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17 pages, 2848 KB  
Article
Retinoic Acid Receptor γ Activity Plays a Critical Role in Regulating Early Mouse Gastruloid Development
by Jide T. Olanipekun, Benjamin Edginton-White, Caitlin McQueen, Geoffrey Brown and William E. B. Johnson
Int. J. Mol. Sci. 2026, 27(9), 3995; https://doi.org/10.3390/ijms27093995 - 29 Apr 2026
Viewed by 141
Abstract
Regulation of all-trans retinoic acid (ATRA) signaling is crucial to early embryonic development. Embryonic stem (ES) cell-derived gastruloids mimic normal development in response to the Wnt/β-catenin agonist CHIR9901, and this study has examined the importance of the activities of RAR (retinoic acid [...] Read more.
Regulation of all-trans retinoic acid (ATRA) signaling is crucial to early embryonic development. Embryonic stem (ES) cell-derived gastruloids mimic normal development in response to the Wnt/β-catenin agonist CHIR9901, and this study has examined the importance of the activities of RAR (retinoic acid receptor) α and γ to gastruloid development. Expression of retinoic acid receptor (RAR)γ within developing gastruloids was spatially restricted to primitive cells that co-expressed ES cell and early progenitor cell markers, i.e., Nanog, Sox2, and Oct4. In contrast, RARα expression was ubiquitous. mRNAs for the key enzymes involved in ATRA synthesis (Aldh1a2) and degradation (Cyp26a1) were not seen in cells that expressed RARγ. Treatment of ES cell-derived gastruloids with physiologically relevant (10 nM) levels of ATRA or with a highly selective RARγ agonist blocked normal developmental processes, preventing symmetry-breaking and axial elongation. This was not seen following treatments with an RARα agonist, where there was a tendency for enhanced axial elongation. Brachyury (TBXT) immuno-positive cells localized in the posterior end of elongated gastruloids in control- and RARα agonist-treated cultures, with Sox2 immuno-positive cells seen more widely, whilst both TBXT and Sox2 immuno-positive cells were randomly distributed throughout ATRA- and RARγ agonist-treated gastruloids. Concurrent treatment of gastruloids with 10 nM ATRA and 100 nM of an RARγ antagonist partially abrogated the ATRA-mediated block to axial elongation. Conversely, 10 nM RARγ antagonist treatments were associated with the formation of multi-axis gastruloid elongations, with comparatively little effect seen after treatments with an RARα antagonist. These findings reveal that RARγ plays a crucial role in the development of embryonic tissues. Full article
(This article belongs to the Section Molecular Biology)
18 pages, 4864 KB  
Review
Brewing Epigenetic Defense: Mechanisms of Coffee Bioactives in the Chemoprevention of Hepatocellular Carcinoma
by Nobuyuki Toshikuni and Masaaki Shimatani
Targets 2026, 4(2), 14; https://doi.org/10.3390/targets4020014 - 29 Apr 2026
Viewed by 95
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality, frequently arising from chronic inflammatory states such as metabolic dysfunction-associated steatotic liver disease and cirrhosis. While extensive epidemiological data demonstrate a strong, dose-dependent inverse association between habitual coffee consumption and HCC incidence, the [...] Read more.
Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality, frequently arising from chronic inflammatory states such as metabolic dysfunction-associated steatotic liver disease and cirrhosis. While extensive epidemiological data demonstrate a strong, dose-dependent inverse association between habitual coffee consumption and HCC incidence, the underlying molecular causality remains incompletely understood. In this comprehensive review, we elucidate the “Coffee Paradox” through the lens of nutriepigenomics. We demonstrate how coffee-derived bioactives—specifically chlorogenic acids, diterpenes, and microbially derived short-chain fatty acids—function as a coordinated epigenetic defense system. These compounds actively inhibit DNA methyltransferases, serve as endogenous histone deacetylase inhibitors via the gut–liver axis, and induce post-transcriptional, tumor-suppressive microRNA networks to halt oncogenic progression. However, to provide a critical and balanced perspective, we also address significant translational challenges. We evaluate conflicting null associations from recent Mendelian randomization studies and highlight the profound variability introduced by specific brewing methods, roasting profiles, and individual pharmacogenomics (e.g., CYP1A2 polymorphisms). Finally, we outline the future of precision hepatology, emphasizing the critical transition from observational epidemiology to clinical application via the utilization of circulating exosomal microRNAs as dynamic liquid biopsies and the development of standardized epi-nutraceuticals. Ultimately, this multi-layered epigenetic framework provides a robust foundation for integrating targeted dietary interventions into the primary prevention of HCC. Full article
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82 pages, 6759 KB  
Review
Toxoplasma gondii as a Direct Cause of Reproductive Dysfunction: Dual Threats to Male and Female Fertility
by Muhammad Farhab, Tariq Sohail, Mohammed Al-Rasheed, Zohaib Saeed and Aftab Shaukat
Vet. Sci. 2026, 13(5), 430; https://doi.org/10.3390/vetsci13050430 - 28 Apr 2026
Viewed by 146
Abstract
Toxoplasma gondii, an obligate intracellular protozoan infecting approximately one-third of the global population, poses a significant yet underappreciated threat to reproductive health in both sexes. Although this parasite has long been linked to birth defects caused by infection during pregnancy, new research [...] Read more.
Toxoplasma gondii, an obligate intracellular protozoan infecting approximately one-third of the global population, poses a significant yet underappreciated threat to reproductive health in both sexes. Although this parasite has long been linked to birth defects caused by infection during pregnancy, new research shows that it also reduces fertility in both sexes through different but related mechanisms. This review synthesizes knowledge on T. gondii-induced reproductive pathology across females and males, examining shared mechanistic themes while respecting tissue-specific differences, and evaluates emerging therapeutic strategies. In females, the parasite establishes persistent uterine reservoirs, triggers decidual immune dysregulation characterized by NK cell cytotoxicity, M1 macrophage polarization, Treg apoptosis, and inflammasome-mediated pyroptosis, while disrupting estrogen and progesterone signaling through both host receptor modulation and intrinsic parasite steroidogenic enzymes (TgCYP450mt, TgMAPR, Tg-HSD). In males, T. gondii breaches the blood–testis barrier, induces germ cell and Leydig cell apoptosis via ER stress and caspase pathways, impairs sperm quality parameters across acute and chronic infection, and disrupts the hypothalamic–pituitary–gonadal axis. Conserved molecular mechanisms—including NLRP3 inflammasome activation, PERK/eIF2α/ATF4/CHOP-mediated ER stress, and oxidative stress—operate in both reproductive tissues. The parasite’s intrinsic steroidogenic capability and bidirectional hormonal manipulation represent a paradigm shift in understanding host–parasite interactions. Conventional antiparasitics face limitations due to poor reproductive sanctuary penetration. Immunomodulatory approaches targeting Trem2, Tim-3, and the NLRP3 inflammasome show promise, along with natural products including Inonotus obliquus polysaccharide and ginseng polysaccharide. Nanomedicine platforms and mRNA vaccine candidates offer new directions for overcoming tissue barrier limitations. Toxoplasma gondii represents a fundamental threat to fertility and pregnancy outcomes rather than merely a risk for congenital infection. Integrated therapeutic strategies addressing direct parasitism, immunopathology, and endocrine disruption are needed. Longitudinal cohort studies, strain-specific mechanistic comparisons, and clinical trials of immunomodulatory adjuncts are urgently required. Full article
(This article belongs to the Special Issue Prevention and Control of Obstetric Diseases in Domestic Animals)
20 pages, 3771 KB  
Article
Transcriptome Analysis Reveals Intensity-Dependent Regulation of UV-B Radiation on Glucosinolate Biosynthesis in Rapeseed Leaves
by Pengpeng Mao, Song Chen, Le Kong, Xiangyu Yao, Weixuan Su, Xiaoying Liu, Yinjian Zheng and Zhigang Xu
Plants 2026, 15(9), 1335; https://doi.org/10.3390/plants15091335 - 28 Apr 2026
Viewed by 214
Abstract
Rapeseed (Brassica napus L.) is a globally important oilseed crop; however, its ‘double-low’ cultivars exhibit substantially reduced glucosinolate levels in vegetative tissues. To investigate whether UV-B radiation could be used to enhance glucosinolate accumulation, we systematically examined the modulation of glucosinolate profiles [...] Read more.
Rapeseed (Brassica napus L.) is a globally important oilseed crop; however, its ‘double-low’ cultivars exhibit substantially reduced glucosinolate levels in vegetative tissues. To investigate whether UV-B radiation could be used to enhance glucosinolate accumulation, we systematically examined the modulation of glucosinolate profiles and associated biosynthetic pathways in leaves of the ‘double-low’ cultivar NY4 under white light (WL) supplemented with two UV-B intensities: low-intensity UV-B (UVBL, 0.1 W m−2) and high-intensity UV-B (UVBH, 0.4 W m−2). Rapeseed seedlings were treated for 21 days under a 16 h photoperiod, and leaf samples were collected at the end of the treatment period, with three biological replicates per condition. Compared with the WL control, UVBL significantly increased total glucosinolate content by 64.57%, driven predominantly by elevated accumulation of progoitrin and neoglucobrassicin. In contrast, UVBH reduced total glucosinolate levels but markedly elevated gluconasturtiin content. Transcriptome analysis revealed that UVBL upregulated key genes involved in glucosinolate biosynthesis (e.g., MAM, IPMDH, CYP79F1, and SOT17/18) and transcription factors (e.g., MYB28, MYB34, MYB51, and MYB122). Conversely, UVBH downregulated genes associated with side-chain elongation of aliphatic glucosinolates and secondary modification of indolic glucosinolate. Collectively, these results demonstrate that low-intensity UV-B radiation can effectively boost total glucosinolate content in rapeseed leaves via transcriptional reprogramming. Full article
(This article belongs to the Section Plant Physiology and Metabolism)
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19 pages, 8761 KB  
Article
Hydrogen-Rich Water Suppresses Dark- and ABA-Induced Postharvest Senescence in Non-Heading Chinese Cabbage (Brassica rapa ssp. chinensis)
by Yong Luo, Xinman Wang, Mengya Yin, Ranze Zhao, Dingyu Zhang and Hongfang Zhu
Antioxidants 2026, 15(5), 554; https://doi.org/10.3390/antiox15050554 - 27 Apr 2026
Viewed by 215
Abstract
Non-heading Chinese cabbage (NHCC) is a highly economically valuable leafy vegetable widely grown in Asian regions. However, it undergoes rapid leaf yellowing and wilting during postharvest storage, which subsequently cause rapid quality decline and loss of nutritional components. Abscisic acid (ABA) promotes postharvest [...] Read more.
Non-heading Chinese cabbage (NHCC) is a highly economically valuable leafy vegetable widely grown in Asian regions. However, it undergoes rapid leaf yellowing and wilting during postharvest storage, which subsequently cause rapid quality decline and loss of nutritional components. Abscisic acid (ABA) promotes postharvest leaf senescence, while hydrogen-rich water (HRW) is widely used in postharvest preservation due to its excellent antioxidant properties; yet, the mechanism through which they interact to regulate postharvest senescence in NHCC remains unclear. Herein we found that exogenous HRW effectively delayed dark- and ABA-induced postharvest leaf senescence in NHCC, significantly maintained chlorophyll content, inhibited oxidative damage, and preserve nutritional components such as soluble sugars and vitamin C. The underlying mechanism was HRW inhibiting chlorophyll degradation by repressing the expression of chlorophyll catabolic genes like NYC1, NYE1, and PPH1. Meanwhile, HRW effectively lowered the accumulation of MDA and H2O2, elevated both the enzymatic activities and transcript abundance of SOD and CAT, and downregulated the transcript levels of RbohB, RbohC, RbohD, and RbohE, thereby maintaining reactive oxygen species (ROS) homeostasis. In addition, HRW negatively regulated ABA biosynthesis by inhibiting the transcript levels of ABA1, ABA2 and ABA3, while promoting the transcription of CYP707A1, CYP707A2 and CYP707A3. It also dampened the transcript abundance of ABA signaling components including PYL5, ABI1, and ABF3, thus blocking ABA signal transduction and alleviating its senescence-promoting effect. Collectively, this study confirms that HRW mitigates leaf senescence induced under dark and ABA conditions in NHCC via multiple synergistic pathways. Full article
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10 pages, 226 KB  
Article
Molecular and Phenotypic Characterization of Multidrug-Resistant Aspergillus fumigatus Clinical Isolates in Republic of Korea
by Yun Ha Lee, Yewon An, Yu Jin Lee, Jihee Lee, Su Yeon Kim and Byung Hak Kang
J. Fungi 2026, 12(5), 302; https://doi.org/10.3390/jof12050302 - 22 Apr 2026
Viewed by 663
Abstract
Genetic diversity and antifungal susceptibility profiles of Aspergillus fumigatus are critical for understanding the evolution of resistance in clinical and environmental settings. We performed comprehensive genomic characterization of A. fumigatus isolates using whole-genome sequencing combined with phenotypic susceptibility assays. SnpEff-based variant annotation identified [...] Read more.
Genetic diversity and antifungal susceptibility profiles of Aspergillus fumigatus are critical for understanding the evolution of resistance in clinical and environmental settings. We performed comprehensive genomic characterization of A. fumigatus isolates using whole-genome sequencing combined with phenotypic susceptibility assays. SnpEff-based variant annotation identified 76,079 single-nucleotide polymorphisms, revealing a high proportion of mutations (78.8%) in upstream and downstream regulatory regions, whereas high-impact coding variants remained rare (0.083%). Several key mutations were identified, including the well-established cyp51A M220V and HMG1 S212P/Y564H mutations. Moreover, a diverse array of peripheral cyp51A polymorphisms (M39I, E402D, N248K, and K372N) was detected, although these variants did not correlate with the resistant phenotypes. Our comparative genomic analysis identified a novel A586T substitution in the FKS1 gene in an isolate with an elevated minimum effective concentration of caspofungin, suggesting its possible association with reduced susceptibility, although functional validation is required. In isolates lacking canonical target-site mutations, the high frequency of regulatory-region variants indicated the involvement of non–target-site mechanisms. This study provides a detailed map of the genomic landscape of A. fumigatus and identifies candidate loci for future functional validation. Our results demonstrate the utility of high-throughput genomic surveillance for monitoring emerging resistance trends and characterizing the genetic background of clinical fungal pathogens. Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
21 pages, 32172 KB  
Article
Honey Lemon Alleviates Alcoholic Liver Disease via Multi-Target Synergistic Mechanisms: An Integrated Study of Network Pharmacology, Molecular Docking, and Animal Experiments
by Yaxi Zhou, Dong Xu, Meichao Bu, Ke Li, Lingyu Gao, Fei Pan, Wenjun Peng, Hualei Chen and Wenli Tian
Foods 2026, 15(8), 1384; https://doi.org/10.3390/foods15081384 - 16 Apr 2026
Viewed by 494
Abstract
Honey lemon (H&L) is a traditional beverage known for its potential liver-protective effects, but its mechanisms against alcoholic liver disease (ALD) remain poorly understood. This study aimed to investigate the hepatoprotective properties of H&L and explore its multi-target mechanisms in alleviating ALD. Using [...] Read more.
Honey lemon (H&L) is a traditional beverage known for its potential liver-protective effects, but its mechanisms against alcoholic liver disease (ALD) remain poorly understood. This study aimed to investigate the hepatoprotective properties of H&L and explore its multi-target mechanisms in alleviating ALD. Using network pharmacology and molecular docking, we identified 26 bioactive compounds in H&L and 335 potential targets associated with ALD. Pathway enrichment analysis revealed that H&L might exert its influence by regulating inflammation, oxidative stress and ethanol metabolism. Molecular docking further demonstrated strong binding interactions between key flavonoids (hesperidin, diosmin, and eriocitrin) and crucial targets, such as AKT1, SRC, STAT3, as well as ethanol-metabolizing enzymes like ADH, ALDH, and CYP2E1. In vivo experiments suggested that H&L alleviated liver injury and significantly improved selected indicators related to ethanol metabolism, oxidative stress, and inflammatory response. For several variables, including ALT/AST, ALDH, IL-6, and hepatic ethanol content, improvement trends were observed, although not all differences reached statistical significance. Overall, the results suggest that the protective effect of H&L against ALD may be associated with a multi-component, multi-target, and multi-pathway mode of action, supporting its potential for further investigation as a functional food candidate. Full article
(This article belongs to the Special Issue Latest Advances in Beehive Products)
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22 pages, 1012 KB  
Review
Oxidative Stress and Alcohol-Related Hepatitis: A Role for Future Therapies
by Francesca D’Arcangelo, Neil Rajoriya and Patricia F. Lalor
Antioxidants 2026, 15(4), 493; https://doi.org/10.3390/antiox15040493 - 16 Apr 2026
Viewed by 495
Abstract
Alcohol-associated Hepatitis (AH) is a rare acute injury caused by alcohol consumption, which can lead to one of the most severe manifestations of liver disease. It is part of the alcohol-related liver diseases (ArLD) spectrum, which represents a major global health burden, with [...] Read more.
Alcohol-associated Hepatitis (AH) is a rare acute injury caused by alcohol consumption, which can lead to one of the most severe manifestations of liver disease. It is part of the alcohol-related liver diseases (ArLD) spectrum, which represents a major global health burden, with oxidative stress and inflammation serving as central, interconnected pathogenic mechanisms. Chronic alcohol (ethanol) consumption induces hepatic reactive oxygen species (ROS) generation through multiple pathways, including cytochrome P450 2E1 (CYP2E1) induction, mitochondrial dysfunction, and NADPH oxidase activation. These oxidative insults trigger a cascade of cellular damage encompassing lipid peroxidation, protein adduct formation, DNA damage, and endoplasmic reticulum stress, ultimately leading to hepatocyte dysfunction and multiple forms of cell death, including apoptosis, necroptosis, pyroptosis, and ferroptosis. The inflammatory response, orchestrated primarily by Kupffer cells and infiltrating neutrophils through Toll-like receptor (TLR) signalling and inflammasome activation, not only amplifies hepatic injury but also promotes fibrogenesis through hepatic stellate cell activation. Neutrophils, characterised by elevated lipocalin-2 expression and spontaneous NETosis in AH, exhibit a paradoxical role by driving both tissue damage and repair. Current therapeutic strategies include corticosteroids, which remain the first-line treatment for severe AH, while emerging therapies targeting the gut–liver axis, hepatic regeneration, and specific molecular targets show promise in clinical trials. This review comprehensively examines the molecular crosstalk between oxidative stress and inflammation in the pathogenesis of AH to highlight current and investigational therapeutic approaches targeting these interconnected pathways. Full article
(This article belongs to the Special Issue Alcohol-Induced Oxidative Stress in Health and Disease, 2nd Edition)
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31 pages, 9123 KB  
Article
Exploring the Biological Potency of Carotenoids Against Alzheimer’s Disease: An Integrated Approach of Molecular Docking and Molecular Dynamics
by Meriem Khedraoui, El Mehdi Karim, Imane Yamari, Abdelkbir Errougui, Doni Dermawan, Nasser Alotaiq and Samir Chtita
Curr. Issues Mol. Biol. 2026, 48(4), 407; https://doi.org/10.3390/cimb48040407 - 16 Apr 2026
Viewed by 367
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder characterized by cholinergic dysfunction, amyloid-β aggregation, mitochondrial stress, and aberrant kinase activity. Carotenoids, naturally occurring pigments with antioxidant and neuroprotective properties, have emerged as promising candidates for AD intervention. In this study, we performed a [...] Read more.
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder characterized by cholinergic dysfunction, amyloid-β aggregation, mitochondrial stress, and aberrant kinase activity. Carotenoids, naturally occurring pigments with antioxidant and neuroprotective properties, have emerged as promising candidates for AD intervention. In this study, we performed a systematic stepwise computational screening of a large carotenoid library (n = 1191) to identify multitarget candidates against AD–related proteins. The workflow consisted of predefined ADMET filtering (oral absorption > 90%, Caco-2 > 0.9, logBB > −1, and absence of major CYP inhibition and toxicity alerts), reducing the dataset to 61 compounds, followed by multi-target molecular docking against AChE, BChE, BACE-1, MAO-B, and GSK3-β. Compounds were ranked using an aggregated mean docking score across all five targets, and the top-performing candidate was subjected to detailed mechanistic analyses. Hopkinsiaxanthin emerged as the highest-ranked multitarget carotenoid and was further evaluated using frontier molecular orbital (FMO) analysis, pharmacophore modeling, 100 ns molecular dynamics (MD) simulations, MM/PBSA binding free energy calculations, and per-residue decomposition. Docking predicted favorable estimated binding affinities toward all targets. MD simulations confirmed stable receptor–ligand complexes with low RMSD values (0.278–0.285 nm). MM/PBSA analysis indicated favorable binding free energies, particularly for GSK3-β (−22.73 kcal/mol) and AChE (−21.50 kcal/mol). Per-residue decomposition identified key hotspot residues driving stabilization. Overall, this structured computational framework identifies Hopkinsiaxanthin as a promising multitarget scaffold and supports its prioritization for experimental validation in AD models. Full article
(This article belongs to the Special Issue Emerging Trends in Bioinformatics and Computational Biology)
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16 pages, 4052 KB  
Article
Identification of CYP450 Family Members and Their Gonadal Expression Profiles in Exopalaemon carinicauda
by Shaoting Jia, Yichen Su, Yashi Hou, Kezhi Gong, Xiaotong Pan, Jianjian Lv and Jitao Li
Animals 2026, 16(8), 1201; https://doi.org/10.3390/ani16081201 - 15 Apr 2026
Viewed by 261
Abstract
The cytochrome P450 (CYP450) superfamily plays important roles in a wide range of biological processes. The classification of CYP450 family members has been studied in some plants and animals; however, there are no reports on CYP450 family members in Exopalaemon carinicauda [...] Read more.
The cytochrome P450 (CYP450) superfamily plays important roles in a wide range of biological processes. The classification of CYP450 family members has been studied in some plants and animals; however, there are no reports on CYP450 family members in Exopalaemon carinicauda. Based on publicly available whole-genome data for E. carinicauda, we identified 58 CYP450 family members based on the genome-wide alignment and analyzed their domains, gene structures and chromosomal locations, as well as physicochemical properties of the encoded proteins. The results revealed that CYP450 family members, widely distributed across multiple chromosomes, exhibit diverse protein properties, gene structures, and conserved motifs. Phylogenetic analysis indicated that these members are primarily clustered into subfamilies 2, 3, and 4, and the mitochondrial clan, showing close genetic relationships with homologous genes from other crustaceans. In this study, we revealed the genetic structural characteristics of the CYP450 family in E. carinicauda. We identified candidate genes for future research on the molecular mechanisms of CYP450 in development and reproduction. These findings are expected to serve as a foundation for further studies in this field. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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17 pages, 318 KB  
Review
Genetic Risk Factors and Clinical Implications of Glaucoma in the Saudi Population: A Review
by Abdullah Faisal Alotaibi, Lojain Mohammed A. Maawadh, Mohammed Naji Obaid Almutairi, Syed Hameed, Rizwan Malik and Khaled K. Abu-Amero
Int. J. Mol. Sci. 2026, 27(8), 3506; https://doi.org/10.3390/ijms27083506 - 14 Apr 2026
Viewed by 312
Abstract
Most glaucoma genetic data derive from European and East Asian cohorts, leaving high-consanguinity Middle Eastern populations under-characterized. This review synthesizes 33 Saudi-specific genetic studies (2014–2024, >9000 participants) to define a population-level glaucoma genetic architecture that diverges substantially from global models and carries direct [...] Read more.
Most glaucoma genetic data derive from European and East Asian cohorts, leaving high-consanguinity Middle Eastern populations under-characterized. This review synthesizes 33 Saudi-specific genetic studies (2014–2024, >9000 participants) to define a population-level glaucoma genetic architecture that diverges substantially from global models and carries direct precision medicine implications. Three findings distinguish the Saudi landscape. First, CYP1B1 functions as the dominant causal gene across both primary congenital glaucoma (PCG) and juvenile-onset open-angle glaucoma (JOAG), accounting for 76–86% of cases, with two founder alleles, p.G61E (penetrance 87.7%) and p.R469W (penetrance 93%), driving severe, early-onset phenotypes. Critically, MYOC and LTBP2, the primary JOAG genes in other populations, carry no pathogenic variants in Saudi cohorts, rendering standard multi-ethnic gene panels inadequate for this population. Second, adult-onset glaucoma follows a distinct polygenic architecture where APOE ε2 confers a near five-fold risk for primary angle-closure glaucoma (OR = 4.82), an effect absent or inconsistent in global datasets, and NOS3 variants associate with primary open-angle glaucoma specifically in men, a sex-stratified signal unreported outside Saudi cohorts. The MTHFR T/T genotype, common in European and Asian POAG patients, is entirely absent locally, indicating population-specific allelic distributions that alter folate-metabolism-related optic nerve susceptibility. Third, ACVR1 rs12997 associates across POAG, PACG, and pseudoexfoliation glaucoma (PXG), positioning BMP/TGF-β signaling as a shared mechanistic pathway spanning multiple subtypes. These findings argue for Saudi-specific genetic panels, CYP1B1-centered cascade testing in consanguineous families, and polygenic risk models incorporating local allele frequencies rather than globally derived weights. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
18 pages, 6980 KB  
Article
Understanding the Chemosensory and Detoxification Mechanisms in the Oriental Fruit Fly, Bactrocera dorsalis
by Saleem Jaffar and Yongyue Lu
Insects 2026, 17(4), 416; https://doi.org/10.3390/insects17040416 - 14 Apr 2026
Viewed by 460
Abstract
Bactrocera dorsalis (Hendel) is a major fruit-feeding pest that poses a severe and persistent threat to the horticulture industry in tropical and subtropical regions. Methyl eugenol (ME) is a powerful male-specific attractant phytochemical and pheromone precursor that has been widely exploited in lure-and-kill [...] Read more.
Bactrocera dorsalis (Hendel) is a major fruit-feeding pest that poses a severe and persistent threat to the horticulture industry in tropical and subtropical regions. Methyl eugenol (ME) is a powerful male-specific attractant phytochemical and pheromone precursor that has been widely exploited in lure-and-kill pest management programs. Upon ingestion, ME is metabolized (E)-coniferyl alcohol (E-CF) and 2-allyl-4,5-dimethoxyphenol (DMP), which are stored in the male rectal glands and released during courtship to attract females. Despite its ecological significance, the fundamental molecular mechanism underlying ME perception remains poorly understood. Here, we performed a comparative transcriptomic analysis of ME-responsive and ME-non-responsive male B. dorsalis across four tissues (head, gut, midleg, and wing). A total of 15,727 genes were annotated, of which 970 were associated with odorant-binding proteins (OBPs), odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), and chemosensory proteins (CSPs), as well as detoxification families comprising cytochrome P450s (CYPs), carboxylesterases (CaEs), glutathione S-transferases (GSTs), and uridine diphosphate (UDP)-glycosyltransferases (UGTs), and the stress-related heat shock proteins (HSPs) genes. Differential expression analysis identified 7222, 7763, and 6105 differentially expressed genes (DEGs) in the head, gut, and wings/midlegs, respectively, between ME-responsive and ME-non-responsive males. Notably, CYPs, UGTs, and HSPs involved in detoxification and stress response were significantly downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that CYPs were significantly enriched in metabolic detoxification pathways. These findings reveal a complex molecular interplay between olfaction and detoxification and suggest that ME induces coordinated genetic pathways supporting survival, reproduction, and environmental adaptability. This knowledge provides a foundation for the development of eco-friendly pest management strategies targeting these molecular mechanisms. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
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31 pages, 4910 KB  
Article
Multi-Omics Reveals Light-Quality-Dependent Phytohormone and Transcription Factor Networks Regulating Flavonoid Biosynthesis in Ludisia discolor
by Mingyue Qiu, Yuman Shi, Tiankai Shen, Kunxiu Cai, Luan Li, Xiaoyue Qiu, Tao Zheng and Ying Chen
Genes 2026, 17(4), 445; https://doi.org/10.3390/genes17040445 - 13 Apr 2026
Viewed by 397
Abstract
Background/Objectives: Ludisia discolor, an endangered medicinal orchid, is a vital source of bioactive flavonoids which requires in vitro tissue culture for propagation and metabolite production. While light quality influences metabolic processes, the mechanisms connecting light conditions, phytohormone signaling, and flavonoid biosynthesis [...] Read more.
Background/Objectives: Ludisia discolor, an endangered medicinal orchid, is a vital source of bioactive flavonoids which requires in vitro tissue culture for propagation and metabolite production. While light quality influences metabolic processes, the mechanisms connecting light conditions, phytohormone signaling, and flavonoid biosynthesis remain unclear. This study investigates how specific light qualities trigger secondary metabolism to improve tissue culture and conservation strategies. Methods: L. discolor was cultivated under strictly regulated LED environments (blue, red, yellow, and green). An integrated multi-omics approach, combining transcriptomic sequencing and targeted metabolomic profiling, was employed to analyze leaves, correlating plant hormone changes with flavonoid metabolite levels. Results: LED light qualities significantly altered flavonoid and phytohormone profiles, yielding 80 unique flavonoids. Blue and red light effectively promoted flavonoid accumulation, whereas yellow light suppressed it. Transcriptomics, validated by qRT-PCR, revealed distinct expression patterns in key structural genes (e.g., 4CL, PAL, CYP73A, FLS, CCoAOMT, C12RT1). Ten transcription factors (including MYB93, bZIP36, bHLH4, and bZIP44) with hormone-responsive cis-elements were co-expressed with 16 structural genes. Notably, blue light induced reactive oxygen species (ROS) signaling, activating phytohormone production (IAA, GA, ABA). These hormones subsequently stimulated transcription factors, increasing the biosynthesis of compounds like neohesperidin and hesperetin. Conclusions: We propose a novel regulatory model where light-induced ROS and phytohormone cascades activate specific transcription factors, enhancing structural gene expression in the flavonoid pathway. These findings elucidate the molecular mechanisms of light-driven secondary metabolism, providing valuable insights for the sustainable agriculture and ex situ conservation of endangered medicinal orchids. Full article
(This article belongs to the Special Issue Abiotic Stress in Plant: Molecular Genetics and Genomics)
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29 pages, 19236 KB  
Article
Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Responses to Ammonia Stress in the Gills of Litopenaeus vannamei Under Low-Salinity Conditions
by Yutong Zhao, Yangyang Ding, Falin Zhou, Xiaojuan Hu, Qibin Yang and Yucheng Cao
Biology 2026, 15(8), 612; https://doi.org/10.3390/biology15080612 - 13 Apr 2026
Viewed by 321
Abstract
High ammonia nitrogen stress significantly compromises the survival of Litopenaeus vannamei under low-salinity conditions. However, existing studies predominantly focus on ammonia nitrogen responses under single stressors or normal seawater salinity. The molecular regulatory mechanisms, metabolic remodeling patterns, and key pathway interactions in shrimp [...] Read more.
High ammonia nitrogen stress significantly compromises the survival of Litopenaeus vannamei under low-salinity conditions. However, existing studies predominantly focus on ammonia nitrogen responses under single stressors or normal seawater salinity. The molecular regulatory mechanisms, metabolic remodeling patterns, and key pathway interactions in shrimp subjected to high ammonia nitrogen stress under low-salinity environment remain unclear. In this study, we employed integrated transcriptomic and metabolomic analyses to unveil the underlying molecular responses and metabolic biomarkers in the gills of L. vannamei to ammonia stress under low-salinity conditions. First, L. vannamei underwent low-salinity acclimation from 30‰ to 5‰ salinity and was then reared for one week to acclimate to the experimental environment. Subsequently, shrimp were treated with 42.32 mg/L ammonia nitrogen for a consecutive 96 h period. Integrated transcriptomic and metabolomic analyses elucidated the stress response patterns in the gills of L. vannamei under low-salinity ammonia nitrogen exposure. Specifically, 352, 802, and 140 differentially expressed genes (DEGs) were identified at 12 h, 48 h, and 96 h post-exposure, respectively. GO and KEGG enrichment analyses revealed that the significant DEGs were primarily enriched in six major pathways: autophagy, immune-related pathway, ABC transporter, fatty acid degradation and metabolism, metabolic pathway, and PPAR signaling pathway. Metabolomic profiling identified numerous differentially accumulated metabolites (DAMs) in both positive and negative ion modes, with significantly altered DAMs mainly consisting of organic acids and their derivatives, phospholipids, and other related metabolites. Key DAMs included taurine, guanosine, 1-palmitoyl-sn-glycero-3-phosphocholine, pseudouridine, and betaine. Integrative multi-omics analysis revealed that L. vannamei mediates stress responses by modulating five core pathways under low-salinity/high-ammonia-nitrogen dual stress: fatty acid degradation and metabolism (e.g., acyl-CoA dehydrogenase short chain (Acads), acetyl-CoA acetyltransferase 2 (ACAT2)), autophagy (e.g., autophagy-related protein 101-like (atg101)), immune regulation pathway (e.g., V-type proton ATPase subunit H-like (VhaSFD), actin-5C-like (Act5C)), metabolic pathway (e.g., molybdopterin synthase catalytic subunit-like (Mocs2B), cytochrome P450 2U1-like (Cyp2b1)), and ABC transporter (e.g., ATP-binding cassette sub-family D member 3-like (ABCD3), ATP-binding cassette sub-family B member 10 (ABCB10)). Through characterization of these core pathways, this study reveals the fundamental mechanisms by which L. vannamei responds to high ammonia nitrogen stress following low-salinity acclimation, providing a theoretical foundation for estuarine shrimp farming. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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Article
Insights into the Interactions of Microalgae and Combined Macrolide Antibiotics: Removal Efficiency, Physiological–Biochemical Responses and Transcriptomic Analysis
by Ting Guan, Junzhuang Wu, Guoxin Tang, Feifan Wu, Wei Gao, Shuhan Ren and Wei Li
Plants 2026, 15(7), 1128; https://doi.org/10.3390/plants15071128 - 7 Apr 2026
Viewed by 493
Abstract
The widespread occurrence of macrolide antibiotics (MLs) in aquatic environments poses potential ecological risks; however, the interactive effects of MLs, especially combined MLs on microalgae and their removal mechanisms, remain poorly understood. This study investigated the removal efficiency, physiological–biochemical responses, and molecular mechanisms [...] Read more.
The widespread occurrence of macrolide antibiotics (MLs) in aquatic environments poses potential ecological risks; however, the interactive effects of MLs, especially combined MLs on microalgae and their removal mechanisms, remain poorly understood. This study investigated the removal efficiency, physiological–biochemical responses, and molecular mechanisms of Chlorella pyrenoidosa under single and combined exposure to erythromycin (ERY) and roxithromycin (ROX) over 14 days. The results demonstrated that antibiotic removal efficiency was concentration-dependent and higher in low-concentration treatment. The removal rates of ERY (0.15 mg/L) and ROX (0.02 mg/L) reached 100% and 66.86%, respectively. Notably, in the combined low-concentration group, the presence of ROX promoted the degradation of ERY, with the removal being 11.06–14.77% higher than in single treatment. Conversely, in high-concentration combined treatments (1.63 mg/L ERY + 0.5 mg/L ROX), the removal of ERY was inhibited and the removal of ROX was comparable with the corresponding single treatment. High-concentration treatment groups and combined-treatment groups significantly inhibited microalgae growth and total chlorophyll content, modified the chlorophyll composition, and induced severe oxidative stress. Correlation analysis revealed that antibiotic removal was positively correlated with cell density, chlorophyll content, CAT, CYP450, and GST activities while negatively correlated with SOD, ROS, and MDA. Transcriptomic analysis revealed significant disruption of xenobiotic metabolism pathways, photosynthesis-related processes, and DNA replication/mismatch repair pathways. Key genes involved in stress signaling (e.g., MKK3, MPK3), detoxification (e.g., CYP97, GSTP), and photosynthesis (e.g., HemL) were differentially regulated, providing molecular evidence for the observed physiological responses and removal behaviors. These findings provide valuable insights for the ecological risk assessment of antibiotic mixtures and the development of microalgae-based wastewater treatment technologies. Full article
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