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Keywords = species-specific gene expression

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13 pages, 7209 KiB  
Article
Evolutionary Analysis of the Land Plant-Specific TCP Interactor Containing EAR Motif Protein (TIE) Family of Transcriptional Corepressors
by Agustín Arce, Camila Schild, Delfina Maslein and Leandro Lucero
Plants 2025, 14(15), 2423; https://doi.org/10.3390/plants14152423 - 5 Aug 2025
Abstract
The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin [...] Read more.
The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin of the TIE family to the early evolution of the embryophyte, while an earlier diversification in algae cannot be ruled out. Strikingly, we found that the number of TIE members is highly constrained compared to the expansion of TCPs in angiosperms. We used co-expression data to identify potential TIE-TCP regulatory targets across Arabidopsis thaliana and rice. Notably, the expression pattern between these species is remarkably similar. TCP Class I and Class II genes formed two distinct clusters, and TIE genes cluster within the TCP Class I group. This study provides a comprehensive evolutionary analysis of the TIE family, shedding light on its conserved role in the regulation of gene transcription in flowering plant development. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)
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19 pages, 3457 KiB  
Article
Transcriptome Analysis Revealed the Immune and Metabolic Responses of Grass Carp (Ctenopharyngodon idellus) Under Acute Salinity Stress
by Leshan Ruan, Baocan Wei, Yanlin Liu, Rongfei Mu, Huang Li and Shina Wei
Fishes 2025, 10(8), 380; https://doi.org/10.3390/fishes10080380 - 5 Aug 2025
Viewed by 135
Abstract
Freshwater salinization, an escalating global environmental stressor, poses a significant threat to freshwater biodiversity, including fish communities. This study investigates the grass carp (Ctenopharyngodon idellus), a species with the highest aquaculture output in China, to elucidate the molecular underpinnings of its [...] Read more.
Freshwater salinization, an escalating global environmental stressor, poses a significant threat to freshwater biodiversity, including fish communities. This study investigates the grass carp (Ctenopharyngodon idellus), a species with the highest aquaculture output in China, to elucidate the molecular underpinnings of its physiological adaptations to fluctuating salinity gradients. We used high-throughput mRNA sequencing and differential gene expression profiling to analyze transcriptional dynamics in intestinal and kidney tissues of grass carp exposed to heterogeneous salinity stressors. Concurrent serum biochemical analyses showed salinity stress significantly increased Na+, Cl, and osmolarity, while decreasing lactate and glucose. Salinity stress exerted a profound impact on the global transcriptomic landscape of grass carp. A substantial number of co-regulated differentially expressed genes (DEGs) in kidney and intestinal tissues were enriched in immune and metabolic pathways. Specifically, genes associated with antigen processing and presentation (e.g., cd4-1, calr3b) and apoptosis (e.g., caspase17, pik3ca) exhibited upregulated expression, whereas genes involved in gluconeogenesis/glycolysis (e.g., hk2, pck2) were downregulated. KEGG pathway enrichment analyses revealed that metabolic and cellular structural pathways were predominantly enriched in intestinal tissues, while kidney tissues showed preferential enrichment of immune and apoptotic pathways. Rigorous validation of RNA-seq data via qPCR confirmed the robustness and cross-platform consistency of the findings. This study investigated the core transcriptional and physiological mechanisms regulating grass carp’s response to salinity stress, providing a theoretical foundation for research into grass carp’s resistance to salinity stress and the development of salt-tolerant varieties. Full article
(This article belongs to the Special Issue Adaptation and Response of Fish to Environmental Changes)
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21 pages, 6621 KiB  
Article
Genome-Wide Identification and Expression Pattern Analysis of the Late Embryogenesis Abundant (LEA) Family in Foxtail Millet (Setaria italica L.)
by Yingying Qin, Yiru Zhao, Xiaoyu Li, Ruifu Wang, Shuo Chang, Yu Zhang, Xuemei Ren and Hongying Li
Genes 2025, 16(8), 932; https://doi.org/10.3390/genes16080932 (registering DOI) - 4 Aug 2025
Viewed by 123
Abstract
Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to [...] Read more.
Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to comprehensively identify SiLEA genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. Methods: Genome-wide identification of SiLEA genes was conducted, followed by phylogenetic reconstruction, cis-acting element analysis of promoters, synteny analysis, and expression profiling. Results: Ninety-four SiLEA genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of SiLEA genes with sorghum and rice orthologs than with Arabidopsis thaliana AtLEA genes. Synteny analysis indicated the LEA gene family expansion through tandem and segmental duplication. Promoter cis-element analysis linked SiLEA genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among SiLEA members, while RT-qPCR verified ABA-induced transcriptional regulation of SiLEA genes. Conclusions: This study identified 94 SiLEA genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated SiASR-2, SiASR-5, and SiASR-6 in both shoots and roots. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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34 pages, 1227 KiB  
Review
Beyond Cutting: CRISPR-Driven Synthetic Biology Toolkit for Next-Generation Microalgal Metabolic Engineering
by Limin Yang and Qian Lu
Int. J. Mol. Sci. 2025, 26(15), 7470; https://doi.org/10.3390/ijms26157470 - 2 Aug 2025
Viewed by 345
Abstract
Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO2 fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent [...] Read more.
Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO2 fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent of CRISPR-Cas systems initially provided precise gene editing via targeted DNA cleavage. This review argues that the true transformative potential lies in moving decisively beyond cutting to harness CRISPR as a versatile synthetic biology “Swiss Army Knife”. We synthesize the rapid evolution of CRISPR-derived tools—including transcriptional modulators (CRISPRa/i), epigenome editors, base/prime editors, multiplexed systems, and biosensor-integrated logic gates—and their revolutionary applications in microalgal engineering. These tools enable tunable gene expression, stable epigenetic reprogramming, DSB-free nucleotide-level precision editing, coordinated rewiring of complex metabolic networks, and dynamic, autonomous control in response to environmental cues. We critically evaluate their deployment to enhance photosynthesis, boost lipid/biofuel production, engineer high-value compound pathways (carotenoids, PUFAs, proteins), improve stress resilience, and optimize carbon utilization. Persistent challenges—species-specific tool optimization, delivery efficiency, genetic stability, scalability, and biosafety—are analyzed, alongside emerging solutions and future directions integrating AI, automation, and multi-omics. The strategic integration of this CRISPR toolkit unlocks the potential to engineer robust, high-productivity microalgal cell factories, finally realizing their promise as sustainable platforms for next-generation biomanufacturing. Full article
(This article belongs to the Special Issue Developing Methods and Molecular Basis in Plant Biotechnology)
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20 pages, 3136 KiB  
Review
The Role of Genomic Islands in the Pathogenicity and Evolution of Plant-Pathogenic Gammaproteobacteria
by Yuta Watanabe, Yasuhiro Ishiga and Nanami Sakata
Microorganisms 2025, 13(8), 1803; https://doi.org/10.3390/microorganisms13081803 - 1 Aug 2025
Viewed by 132
Abstract
Genomic islands (GIs) including integrative and conjugative elements (ICEs), prophages, and integrative plasmids are central drivers of horizontal gene transfer in bacterial plant pathogens. These elements often carry cargo genes encoding virulence factors, antibiotic and metal resistance determinants, and metabolic functions that enhance [...] Read more.
Genomic islands (GIs) including integrative and conjugative elements (ICEs), prophages, and integrative plasmids are central drivers of horizontal gene transfer in bacterial plant pathogens. These elements often carry cargo genes encoding virulence factors, antibiotic and metal resistance determinants, and metabolic functions that enhance environmental adaptability. In plant-pathogenic species such as Pseudomonas syringae, GIs contribute to host specificity, immune evasion, and the emergence of novel pathogenic variants. ICEclc and its homologs represent integrative and mobilizable elements whose tightly regulated excision and transfer are driven by a specialized transcriptional cascade, while ICEs in P. syringae highlight the ecological impact of cargo genes on pathogen virulence and fitness. Pathogenicity islands further modulate virulence gene expression in response to in planta stimuli. Beyond P. syringae, GIs in genera such as Erwinia, Pectobacterium, and Ralstonia underpin critical traits like toxin biosynthesis, secretion system acquisition, and topoisomerase-mediated stability. Leveraging high-throughput genomics and structural biology will be essential to dissect GI regulation and develop targeted interventions to curb disease spread. This review synthesizes the current understanding of GIs in plant-pathogenic gammaproteobacteria and outlines future research priorities for translating mechanistic insights into sustainable disease control strategies. Full article
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23 pages, 3297 KiB  
Article
Phenotypic Changes and Oxidative Stress in THP-1 Macrophages in Response to Vanilloids Following Stimulation with Allergen Act d 1 and LPS
by Milena Zlatanova, Jovana Grubač, Jovana Trbojević-Ivić and Marija Gavrović-Jankulović
Antioxidants 2025, 14(8), 949; https://doi.org/10.3390/antiox14080949 (registering DOI) - 1 Aug 2025
Viewed by 303
Abstract
Activation of macrophages plays a key role in both inflammation and oxidative stress, key features of many chronic diseases. Pro-inflammatory M1-like macrophages, in particular, contribute to pro-oxidative environments and are a frequent focus of immunological research. This research examined the effects of kiwifruit [...] Read more.
Activation of macrophages plays a key role in both inflammation and oxidative stress, key features of many chronic diseases. Pro-inflammatory M1-like macrophages, in particular, contribute to pro-oxidative environments and are a frequent focus of immunological research. This research examined the effects of kiwifruit allergen Act d 1, in comparison to LPS, on THP-1 macrophages in vitro differentiated under optimized conditions, both in the presence and in the absence of selected vanilloids. THP-1 monocyte differentiation was optimized by varying PMA exposure and resting time. Act d 1 induced M1-like phenotypic changes comparable to LPS, including upregulation of CD80, IL-1β and IL-6 secretion, gene expression of iNOS and NF-κB activation, in addition to increased reactive oxygen species (ROS) and catalase activity. Treatment with specific vanilloids mitigated these responses, primarily through reduced oxidative stress and NF-κB activation. Notably, vanillin (VN) was the most effective, also reducing CD80 expression and IL-1β levels. These results suggest that vanilloids can affect pro-inflammatory signaling and oxidative stress in THP-1 macrophages and highlight their potential to alter inflammatory conditions characterized by similar immune responses. Full article
(This article belongs to the Section Natural and Synthetic Antioxidants)
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29 pages, 10502 KiB  
Article
A Comparative Bioinformatic Investigation of the Rubisco Small Subunit Gene Family in True Grasses Reveals Novel Targets for Enhanced Photosynthetic Efficiency
by Brittany Clare Thornbury, Tianhua He, Yong Jia and Chengdao Li
Int. J. Mol. Sci. 2025, 26(15), 7424; https://doi.org/10.3390/ijms26157424 - 1 Aug 2025
Viewed by 150
Abstract
Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the [...] Read more.
Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes. Full article
(This article belongs to the Special Issue Molecular Genetics, Genomics and Breeding in Field Crops)
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14 pages, 2882 KiB  
Article
Babesia bovis Enolase Is Expressed in Intracellular Merozoites and Contains B-Cell Epitopes That Induce Neutralizing Antibodies In Vitro
by Alma Cárdenas-Flores, Minerva Camacho-Nuez, Massaro W. Ueti, Mario Hidalgo-Ruiz, Angelina Rodríguez-Torres, Diego Josimar Hernández-Silva, José Guadalupe Gómez-Soto, Masahito Asada, Shin-ichiro Kawazu, Alma R. Tamayo-Sosa, Rocío Alejandra Ruiz-Manzano and Juan Mosqueda
Vaccines 2025, 13(8), 818; https://doi.org/10.3390/vaccines13080818 - 31 Jul 2025
Viewed by 229
Abstract
Background: Bovine babesiosis, caused by the tick-borne apicomplexan parasite Babesia spp., is an economically significant disease that threatens the cattle industry worldwide. Babesia bovis is the most pathogenic species, leading to high morbidity and mortality in infected animals. One promising approach to [...] Read more.
Background: Bovine babesiosis, caused by the tick-borne apicomplexan parasite Babesia spp., is an economically significant disease that threatens the cattle industry worldwide. Babesia bovis is the most pathogenic species, leading to high morbidity and mortality in infected animals. One promising approach to vaccination against bovine babesiosis involves the use of multiple protective antigens, offering advantages over traditional live-attenuated vaccines. Tools such as immunobioinformatics and reverse vaccinology have facilitated the identification of novel antigens. Enolase, a “moonlighting” enzyme of the glycolytic pathway with demonstrated vaccine potential in other pathogens, has not yet been studied in B. bovis. Methods: In this study, the enolase gene from two B. bovis isolates was successfully identified and sequenced. The gene, consisting of 1366 base pairs, encodes a predicted protein of 438 amino acids. Its expression in intraerythrocytic parasites was confirmed by RT-PCR. Two peptides containing predicted B-cell epitopes were synthesized and used to immunize rabbits. Hyperimmune sera were then analyzed by ELISA, confocal microscopy, Western blot, and an in vitro neutralization assay. Results: The hyperimmune sera showed high antibody titers, reaching up to 1:256,000. Specific antibodies recognized intraerythrocytic merozoites by confocal microscopy and bound to a ~47 kDa protein in erythrocytic cultures of B. bovis as detected by Western blot. In the neutralization assay, antibodies raised against peptide 1 had no observable effect, whereas those targeting peptide 2 significantly reduced parasitemia by 71.99%. Conclusions: These results suggest that B. bovis enolase contains B-cell epitopes capable of inducing neutralizing antibodies and may play a role in parasite–host interactions. Enolase is therefore a promising candidate for further exploration as a vaccine antigen. Nonetheless, additional experimental studies are needed to fully elucidate its biological function and validate its vaccine potential. Full article
(This article belongs to the Special Issue Vaccines against Arthropods and Arthropod-Borne Pathogens)
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26 pages, 14851 KiB  
Article
Degradation of Synthetic Restoration Materials by Xerotolerant/Xerophilic Fungi Contaminating Canvas Paintings
by Amela Kujović, Katja Kavkler, Michel Alexander Wilson-Hernandez, Miloš Vittori, Luen Zidar, Cene Gostinčar, Kristina Sepčić, Yordanis Pérez-Llano, Ramón Alberto Batista-García, Nina Gunde-Cimerman and Polona Zalar
J. Fungi 2025, 11(8), 568; https://doi.org/10.3390/jof11080568 - 30 Jul 2025
Viewed by 281
Abstract
Canvas paintings are prone to biodeterioration due to their complex chemical composition, which can support fungal growth even under controlled conditions. This study evaluated the susceptibility of common synthetic restoration materials—Lascaux glues (303 HV, 498 HV), Acrylharz P550, BEVA 371, Laropal A81, and [...] Read more.
Canvas paintings are prone to biodeterioration due to their complex chemical composition, which can support fungal growth even under controlled conditions. This study evaluated the susceptibility of common synthetic restoration materials—Lascaux glues (303 HV, 498 HV), Acrylharz P550, BEVA 371, Laropal A81, and Regalrez 1094—to degradation by fourteen xerotolerant/xerophilic fungal strains. All tested Aspergillus and Penicillium species extensively colonized, especially artificially aged materials. FTIR-PAS analysis revealed chemical changes in carbonyl and C–H bonds in Laropal A81 and Regalrez 1094 colonized by Aspergillus spp. Scanning electron microscopy (SEM) imaging showed thinning of Lascaux glues and deformation of Regalrez 1094. Transcriptomic profiling of A. puulaauensis grown on Lascaux 498 HV and Regalrez 1094 identified altered expression of genes coding for esterases and oxidases, enzymes involved in synthetic polymer degradation. Esterase activity assays using 4-nitrophenol-based substrates confirmed significant enzymatic activity correlating with the presence of ester bonds. These findings highlight the vulnerability of synthetic restoration materials, specifically Laropal A81, Regalrez 1094, and Lascaux glues, to extremophilic fungi thriving in environments with low water activity. The results emphasize the urgent need for specific knowledge on fungi and their metabolic pathways to use/develop more durable conservation materials and strategies to protect cultural heritage objects from biodeterioration. Full article
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19 pages, 13626 KiB  
Article
Genome-Wide Identification and Co-Expression Analysis of WRKY Genes Unveil Their Role in Regulating Anthocyanin Accumulation During Euscaphis japonica Fruit Maturation
by Bobin Liu, Qingying Wang, Dongmei He, Xiaqin Wang, Guiliang Xin, Xiaoxing Zou, Daizhen Zhang, Shuangquan Zou and Jiakai Liao
Biology 2025, 14(8), 958; https://doi.org/10.3390/biology14080958 - 29 Jul 2025
Viewed by 269
Abstract
Anthocyanins, crucial water-soluble pigments in plants, determine coloration in floral and fruit tissues, while fulfilling essential physiological roles in terms of plant growth, development, and stress adaptation. The biosynthesis of anthocyanins is transcriptionally regulated by WRKY factors, one of the largest plant-specific transcription [...] Read more.
Anthocyanins, crucial water-soluble pigments in plants, determine coloration in floral and fruit tissues, while fulfilling essential physiological roles in terms of plant growth, development, and stress adaptation. The biosynthesis of anthocyanins is transcriptionally regulated by WRKY factors, one of the largest plant-specific transcription factor families. Euscaphis japonica is an East Asian species, prized for its exceptionally persistent butterfly-shaped fruits that undergo pericarp dehiscence, overturning, and a color transition to scarlet red. This species represents an ideal system for studying anthocyanin regulation. However, the mechanisms by which WRKY transcription factors orchestrate anthocyanin accumulation during this process remain unknown. In this study, we identified 87 WRKY genes (EjaWRKYs) from the E. japonica genome. Phylogenetic analysis was used to classify these genes into three primary groups, with five subgroups, revealing conserved gene structures and motif compositions, supported by collinearity and comparative synteny analyses. Crucially, ten EjaWRKYs exhibited peak expression during the mature fruit stages, showing positive correlations with key anthocyanin biosynthesis genes. Functional validation through the use of transient transactivation assays in Nicotiana benthamiana confirmed that the five selected EjaWRKYs bind W-box elements and strongly activate reporter gene expression. Our results reveal EjaWRKYs’ regulation of anthocyanin accumulation in E. japonica fruit, provide the first comprehensive WRKY family characterization of this species, and establish a foundation for manipulating ornamental traits in horticultural breeding. Full article
(This article belongs to the Special Issue Recent Advances in Biosynthesis and Degradation of Plant Anthocyanin)
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22 pages, 1674 KiB  
Article
The Ghrelin Analog GHRP-6, Delivered Through Aquafeeds, Modulates the Endocrine and Immune Responses of Sparus aurata Following IFA Treatment
by Leandro Rodríguez-Viera, Anyell Caderno, Rebeca Martinez, Gonzalo Martinez-Rodríguez, Milagrosa Oliva, Erick Perera, Juan Miguel Mancera and Juan Antonio Martos-Sitcha
Biology 2025, 14(8), 941; https://doi.org/10.3390/biology14080941 - 25 Jul 2025
Viewed by 402
Abstract
The aquaculture industry has experienced considerable growth in recent decades, stimulating research into sustainable and functional feed formulations, mainly related to using high-quality, safe, and environmentally friendly feed ingredients. The employment of immunomodulatory additives is a promising strategy to enhance fish health and [...] Read more.
The aquaculture industry has experienced considerable growth in recent decades, stimulating research into sustainable and functional feed formulations, mainly related to using high-quality, safe, and environmentally friendly feed ingredients. The employment of immunomodulatory additives is a promising strategy to enhance fish health and performance. In this study, the effects of the ghrelin analog GHRP-6 peptide included in the diet (500 µg/kg of feed) on the endocrine and immune responses of Sparus aurata following Incomplete Freund’s adjuvant (IFA) treatment were assessed. After 97 days, fish were intraperitoneally injected with 100 µL of saline solution or IFA/100 g fish and sampled 72 h post-injection. Our results indicated that fish fed GHRP-6 maintained stable plasma levels of lactate, triglycerides, and cortisol after IFA treatment, in contrast to control-fed fish, which showed significant metabolic stress. Circulating immunoglobulin levels enhanced significantly in the GHRP-6/IFA group, suggesting a stimulated humoral immune response. Transcriptomics analysis revealed that the anterior intestine was the most responsive tissue, with upregulation of il10, il15, il34, and mx1, indicating mucosal immune activation. In the spleen, GHRP-6-fed fish increased il8, il10, and ighm expression, highlighting a balanced pro- and anti-inflammatory response and support for adaptive immunity. Multivariate analysis confirmed that dietary GHRP-6 modulates immune gene expression in a tissue- and stimulus-specific manner, without inducing histological alterations in the intestine or spleen. Taken together, these preliminary results indicate that this peptide is a viable and safe dietary supplement to improve immune resilience and increase the production efficiency of S. aurata and suggest a protective effect on the fish’s immune system in this species. Full article
(This article belongs to the Special Issue Aquatic Animal Nutrition and Feed)
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19 pages, 2974 KiB  
Article
PI3K/Akt1 Pathway Suppression by Quercetin–Doxorubicin Combination in Osteosarcoma Cell Line (MG-63 Cells)
by Mehmet Uğur Karabat and Mehmet Cudi Tuncer
Medicina 2025, 61(8), 1347; https://doi.org/10.3390/medicina61081347 - 25 Jul 2025
Viewed by 214
Abstract
Background and Objectives: This study aimed to investigate the anticancer effects and potential synergistic interactions of quercetin (Q) and doxorubicin (Dox) on the MG-63 osteosarcoma (OS) cell line. Specifically, the effects of these agents on cell viability, apoptosis, reactive oxygen species (ROS) [...] Read more.
Background and Objectives: This study aimed to investigate the anticancer effects and potential synergistic interactions of quercetin (Q) and doxorubicin (Dox) on the MG-63 osteosarcoma (OS) cell line. Specifically, the effects of these agents on cell viability, apoptosis, reactive oxygen species (ROS) generation, antioxidant defense, and the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt1) signaling pathway were evaluated. Material and Methods: MG-63 cells were cultured and treated with varying concentrations of Q and Dox, both individually and in combination (fixed 5:1 molar ratio), for 48 h. Cell viability was assessed using an MTT assay, and IC50 values were calculated. Synergistic effects were analyzed using the Chou–Talalay combination index (CI). Apoptosis was evaluated via Annexin V-FITC/PI staining and caspase-3/7 activity. ROS levels were quantified using DCFH-DA probe, and antioxidant enzymes (SOD, GPx) were measured spectrophotometrically. Gene expression (Runx2, PI3K, Akt1, caspase-3) was analyzed by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Results: Q and Dox reduced cell viability in a dose-dependent manner, with IC50 values of 70.3 µM and 1.14 µM, respectively. The combination treatment exhibited synergistic cytotoxicity (CI < 1), especially in the Q50 + Dox5 group (CI = 0.23). Apoptosis was significantly enhanced in the combination group, evidenced by increased Annexin V positivity and caspase-3 activation. ROS levels were markedly elevated, while antioxidant enzyme activities declined. RT-qPCR revealed upregulation of caspase-3 and downregulation of Runx2, PI3K, and Akt1 mRNA levels. Conclusions: The combination of Q and Dox exerts synergistic anticancer effects in MG-63 OS cells by inducing apoptosis, elevating oxidative stress, suppressing antioxidant defense, and inhibiting the PI3K/Akt1 signaling pathway and Runx2 expression. These findings support the potential utility of Q as an adjuvant to enhance Dox efficacy in OS treatment. Full article
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18 pages, 3973 KiB  
Article
Identification and Characterization of Static Craniofacial Defects in Pre-Metamorphic Xenopus laevis Tadpoles
by Emilie Jones, Jay Miguel Fonticella and Kelly A. McLaughlin
J. Dev. Biol. 2025, 13(3), 26; https://doi.org/10.3390/jdb13030026 - 25 Jul 2025
Viewed by 340
Abstract
Craniofacial development is a complex, highly conserved process involving multiple tissue types and molecular pathways, with perturbations resulting in congenital defects that often require invasive surgical interventions to correct. Remarkably, some species, such as Xenopus laevis, can correct some craniofacial abnormalities during [...] Read more.
Craniofacial development is a complex, highly conserved process involving multiple tissue types and molecular pathways, with perturbations resulting in congenital defects that often require invasive surgical interventions to correct. Remarkably, some species, such as Xenopus laevis, can correct some craniofacial abnormalities during pre-metamorphic stages through thyroid hormone-independent mechanisms. However, the full scope of factors mediating remodeling initiation and coordination remain unclear. This study explores the differential remodeling responses of craniofacial defects by comparing the effects of two pharmacological agents, thioridazine-hydrochloride (thio) and ivermectin (IVM), on craniofacial morphology in X. laevis. Thio-exposure reliably induces a craniofacial defect that can remodel in pre-metamorphic animals, while IVM induces a permanent, non-correcting phenotype. We examined developmental changes from feeding stages to hindlimb bud stages and mapped the effects of each agent on the patterning of craniofacial tissue types including: cartilage, muscle, and nerves. Our findings reveal that thio-induced craniofacial defects exhibit significant consistent remodeling, particularly in muscle, with gene expression analysis revealing upregulation of key remodeling genes, matrix metalloproteinases 1 and 13, as well as their regulator, prolactin.2. In contrast, IVM-induced defects show no significant remodeling, highlighting the importance of specific molecular and cellular factors in pre-metamorphic craniofacial correction. Additionally, unique neuronal profiles suggest a previously underappreciated role for the nervous system in tissue remodeling. This study provides novel insights into the molecular and cellular mechanisms underlying craniofacial defect remodeling and lays the groundwork for future investigations into tissue repair in vertebrates. Full article
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21 pages, 13309 KiB  
Article
Genome-Wide Identification, Evolution and Expression Analysis of GRAS Transcription Factor Gene Family Under Viral Stress in Nicotiana benthamiana
by Keyan Yao, Shuhao Cui, Songbai Zhang, Hao Cao, Long He and Jie Chen
Plants 2025, 14(15), 2295; https://doi.org/10.3390/plants14152295 - 25 Jul 2025
Viewed by 328
Abstract
The GRAS gene family not only performs a variety of regulatory functions in plant growth and development but also plays a key role in the defense mechanisms of plants in response to environmental stresses. Although GRASs have been identified in many species, research [...] Read more.
The GRAS gene family not only performs a variety of regulatory functions in plant growth and development but also plays a key role in the defense mechanisms of plants in response to environmental stresses. Although GRASs have been identified in many species, research on them in Nicotiana benthamiana remains relatively limited until now. In this study, we comprehensively analyzed the GRAS gene family in N. benthamiana plants. Phylogenetic analysis displayed that all identified NbGRASs were classified into eight different subfamilies. Gene duplication analysis revealed that segmental duplication was the main driving force for the expansion of the NbGRAS gene family, with a total of 40 segmental duplication pairs identified. NbGRASs were unevenly distributed across the 19 chromosomes. Additionally, both gene families exhibited a relatively weak codon usage bias, a pattern shaped by mutational and selective pressures. Expression analysis showed that NbGRASs had tissue-specific expression patterns, with relatively high expression levels being observed in leaves and roots. The expression of NbGRASs was significantly changed under tomato yellow leaf curl virus or bamboo mosaic virus infection, suggesting that these NbGRASs can be involved in the plant’s antiviral response. These findings provide new perspectives for in-depth understanding of the evolution and functions of the GRAS gene family in N. benthamiana. Full article
(This article belongs to the Section Plant Protection and Biotic Interactions)
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24 pages, 5977 KiB  
Article
An Investigation into the Evolutionary Characteristics and Expression Patterns of the Basic Leucine Zipper Gene Family in the Endangered Species Phoebe bournei Under Abiotic Stress Through Bioinformatics
by Yizhuo Feng, Almas Bakari, Hengfeng Guan, Jingyan Wang, Linping Zhang, Menglan Xu, Michael Nyoni, Shijiang Cao and Zhenzhen Zhang
Plants 2025, 14(15), 2292; https://doi.org/10.3390/plants14152292 - 25 Jul 2025
Viewed by 322
Abstract
The bZIP gene family play a crucial role in plant growth, development, and stress responses, functioning as transcription factors. While this gene family has been studied in several plant species, its roles in the endangered woody plant Phoebe bournei remain largely unclear. This [...] Read more.
The bZIP gene family play a crucial role in plant growth, development, and stress responses, functioning as transcription factors. While this gene family has been studied in several plant species, its roles in the endangered woody plant Phoebe bournei remain largely unclear. This study comprehensively analyzed the PbbZIP gene family in P. bournei, identifying 71 PbbZIP genes distributed across all 12 chromosomes. The amino acid count in these genes ranged from 74 to 839, with molecular weights varying from 8813.28 Da to 88,864.94 Da. Phylogenetic analysis categorized the PbbZIP genes into 12 subfamilies (A-K, S). Interspecific collinearity analysis revealed homologous PbbZIP genes between P. bournei and Arabidopsis thaliana. A promoter cis-acting element analysis indicated that PbbZIP genes contain various elements responsive to plant hormones, stress signals, and light. Additionally, expression analysis of public RNA-seq data showed that PbbZIP genes are distributed across multiple tissues, exhibiting distinct expression patterns specific to root bark, root xylem, stem bark, stem xylem, and leaves. We also performed qRT-PCR analysis on five representative PbbZIP genes (PbbZIP14, PbbZIP26, PbbZIP32, PbbZIP67, and PbbZIP69). The results demonstrated significant differences in the expression of PbbZIP genes under various abiotic stress conditions, including salt stress, heat, and drought. Notably, PbbZIP67 and PbbZIP69 exhibited robust responses under salt or heat stress conditions. This study confirmed the roles of the PbbZIP gene family in responding to various abiotic stresses, thereby providing insights into its functions in plant growth, development, and stress adaptation. The findings lay a foundation for future research on breeding and enhancing stress resistance in P. bournei. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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