons may be a regulatory target for i6A-modified tRNAs. Understanding the temporal nature of the i6A modification status of tRNAs would help us determine the regulatory potential of MiaA and its potential interplay with leucine codon frequency. In this work, we set out to uncover additional information about the synthesis of the MiaA. MiaA synthesis is primarily driven at the transcriptional level from multiple promoters in a complex operon. However, very little is known about the post-transcriptional regulation of MiaA, including the role of sRNAs in its synthesis. To determine the role of small RNAs (sRNAs) in the regulation of miaA, we constructed a chromosomal miaA-lacZ translational fusion driven by the arabinose-responsive PBAD promoter and used it to screen against an Escherichia coli sRNA library (containing sRNAs driven by the IPTG-inducible PLac promoter). Our genetic screen and quantitative β-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators of miaA expression in E. coli. Consistent with our hypothesis that CsrA regulates miaA post-transcriptional gene expression through binding to the miaA mRNA 5′ UTR, and CsrB binds and regulates miaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion of csrA significantly reduced expression of the reporter fusion as well as reducing miaA mRNA levels. These results suggest that under conditions where CsrA is inhibited, miaA mRNA translation and thus MiaA-dependent tRNA modification may be limited. Full article
(This article belongs to the Special Issue Role of RNA Decay in Bacterial Gene Regulation)
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19 pages, 5589 KB  
Article
Identification and Morphophysiological Characterization of Oryzalin-Induced Polyploids and Variants in Lysimachia xiangxiensis
by Yuanshan Zhang, Guanqun Chen, Ruixue Shen, Qiujing Li and Xiaohui Shen
Horticulturae 2025, 11(6), 654; https://doi.org/10.3390/horticulturae11060654 - 9 Jun 2025
Viewed by 805
Abstract
This study investigated the effects of oryzalin treatments on the induction of polyploids and variants, as well as their subsequent morphological and physiological characteristics, in Lysimachia xiangxiensis, a perennial herbaceous plant belonging to the Primulaceae family that is known for its ornamental value. [...] Read more.
This study investigated the effects of oryzalin treatments on the induction of polyploids and variants, as well as their subsequent morphological and physiological characteristics, in Lysimachia xiangxiensis, a perennial herbaceous plant belonging to the Primulaceae family that is known for its ornamental value. A total of 52 of the 162 treated stem segments survived after treatments and further developed into plantlets, and significant morphological changes in leaf color and growth status were observed. Using flow cytometry and chromosome counting, plants are categorized into the three variant types (VT1, VT2, and VT3), that is, VT1 and VT2 were diploid aneuploids, while VT3 was triploid. The optimized polyploid induction scheme involved treatment with 0.001% oryzalin for 4 days, resulting in an induction rate of up to 100%. Higher concentrations and longer exposure durations resulted in lower survival and polyploid induction rates of all stem segments during the above-mentioned processing. Observation of morphological features indicated that triploid VT3 vines were longer, with larger and thicker leaves and more guard cells, but lower stomatal density, compared with diploid aneuploids or the wild type. Polyploids outperformed other types in terms of chlorophyll content, net photosynthesis rate, stomatal conductance, and intercellular CO2 concentration, but had a lower flavonoid content. The results demonstrate that oryzalin can effectively induce polyploidy and variants in L. xiangxiensis, resulting in beneficial changes in morphology and physiological characteristics; this should provide valuable insight into the improvement of excellent varieties in plants. Full article
(This article belongs to the Section Propagation and Seeds)
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13 pages, 1092 KB  
Opinion
Epigenetic DNA Methylation Under the Influence of Low-Dose Ionizing Radiation, and Supplementation with Vitamin B12 and Folic Acid: Harmful or Beneficial for Professionals?
by Borivoje Savic, Bozidar Savic and Svetlana Stanojlovic
Epigenomes 2025, 9(2), 17; https://doi.org/10.3390/epigenomes9020017 - 31 May 2025
Viewed by 2066
Abstract
This review paper highlights the importance of educating current and future professionals about epigenetic mechanisms and recognizing epigenetics as a crucial model for protection against ionizing radiation. Two basic models for radiation-induced DNA damage are currently in use. The association between mutations and [...] Read more.
This review paper highlights the importance of educating current and future professionals about epigenetic mechanisms and recognizing epigenetics as a crucial model for protection against ionizing radiation. Two basic models for radiation-induced DNA damage are currently in use. The association between mutations and chromosomal aberrations provides a framework for analyzing risks at low radiation doses and exposure to small doses. However, there is no monitoring of epigenetic changes in professionals exposed to low doses of ionizing radiation. Epigenetic events regulate gene activity and expression not only during cell development and differentiation but also in response to environmental stimuli, such as ionizing radiation. Furthermore, the potential occurrence of malignant and hereditary diseases at low doses of ionizing radiation is linearly correlated and is considered a scientifically accepted assumption, despite recognized scientific limitations associated with this assessment. The aim of this review is to integrate novel and intriguing radiobiological paradigms regarding the effects of ionizing radiation on DNA methylation and epigenetic regulation of the DNA molecule. Several hypothesized biological responses to ionizing radiation are examined, linking them to epigenetic mechanisms involved in health risk assessment for professionals. The second part of the review includes published research related to epigenetics, supplementation, and virus reactivation in the context of epigenetic modifications of the DNA molecule. We hypothesize that different cycles lead to changes in the epigenome, which may be associated with the reactivation of certain viruses and the deficiency of specific dietary elements. These findings are linked to minimal deficiencies in vitamin B12 and folic acid, which may contribute to epigenomic changes. This aspect is crucial for the immune status of individuals working in high-risk environments. Full article
(This article belongs to the Special Issue Features Papers in Epigenomes 2025)
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29 pages, 1026 KB  
Article
Vitamin D Supplementation During Pregnancy and Maternal and Neonatal Vitamin D Status at ≤32 Weeks Gestation: Romanian Prospective Observational Cohort Study
by Ioana Andrada Radu, Manuela Cucerea, Cristian Gheonea, Radu Chicea, Dumitru Alin Teacoe, Bianca Ioana Mutică, Samuel Bogdan Todor, Gabriela Boța, Dragoș Popescu, Bianca Cosmina Coțovanu and Maria Livia Ognean
Children 2025, 12(6), 682; https://doi.org/10.3390/children12060682 - 26 May 2025
Viewed by 1729
Abstract
Background: Recently, vitamin D deficiency (VDD) has been described as a pandemic, affecting all groups of the population. Pregnant women and preterm infants are particularly vulnerable to vitamin D deficiency. Objectives: We aimed to evaluate the maternal and neonatal vitamin D [...] Read more.
Background: Recently, vitamin D deficiency (VDD) has been described as a pandemic, affecting all groups of the population. Pregnant women and preterm infants are particularly vulnerable to vitamin D deficiency. Objectives: We aimed to evaluate the maternal and neonatal vitamin D status in relation with maternal vitamin D supplementations during pregnancy and to identify demographic, social, and healthcare risk factors for maternal VDD and vitamin D insufficiency in women delivering at ≤32 weeks of gestation. Methods: This prospective observational study was developed in the regional level III maternity unit of the Clinical County Emergency Hospital Sibiu. It included all admitted mothers who delivered at ≤32 weeks of gestation and their infants between 1 March 2022 and 28 February 2025. Infant deaths in the first 24 h of life, major congenital defects, chromosomal abnormalities, the admission of outborn infants without their mothers, or the transfer of the mother more than 48 h after birth were used as exclusion criteria. Maternal and neonatal data were collected from medical records. Data on maternal vitamin D supplementation were collected through interviews. Univariate and multivariate logistic regressions, linear regression, and predictive models were performed for data analysis. Results: A total of 146 mothers (median (IQR) age 30 (24–35) years) and their 164 preterm infants born at ≤32 weeks of gestation (median gestational age of 30 (27–31) weeks and birth weight of 1200 (900–1527) g) were included in this study. Only 43.15% of the mothers used multivitamins containing vitamin D during pregnancy, and 10.96% used specific vitamin D supplements. Vitamin D supplementation was used for a median of 4 (3–5) months at a median dose of 800 (250–1500) IU/day. Severe VDD (25(OH)D < 10 ng/mL), VDD (25(OH)D < 20 ng/mL), VDI (25(OH)D 20–29 ng/mL) were found in 19.86%, 55.48%, and 23.97% of the mothers and 16.46%, 58.53%, and 25.61% of their infants, respectively. A significant correlation was found between the maternal and neonatal status (r = 0.684, r2 = 0.468, p < 0.001, B = 0.62). Both the maternal and neonatal vitamin D status were correlated with the vitamin D duration and dose used for supplementation during pregnancy. The logistic regression analysis showed that birth during a cold season and increased parity are independently associated with severe maternal VDD, while birth during the cold season and a lower educational status were independently associated with maternal VDD. Only an absent vitamin D supplementation (in the form of a multivitamin or specific vitamin D supplements) has been proven as an independent risk factor for VDI. Conclusions: Our findings revealed a worrisome prevalence of severe VDD, VDD, and VDI in mothers delivering very prematurely and in their infants. Additionally, less than half of the mothers in this study used vitamin D supplements during pregnancy despite the national recommendations. The professionals involved in advising pregnant women and policymakers should find solutions to improve the vitamin D status in these vulnerable groups of the population. Full article
(This article belongs to the Special Issue New Trends in Perinatal and Pediatric Epidemiology)
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