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Search Results (1,393)

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22 pages, 2422 KiB  
Article
A Conserved N-Terminal Di-Arginine Motif Stabilizes Plant DGAT1 and Modulates Lipid Droplet Organization
by Somrutai Winichayakul, Hong Xue and Nick Roberts
Int. J. Mol. Sci. 2025, 26(15), 7406; https://doi.org/10.3390/ijms26157406 (registering DOI) - 31 Jul 2025
Abstract
Diacylglycerol-O-acyltransferase 1 (DGAT1, EC 2.3.1.20) is a pivotal enzyme in plant triacylglycerol (TAG) biosynthesis. Previous work identified conserved di-arginine (R) motifs (R-R, R-X-R, and R-X-X-R) in its N-terminal cytoplasmic acyl-CoA binding domain. To elucidate their functional significance, we engineered R-rich sequences in the [...] Read more.
Diacylglycerol-O-acyltransferase 1 (DGAT1, EC 2.3.1.20) is a pivotal enzyme in plant triacylglycerol (TAG) biosynthesis. Previous work identified conserved di-arginine (R) motifs (R-R, R-X-R, and R-X-X-R) in its N-terminal cytoplasmic acyl-CoA binding domain. To elucidate their functional significance, we engineered R-rich sequences in the N-termini of Tropaeolum majus and Zea mays DGAT1s. Comparative analysis with their respective non-mutant constructs showed that deleting or substituting R with glycine in the N-terminal region of DGAT1 markedly reduced lipid accumulation in both Camelina sativa seeds and Saccharomyces cerevisiae cells. Immunofluorescence imaging revealed co-localization of non-mutant and R-substituted DGAT1 with lipid droplets (LDs). However, disruption of an N-terminal di-R motif destabilizes DGAT1, alters LD organization, and impairs recombinant oleosin retention on LDs. Further evidence suggests that the di-R motif mediates DGAT1 retrieval from LDs to the endoplasmic reticulum (ER), implicating its role in dynamic LD–ER protein trafficking. These findings establish the conserved di-R motifs as important regulators of DGAT1 function and LD dynamics, offering insights for the engineering of oil content in diverse biological systems. Full article
(This article belongs to the Special Issue Modern Plant Cell Biotechnology: From Genes to Structure, 2nd Edition)
16 pages, 4253 KiB  
Article
Integrative Analysis of Iso-Seq and RNA-Seq Identifies Key Genes Related to Fatty Acid Biosynthesis and High-Altitude Stress Adaptation in Paeonia delavayi
by Qiongji He, Wenjue Yuan, Rui Wang, Wengao Yang, Guiqing He, Jinglong Cao, Yan Li, Lei Ye, Zhaoguang Li and Zhijiang Hou
Genes 2025, 16(8), 919; https://doi.org/10.3390/genes16080919 - 30 Jul 2025
Abstract
Background/Objectives: Paeonia delavayi, a high-altitude-adapted medicinal and oil-producing plant, exhibits broad elevational distribution. Understanding how environmental factors regulate its growth across altitudes is critical for optimizing cultivation and exploiting its economic potential. Methods: In this study, we conducted a comprehensive Iso-Seq and [...] Read more.
Background/Objectives: Paeonia delavayi, a high-altitude-adapted medicinal and oil-producing plant, exhibits broad elevational distribution. Understanding how environmental factors regulate its growth across altitudes is critical for optimizing cultivation and exploiting its economic potential. Methods: In this study, we conducted a comprehensive Iso-Seq and RNA-seq analysis to elucidate the transcriptional profile across diverse altitudes and three seed developmental stages. Results: Using Pacbio full-length cDNA sequencing, we identified 39,267 full-length transcripts, with 80.03% (31,426) achieving successful annotation. RNA-seq analysis uncovered 11,423 and 9565 differentially expressed genes (DEGs) in response to different altitude and developmental stages, respectively. KEGG analysis indicated that pathways linked to fatty acid metabolism were notably enriched during developmental stages. In contrast, pathways associated with amino acid and protein metabolism were significantly enriched under different altitudes. Furthermore, we identified 34 DEGs related to fatty acid biosynthesis, including genes encoding pivotal enzymes like biotin carboxylase, carboxyl transferase subunit alpha, malonyl-CoA-acyl carrier protein transacylase, 3-oxoacyl-ACP reductase, 3-hydroxyacyl-ACP dehydratase, and stearoyl-ACP desaturase enoyl-ACP reductase. Additionally, ten DEGs were pinpointed as potentially involved in high-altitude stress response. Conclusions: These findings provide insights into the molecular mechanisms of fatty acid biosynthesis and adaptation to high-altitude stress in peony seeds, providing a theoretical foundation for future breeding programs aimed at enhancing seed quality. Full article
(This article belongs to the Section Genes & Environments)
22 pages, 2795 KiB  
Article
Environmental Stressors Modulating Seasonal and Daily Carbon Dioxide Assimilation and Productivity in Lessonia spicata
by Macarena Troncoso, Zoë L. Fleming, Félix L. Figueroa, Nathalie Korbee, Ronald Durán, Camilo Navarrete, Cecilia Rivera and Paula S. M. Celis-Plá
Plants 2025, 14(15), 2341; https://doi.org/10.3390/plants14152341 - 29 Jul 2025
Viewed by 115
Abstract
Carbon dioxide (CO2) emissions due to human activities are responsible for approximately 80% of the drivers of global warming, resulting in a 1.1 °C increase above pre-industrial temperatures. This study quantified the CO2 assimilation and productivity of the brown macroalgae [...] Read more.
Carbon dioxide (CO2) emissions due to human activities are responsible for approximately 80% of the drivers of global warming, resulting in a 1.1 °C increase above pre-industrial temperatures. This study quantified the CO2 assimilation and productivity of the brown macroalgae Lessonia spicata in the central Pacific coast of Chile, across seasonal and daily cycles, under different environmental stressors, such as temperature and solar irradiance. Measurements were performed using an infra-red gas analysis (IRGA) instrument which had a chamber allowing for precise quantification of CO2 concentrations; additional photophysiological and biochemical responses were also measured. CO2 assimilation, along with the productivity and biosynthesis of proteins and lipids, increased during the spring, coinciding with moderate temperatures (~14 °C) and high photosynthetically active radiation (PAR). Furthermore, the increased production of photoprotective and antioxidant compounds, including phenolic compounds, and carotenoids, along with the enhancement of non-photochemical quenching (NPQ), contribute to the effective photoacclimation strategies of L. spicata. Principal component analysis (PCA) revealed seasonal associations between productivity, reactive oxygen species (ROSs), and biochemical indicators, particularly during the spring and summer. These associations, further supported by Pearson correlation analyses, suggest a high but seasonally constrained photoacclimation capacity. In contrast, the reduced productivity and photoprotection observed in the summer suggest increased physiological vulnerability to heat and light stress. Overall, our findings position L. spicata as a promising nature-based solution for climate change mitigation. Full article
(This article belongs to the Special Issue Marine Macrophytes Responses to Global Change)
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15 pages, 4581 KiB  
Article
Co-Culture with Two Soil Fungal Strains Enhances Growth and Secondary Metabolite Biosynthesis in Cordyceps takaomontana
by Junyi Chen, Minghao Ding, Donglan He, Dengxian Zhang, Ming Wang, Yulan Xiang and Tianya Liu
J. Fungi 2025, 11(8), 559; https://doi.org/10.3390/jof11080559 - 29 Jul 2025
Viewed by 199
Abstract
Cordyceps takaomontana is a medicinal fungus with significant pharmacological value, but how soil microbes promote its growth remains unclear. We established a solid-state co-culture system involving C. takaomontana synnemata and its native soil fungi of Fusarium paeoniae and Bjerkandera minispora. Both F. [...] Read more.
Cordyceps takaomontana is a medicinal fungus with significant pharmacological value, but how soil microbes promote its growth remains unclear. We established a solid-state co-culture system involving C. takaomontana synnemata and its native soil fungi of Fusarium paeoniae and Bjerkandera minispora. Both F. paeoniae and B. minispora significantly promoted synnematal growth and enhanced antioxidant enzyme activities. Total triterpenoid content increased substantially. F. paeoniae markedly elevated levels of ergosterol peroxide, whereas B. minispora boosted accumulation of L-arabinose, ergotamine, and euphol. Metabolomics revealed that both fungi activated key metabolic pathways (including ABC transporters, mineral absorption, and protein digestion/absorption). F. paeoniae uniquely upregulated phenylalanine metabolism. This work elucidates the metabolic mechanisms underlying growth promotion of C. takaomontana mediated by F. paeoniae and B. minispora as well as deciphers potential pharmacologically active metabolites. These findings provide a foundation for strategically improving artificial cultivation and developing functional microbial inoculants. Full article
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25 pages, 4453 KiB  
Article
Regulatory Mechanisms of Exogenous Gibberellin on Seed Germination and Transcriptomic Responses in Lomatogonium rotatum
by Kefan Cao, Yingtong Mu, Sihai Lu and Yanyan Zhao
Genes 2025, 16(8), 878; https://doi.org/10.3390/genes16080878 - 26 Jul 2025
Viewed by 222
Abstract
Gibberellins (GAs) are essential phytohormones that regulate seed dormancy release and germination. Lomatogonium rotatum (L.) Fries ex Nym is a traditional medicinal plant whose seed germination is often hindered by physiological dormancy. In this study, we systematically investigated the effects of exogenous GA [...] Read more.
Gibberellins (GAs) are essential phytohormones that regulate seed dormancy release and germination. Lomatogonium rotatum (L.) Fries ex Nym is a traditional medicinal plant whose seed germination is often hindered by physiological dormancy. In this study, we systematically investigated the effects of exogenous GA3 on the seed germination of L. rotatum and elucidated the underlying molecular regulatory mechanisms via transcriptomic analysis. GA3 treatment (500 mg/L for 24 h) significantly improved the germination rate, vigor index, and other germination traits. RNA-seq analysis identified time-dependent transcriptional changes in GA3-treated seeds across three developmental stages (24 h, 72 h, and 96 h). KEGG enrichment and K-means clustering revealed dynamic actiSvation of hormonal signaling, secondary metabolism, and DNA replication pathways. WGCNA uncovered two hormone-responsive co-expression modules (Red and Lightcyan) corresponding to early and late stages of germination, respectively. Key genes related to ABA and GA biosynthesis and signal transduction showed phase-specific expression, highlighting the coordinated hormonal regulation during seed germination. Our findings provide new insights into the molecular basis of GA3-regulated seed germination and offer theoretical support for the cultivation and utilization of L. rotatum. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 1425 KiB  
Article
Blackberry (Rubus spp. Xavante Cultivar) Oil-Loaded PCL Nanocapsules: Sustainable Bioactive for In Vitro Collagen-Boosting Skincare
by Daniela F. Maluf, Brenda A. Lopes, Mariana D. Miranda, Luana C. Teixeira, Ana P. Horacio, Amanda Jansen, Madeline S. Correa, Guilherme dos Anjos Camargo, Jessica Mendes Nadal, Jane Manfron, Patrícia M. Döll-Boscardin and Paulo Vitor Farago
Cosmetics 2025, 12(4), 159; https://doi.org/10.3390/cosmetics12040159 - 25 Jul 2025
Viewed by 310
Abstract
Background: Blackberry seed oil (BSO), obtained from Rubus spp. Xavante cultivar via supercritical CO2 extraction, contains bioactive lipids and antioxidants, but its cosmetic application is limited by poor solubility and stability. Nanoencapsulation with poly(ε-caprolactone) (PCL) can overcome these limitations. Methods: BSO was [...] Read more.
Background: Blackberry seed oil (BSO), obtained from Rubus spp. Xavante cultivar via supercritical CO2 extraction, contains bioactive lipids and antioxidants, but its cosmetic application is limited by poor solubility and stability. Nanoencapsulation with poly(ε-caprolactone) (PCL) can overcome these limitations. Methods: BSO was characterized by Ultra-High-Performance Liquid Chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry and incorporated into PCL nanocapsules (NCBSO) using the preformed polymer deposition method. Physicochemical properties, stability (at 4 °C, room temperature, and 37 °C for 90 days), cytotoxicity, and collagen production were assessed in human fibroblasts. Additionally, a predictive in silico analysis using PASS Online, Molinspiration, and SEA platforms was performed to identify the bioactivities of major BSO compounds related to collagen synthesis, antioxidant potential, and anti-aging effects. Results: NCBSO showed a nanometric size of ~267 nm, low polydispersity (PDI < 0.2), negative zeta potential (−28 mV), and spherical morphology confirmed by FE-SEM. The dispersion remained stable across all tested temperatures, preserving pH and colloidal properties. In particular, BSO and NCBSO at 100 µg.mL−1 significantly enhanced in vitro collagen production by 170% and 200%, respectively, compared to untreated cells (p < 0.01). Superior bioactivity was observed for NCBSO. The in silico results support the role of key compounds in promoting collagen biosynthesis and protecting skin structure. No cytotoxic effects were achieved. Conclusions: The nanoencapsulation of BSO into PCL nanocapsules ensured formulation stability and potentiated collagen production. These findings support the potential of NCBSO as a promising candidate for future development as a collagen-boosting cosmeceutical. Full article
(This article belongs to the Special Issue Advanced Cosmetic Sciences: Sustainability in Materials and Processes)
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21 pages, 1285 KiB  
Article
Stage-Specific Transcriptomic Insights into Seed Germination and Early Development in Camellia oleifera Abel.
by Zhen Zhang, Caixia Liu, Ying Zhang, Zhilong He, Longsheng Chen, Chengfeng Xun, Yushen Ma, Xiaokang Yuan, Yanming Xu and Rui Wang
Plants 2025, 14(15), 2283; https://doi.org/10.3390/plants14152283 - 24 Jul 2025
Viewed by 177
Abstract
Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. [...] Read more.
Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article
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22 pages, 3771 KiB  
Article
Integrated Transcriptome and Metabolome Analyses Uncover Cholesterol-Responsive Gene Networks
by Ruihao Zhang, Qi Sun, Lixia Huang and Jian Li
Int. J. Mol. Sci. 2025, 26(15), 7108; https://doi.org/10.3390/ijms26157108 - 23 Jul 2025
Viewed by 308
Abstract
Cholesterol stress profoundly modulates cellular processes, but its underlying mechanisms remain incompletely understood. To investigate cholesterol-responsive networks, we performed integrated transcriptome (RNA-seq) and metabolome (LC-MS) analyses on HeLa cells treated with cholesterol for 6 and 24 h. Through transcriptomic analysis of cholesterol-stressed HeLa [...] Read more.
Cholesterol stress profoundly modulates cellular processes, but its underlying mechanisms remain incompletely understood. To investigate cholesterol-responsive networks, we performed integrated transcriptome (RNA-seq) and metabolome (LC-MS) analyses on HeLa cells treated with cholesterol for 6 and 24 h. Through transcriptomic analysis of cholesterol-stressed HeLa cells, we identified stage-specific responses characterized by early-phase stress responses and late-phase immune-metabolic coordination. This revealed 1340 upregulated and 976 downregulated genes after a 6 h cholesterol treatment, including induction and suppression of genes involved in cholesterol efflux and sterol biosynthesis, respectively, transitioning to Nuclear Factor kappa-B (NF-κB) activation and Peroxisome Proliferator-Activated Receptor (PPAR) pathway modulation by 24 h. Co-expression network analysis prioritized functional modules intersecting with differentially expressed genes. We also performed untargeted metabolomics using cells treated with cholesterol for 6 h, which demonstrated extensive remodeling of lipid species. Interestingly, integrated transcriptomic and metabolic analysis uncovered GFPT1-driven Uridine Diphosphate-N-Acetylglucosamine (UDP-GlcNAc) accumulation and increased taurine levels. Validation experiments confirmed GFPT1 upregulation and ANGPTL4 downregulation through RT-qPCR and increased O-GlcNAcylation via Western blot. Importantly, clinical datasets further supported the correlations between GFPT1/ANGPTL4 expression and cholesterol levels in Non-Alcoholic Steatohepatitis (NASH) liver cancer patients. This work establishes a chronological paradigm of cholesterol sensing and identifies GFPT1 and ANGPTL4 as key regulators bridging glycosylation and lipid pathways, providing mechanistic insights into cholesterol-associated metabolic disorders. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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22 pages, 8995 KiB  
Article
Comparative Transcriptomics and Metabolomics Uncover the Molecular Basis of Leaf Rust Resistance in Contrasting Leymus chinensis Germplasms
by Wenxin Gao, Peng Gao, Fenghui Guo and Xiangyang Hou
Int. J. Mol. Sci. 2025, 26(15), 7042; https://doi.org/10.3390/ijms26157042 - 22 Jul 2025
Viewed by 153
Abstract
Leymus chinensis (Trin.) Tzvel., a vital native forage grass in northern China for ecological restoration and livestock production, faces severe yield losses and grassland degradation due to rust (Puccinia spp.) infection. Current control strategies, reliant on chemical interventions, are limited by evolving [...] Read more.
Leymus chinensis (Trin.) Tzvel., a vital native forage grass in northern China for ecological restoration and livestock production, faces severe yield losses and grassland degradation due to rust (Puccinia spp.) infection. Current control strategies, reliant on chemical interventions, are limited by evolving resistance risks and environmental concerns, while rust-resistant breeding remains hindered by insufficient molecular insights. To address this, we systematically evaluated rust resistance in 24 L. chinensis germplasms from diverse geographic origins, identifying six highly resistant (HR) and five extremely susceptible (ES) genotypes. Integrating transcriptomics and metabolomics, we dissected molecular responses to Puccinia infection, focusing on contrasting HR (Lc71) and ES (Lc5) germplasms at 48 h post-inoculation. Transcriptomic analysis revealed 1012 differentially expressed genes (DEGs: 247 upregulated, 765 downregulated), with enrichment in cell wall biosynthesis and photosynthesis pathways but suppression of flavonoid synthesis. Metabolomic profiling identified 287 differentially accumulated metabolites (DAMs: 133 upregulated, 188 downregulated), showing significant downregulation of pterocarpans and flavonoids in HR germplasms, alongside upregulated cutin synthesis-related metabolites. Multi-omics integration uncovered 79 co-enriched pathways, pinpointing critical regulatory networks: (1) In the nucleotide metabolism pathway, genes Lc5Ns011910, Lc1Xm057211, and Lc4Xm043884 exhibited negative cor-relations with metabolites Deoxycytidine and Cytosine. (2) In flavonoid biosynthesis, Lc2Xm054924, Lc4Xm044161, novel.8850, Lc2Ns006303, and Lc7Ns021884 were linked to naringenin and naringenin-7-O-glucoside accumulation. These candidate genes likely orchestrate rust resistance mechanisms in L. chinensis. Our findings advance the molecular understanding of rust resistance and provide actionable targets for breeding resilient germplasms. Full article
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16 pages, 7336 KiB  
Article
Identification of Quality-Related Genomic Regions and Candidate Genes in Silage Maize by Combining GWAS and Meta-Analysis
by Yantian Lu, Yongfu Ding, Can Xu, Shubin Chen, Chunlan Xia, Li Zhang, Zhiqing Sang and Zhanqin Zhang
Plants 2025, 14(15), 2250; https://doi.org/10.3390/plants14152250 - 22 Jul 2025
Viewed by 306
Abstract
Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage [...] Read more.
Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage maize quality. In this study, a GWAS was conducted on 580 inbred lines of silage maize, and a meta-analysis was performed on 477 quantitative trait loci (QTLs) from 34 studies. The analysis identified 27 significant single nucleotide polymorphisms (SNPs) and 87 consensus QTLs (cQTLs), with 7 cQTLs associated with multiple quality traits. By integrating the SNPs identified through association mapping, one SNP was found to overlap with the cQTL interval related to crude protein, neutral detergent fiber, and starch content. Furthermore, enrichment analysis predicted 300 and 5669 candidate genes through GWAS and meta-analysis, respectively, highlighting pathways such as cellular metabolism, the biosynthesis of secondary metabolites, ribosome function, carbon metabolism, protein processing in the endoplasmic reticulum, and amino acid biosynthesis. The examination of 13 candidate genes from three co-located regions revealed Zm00001d050977 as a cytochrome P450 family gene, while the other 2 genes primarily encode proteins involved in stress responses and other biological pathways. In conclusion, this research presents a methodology combining GWAS and meta-analysis to identify genomic regions and potential genes influencing quality traits in silage maize. These findings serve as a foundation for the identification of significant QTLs and candidate genes crucial for improving silage maize quality. Full article
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26 pages, 3710 KiB  
Article
Global Transcriptome and Weighted Gene Co-Expression Network Analyses of Cold Stress Responses in Chinese Cabbage
by Jizong Zhang, Songtao Liu, Huibin Li, Mengmeng Sun, Baoyue Yan, Peng Zhang and Lifeng Zhang
Genes 2025, 16(7), 845; https://doi.org/10.3390/genes16070845 - 20 Jul 2025
Viewed by 368
Abstract
Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome [...] Read more.
Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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27 pages, 3394 KiB  
Article
Integrative Multi-Omics Profiling of Rhabdomyosarcoma Subtypes Reveals Distinct Molecular Pathways and Biomarker Signatures
by Aya Osama, Ahmed Karam, Abdelrahman Atef, Menna Arafat, Rahma W. Afifi, Maha Mokhtar, Taghreed Khaled Abdelmoneim, Asmaa Ramzy, Enas El Nadi, Asmaa Salama, Emad Elzayat and Sameh Magdeldin
Cells 2025, 14(14), 1115; https://doi.org/10.3390/cells14141115 - 20 Jul 2025
Viewed by 638
Abstract
Rhabdomyosarcoma (RMS), the most common pediatric soft tissue sarcoma, comprises embryonal (ERMS) and alveolar (ARMS) subtypes with distinct histopathological features, clinical outcomes, and therapeutic responses. To better characterize their molecular distinctions, we performed untargeted plasma proteomics and metabolomics profiling in children with ERMS [...] Read more.
Rhabdomyosarcoma (RMS), the most common pediatric soft tissue sarcoma, comprises embryonal (ERMS) and alveolar (ARMS) subtypes with distinct histopathological features, clinical outcomes, and therapeutic responses. To better characterize their molecular distinctions, we performed untargeted plasma proteomics and metabolomics profiling in children with ERMS (n = 18), ARMS (n = 17), and matched healthy controls (n = 18). Differential expression, functional enrichment (GO, KEGG, RaMP-DB), co-expression network analysis (WGCNA/WMCNA), and multi-omics integration (DIABLO, MOFA) revealed distinct molecular signatures for each subtype. ARMS displayed elevated oncogenic and stemness-associated proteins (e.g., cyclin E1, FAP, myotrophin) and metabolites involved in lipid transport, fatty acid metabolism, and polyamine biosynthesis. In contrast, ERMS was enriched in immune-related and myogenic proteins (e.g., myosin-9, SAA2, S100A11) and metabolites linked to glutamate/glycine metabolism and redox homeostasis. Pathway analyses highlighted subtype-specific activation of PI3K-Akt and Hippo signaling in ARMS and immune and coagulation pathways in ERMS. Additionally, the proteomics and metabolomics datasets showed association with clinical parameters, including disease stage, lymph node involvement, and age, demonstrating clear molecular discrimination consistent with clinical observation. Co-expression networks and integrative analyses further reinforced these distinctions, uncovering coordinated protein–metabolite modules. Our findings reveal novel, subtype-specific molecular programs in RMS and propose candidate biomarkers and pathways that may guide precision diagnostics and therapeutic targeting in pediatric sarcomas. Full article
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24 pages, 3329 KiB  
Article
Isolation of a Novel Streptomyces sp. TH05 with Potent Cyanocidal Effects on Microcystis aeruginosa
by Xuhan Wang, Siqi Zhu, Shenchen Tao, Shaoyong Zhang, Ruijun Wang and Liqin Zhang
Toxins 2025, 17(7), 354; https://doi.org/10.3390/toxins17070354 - 17 Jul 2025
Viewed by 431
Abstract
In this paper, cultivable actinobacteria were isolated, cultured, and identified from the heavily algal-bloomed waters of Taihu Lake using 16S rRNA gene sequencing. Among the isolates, a single strain exhibiting vigorous cyanocidal activity against Microcystis aeruginosa FACHB-905 was selected for further investigation. The [...] Read more.
In this paper, cultivable actinobacteria were isolated, cultured, and identified from the heavily algal-bloomed waters of Taihu Lake using 16S rRNA gene sequencing. Among the isolates, a single strain exhibiting vigorous cyanocidal activity against Microcystis aeruginosa FACHB-905 was selected for further investigation. The cyanocidal efficacy and underlying mechanisms of this strain, designated TH05, were assessed through using chlorophyll content, cyanobacterial inhibition rate, and cyanobacterial cell morphology measurements. In addition, oxidative stress responses, expression of key functional genes in FACHB-905, and variations in microcystin concentrations were comprehensively evaluated. Cyanobacterial blooms caused by Microcystis aeruginosa pose serious ecological and public health threats due to the release of microcystins (MCs). In this study, we evaluated the cyanocidal activity and mechanism of a novel actinomycete strain, Streptomyces sp. TH05. Optimization experiments revealed that a light–dark cycle of 12 h/12 h, temperature of 25 °C, and pH 7 significantly enhanced cyanocidal efficacy. Under these conditions, TH05 achieved an 84.31% inhibition rate after seven days of co-cultivation with M. aeruginosa. Scanning electron microscopy revealed two distinct cyanocidal modes: direct physical attachment of TH05 mycelia to cyanobacterial cells, causing cell wall disruption, and indirect membrane damage via extracellular bioactive compounds. Biochemical analyses showed increased levels of malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) during the first five days, peaking at 2.47-, 2.12-, and 1.91-fold higher than control levels, respectively, indicating elevated oxidative stress. Gene expression analysis using elf-p as a reference showed that TH05 modulated key genes associated with photosynthesis (PsaB, PstD1, PstD2, RbcL), DNA repair and stress response (RecA, FtsH), and microcystin biosynthesis (McyA, McyD). All genes were upregulated except for RbcL, which was downregulated. In parallel, microcystin content peaked at 32.25 ng/L on day 1 and decreased to 16.16 ng/L by day 9, which was significantly lower than that of the control group on day 9 (29.03 ng/L). These findings suggest that strain TH05 exhibits potent and multifaceted cyanocidal activity, underscoring its potential for application in the biological control of cyanobacterial blooms. Full article
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12 pages, 2098 KiB  
Article
A High-Efficiency Transient Expression System Reveals That CjMYB5 Positively Regulates Anthocyanin Biosynthesis in Camellia japonica
by Menglong Fan, Hong Jiang, Si Wu, Zhixin Song, Ying Zhang, Xinlei Li and Yan Wang
Horticulturae 2025, 11(7), 839; https://doi.org/10.3390/horticulturae11070839 - 16 Jul 2025
Viewed by 284
Abstract
The establishment of a transient expression system in petals is significant for elucidating gene functions in flowering trees characterized by a prolonged juvenile phase. Genetic improvements in Camellia japonica have been hindered due to the absence of a functional validation platform. In this [...] Read more.
The establishment of a transient expression system in petals is significant for elucidating gene functions in flowering trees characterized by a prolonged juvenile phase. Genetic improvements in Camellia japonica have been hindered due to the absence of a functional validation platform. In this study, we explored an Agrobacterium-mediated and readily observable transient expression system in camellia petals to systematically optimize four critical factors affecting transformation efficiency. As a result, the bud stage, ‘Banliuxiang’ genotype, OD600 of 1.0, and 1-day co-cultivation achieved the highest intensity of transient expression, and overexpression of the Ruby1 reporter gene induced substantial anthocyanin synthesis, manifested as distinct red pigmentation. Furthermore, the optimized transient expression system revealed that the R2R3-MYB transcription factor CjMYB5, which interacted with CjGL3, promoted anthocyanin biosynthesis in camellia petals by transactivating key DFR structural genes. This transient expression platform not only advances functional genomics studies in ornamental woody species but also lays a foundation for molecular breeding programs in C. japonica. Full article
(This article belongs to the Special Issue Germplasm, Genetics and Breeding of Ornamental Plants)
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Article
Integrative Analysis of Transcriptomics and Metabolomics Provides Insights into Meat Quality Differences in Hu Sheep with Different Carcass Performance
by Xiaoxue Zhang, Liming Zhao, Huibin Tian, Zongwu Ma, Qi Zhang, Mengru Pu, Peiliang Cao, Deyin Zhang, Yukun Zhang, Yuan Zhao, Jiangbo Cheng, Quanzhong Xu, Dan Xu, Xiaobin Yang, Xiaolong Li, Weiwei Wu, Fadi Li and Weimin Wang
Foods 2025, 14(14), 2477; https://doi.org/10.3390/foods14142477 - 15 Jul 2025
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Abstract
Meat quality is a critical determinant of consumer preference and economic value in the livestock industry. However, the relationship between carcass performance and meat quality remains poorly understood. In our study, we conducted an integrative analysis of transcriptomics and metabolomics to investigate the [...] Read more.
Meat quality is a critical determinant of consumer preference and economic value in the livestock industry. However, the relationship between carcass performance and meat quality remains poorly understood. In our study, we conducted an integrative analysis of transcriptomics and metabolomics to investigate the molecular mechanisms underlying meat quality differences in Hu sheep with high (HHS, n = 10) and low (LHS, n = 10) carcass performance. Phenotypic analysis revealed that the HHS group exhibited superior meat quality traits, including higher intramuscular fat (IMF) content (reflected in elevated marbling scores), along with lower shear force, drip loss, and cooking loss, compared to the LHS group. Transcriptomic analysis identified 376 differentially expressed genes (DEGs) enriched in pathways linked to lipid metabolism, such as the PPAR signaling pathway and long-chain fatty acid metabolic process. Weighted gene co-expression network analysis (WGCNA) revealed important modules and key genes (e.g., ELOVL6, PLIN1, and ARHGEF2) associated with meat quality traits. Metabolomic profiling identified 132 differentially accumulated metabolites (DAMs), with significant enrichment in amino acid metabolism pathways, including D-amino acid metabolism, arginine biosynthesis, and glycine, serine, and threonine metabolism. Integrative analysis of transcriptomic and metabolomic data highlighted six co-enriched pathways, such as the mTOR signaling pathway and amino acid metabolism, underscoring their role in regulating meat quality. These findings provide valuable insights into the genetic and metabolic networks driving meat quality variation and offer potential biomarkers for genetic selection and nutritional strategies to enhance both carcass yield and eating quality in Hu sheep. This research enhances knowledge of the molecular basis of meat quality and supports precision breeding in livestock production. Full article
(This article belongs to the Section Meat)
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