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29 pages, 5971 KB  
Article
Comprehensive Analysis of 122 Guinea Fowl Genomes Across Three Continents Delineates Their Domestication and Evolutionary Patterns with Special Reference to India
by Simmi Tomar, Sheikh Firdous Ahmad, Munish Gangwar, Manoharan Azhaguraja, Alisha Kush, Abha Trivedi, Ravi Kumar Gandham and Ashok Kumar Tiwari
Int. J. Mol. Sci. 2026, 27(7), 2994; https://doi.org/10.3390/ijms27072994 - 25 Mar 2026
Viewed by 712
Abstract
The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and [...] Read more.
The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and understand the evolutionary dynamics of guinea fowl populations (wild and domestic) across three continents, utilizing whole-genome sequencing data from 122 genomes. The population structure analyses (ADMIXTURE, PCA, phylogeny, FST, LD, and MAF) revealed that Indian guinea fowl (CARI) shared close ancestry with Iranian (IRAD) and Chinese (CHID) domesticated populations while remaining distinct from wild lineages. The runs of homozygosity (ROH) identified 49,088 segments, with short fragments (ROHs) preponderant in Indian and domestic populations, reflecting historical inbreeding and effects of domestication cum selection. Copy number variation (CNV) analysis revealed 105,178 CNVs concatenated into 40,067 CNV regions (CNVRs) across 11 populations, establishing the first CNV atlas for guinea fowl at the global level. Gene annotation of overlapping ROH and CNVRs revealed 1080 common candidates across Asian guinea fowl populations, i.e., the Indian guinea fowl (CARI), IRAD, and CHID, including FOS, EPAS1, CD74, and CSF1R. These genes have earlier been associated with immune regulation, stress response, and thermal adaptation. Selection signature scans, integrating intra-population (iHS) and inter-population (XP-EHH) approaches, uncovered genes under positive selection linked to immune response (like BCL11B, IL18, and GPC3), thermo-tolerance (like TRPV4 and BAG3), lipid metabolism (like AACS and ELOVL4), and pigmentation (BCO2). These signatures highlight the molecular basis of resilience in guinea fowl and their potential to withstand climate-induced stresses. This study presents the first global CNV atlas for guinea fowl and provides the first comprehensive genomic characterization of the Indian domestic population, integrating ROH, CNV, and selection signature analyses. It offers a comprehensive assessment of guinea fowl genomes (wild and domesticated) across three continents, offering insights into domestication, evolutionary dynamics, and the genetic basis of their adaptation and resilience. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 2790 KB  
Article
Transcriptomic Analysis of High and Low Lipid Droplet Deposition Subpopulations of Chicken Preadipocytes Based on SSC Sorting
by Boyu Wang, Yantao Li, Yake Wang, Jiayi Chen, Jiali Wang, Xiaoping Li and Zhenhui Li
Animals 2026, 16(6), 885; https://doi.org/10.3390/ani16060885 - 12 Mar 2026
Viewed by 583
Abstract
Fat deposition plays a crucial role in regulating the production performance and meat quality of broilers. Although the heterogeneity of mammalian adipocytes has been extensively studied, research on the molecular mechanisms underlying differences in lipid droplet accumulation in avian adipocytes remains limited. This [...] Read more.
Fat deposition plays a crucial role in regulating the production performance and meat quality of broilers. Although the heterogeneity of mammalian adipocytes has been extensively studied, research on the molecular mechanisms underlying differences in lipid droplet accumulation in avian adipocytes remains limited. This study confirmed a significant positive correlation (R2 > 0.81, p < 0.001) between the SSC signal and lipid droplet content via fluorescence staining of lipid droplets, Oil Red O staining, and triglyceride (TG) quantification. Based on this, a label-free sorting strategy using SSC signals was established to sort differentiated chicken preadipocytes, obtaining high lipid droplet (H) and low lipid droplet (L) subpopulations, which were subsequently subjected to transcriptome sequencing and differential gene expression (DEG) analysis, followed by GO and KEGG enrichment analysis. The results indicated no significant differences in the expression of adipogenesis marker genes (PPARG, LPL, CD36, PLIN1, PLIN2) between the high lipid droplet (H) and low lipid droplet (L) groups, suggesting that both groups are at similar stages of differentiation. KEGG analysis revealed that both the H vs. NC and L vs. NC comparisons were enriched in common pathways, including the PPAR signaling pathway, ECM–receptor interaction, focal adhesion, cytokine–receptor interaction, and calcium–Apelin signaling pathway, suggesting that both groups of cells had activated the adipogenesis program. GO analysis showed that, in both H vs. NC and L vs. NC comparisons, differentially expressed genes (DEGs) were enriched in biological processes (BPs) related to cell adhesion, nucleosome assembly, chromatin remodeling, and receptor activity, as well as cellular components (CCs) such as the extracellular matrix, cytoskeleton, and nucleosome organization, indicating extensive gene reprogramming and activation of signaling transduction during differentiation. In the H vs. L comparison, enriched pathways included ABC transporters, ECM–receptor interaction, focal adhesion, gap junctions, microtubule-related processes, and neuroactive ligand–receptor interactions, involving lipid transmembrane transport, cytoskeleton stabilization, and signal transduction regulation, suggesting that high lipid droplet cells are more mature in lipid droplet transport, storage, and homeostasis maintenance. GO enrichment results further supported this conclusion, as H vs. L specifically enriched processes related to microtubule-related processes, cell cycle, and redox reactions (BPs), as well as chromosome organization, cytoskeleton, and motor activity (CC/MF), indicating that high lipid droplet cells maintain lipid droplet fusion and metabolic homeostasis via enhanced microtubule transport and antioxidant regulation. Differential gene analysis revealed that the L group upregulated genes associated with fatty acid synthesis and elongation (ACACA, FASN, SCD, FADS2, ELOVL1), cholesterol and isoprenoid biosynthesis (HMGCR, SQLE, MSMO1, DHCR7, DHCR24, FDPS, LSS), and fatty acid oxidation (PPARA, PPARD, ACAD11, SIRT5), reflecting a metabolic characteristic of concurrent lipid synthesis and mobilization; the H group, conversely, upregulated genes associated with lipid droplet formation and storage (G0S2, MOGAT1, GPAT4, PLIN4, AUP1), lipid transport (ABCA1, ABCA2, ABCG1, OSBPL3, VLDLR), and antioxidant defense (GPX3, GPX4, HMOX1), exhibiting a storage and homeostasis-oriented metabolic state. In the NC, L, and H groups, the expression of five genes—GEM, SPP1, ABCA1, PDLIM3, and ITGA8—showed a gradual increase, suggesting that these genes were associated with preadipocyte differentiation and lipid droplet deposition. In summary, although the high and low lipid droplet subpopulations of chicken preadipocytes exhibit similar differentiation states, they form distinct metabolic orientations. The L group is characterized by active lipid synthesis, fatty acid oxidation, and membrane lipid remodeling, while the H group predominantly features lipid droplet storage, lipid transport, and antioxidant homeostasis. This study highlights the molecular mechanisms underlying the metabolic heterogeneity of avian adipocytes and provides a theoretical basis for poultry fat deposition regulation and genetic improvement. Full article
(This article belongs to the Section Poultry)
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14 pages, 401 KB  
Article
Use of Epigenetic Markers to Predict Age and Smoking Status in an Italian Population Sample
by Domenico Colloca, Matteo Manfredini, Fabiano Gentile, Alberto Marino, Maria Carla Gerra and Cristina Dallabona
Forensic Sci. 2026, 6(1), 20; https://doi.org/10.3390/forensicsci6010020 - 19 Feb 2026
Viewed by 552
Abstract
Background/Objectives: DNA profiling in forensic investigation typically compares genetic profiles, usually derived from the analysis of STR markers. However, this method has limitations when there is no biological reference sample or match in the DNA database. The aim of the current study [...] Read more.
Background/Objectives: DNA profiling in forensic investigation typically compares genetic profiles, usually derived from the analysis of STR markers. However, this method has limitations when there is no biological reference sample or match in the DNA database. The aim of the current study is thus to replicate, in an Italian cohort, epigenetic markers previously identified in the literature for distinguishing tobacco smokers from non-smokers or estimating chronological age, so as to help narrow down the pool of suspects. Methods: DNA methylation at four CpG dinucleotides located around the cg05575921 site of the AHRR gene, widely associated with tobacco consumption, was measured. Additionally, five CpG dinucleotides in the ELOVL2, FHL2, KLF14, TRIM59, and C1orf132 genes were examined for chronological age estimation in buccal swab samples of 102 volunteers through pyrosequencing. Results: A multiple linear regression model for estimating chronological age shows that ELOVL2-C7, C1orf132-C1, and TRIM59-C7 have a significant effect on age. In this model, the prediction error increases with age. Two logistic regression models were used for determining smoker/non-smoker status, proving that two CpG sites significantly influence the odds of being classified as a smoker. When ex-smokers are included in the non-smoking group, the model correctly classifies the two conditions in about 80% of cases. Conclusions: The results demonstrate that the models generated from pyrosequencing data are useful for identifying tobacco smokers and estimating an individual’s chronological age, particularly for younger subjects. Further studies are needed to develop models with higher predictive accuracy and to integrate these tools into regular forensic practice. Full article
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17 pages, 1104 KB  
Review
Multi-Target Strategies for Enhancing Ceramide Production: A Review of Bioactive Ingredients in Cosmetic Science
by Jihye Maeng, Sekyoo Jeong, Hyunjung Kim and Gaewon Nam
Cosmetics 2026, 13(1), 8; https://doi.org/10.3390/cosmetics13010008 - 1 Jan 2026
Viewed by 2111
Abstract
Ceramides are central to stratum corneum barrier organization and hydration. Beyond topical replenishment, ceramide-stimulating strategies increasingly aim to enhance endogenous ceramide biosynthesis, processing, and homeostatic remodeling in coordination with keratinocyte differentiation. In this review, we summarize the three major metabolic routes that shape [...] Read more.
Ceramides are central to stratum corneum barrier organization and hydration. Beyond topical replenishment, ceramide-stimulating strategies increasingly aim to enhance endogenous ceramide biosynthesis, processing, and homeostatic remodeling in coordination with keratinocyte differentiation. In this review, we summarize the three major metabolic routes that shape epidermal ceramide output—de novo synthesis, salvage, and sphingomyelin hydrolysis—and organize representative bioactive ingredients by their primary molecular targets rather than by origin. Specifically, we map ingredients to tractable regulatory nodes, including transcriptional “liposensors” (PPAR/LXR), the induction of biosynthetic/elongation and processing enzymes (e.g., SPT, CerS3, ELOVL4), the provision of structural substrates and precursors (e.g., linoleate-rich lipids and glycosylceramides), salvage-pathway sphingoid bases that can reshape ceramide subclass output, and metabolic sensing/stress-response pathways centered on AMPK–mTOR–SIRT1/autophagy. Across these mechanisms, agents spanning botanical and fermented extracts, vitamins, sphingoid intermediates, lipid precursors, and pathway modulators (including autophagy-focused probes) have been reported to increase ceramide abundance and, in some contexts, favor barrier-relevant ultra-long-chain species and ω-O-acylceramides that support lamellar organization and the corneocyte lipid envelope. Translational and clinical studies in dry, sensitive, and aged skin generally associate such interventions with improved barrier function and reduced dryness. Aligning ingredient selection with defined biosynthetic and processing checkpoints—and verifying outcomes with lipidomics alongside clinical endpoints—may accelerate the development of evidence-based, ceramide-stimulating cosmetics. Full article
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23 pages, 6560 KB  
Article
Cross-Species Transcriptomic and Metabolomic Analysis Reveals Conserved and Divergent Fatty Acid Metabolic Regulatory Strategies During Mammalian Oocyte Maturation
by Mostafa Elashry, Yassin Kassim, Bingjie Hu, Hao Sheng, Guangjun Xu, Hagar Elashry and Kun Zhang
Int. J. Mol. Sci. 2026, 27(1), 397; https://doi.org/10.3390/ijms27010397 - 30 Dec 2025
Cited by 1 | Viewed by 1747
Abstract
Mammalian oocyte maturation is a metabolically demanding process relying on lipid metabolism that supplies energy, structural substrates, and signaling mediators. However, a comprehensive cross-species understanding of the dynamic requirement for lipids during this process remains elusive, hindering the optimization of assisted reproductive technologies. [...] Read more.
Mammalian oocyte maturation is a metabolically demanding process relying on lipid metabolism that supplies energy, structural substrates, and signaling mediators. However, a comprehensive cross-species understanding of the dynamic requirement for lipids during this process remains elusive, hindering the optimization of assisted reproductive technologies. Utilizing an integrated single-cell transcriptomic and targeted lipidomic approach, we mapped the metabolic landscape of bovine oocyte maturation. Our analysis uncovered a global transcriptional downregulation, with 3259 genes suppressed during the transition from the germinal vesicle (GV) to the metaphase II (MII) stage. This was particularly apparent in lipid catabolism pathways (e.g., for ACAA1), while mitochondrial energy production genes (ATP6) were upregulated. Lipidomics indicated a selective depletion of saturated fatty acids (SFAs; e.g., C16:0, C18:0) in MII oocytes, while monounsaturated (MUFAs) and polyunsaturated fatty acids (PUFAs) were preferentially retained. Integrated network analysis specified hexadecanoic acid (C16:0) as a central metabolic hub, which rewires its interactions from biosynthetic genes (FASN, ELOVL6) in GV oocytes to degradative enzymes (ACADVL, HADH) in MII oocytes. Expanding to a cross-species transcriptomic atlas, we identified a core set of 59 lipid metabolism genes conserved across bovine, mouse, and human oocytes. Despite this conservation, we discovered stark species-specific regulatory strategies: bovine and human oocytes significantly downregulated fatty acid degradation and elongation post-maturation, whereas murine oocytes maintain pathway activity, upregulating key regulators like Acsl3. Our work unveils an evolutionarily conserved core lipid metabolic program in mammalian oocytes that is adaptively tuned to meet species-specific physiological demands. Bovine and human oocytes prioritize catabolic flexibility, using SFAs for energy, while mouse oocytes maintain their anabolic capacity for membrane biosynthesis. These findings provide a transformative resource for the field, offering biomarkers for oocyte quality and a rationale for enhancing species-tailored lipid formulations to develop in vitro maturation systems and amend reproductive outcomes in both agriculture and medicine. Full article
(This article belongs to the Section Molecular Biology)
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15 pages, 1746 KB  
Article
Gene-Polymorphism Effects on Growth Efficiency in the Kalmyk Breed of Central Asia
by Nurlybay Kazhgaliyev, Kaster Nurgulsim, Miras Gabbassov, Aizhan Makhanbetova, Assylbek Zhanabayev, Ascar Terlikbayev, Tolegen Assanbayev, Maxat Toishimanov and Tlekbol Sharapatov
Genes 2026, 17(1), 1; https://doi.org/10.3390/genes17010001 - 19 Dec 2025
Viewed by 780
Abstract
Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in [...] Read more.
Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in the CRTC2 and ELOVL6 genes on intramuscular fat content and to evaluate their associations with growth and meat quality traits in 18-month-old Kalmyk heifers raised under different environmental conditions. Methods: A total of 400 clinically healthy Kalmyk heifers (200 from LLP “Qazaq Asyldary” and 200 from LLP “Agrofirma Turikpen”) were examined. All animals originated from closed breeding herds, and only unrelated individuals without common ancestors to the third generation were included. Zootechnical measurements— live weight, withers height, chest depth, chest girth, and body length—were performed twice by a trained specialist. Backfat thickness and musculus longissimus dorsi depth were measured postmortem. Blood samples were collected for genomic DNA extraction using the GeneJET purification kit, and DNA quality was assessed by Nanodrop, Qubit, and agarose gel electrophoresis. Target fragments of CRTC2 and ELOVL6 were amplified (150–200 bp) and sequenced on an ABI 3500 system. SNP identification, allele frequencies, and genotyping were performed by alignment to the Bos taurus ARS-UCD1.2 reference genome. Statistical analyses were conducted in RStudio using linear and mixed models with “farm” as a random effect. Results: Only one informative polymorphism, g.133528A>G in ELOVL6, was detected. Three genotypes (AA, AG, GG) were observed, with the heterozygous AG genotype showing significantly higher live weight, greater body length, and improved linear measurements compared to AA and GG. No significant associations were detected with backfat thickness or muscle depth. The g.133528A>G polymorphism in ELOVL6 positively influences growth traits without increasing fatness, aligning with the naturally lean phenotype of Kalmyk cattle. Conclusions: The AG genotype may serve as a promising marker for selecting faster-growing animals in marker-assisted breeding programs. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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30 pages, 6956 KB  
Article
Hepatoprotective, Antioxidant, and Anti-Hyperlipidemic Effects of Kefir Milk in High-Fat Diet-Induced Obesity: Insights from Gas Chromatography-Mass Spectrometry Profiling, Molecular Docking of Kefiran, and Liver Function Restoration
by Imen Hammami, Sonia Ben Younes, Ridha Ben Ali, Fatma Arrari, Afef Nahdi, Michèle Véronique El May, Rym Baati, Eduardo Alberto López-Maldonado and Abada Mhamdi
Antioxidants 2025, 14(12), 1500; https://doi.org/10.3390/antiox14121500 - 14 Dec 2025
Viewed by 1629
Abstract
The prevalence of chronic diseases, including obesity and related endocrine disorders, has risen significantly in recent decades. As a result, there has been growing interest in fermented foods with probiotic properties, such as kefir, which have potential health benefits. This study aimed to [...] Read more.
The prevalence of chronic diseases, including obesity and related endocrine disorders, has risen significantly in recent decades. As a result, there has been growing interest in fermented foods with probiotic properties, such as kefir, which have potential health benefits. This study aimed to evaluate the hepatoprotective and antioxidant effects of kefir milk (KM) in a high-fat diet (HFD)-induced obesity rat model, complemented by in silico molecular docking studies with antioxidant enzymes. Twenty-four adult rats were divided into four groups: control (1 mL/100 g bw semi-skimmed cow milk), KM (1 mL/100 g bw kefir milk), HFD (1 mL/100 g bw semi-skimmed cow milk + high-fat diet), and KM/HFD (1 mL/100 g bw kefir milk + high-fat diet). After 60 days of treatment, biochemical assays and histological examinations were performed to assess the effects on lipid profiles and organ health. Kefir milk demonstrated significant antioxidant activity, with increased total phenolic content and enhanced DPPH, ABTS, and FRAP radical scavenging activities compared to commercial milk. Furthermore, KM administration protected against liver metabolic disruptions (ALT, AST, and LDH) induced by the high-fat diet and reduced lipid peroxidation in liver and testis tissues. KM supplementation also increased the activity of key antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). Additionally, KM improved the fatty acid composition and decreased the de novo lipogenesis (DNL) index, as well as enzyme activities (SCD and Elovl6) associated with the high-fat diet. Histological analysis of liver, pancreas, and heart tissues revealed that kefir milk attenuated structural damage caused by the high-fat diet, suggesting its protective role in oxidative stress regulation and organ function. These findings underscore the potential of kefir milk as a functional food for preventing metabolic disturbances and liver damage associated with obesity. Full article
(This article belongs to the Special Issue Phenolic Antioxidants in Functional Foods and Nutraceuticals)
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18 pages, 6370 KB  
Article
Molecular Mechanisms Underlying Divergent Biochemical Compositions in Longissimus Dorsi of Huainan and Yunan Black Pigs: Insights from Fatty Acids, Amino Acids, and Transcriptomic Profiling
by Yuliang Wen, Chengshui Liao, Ruibiao Wang, Bo Wen, Weiyu Luo, Wei Zhang, Chunling Zhu, Huarun Sun, Longfei Zhang, Xuehan Liu, Jiyuan Shen, Yuping Xiang, Hao Li, Jianhe Hu, Yueyu Bai, Ke Ding and Lei Wang
Agriculture 2025, 15(24), 2532; https://doi.org/10.3390/agriculture15242532 - 6 Dec 2025
Viewed by 724
Abstract
This study investigated meat quality, nutritional characteristics, and transcriptomic regulation in Yunan (YN) black pigs and Huainan (HN) black pigs (n = 6 each). Analysis of fatty acid composition revealed that HN black pigs possessed significantly higher levels of most fatty acids compared [...] Read more.
This study investigated meat quality, nutritional characteristics, and transcriptomic regulation in Yunan (YN) black pigs and Huainan (HN) black pigs (n = 6 each). Analysis of fatty acid composition revealed that HN black pigs possessed significantly higher levels of most fatty acids compared to YN black pigs. Notably, the contents of monounsaturated fatty acid C18:1n9c and polyunsaturated fatty acid C18:2n6c in HN black pigs were 1.94-fold and 2.65-fold higher, respectively, than those in YN black pigs. The α-linolenic acid content was also significantly elevated in HN black pigs, indicating an overall higher fatty acid content. Regarding amino acid differences, HN black pigs exhibited significantly higher levels of aspartic acid, glutamic acid, histidine, as well as superior composition of total amino acids, total umami amino acids, and essential amino acids, which contribute to enhanced flavor characteristics and nutritional balance. Transcriptome analysis identified 526 differentially expressed genes in HN vs. YN. KEGG enrichment analysis showed that these genes were involved in many adipogenesis and lipid metabolism signaling pathways, such as biosynthesis of unsaturated fatty acids, fatty acid elongation, apelin signaling pathway and lysine degradation. By integrating transcriptome and protein–protein interaction (PPI) network analyses, we identified key meat quality-related genes: ELOVL6, PRKAG3, ROCK2, and MYH11. miRNA profiling identified ssc-miR-133b, ssc-miR-206, and miR-205 as key regulators of meat quality. This study provides a valuable theoretical foundation for understanding the molecular mechanisms underlying pork quality and offers insights for its future improvement. Full article
(This article belongs to the Section Farm Animal Production)
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19 pages, 16657 KB  
Article
Integrated Transcriptomic and Metabolomic Analysis of the Mechanism of Intramuscular Fat Differences in Wandong Cattle
by Fenglou He, Han Liu, Yakun Yao, Zhanhong Qiao, Xinye Li, Chao Chen, Xiaokang Lv, Ke Ji and Jinling Hua
Int. J. Mol. Sci. 2025, 26(23), 11557; https://doi.org/10.3390/ijms262311557 - 28 Nov 2025
Cited by 1 | Viewed by 953
Abstract
This study aimed to collaboratively investigate the mechanism of variations in intramuscular fat (IMF) content in Wandong cattle using transcriptomics and metabolomics techniques. Longissimus dorsi (LD) muscle samples were collected from thirteen free-range Wandong cattle in Fengyang County, Anhui Province, China. From this [...] Read more.
This study aimed to collaboratively investigate the mechanism of variations in intramuscular fat (IMF) content in Wandong cattle using transcriptomics and metabolomics techniques. Longissimus dorsi (LD) muscle samples were collected from thirteen free-range Wandong cattle in Fengyang County, Anhui Province, China. From this initial cohort, eight animals closely matched in age and body weight were selected. Based on IMF content measured by Soxhlet extraction, these eight cattle were divided into two groups: the high-IMF (HF, n = 4) and low-IMF (LF, n = 4) groups. Subsequent analyses were performed on integrated datasets comprising the transcriptome, metabolome, and fatty acid profile. The results revealed a significant increase in IMF in the HF group compared to the LF group (p < 0.05). Specifically, α-linolenic acid (C18:3n3) and γ-linolenic acid (C18:3n6) were significantly more abundant in the LF group compared to the HF group (p < 0.05), whereas oleic acid (C18:1n9c) and cis-9-palmitoleic acid (C16:1) predominated in the HF group. However, saturated fatty acids (SFAs), such as myristic acid (C14:0), palmitic acid (C16:0), stearic acid (C18:0), and Margaric acid (C17:0), did not show significant differences (p > 0.05). A total of 9164 differentially expressed genes (DEGs) were identified via transcriptome analysis, with 2202 genes upregulated and 6962 genes downregulated in the HF group compared to the LF group. The expression profiles exhibited a distinct pattern, characterized by the upregulation of genes such as FABP1, SREBF1, and LIPE, while genes including SCD, PPARGC1A, and LEP were downregulated. GO enrichment analysis demonstrated that the majority of DEGs were predominantly abundant across 25 distinct functional categories distributed across the three primary ontologies. KEGG pathway analysis further identified 341 significantly enriched signaling pathways in the HF group (p < 0.05), predominantly involving metabolic pathways, FoxO, AMPK, and PPAR signaling pathways. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics analysis revealed 404 differential accumulated metabolites (DAMs), with 187 in positive ion mode and 217 in negative ion mode (p < 0.05). These DAMs were notably enriched in pathways such as glycerophospholipid metabolism, terpene and steroid biosynthesis, fatty acid degradation, and fatty acid metabolism. Notably, C16:1, C18:1n9c, arachidonic acid (peroxide free) (C20:4n6), oleoyl-L-carnitine, and linoleoyl-carnitine were identified as key players in lipid metabolism. Integrating transcriptomics with metabolomics data unveiled significant associations between DAMs linked to lipid metabolism and DEGs. Specifically, C18:1n9c exhibited a positive correlation with LPIN3, while C16:1 showed negative associations with PPAP2B, PPAP2A, CDS2, HADHA, LPL, HSD17B12, ELOVL5, ACSL1, and ACOX1, and positive correlations with PLA2G15, CDIPT, AGPSBG1, and GPD1. In summary, the variation in IMF content in Wandong cattle is co-regulated by key genes (SREBF1, ACSL1, SCD) via the AMPK, PPAR, and FoxO signaling pathways, coupled with alterations in specific fatty acid metabolites such as C18:1n9c, C16:1, and C20:4n6. These findings provide critical molecular insights for the genetic selection and breeding of Wandong cattle, which are renowned for their superior meat quality. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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26 pages, 7389 KB  
Article
Lipid Composition and Thermotropic Properties of Meibum of Animal Models and Humans with Meibomian Gland Dysfunction
by Igor A. Butovich, Jadwiga C. Wojtowicz, Amber Wilkerson and Seher Yuksel
Int. J. Mol. Sci. 2025, 26(23), 11434; https://doi.org/10.3390/ijms262311434 - 26 Nov 2025
Cited by 1 | Viewed by 1013
Abstract
Meibum—a lipid-rich secretion produced by holocrine Meibomian glands (MG)—plays a central role in maintaining ocular surface homeostasis in humans. Previously, changes in MG lipidomes induced by inactivation of critical genes of meibogenesis, such as Elovl3, Soat1, Awat2, Sdr16c5/Sdr16c6, and [...] Read more.
Meibum—a lipid-rich secretion produced by holocrine Meibomian glands (MG)—plays a central role in maintaining ocular surface homeostasis in humans. Previously, changes in MG lipidomes induced by inactivation of critical genes of meibogenesis, such as Elovl3, Soat1, Awat2, Sdr16c5/Sdr16c6, and others were shown to cause MG dysfunction (MGD) and dry eye in experimental animals. Here, we describe the impact of the changes in the lipid composition of meibum on its protective properties, specifically physiologically relevant thermotropic characteristics, using various mutant and wild-type animal models, and comparing them with healthy human subjects and patients with MGD. Meibum samples were analyzed using liquid chromatography/mass spectrometry (LC/MS) and differential scanning microcalorimetry (DSC). We found that any change in the balance between major lipid classes in meibum—wax esters, cholesteryl esters, triacylglycerols, and free cholesterol—cause detrimental changes in its thermotropic properties, loss of cohesiveness, and abnormal expressibility from MG, resulting in MGD-like phenotypes of the eyes and adnexa. We conclude that tested knockout mice can be valuable models for modeling and studying MGD. A combination of LC/MS and DSC can be a powerful diagnostic tool and may help to diagnose MGD and other pathologies, as well as determine their molecular mechanisms. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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20 pages, 2441 KB  
Article
Magnesium Promotes Growth–Metabolism Balance in Juvenile Largemouth Bass (Micropterus salmoides) and Modulates Antioxidant–Inflammatory–Apoptotic Responses Under Heat Stress
by Junjie Qin, Dongyu Huang, Hualiang Liang, Xiaoru Chen, Jiaze Gu, Mingchun Ren and Lu Zhang
Antioxidants 2025, 14(12), 1394; https://doi.org/10.3390/antiox14121394 - 23 Nov 2025
Cited by 1 | Viewed by 1046
Abstract
This study addressed the optimal magnesium (Mg) requirement for juvenile largemouth bass (Micropterus salmoides) and assessed the effects of dietary Mg supplementation on growth performance, nutrient metabolism, and alleviation of heat stress in it. In this study, six diets with varying [...] Read more.
This study addressed the optimal magnesium (Mg) requirement for juvenile largemouth bass (Micropterus salmoides) and assessed the effects of dietary Mg supplementation on growth performance, nutrient metabolism, and alleviation of heat stress in it. In this study, six diets with varying Mg levels (1.01, 1.26, 1.78, 2.24, 2.35, and 2.51 g/kg), designated as MG1, MG2, MG3, MG4, MG5, and MG6, respectively, were formulated using MgSO4·7H2O as the Mg source. These diets were fed to juvenile M. salmoides (initial body weight 2.27 ± 0.02 g) for 8 weeks. The growth performance of the MG4 group was significantly improved. In addition, Plasma GLU, LDL-C, and TG levels were significantly reduced in the MG4 group, while plasma HDL-C levels were increased. In terms of gene expression, glut2, g6pdh, ppar-γ, fas, elovl2, acc, and igf-1 were significantly upregulated in the MG4 and MG5 groups, while g6pase and ppar-α were significantly downregulated in the MG5 group. In the heat stress test, MG4 group exhibited enhanced antioxidant capacity, as evidenced by decreased plasma MDA levels and increased CAT activity, coupled with enhanced gill Na+/K+-ATPase activity. Gene expression results also showed that il-10 and bcl-2 were significantly upregulated in the MG4 group, while nf-κb, ifn-γ, il-8, tnf-α, casp3, casp8, bax, jnk2 and ask1 were significantly downregulated. Furthermore, the results of TUNEL immunofluorescence labeling analysis showed that the apoptotic index was significantly decreased in the MG2-MG6 groups. Overall, appropriate dietary Mg levels promoted growth performance, improved glucose metabolism, and induced lipid deposition in juvenile M. salmoides. Notably, Mg reduced oxidative damage by enhancing antioxidant enzyme activity, thereby modulating heat stress-induced Antioxidant–Inflammatory–Apoptotic of juvenile M. salmoides. Based on quadratic regression analysis of SGR and FCR, the optimal Mg requirement for juvenile M. salmoides was 2.04, and 2.15 g/kg, respectively. Full article
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16 pages, 17995 KB  
Article
Transcriptome Analysis Reveals Circadian Rhythmic Regulation of Lipid Metabolism and Immune Function in Chicken Livers
by Jiahua Li, Jie Dong, Minjie Huang, Yuting Jin, Xiaodong Tan and Deqian Wang
Animals 2025, 15(22), 3241; https://doi.org/10.3390/ani15223241 - 8 Nov 2025
Cited by 1 | Viewed by 1233
Abstract
Liver rhythm has a significant effect on lipid metabolism and immune function in chickens. However, reports on its underlying mechanisms and key genes are relatively scarce. We collected liver samples at seven time points during one light/dark cycle and investigated the candidate genes [...] Read more.
Liver rhythm has a significant effect on lipid metabolism and immune function in chickens. However, reports on its underlying mechanisms and key genes are relatively scarce. We collected liver samples at seven time points during one light/dark cycle and investigated the candidate genes and pathways related to hepatic rhythm through transcriptomic sequencing. Trend analysis revealed that the expression of genes in Profile 5 exhibited rhythmic fluctuations, and these genes (e.g., FAM21C, SRSF4, and TLR2A) were enriched in immune function and biological rhythm. The genes (e.g., MSMO1, ELOVL2, and HMGCR) in Profile 2 that were related to lipid metabolism also exhibited a rhythmic trend. A total of 845 differentially expressed genes (e.g., MSMO1 and FAM21C) were detected between light/dark conditions. Lipid metabolism and immune functions showed the most changes between the two conditions. Immune-related processes (e.g., autophagy) were more active in the light phase, while in the dark phase, lipid metabolism (e.g., sterol biosynthesis) was more active. Weighted gene coexpression network analysis revealed that the tan (including C1QA, TLR2A, and others) and cyan (including ELOVL2, IARS1, and others) modules were strongly associated with the hepatic circadian rhythm. Cosinor analysis revealed that 9 lipid-related genes (e.g., MSMO1, HMGCR1, and ELOVL2) and 11 immune-related genes (e.g., FAM21C, TLR4, and TLR2A) exhibited significant rhythmic expression. These findings revealed rhythmic changes in hepatic immune and lipid metabolism, providing important insights into the regulation of disease resistance and lipid deposition in chickens. Full article
(This article belongs to the Section Animal Physiology)
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11 pages, 1490 KB  
Article
RNA Signature as Potential Diagnostic Marker for Differentiation of Pancreatic Cysts: A Pilot Study
by Olga Freylikhman, Sabina Seyfedinova, Valeriia Kamalova, Aleksandra Vatian, Alexander Boukhanovsky, Anna Kostareva, Evgenii Solonitsyn and Olga Kalinina
Int. J. Mol. Sci. 2025, 26(19), 9680; https://doi.org/10.3390/ijms26199680 - 4 Oct 2025
Viewed by 1230
Abstract
The accurate classification of pancreatic cystic lesions remains clinically challenging due to overlapping imaging features and variable malignant potential. Mucinous cystic neoplasms, in particular, require early identification given their premalignant nature. RNA profiling presents a promising alternative to current diagnostic limitations—a molecular lens [...] Read more.
The accurate classification of pancreatic cystic lesions remains clinically challenging due to overlapping imaging features and variable malignant potential. Mucinous cystic neoplasms, in particular, require early identification given their premalignant nature. RNA profiling presents a promising alternative to current diagnostic limitations—a molecular lens sharpened by AI-driven pattern recognition. This study aimed to evaluate the diagnostic potential of RNA signatures for differentiating pancreatic cyst subtypes and to clarify their roles in their pathophysiology. The study included 31 patients with pancreatic lesions who underwent endoscopic ultrasound-guided fine-needle aspiration. RNA was extracted from cyst fluid, tissue, and peripheral blood. Expression of 17 target genes was analyzed using qPCR. Gene expression patterns were compared across mucinous cystic neoplasms, serous cystic neoplasms, pseudocysts, adenocarcinoma, and chronic pancreatitis cohorts. Diagnostic accuracy was evaluated via ROC analysis. Mucinous cysts exhibited significant overexpression of MUC1, ITGA2, ELOVL6, and MUC5AC genes compared to serous cysts and pseudocysts. PKM gene expression correlated with increasing malignant potential. In blood plasma, only MUC1, MUC4, and PYGL were elevated in adenocarcinoma compared to mucinous neoplasms. We identified a distinct RNA signature that can distinguish mucinous cystic neoplasms from benign cystic lesions (serous cysts and pseudocysts), which could be useful for guiding patient management and improving clinical outcomes. Validation in broader cohorts is essential for clinical implementation. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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13 pages, 670 KB  
Review
Characteristic Gene Alterations During Fatty Acid Metabolism in the Goose Liver
by Anna Koseniuk
Genes 2025, 16(10), 1137; https://doi.org/10.3390/genes16101137 - 25 Sep 2025
Viewed by 1821
Abstract
The development of hepatic steatosis in geese is a complex, multistage process involving genes related to lipid synthesis, transport, storage, and metabolism. Key genes activated during this process include ME1 (malic enzyme 1), SCD1 (stearoyl-CoA desaturase), ACSL1 (acyl-CoA synthetase long-chain family member 1), [...] Read more.
The development of hepatic steatosis in geese is a complex, multistage process involving genes related to lipid synthesis, transport, storage, and metabolism. Key genes activated during this process include ME1 (malic enzyme 1), SCD1 (stearoyl-CoA desaturase), ACSL1 (acyl-CoA synthetase long-chain family member 1), and ELOVL6 (elongation of very-long-chain fatty acids protein 6). The expression of these genes varies depending on the tissue, breed, and metabolic context. Geese possess a unique ability to develop hepatic steatosis (fatty liver) without accompanying inflammation or liver damage. This condition typically arises from overfeeding, either through carbohydrates or fats, leading to significant triglyceride accumulation in hepatocytes. Importantly, this state remains reversible and is considered non-pathological. The physiological and molecular changes observed in overfed geese, particularly regarding liver lipid accumulation and serum enzyme activity, closely resemble those found in human non-alcoholic fatty liver disease (NAFLD). This similarity makes geese an excellent biomedical model for studying NAFLD. Overfeeding initiates a cascade of enzymatic reactions that regulate lipid metabolism at the genetic level. These reactions decrease circulating free fatty acids and glucose while promoting triglyceride storage in the liver. The aim of this study is to synthesize current knowledge on the genetic regulation of fatty acid metabolism in geese, highlighting how these genes coordinate the processes of activation, desaturation, synthesis, and elongation during induced steatosis. Moreover, the summarized effects of different diet supplements will enhance goose feeding strategies for foie gras production. Full article
(This article belongs to the Special Issue Genetic Breeding of Poultry)
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12 pages, 1214 KB  
Article
Tissue-Specific Differences in Fatty Acid Content and Desaturase Activity Between the Liver and Spinal Cord of Diabetic ZDF Rats
by Katarína Orešanská, Mária Chomová, Janka Kubincová, Ladislav Turecký and Monika Ďurfinová
Biology 2025, 14(9), 1205; https://doi.org/10.3390/biology14091205 - 6 Sep 2025
Viewed by 1047
Abstract
Imbalance in fatty acid (FA) metabolism is a critical factor in the development of type 2 diabetes (T2D). This study examined fatty acid composition and desaturase activities in the liver and spinal cord of male Zucker diabetic fatty (ZDF) rats, a genetic model [...] Read more.
Imbalance in fatty acid (FA) metabolism is a critical factor in the development of type 2 diabetes (T2D). This study examined fatty acid composition and desaturase activities in the liver and spinal cord of male Zucker diabetic fatty (ZDF) rats, a genetic model of T2D. Heterozygous lean ZDF fa/+ animals served as controls, while homozygous obese ZDF fa/fa animals represented the diabetic group. FA profiles were determined by gas chromatography, and the activities of Δ5-desaturase (FADS1), Δ6-desaturase (FADS2), Δ9-desaturase (SCD1), and elongase of very long-chain fatty acids (ELOVL) were estimated. T2D rats displayed significantly elevated levels of monounsaturated fatty acids (MUFAs) and increased SCD1 activity in both the liver and spinal cord. In contrast, polyunsaturated fatty acids (PUFAs), particularly arachidonic acid (AA, C20:4 n-6), were reduced. Since AA plays a fundamental role in neuronal membrane structure and signaling pathways, these alterations have particular relevance to nervous system function. Tissue-specific alterations further suggested impaired FADS1 activity in the liver and reduced elongase/FADS2 activity in the spinal cord. These findings suggest that desaturase imbalance and FA remodeling in the spinal cord might represent characteristic features of T2D and that altered FA metabolism within the nervous system may potentially serve as an early indicator of neuropathy or a predictor of increased susceptibility to diabetes-related complications. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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