Biology

2 pages, 144 KiB

Open AccessRetraction

RETRACTED: Rehman et al. Piperine Regulates Nrf-2/Keap-1 Signalling and Exhibits Anticancer Effect in Experimental Colon Carcinogenesis in Wistar Rats. Biology 2020, 9, 302

by Muneeb U. Rehman, Summya Rashid, Azher Arafah, Wajhul Qamar, Rana M. Alsaffar, Ajaz Ahmad, Nada M. Almatroudi, Saeed M. A. Alqahtani, Shahzada Mudasir Rashid and Sheikh Bilal Ahmad

Biology 2025, 14(5), 464; https://doi.org/10.3390/biology14050464 (registering DOI) - 25 Apr 2025

Abstract

The journal retracts the article, “Piperine Regulates Nrf-2/Keap-1 Signalling and Exhibits Anticancer Effect in Experimental Colon Carcinogenesis in Wistar Rats” [...] Full article

(This article belongs to the Special Issue Bioactivity of Medicinal Plants and Extracts)

19 pages, 788 KiB

Open AccessReview

Omega-3 Fatty Acids and Exercise in Obesity Management: Independent and Synergistic Benefits in Metabolism and Knowledge Gaps

by Viviana Sandoval, Álvaro Vergara-Nieto, Amanda Bentes, Saulo Silva, Carolina Núñez and Sergio Martínez-Huenchullán

Biology 2025, 14(5), 463; https://doi.org/10.3390/biology14050463 - 24 Apr 2025

Abstract

Obesity is a significant global health issue, profoundly affecting metabolic and cardiovascular health and other related chronic conditions. In Chile, the prevalence of obesity is among the highest within the Organisation for Economic Cooperation and Development (OECD) countries, highlighting a critical public health [...] Read more.

Obesity is a significant global health issue, profoundly affecting metabolic and cardiovascular health and other related chronic conditions. In Chile, the prevalence of obesity is among the highest within the Organisation for Economic Cooperation and Development (OECD) countries, highlighting a critical public health challenge. This narrative review examines current evidence on the independent and potential synergistic roles of omega-3 fatty acids and exercise in managing obesity-related metabolic dysfunction. Omega-3 fatty acids, particularly eicosapentaenoic acid (EPA), have been shown to lower triglyceride levels, enhance lipid metabolism, and modulate inflammation via pathways involving peroxisome proliferator-activated receptors (PPARs) and sterol regulatory element-binding protein-1c (SREBP-1c). Exercise interventions, such as moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT), provide distinct yet complementary metabolic benefits. Specifically, MICT improves body fat distribution and mitochondrial efficiency, whereas HIIT has notable effects on metabolic adaptability and insulin signaling. Additionally, emerging evidence points toward a potential role of the kinin-kallikrein system, particularly kallikrein 7 (KLK7), in obesity-associated insulin resistance. Despite these promising findings, several knowledge gaps persist regarding optimal dosing, intervention timing, population-specific effects, and the exact mechanisms behind the potential synergistic interactions between omega-3 supplementation and structured exercise. This review emphasizes the importance of conducting further research, particularly controlled clinical trials, to clarify these combined interventions’ effectiveness and establish targeted therapeutic strategies tailored to individual metabolic profiles. Full article

(This article belongs to the Section Physiology)

► Show Figures

Figure 1

47 pages, 1408 KiB

Open AccessArticle

Stability Analysis of a Four-Species Periodic Diffusive Predator–Prey System with Delay and Feedback Control

by Lili Jia and Changyou Wang

Biology 2025, 14(5), 462; https://doi.org/10.3390/biology14050462 - 24 Apr 2025

Abstract

In this work, we present a novel four-species periodic diffusive predator–prey model, which incorporates delay and feedback control mechanisms, marking substantial progress in ecological modeling. This model offers a more realistic and detailed portrayal of the intricate dynamics of predator–prey interactions. Our primary [...] Read more.

In this work, we present a novel four-species periodic diffusive predator–prey model, which incorporates delay and feedback control mechanisms, marking substantial progress in ecological modeling. This model offers a more realistic and detailed portrayal of the intricate dynamics of predator–prey interactions. Our primary objective is to establish the existence of a periodic solution for this new model, which depends only on time variables and is independent of spatial variables (we refer to it as a spatially homogeneous periodic solution). By employing the comparison theorem and the fixed point theorem tailored for delay differential equations, we derive a set of sufficient conditions that guarantee the emergence of such a solution. This analytical framework lays a solid mathematical foundation for understanding the periodic behaviors exhibited by predator–prey systems with delayed and feedback-regulated interactions. Moreover, we explore the global asymptotic stability of the aforementioned periodic solution. We organically combine Lyapunov stability theory, upper and lower solution techniques for partial differential equations with delay, and the squeezing theorem for limits to formulate additional sufficient conditions that ensure the stability of the periodic solution. This stability analysis is vital for forecasting the long-term outcomes of predator–prey interactions and evaluating the model’s resilience against disturbances. To validate our theoretical findings, we undertake a series of numerical simulations. These simulations not only corroborate our analytical results but also further elucidate the dynamic behaviors of the four-species predator–prey model. Our research enhances our understanding of the complex interactions within ecological systems and carries significant implications for the conservation and management of biological populations. Full article

(This article belongs to the Topic Conservation at the Crossroads: Forest Ecology, Wildlife Dynamics, and Emerging Challenges for Ecosystem Resilience)

22 pages, 1455 KiB

Open AccessReview

Cross-Kingdom DNA Methylation Dynamics: Comparative Mechanisms of 5mC/6mA Regulation and Their Implications in Epigenetic Disorders

by Yu Liu, Ying Wang, Dapeng Bao, Hongyu Chen, Ming Gong, Shujing Sun and Gen Zou

Biology 2025, 14(5), 461; https://doi.org/10.3390/biology14050461 - 24 Apr 2025

Abstract

DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns—characterized by spatial-temporal dysregulation and stochastic molecular noise—serve as key drivers of diverse [...] Read more.

DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns—characterized by spatial-temporal dysregulation and stochastic molecular noise—serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Regulation of Gene Expression)

► Show Figures

Figure 1

18 pages, 746 KiB

Open AccessReview

Animal Models in Rheumatoid Arthritis: Is There a Correlation Between Autoantibodies in Human Pathology and Animal Models?

by Miguel Marco-Bonilla, Maria Fresnadillo, Macarena de la Riva-Bueno, Gabriel Herrero-Beaumont, Raquel Largo and Aránzazu Mediero

Biology 2025, 14(5), 460; https://doi.org/10.3390/biology14050460 - 24 Apr 2025

Abstract

RA is a chronic autoimmune disease characterized by synovial inflammation and joint damage, driven by autoantibodies such as ACPA, anti-CarP and RF. These autoantibodies, influenced by genetic and environmental factors, play a crucial role in RA pathogenesis through post-translational modifications like citrullination, carbamylation, [...] Read more.

RA is a chronic autoimmune disease characterized by synovial inflammation and joint damage, driven by autoantibodies such as ACPA, anti-CarP and RF. These autoantibodies, influenced by genetic and environmental factors, play a crucial role in RA pathogenesis through post-translational modifications like citrullination, carbamylation, and acetylation. The early detection of ACPA provides a potential window for intervention, while anti-CarP antibodies correlate with severe disease progression and RF aids in diagnosis. Translating these findings from human pathology to animal models presents significant challenges. Although the presence of adaptative immune cells (T cells) is well defined in animal models of RA, studies yield inconsistent results regarding autoantibody production and implication in the disease onset and progression, with varying detectability of ACPA, anti-CarP antibodies, and RF across different species and models. The collagen-induced arthritis (CIA) model shows PAD4 expression and citrullinated protein presence but inconsistent ACPA detection, while the K/BxN model elucidates the pathogenicity of anti-GPI autoantibodies and implicates Fcγ receptors in disease processes. Therefore, further research is needed to bridge the gap between animal models and human RA pathology. Future studies should focus on developing more representative animal models, exploring pharmacological targets and pathways that involve the interplay between anti-inflammatory and autoimmune responses, and investigating the complex interplay between genetic predisposition, environmental triggers, and autoimmune mechanisms. This approach may lead to improved early diagnostic tools, targeted therapies, and potentially preventive strategies for RA, ultimately enhancing patient outcomes and quality of life. Full article

(This article belongs to the Special Issue Animal Models of Arthritis)

► Show Figures

Graphical abstract

15 pages, 2895 KiB

Open AccessArticle

Transcriptome and Metabolome Analyses Reveal High-Altitude Adaptation in the Qinghai Toad-Headed Lizard Phrynocephalus vlangalii

by Jun Zhong, Jian Chen, Yu-Hong Lu, Yu-Fei Huang, Ming-Sheng Hong and Xiang Ji

Biology 2025, 14(5), 459; https://doi.org/10.3390/biology14050459 - 24 Apr 2025

Abstract

The plateau environments are always harsh, with low pressure, low oxygen, and low temperature, which are detrimental to the survival of organisms. The Qinghai toad-headed lizard Phrynocephalus vlangalii has a wide range of altitude adaptation from 2000 to 4600 m. But it is [...] Read more.

The plateau environments are always harsh, with low pressure, low oxygen, and low temperature, which are detrimental to the survival of organisms. The Qinghai toad-headed lizard Phrynocephalus vlangalii has a wide range of altitude adaptation from 2000 to 4600 m. But it is still unclear how organisms maintain tissue function by balancing energy supply and demand changes in high-altitude environments of P. vlangalii. We investigated the plateau metabolic adaptation through transcriptome and metabolome analyses of P. vlangalii from three populations at different altitudes of the Qinghai-Tibet Plateau. The genes related to carbohydrate metabolism were significantly down-regulated at the high altitude. The metabolites alpha-D-glucose 1-phosphate, beta-D-fructose 6-phosphate, D-glycerate 1,3-diphosphate, 3-phosphoglycerate, and phosphoenolpyruvate in glycolysis/gluconeogenesis were down-regulated, too. The lipid metabolic and fatty acid synthase-related genes were up-regulated at a high altitude. In conclusion, the glycogen utilization-related genes and metabolites experienced broad down-regulation, while lipid-related genes and metabolites had a clear trend of up-regulation. Thus, we suggest that P. vlangalii tends to increase lipid utilization and reduce the dependence on glycogen consumption to acclimatize to the high-altitude environment. Full article

(This article belongs to the Topic Conservation at the Crossroads: Forest Ecology, Wildlife Dynamics, and Emerging Challenges for Ecosystem Resilience)

► Show Figures

Figure 1

16 pages, 4088 KiB

Open AccessArticle

Whole Genome Sequencing of Kodamaea ohmeri SSK and Its Characterization for Degradation of Inhibitors from Lignocellulosic Biomass

by Yong-Qiang Yang, Xu Li, Zhi-Fei Wang, Yu-Long Deng, Zhen-Zhi Wang, Xing-Yu Fang, Mao-Dong Zhang, Wei Sun, Xin-Qing Zhao, Zhi-Qiang Liu and Feng-Li Zhang

Biology 2025, 14(5), 458; https://doi.org/10.3390/biology14050458 - 24 Apr 2025

Abstract

Lignocellulosic biomass is widely recognized as a renewable resource for bioconversion. However, the presence of inhibitors such as furfural, 5-HMF, and acetic acid can inhibit cell growth, thereby affecting the overall efficiency of the bioconversion process. The studies on the degradation of lignocellulosic [...] Read more.

Lignocellulosic biomass is widely recognized as a renewable resource for bioconversion. However, the presence of inhibitors such as furfural, 5-HMF, and acetic acid can inhibit cell growth, thereby affecting the overall efficiency of the bioconversion process. The studies on the degradation of lignocellulosic hydrolysate inhibitors by Saccharomyces cerevisiae have been limited. In this research, a yeast strain Kodamaea ohmeri can degrade inhibitors furfural, 5-HMF, and acetic acid, and the genome sequence of the strain was analyzed. Furthermore, the molecular detoxification mechanism of K. ohmeri SSK against lignocellulosic hydrolysate inhibitors was predicted using whole genome sequencing. Annotation based on the COG/KEGG databases identified 57 key detoxification genes, including the alcohol dehydrogenase (ADH) gene, aldo-keto/aldehyde reductase (AKR/ARI) gene, and aldehyde dehydrogenase (ALDH) gene. Stress tolerance experiments revealed that the maximum tolerance concentration for the strain was 5.2 g/L of furfural, 2.5 g/L of 5-HMF, and 5.9 g/L of acetic acid, respectively. A NAD(P)⁺-dependent bifunctional enzyme with possible ADH and ARI activities was found by conserved domain analysis. Phylogenetic analysis indicated that this enzyme shared 99% homology with the detoxification enzyme from S. cerevisiae S288C (GenBank: Q04894.1). This study represents the first comprehensive analysis of the inhibitor detoxification network in K. ohmeri SSK from a genome perspective, providing theoretical targets and design strategies for developing highly efficient biorefinery strains. Full article

(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))

► Show Figures

Figure 1

13 pages, 4655 KiB

Open AccessArticle

Cloning, Expression, and Bioinformatics Analysis of the AvFD1 Gene in Amomum villosum Lour

by Duo Wang, Yating Zhu, Shuang Li, Hongyou Zhao, Chongnan Wang, Qianxia Li, Yanfang Wang, Chunyong Yang, Ge Li, Yanqian Wang and Lixia Zhang

Biology 2025, 14(5), 457; https://doi.org/10.3390/biology14050457 - 24 Apr 2025

Abstract

As a perennial medicinal plant in the Zingiber genus, Amomum villosum Lour. faces agricultural challenges due to its prolonged vegetative and reproductive growth phases, which hinder efficient pollination and delay fruiting. To address this limitation, the present study aimed to identify the FD [...] Read more.

As a perennial medicinal plant in the Zingiber genus, Amomum villosum Lour. faces agricultural challenges due to its prolonged vegetative and reproductive growth phases, which hinder efficient pollination and delay fruiting. To address this limitation, the present study aimed to identify the FD gene involved in regulating flowering in A. villosum to provide a basis for research on the molecular mechanisms of early fruiting cultivars. Based on the differentially expressed gene AvFD1 obtained from the transcriptome database of early fruiting plants and controls, specific primers were designed for PCR to clone the full-length sequence of AvFD1. The characteristics of the cloned AvFD1 gene were analyzed using online bioinformatics software. The expression profiles of AvFD1 in various tissues and in 1- and 2-year bearing A. villosum varieties were investigated by quantitative real-time PCR. This study successfully cloned the FD1 gene sequence of A. villosum, marking the first reported characterization of this gene in the species. Tissue-specific expression analysis revealed significantly elevated AvFD1 expression levels in stolon tips and flower buds compared to tender leaves, suggesting its potential role as a positive regulator of flowering initiation. The obtained sequence establishes essential molecular data for subsequent functional validation of AvFD1 in A. villosum. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Graphical abstract

20 pages, 1221 KiB

Open AccessReview

Experimental PTSD Models in Zebrafish: A Systematic Review of Behavioral, Neurochemical, and Molecular Outcomes

by Alexey Sarapultsev, Evgenii Gusev, Desheng Hu and Maria Komelkova

Biology 2025, 14(5), 456; https://doi.org/10.3390/biology14050456 - 23 Apr 2025

Abstract

Post-traumatic stress disorder (PTSD) is a complex psychiatric condition characterized by persistent behavioral and neurobiological alterations following trauma. Although rodent models are commonly used to study PTSD, zebrafish (Danio rerio) have emerged as a promising alternative due to their genetic similarity [...] Read more.

Post-traumatic stress disorder (PTSD) is a complex psychiatric condition characterized by persistent behavioral and neurobiological alterations following trauma. Although rodent models are commonly used to study PTSD, zebrafish (Danio rerio) have emerged as a promising alternative due to their genetic similarity to humans, conserved stress response systems, and high-throughput capabilities. This systematic review evaluates 33 experimental studies on zebrafish PTSD models, focusing on behavioral, neurochemical, and molecular outcomes. Chronic unpredictable stress (CUS/UCS) paradigms of 14–15 days were identified as the most reliable for inducing PTSD-like phenotypes, consistently resulting in anxiety-like behaviors, cortisol dysregulation, and gene expression changes. In contrast, acute stress models produced transient effects, and social defeat paradigms showed methodological variability. Chronic models frequently demonstrated neurotransmitter imbalances, oxidative stress, and upregulation of inflammatory and neuroplasticity-related genes. However, the literature revealed challenges, including protocol heterogeneity, limited sex-specific analyses, and constraints in longitudinal biomarker tracking. Future directions include epigenetic profiling, environmental standardization, and cross-species validation. When used with methodological rigor, zebrafish offer a powerful and translationally relevant platform to study PTSD mechanisms and screen novel interventions. Full article

(This article belongs to the Special Issue Social Behavior in Zebrafish)

► Show Figures

Figure 1

18 pages, 4050 KiB

Open AccessArticle

Curcumin Nanocarriers in the Protection Against Iron- and Alcohol-Induced Oxidative Stress in a Cellular Model of Liver Disease

by Lucy Petagine, Mohammed G. Zariwala, Satyanarayana Somavarapu, Stefanie Ho Yi Chan and Vinood B. Patel

Biology 2025, 14(5), 455; https://doi.org/10.3390/biology14050455 - 23 Apr 2025

Abstract

During chronic alcohol misuse, hepatic iron overload occurs, leading to exacerbated oxidative stress and liver injury. The aim was to study formulations encapsulated with the antioxidant curcumin to assess their ability protect against oxidative stress in a model of alcohol-related liver disease (ALD) [...] Read more.

During chronic alcohol misuse, hepatic iron overload occurs, leading to exacerbated oxidative stress and liver injury. The aim was to study formulations encapsulated with the antioxidant curcumin to assess their ability protect against oxidative stress in a model of alcohol-related liver disease (ALD) combined with iron. HepG2 (VL-17A) cells were treated with iron (50 µM) alone or with alcohol (200 to 350 mM) over 72 h and markers of oxidative damage, cell death, and mitochondrial function were assessed. Nanoformulations encapsulating curcumin were also studied. VL-17A cells treated with both ethanol and iron showed significant decreases in cell viability (64%, p < 0.0001) when compared to control, and a 56% decrease (p = 0.0279) when compared to iron-only treatment. Iron-alone treatment caused a 115% increase (p < 0.0001) in ROS at 48 h as well as increases of up to 118% when treated with 200 mM ethanol + 50 μM iron (p < 0.0001), compared to control DMEM. The study found that 10 µM curcumin DSPE-PEG increased cell viability by 17% and 41% when compared to control and iron treatment alone, respectively. Formulations reduced ROS by 36% (p = 0.0015) when compared to iron-alone treatment. In summary, encapsulated curcumin provided antioxidant capacity and reduced oxidative stress, demonstrating the therapeutic potential for curcumin formulations in ALD combined with iron dysregulation. Full article

(This article belongs to the Special Issue Recent Advances in Metabolic Disorders)

► Show Figures

Figure 1

16 pages, 1926 KiB

Open AccessArticle

The Evaluation of Significance of Uncoupling Protein Genes UCP1, UCP2, UCP3, UCP4, UCP5, and UCP6 in Human Adaptation to Cold Climates

by Alena A. Nikanorova, Nikolay A. Barashkov, Vera G. Pshennikova, Sergey S. Nakhodkin, Georgii P. Romanov, Aisen V. Solovyev and Sardana A. Fedorova

Biology 2025, 14(5), 454; https://doi.org/10.3390/biology14050454 - 23 Apr 2025

Abstract

Six isoforms of uncoupling proteins (UCPs) exist, spanning from UCP1 to UCP6. A precise physiological function has only been established for UCP1, which is involved in non-shivering thermogenesis, but the functions of other UCPs are still not fully defined. Therefore, the purpose of [...] Read more.

Six isoforms of uncoupling proteins (UCPs) exist, spanning from UCP1 to UCP6. A precise physiological function has only been established for UCP1, which is involved in non-shivering thermogenesis, but the functions of other UCPs are still not fully defined. Therefore, the purpose of the present study is to search for indications of the involvement of nine polymorphic variants of UCP1-6 genes in human adaptation to cold climates using four criteria: (1) the presence of associations of polymorphic variants of UCP genes with levels of thyroid-stimulating hormone, free triiodothyronine, and free thyroxine; (2) the presence of associations of polymorphic variants of UCP genes with changes in thyroid homeostasis (SPINA); (3) the presence of associations of polymorphic variants of UCP genes with body surface area; (4) the presence of signals of directional selection to cold climate for polymorphic variants of UCP genes. As a result of the evaluation, the highest scores for cold adaptation traits were recorded for polymorphic variants rs3811787 of the UCP1 gene and rs1800849 of the UCP3 gene. We suggest that the results obtained indicate the importance of uncoupling proteins UCP1 and UCP3 in human adaptation to cold through processes of non-shivering and shivering thermogenesis. Full article

(This article belongs to the Special Issue Unveiling Novel Gene Functions: Mechanisms, Evolution and Applications)

► Show Figures

Figure 1

13 pages, 4098 KiB

Open AccessArticle

Effects of Toxic Organic Compounds on Tenebrio molitor and Its Parasite Gregarina steini

by Denis Rybalka and Viktor Brygadyrenko

Biology 2025, 14(5), 453; https://doi.org/10.3390/biology14050453 - 23 Apr 2025

Abstract

Environmental pollution by toxic compounds affects various species of living organisms, their life cycles, and symbiotic relationships. This study investigated the host-parasite relationship between Tenebrio molitor Linnaeus, 1758 (Coleoptera, Tenebrionidae) and Gregarina steini Berthold, 1827 (Eugregarinorida, Gregarinida) under exposure to aniline, formaldehyde, and [...] Read more.

Environmental pollution by toxic compounds affects various species of living organisms, their life cycles, and symbiotic relationships. This study investigated the host-parasite relationship between Tenebrio molitor Linnaeus, 1758 (Coleoptera, Tenebrionidae) and Gregarina steini Berthold, 1827 (Eugregarinorida, Gregarinida) under exposure to aniline, formaldehyde, and o-xylene at different concentrations. For laboratory studies, 480 larvae of T. molitor and five concentrations of the studied organic compounds were used. Groups of T. molitor, each consisting of ten individuals, were subjected to the tested compounds for 10 days following the initial weight measurement. We measured the body weight and survival rate of T. molitor and the number of G. steini in them to assess the impact of the tested organic compounds on the host-parasite relationship. For all the compounds studied, a decrease in body weight and high mortality were observed in T. molitor at high concentrations. The lethality of the studied organic compounds was concentration-dependent. o-Xylene showed low toxicity at lower concentrations (10.4 and 26.0 mg/kg of feed), with a survival rate of 93.3% and 86.7%, respectively. At a concentration of 10.4 mg/kg, no lethal cases in T. molitor were observed. At higher concentrations (78 and 104 mg/kg feed), T. molitor mortality significantly increased to 33.3% and 53.3%, respectively. Full article

► Show Figures

Figure 1

20 pages, 5242 KiB

Open AccessArticle

Metabonomics Analysis Reveals the Influence Mechanism of Three Potassium Levels on the Growth, Metabolism and Accumulation of Medicinal Components of Bupleurum scorzonerifolium Willd. (Apiaceae)

by Jialin Sun, Jianhao Wu, Alyaa Nasr, Zhonghua Tang, Weili Liu, Xiubo Liu and Wei Ma

Biology 2025, 14(5), 452; https://doi.org/10.3390/biology14050452 - 22 Apr 2025

Abstract

Bupleurum scorzonerifolium Willd. is a commonly used bulk Chinese herbal remedy. Due to the large-scale mining of wild Bupleurum scorzonerifolium Willd., its natural resources are gradually exhausted. In addition, there are some problems in Bupleurum scorzonerifolium Willd. cultivation, such as lack of guidance, [...] Read more.

Bupleurum scorzonerifolium Willd. is a commonly used bulk Chinese herbal remedy. Due to the large-scale mining of wild Bupleurum scorzonerifolium Willd., its natural resources are gradually exhausted. In addition, there are some problems in Bupleurum scorzonerifolium Willd. cultivation, such as lack of guidance, excessive application of fertilizers and so on, which lead to the yield and quality of Bupleurum to be below the standard value. Therefore, it is significant to clarify the regulation of quality and yield under different levels of fertilizers. In this study, three different levels of potassium fertilizer were applied; then, the metabolites in different parts of Bupleurum were analyzed by gas chromatography–mass spectrometry (GC–MS) to detect the alterations in the metabolic spectrum and recognize both the accumulation and distribution of key metabolites in response to each level of potassium fertilizer. The contents of various mineral elements, such as sodium, calcium, potassium, magnesium, manganese, zinc, iron, and copper, in different parts of Bupleurum under different potassium levels were determined. Potassium fertilizer had a significant impact on the absorption and distribution of these mineral elements. There were synergistic and antagonistic effects between each element and K⁺. The results showed that low and high potassium levels could promote the progression of main shoots and roots, but inhibited the accumulation of dry matter in lateral shoots and flowers. Low potassium levels stimulated the content of saikosaponin a in all plant parts, while high potassium levels inhibited the accumulation of most saikosaponin a,c and d. A total of 77 metabolites were identified by GC–MS, of which glycerol, d-glucose, silane and copper phthalocyanine were highlighted as the key metabolites in response to potassium fertilizer. The abovementioned metabolites are mapped into insulin signaling pathways, streptomycin biosynthesis, galactose metabolism and other metabolic pathways, sustaining the metabolic regulation of Bupleurum scorzonerifolium Willd. Full article

(This article belongs to the Special Issue Research Progress on Salt Stress in Plants)

► Show Figures

Figure 1

15 pages, 9108 KiB

Open AccessStudy Protocol

Habitat Suitability Shifts of Eucommia ulmoides in Southwest China Under Climate Change Projections

by Qi Liu, Longjiang Liu, Juan Xue, Peiyao Shi and Shanshan Liang

Biology 2025, 14(4), 451; https://doi.org/10.3390/biology14040451 - 21 Apr 2025

Abstract

As a Chinese endemic species with dual medicinal–industrial importance, Eucommia ulmoides faces habitat challenges under climate change. Using 21 bioclimatic variables and 704 occurrence records, we modeled current and future (2021–2100) distributions via MaxEnt 3.4.4 and ArcGIS 10.8. The results indicate the following: [...] Read more.

As a Chinese endemic species with dual medicinal–industrial importance, Eucommia ulmoides faces habitat challenges under climate change. Using 21 bioclimatic variables and 704 occurrence records, we modeled current and future (2021–2100) distributions via MaxEnt 3.4.4 and ArcGIS 10.8. The results indicate the following: (1) current optimal habitats cluster in the mid-elevation valleys of Daba–Wuling Mountains (Guizhou–Chongqing core); (2) SSP5-8.5 projections suggest a 19.2% reduction in high-suitability areas by 2081–2100 versus SSP1-2.6; and (3) distribution centroids migrate southward under both scenarios. Our multi-temporal analysis provides actionable intelligence for ex situ conservation and agroforestry planning. Full article

► Show Figures

Graphical abstract

12 pages, 1070 KiB

Open AccessArticle

Seminal F₂-IsoP and RvD1 Levels in Idiopathic Infertile Men

by Elena Moretti, Giulia Collodel, Caterina Marcucci, Laura Liguori, Laura Gambera and Cinzia Signorini

Biology 2025, 14(4), 450; https://doi.org/10.3390/biology14040450 - 21 Apr 2025

Abstract

30 percent of infertile men are diagnosed with idiopathic infertility. This study aimed to assess oxidative stress in the semen of 77 patients with idiopathic infertility by measuring F₂-isoprostane (F₂-IsoP), resolvin D1 (RvD1) levels, and semen parameters. The presence [...] Read more.

30 percent of infertile men are diagnosed with idiopathic infertility. This study aimed to assess oxidative stress in the semen of 77 patients with idiopathic infertility by measuring F₂-isoprostane (F₂-IsoP), resolvin D1 (RvD1) levels, and semen parameters. The presence and localization of 8-IsoProstaglandin F_2α were determined using immunofluorescence. No significant correlations were observed for F₂-IsoP and RvD1 levels with the semen variables. Based on F₂-IsoP levels, individuals were classified into two groups: Group 1 (F₂-IsoPs ≤ 29.96 ng/mL, 51%) and Group 2 (F₂-IsoPs > 29.96 ng/mL, 49%). In comparison to Group 1, Group 2 showed significantly higher F₂-IsoP levels (13.33 ng/mL vs. 44.80 ng/mL; p < 0.05), a lower progressive motility percentage (30% vs. 25%; p < 0.05), and increased RvD1 levels (36.09% vs. 44.94%). Immunofluorescence analysis revealed a different localization of 8-IsoProstaglandin F_2α in the ejaculated sperm of Group 1 compared to that observed in Group 2. A weak signal was detected in the sperm tail (Group 1, 79.1% vs. Group 2, 36.9; p < 0.01). In spermatozoa of Group 2 patients, a strong signal in the acrosome, midpiece, and tail was highlighted. These findings suggest the need to test oxidative stress during routine semen analysis in patients with idiopathic infertility to improve diagnosis and treatment. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

► Show Figures

Figure 1

12 pages, 2110 KiB

Open AccessArticle

Genetic Diversity and Structure of Korean Pacific Oyster (Crassostrea gigas) for Determining Selective Breeding Groups

by Kang-Rae Kim, Dain Lee, Kyung-Hee Kim, Hyun Chul Kim, So Hee Kim, Su Jin Park and Deok-Chan Lee

Biology 2025, 14(4), 449; https://doi.org/10.3390/biology14040449 - 21 Apr 2025

Abstract

This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas [...] Read more.

This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas was relatively low. Analysis using AMOVA, genetic differentiation, and DAPC revealed a genetic structure that was consistent with one group. This study identified reference populations to be used for selective breeding to increase the genetic diversity of Korean C. gigas and provided essential data on genetic diversity and structure for future selective breeding efforts in C. gigas. Full article

(This article belongs to the Special Issue Genetic Variability within and between Populations)

► Show Figures

Figure 1

21 pages, 3935 KiB

Open AccessArticle

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Hippophae salicifolia

by Zhefei Zeng, Chunmin Mao, Zhuo Shang, Ngawang Norbu, Ngawang Bonjor, Xiaoyan Jia, Wei Li, Wenju Zhang, Junwei Wang and La Qiong

Biology 2025, 14(4), 448; https://doi.org/10.3390/biology14040448 - 20 Apr 2025

Abstract

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 [...] Read more.

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 tRNA, three rRNA, and three pseudogenes). We identified extensive repetitive elements, including 188 SSRs, 20 tandem repeats, and 455 dispersed repeats, and explored their potential roles in genome evolution. Codon usage analysis showed a bias for codons ending in A or U, while RNA editing analysis revealed 415 sites that mostly convert hydrophilic to hydrophobic amino acids. Phylogenetic and collinearity analyses clarified evolutionary relationships within Hippophae and uncovered genome rearrangements. In addition, extensive gene transfer was detected between the mitochondrial and chloroplast genomes. Ka/Ks and nucleotide diversity analyses indicate that most genes are under purifying selection, with some possibly undergoing positive selection. Overall, these findings enhance our understanding of the structural and evolutionary features of the H. salicifolia mitochondrial genome and provide valuable insights for the genetic improvement and conservation of Hippophae species. Full article

► Show Figures

Figure 1

15 pages, 906 KiB

Open AccessArticle

Effects of Varying Dietary Concentrations of Menadione Nicotinamide Bisulphite (VK₃) on Growth Performance, Muscle Composition, Liver and Muscle Menaquinone-4 Concentration, and Antioxidant Capacities of Coho Salmon (Oncorhynchus kisutch) Alevins

by Han Zhang, Leyong Yu, Abdur Rahman, Sattanathan Govindharajan, Lingyao Li, Hairui Yu and Muhammad Waqas

Biology 2025, 14(4), 447; https://doi.org/10.3390/biology14040447 - 20 Apr 2025

Abstract

Vitamin K₃ (VK₃) is an essential micronutrient for fish growth and metabolism. To determine the optimal required dietary concentration of VK, a 12-week-long trial was planned to investigate the impact of VK₃ on growth performance, muscle composition, liver menaquinone-4 [...] Read more.

Vitamin K₃ (VK₃) is an essential micronutrient for fish growth and metabolism. To determine the optimal required dietary concentration of VK, a 12-week-long trial was planned to investigate the impact of VK₃ on growth performance, muscle composition, liver menaquinone-4 (MK-4), whole-body MK-4 concentration, and antioxidant capacity (T-AOC) in coho salmon alevins. A total of 2100 coho salmon alevins were divided into twenty-one tanks, with 100 alevins in each tank, and three tanks represented one group. Each of the seven groups were randomly assigned to one of the experimental diets formulated with varying levels of menadione nicotinamide bisulphite (VK₃), i.e., 0.16 (control), 5.25, 10.22, 14.93, 20.51, 40.09, and 59.87 mg/kg, respectively. The results revealed that the inclusion of VK₃ from 5.25 to 40.09 mg/kg improved (p < 0.05) the survival rate (SR), weight gain (WG), specific growth rate (SGR), and feed conversion ratio (FCR), while no effect (p > 0.05) was observed on the hepatosomatic index (HSI), viscerosomatic index (VSI), Fulton’s condition factor (K), and muscle composition. The whole-body MK-4, liver MK-4, liver T-AOC, total superoxide dismutase (T-SOD), and catalase (CAT) enzymes were also increased (p < 0.05). Malondialdehyde (MDA) contents were reduced (p < 0.05) in all supplemented groups with a decreasing trend. The predicted optimal required dietary concentrations of VK₃ were found to be 34.0, 43.5, 38.54, and 31.97 mg/kg based on WG, SGR, liver MK-4 concentration, and T-AOC, respectively, by quadratic regression analysis. It is concluded that the dietary VK₃ has improved the growth performance and antioxidant status in alevins during early development in the range of 31.97 to 43.5 mg/kg diet. Full article

(This article belongs to the Special Issue Nutrition, Environment, and Fish Physiology)

► Show Figures

Figure 1

20 pages, 7607 KiB

Open AccessArticle

Identification of the Dof Gene Family in Quinoa and Its Potential Role in Regulating Flavonoid Synthesis Under Different Stress Conditions

by Guangtao Qian, Jinrong Yang, Mingyu Wang and Lixin Li

Biology 2025, 14(4), 446; https://doi.org/10.3390/biology14040446 - 20 Apr 2025

Abstract

Quinoa (Chenopodium quinoa Willd.), often referred to as the “golden grain”, is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, [...] Read more.

Quinoa (Chenopodium quinoa Willd.), often referred to as the “golden grain”, is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, antiviral, anticancer, and antidepressant properties. The DNA binding with one finger (Dof) transcription factor is crucial for regulating growth, development, and stress responses. However, the identification of the Dof family using the latest quinoa genomic data and its function in abiotic stress response have not been fully elucidated. Here, 36 CqDof genes were identified from the quinoa genome and classified into ten subfamilies through phylogenetic analysis. Physicochemical property analysis predicted that CqDofs predominantly encode basic, hydrophilic, and unstable nuclear proteins. CqDofs were distributed across 15 chromosomes, with segmental duplication being the primary driver of their expansion. Subsequently, basic information on CqDofs was systematically analyzed, including conserved motifs, gene structure, cis-acting elements, and expression patterns. Notably, the promoter regions of all CqDof genes were enriched with cis-acting elements related to light responsiveness. Further analysis revealed that red and blue light significantly affected CqDof expression and flavonoid accumulation (epigallocatechin, rutin, naringenin, morin, pinocembrin, quercetin-7-O-rutinoside, quercetin-3-O-glucoside, and naringenin), in which 5 CqDofs exhibited a pronounced response to both light conditions and showed a significant correlation with flavonoid levels. Finally, RT-PCR analysis indicated that the expression levels of CqDofs (except CqDof21) were significantly upregulated under drought, salt, and saline-alkali stresses. These findings lay the groundwork for future studies on how CqDofs regulate flavonoid biosynthesis under different light qualities and function in abiotic stress. Full article

► Show Figures

Figure 1

Journal Description

Biology

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI