Biology

15 pages, 1056 KB

Open AccessArticle

Proteome Analysis of Daily Urine Samples of Pregnant Rats Unveils Developmental Processes of Fetus as Well as Physiological Changes in Mother Rats

by Haitong Wang, Linna Ge, Sijie Chen, Longqin Sun, Wei Sun and Youhe Gao

Biology 2025, 14(12), 1700; https://doi.org/10.3390/biology14121700 (registering DOI) - 28 Nov 2025

Abstract

Significant physiological changes occur in both the fetus and the mother during pregnancy. Urine proteins have been shown to reflect a wide range of physiological and pathological changes in the body. This study employed low-abundance protein-enriched magnetic nanobeads to conduct an in-depth analysis [...] Read more.

Significant physiological changes occur in both the fetus and the mother during pregnancy. Urine proteins have been shown to reflect a wide range of physiological and pathological changes in the body. This study employed low-abundance protein-enriched magnetic nanobeads to conduct an in-depth analysis of the daily changes in urine proteins throughout the entire pregnancy of rats. Based on the 3455 identified urine proteins, fetal and maternal dynamic changes were observed in the pregnancy group compared to the control group, including blastocyst formation and cell division in the early stage of pregnancy. In addition, the morphogenesis- and development-related organs and tissues are significantly enriched at different stages of pregnancy. The 9th day after pregnancy is the stage when organ development is most concentrated, especially the nervous system and vasculature development. During the late stage of pregnancy, maternal-specific changes were observed, such as lactation. These results indicate that urine protein can reflect the fetal and maternal dynamic physiological alterations during pregnancy, which suggests the potential value of urine protein analysis in pregnancy health monitoring. It is emphasized that the analysis focuses on the daily variations in the urine proteins, as these daily changes are expected to reveal more dynamic and detailed information about the physiological processes during pregnancy. Full article

(This article belongs to the Special Issue The Biology of Animal Reproduction)

18 pages, 1489 KB

Open AccessArticle

A Multi-Breed GWAS for Carcass Weight in Jeju Black Cattle and Hanwoo × Jeju Black Crossbreds

by Miyoung Won, Jongan Lee, Sang-Min Shin, Seung-Eun Lee, Won-Jae Kim, Eun-Tae Kim, Tae-Hee Kim, Hee-Bok Park and Borhan Shokrollahi

Biology 2025, 14(12), 1699; https://doi.org/10.3390/biology14121699 (registering DOI) - 28 Nov 2025

Abstract

Carcass weight (CW) is a major determinant of beef yield and market value in Korea, yet the genetic basis of this trait remains largely unexplored in cattle from Jeju Island. In this study, we performed a genome-wide association study (GWAS) using both a [...] Read more.

Carcass weight (CW) is a major determinant of beef yield and market value in Korea, yet the genetic basis of this trait remains largely unexplored in cattle from Jeju Island. In this study, we performed a genome-wide association study (GWAS) using both a mixed linear model (MLM) and the FarmCPU approach, followed by pathway and network analyses to identify loci and biological functions underlying CW variation. A total of 256 Jeju cattle (92 Jeju Black and 164 Jeju Black × Hanwoo crossbreds) were initially sampled. One crossbred sample failed genotyping, leaving 255 animals (92 Jeju Black and 163 crossbreds) for analysis. Animals were genotyped using the Illumina BovineSNP50 v3 BeadChip, and 39,055 high-quality single nucleotide polymorphisms (SNPs) were retained after quality control. The MLM analysis detected no genome-wide significant associations, whereas the FarmCPU analysis identified six significant loci on Bos taurus chromosomes 3, 5, 6, 10, and 13, each explaining 2.55–9.58% of the phenotypic variance. Candidate genes located near these loci included EIF2B3, HECTD3, SOX5, KLF6, PHACTR3, and two uncharacterized protein-coding genes. Functional enrichment analysis identified biologically relevant pathways including lysine degradation, tryptophan metabolism, glycerolipid metabolism, fatty acid biosynthesis, extracellular matrix–receptor interaction, and signaling cascades such as PI3K–Akt and Rap1, although most pathways were not statistically significant after FDR correction. Protein–protein interaction (PPI) network analysis using STRING highlighted modules of signaling, extracellular matrix, and metabolic genes. These clusters suggest that coordinated interactions among these pathways contribute to carcass growth and development. These findings provide new insights into the molecular basis of CW in Jeju Black and Hanwoo × Jeju Black crossbred cattle and identify candidate genes and pathways that may be useful for genomic selection and the sustainable improvement of Jeju Black cattle populations. Full article

(This article belongs to the Special Issue Advances in Animal Functional Genomics)

23 pages, 1921 KB

Open AccessArticle

Multi-Omics Tumor Immunogenicity Score Predicts Immunotherapy Outcome and Survival

by Axel Gschwind, Nadja Ballin, Alexander Ott, Andrea Forschner, Amelie Knapp, Öznur Öner, Michael Bitzer, Ghazaleh Tabatabai, Andreas Hartkopf, Thorben Groß, Markus Reitmajer, Christopher Schroeder, Stephan Ossowski and Sorin Armeanu-Ebinger

Biology 2025, 14(12), 1698; https://doi.org/10.3390/biology14121698 (registering DOI) - 28 Nov 2025

Abstract

Background: Tumor immunogenicity is a concept for modeling the susceptibility of tumors to immune checkpoint inhibitors (ICIs) and other immunotherapies. Single biomarkers, such as tumor mutation burden (TMB) or PDL1 expression, have been shown to correlate with ICI outcomes but are poor predictors [...] Read more.

Background: Tumor immunogenicity is a concept for modeling the susceptibility of tumors to immune checkpoint inhibitors (ICIs) and other immunotherapies. Single biomarkers, such as tumor mutation burden (TMB) or PDL1 expression, have been shown to correlate with ICI outcomes but are poor predictors of overall and progression-free survival (OS, PFS). Complex machine learning models that integrate multiple biomarkers have shown improved predictions but often lack clear a priori interpretability. In this study, we developed a coherent Multi-Omics Tumor Immunogenicity score (MOTIscore) that combines immunogenicity biomarkers derived from genomic and transcriptomic data and demonstrated its generalizability across multiple cancer types. Methods: Several immunogenicity biomarkers, including TMB, neoantigen burden, T-cell receptor repertoire, PDL1 expression, B2M expression, and variants in pathways of ICI response and resistance, were integrated using a weighted sum scoring scheme. The weights were determined using statistical tests in a large melanoma ICI cohort. We compared the MOTIscore with a machine learning (ML) model trained using the same biomarkers and evaluated the model using melanoma, gastric cancer, and pan-cancer datasets. Results: MOTIscore achieved results similar to those of the ML model in predicting ICI in melanoma and gastric cancer, with both outperforming TMB. Gastric cancer and melanoma patients with high MOTIscores had a significantly extended overall and progression-free survival. Gene set enrichment analysis revealed the enrichment of immune-related pathways in patients with high MOTIscores. Differential expression analysis between patients with high and low immunogenicity identified highly expressed C-X-C motif chemokine ligands as important characteristics associated with successful ICI therapy and significantly improved PFS. MOTIscores varied widely across cancers treated in the molecular tumor board at our hospital and showed distinct distributions between non-immunogenic and immunogenic cancer types. Conclusions: MOTIscore demonstrated improved ICI outcome predictions compared to single-omics biomarkers. Patients with higher tumor immunogenicity also show significantly improved OS and PFS in melanoma and gastric cancer. The results demonstrate the potential use of the MOTIscore to prioritize ICI in personalized cancer treatment. However, ICI outcomes and survival should be investigated in prospective studies, and additional cancer types and larger patient cohorts are needed. Full article

(This article belongs to the Special Issue Emerging Hallmarks in Cancer Immunology)

12 pages, 5163 KB

Open AccessArticle

Morphology and Histological Observation of the Male Reproductive System in the Swimming Crab (Portunus trituberculatus)

by Hao Wang, Nahayo Viateur, Litao Wan, Peng Tan, Jie He and Lijian Xue

Biology 2025, 14(12), 1697; https://doi.org/10.3390/biology14121697 (registering DOI) - 28 Nov 2025

Abstract

The swimming crab (Portunus trituberculatus) is an economically important marine crab species in China. Understanding the structure and function of the male reproductive system in the swimming crab is crucial for increasing reproductive efficiency. Although studies on its reproductive biology have [...] Read more.

The swimming crab (Portunus trituberculatus) is an economically important marine crab species in China. Understanding the structure and function of the male reproductive system in the swimming crab is crucial for increasing reproductive efficiency. Although studies on its reproductive biology have increased in recent years, the ultrastructure of the male copulatory system remains insufficiently explored. In this study, gonadal tissues [testes (T), anterior vas deferens (AVD), middle vas deferens (MVD), posterior vas deferens (PVD)] and copulatory organs [first gonopod (G1), second gonopod (G2), penis] of P. trituberculatus were sampled as experimental materials, and we systematically investigated the morphological and functional characteristics of male reproductive and copulatory organs in P. trituberculatus using anatomical, stereomicroscopic and scanning electron microscopic techniques. The results indicate that the male copulatory system comprises the G1, G2, and the penis. The G1 shows a tubular structure, with its endopodite bearing spines that anchor the female during copulation. The G2 is short, stout, solid and rod-shaped, with surface folds and blunt teeth, indicating its role in propelling the spermatophore within the G1. The penis is flexible and covered with elongated, rigid setae. Internally, the reproductive system displays a bilaterally symmetrical “H”-shaped architecture, consisting of the testes; anterior, middle, and posterior vas deferens; and the ejaculatory ducts. These segments have different structures and function in forming, storing, and transporting spermatophores. These findings provide important insights into the reproductive strategies and mating mechanisms of P. trituberculatus. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters (2nd Edition))

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14 pages, 871 KB

Open AccessArticle

Comprehensive Analysis of Mitochondrial Genomic Characteristics and Phylogenetic Analysis of the Plant Genus Ipomoea (Convolvulaceae) Species

by Mengya Xiao, Cheng Zhang, Wenbang Hou and Youjun Li

Biology 2025, 14(12), 1696; https://doi.org/10.3390/biology14121696 (registering DOI) - 28 Nov 2025

Abstract

The genus Ipomoea, belonging to the order Solanales and the family Convolvulaceae, is the largest genus within its family, comprising approximately 500 species [...] Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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23 pages, 5137 KB

Open AccessArticle

Nutritional Quality Fingerprinting of Wild and Farmed Cyprinus carpio: A UHPLC-MS/MS-Based Traceability Strategy

by Lang Zhang, Wenya Ji, Wenwen Suo, Ziwei Song, Wei Yang, Xinbin Duan, Jizhou Lv, Lei Gao, Liting Ye, Zhen Li, Yali Yu and Hui Zhang

Biology 2025, 14(12), 1695; https://doi.org/10.3390/biology14121695 (registering DOI) - 28 Nov 2025

Abstract

In the context of the ten-year fishing ban on the Yangtze River, illegal poaching for profit persists. To support the enforcement of this ban and protect the river’s ecosystem, an efficient and precise method for distinguishing between wild and farmed common carp is [...] Read more.

In the context of the ten-year fishing ban on the Yangtze River, illegal poaching for profit persists. To support the enforcement of this ban and protect the river’s ecosystem, an efficient and precise method for distinguishing between wild and farmed common carp is essential. This study utilized ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) combined with metabolomics technology to analyze and compare the metabolic differences between wild and farmed common carp. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) revealed a clear separation between the two groups, which was further verified by metabolic fingerprint profiles. Moreover, 16 metabolites with high discriminatory potential were identified from 491 differentially metabolites, such as phytosphingosine, succinic acid and threonine. In addition, a cluster analysis of the differential metabolites classified them into four classes: peptides, fatty acyls, steroids and steroid derivatives, and glycerophospholipids. Furthermore, candidate biomarkers, including 3-hydroxybutyrylcarnitine, 3-hydroxyhexanoylcarnitine and jasminoside were identified to potential distinguish wild populations. To our knowledge, this is the first study to apply metabolomics technology to differentiate wild from farmed common carp, providing a new theoretical basis for ecological restoration efforts in the context of the Yangtze River fishing ban. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

36 pages, 2885 KB

Open AccessArticle

Influence of Plant Developmental Phase and Irrigation Level on Cultivable Microbiome of Maize Root

by Carina Sá, Clarisse Brígido, Cátia Fidalgo, Adília Pires, Artur Alves, Etelvina Figueira and Paulo Cardoso

Biology 2025, 14(12), 1694; https://doi.org/10.3390/biology14121694 (registering DOI) - 28 Nov 2025

Abstract

Plant growth-promoting bacteria can help plants survive in stressful environments. Here, we describe the isolation of root-surface and endophytic bacteria from maize roots at two different phases of the plant life cycle (vegetative and reproductive), grown under three different water regimes (100%, 50%, [...] Read more.

Plant growth-promoting bacteria can help plants survive in stressful environments. Here, we describe the isolation of root-surface and endophytic bacteria from maize roots at two different phases of the plant life cycle (vegetative and reproductive), grown under three different water regimes (100%, 50%, and 0%). Isolates were typed using BOX-PCR to identify unique genetic fingerprints, resulting in a total of 400 strains. These strains were screened for osmotic stress tolerance using 15% polyethylene glycol 6000. Isolates were also tested for bacterial plant growth-promoting traits, including the ability to produce siderophores, indole-3-acetic acid synthesis, and phosphate solubilization, both in the presence and absence of osmotic stress. The results showed that in the reproductive phase, a higher percentage of endophytic and rhizoplane bacteria were tolerant to osmotic stress. Additionally, the highest values of alginate and siderophore production by rhizoplane bacteria were also observed in the reproductive phase. These findings suggest that isolation of maize bacteria should consider the plant’s developmental phase and hydric stress conditions to effectively select bacterial strains that enhance crop resilience in drought-affected areas. Full article

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16 pages, 2751 KB

Open AccessArticle

Drosophila miR-33-5p Suppresses Cell Growth by Inhibiting ERK Signaling

by Taeheon Lee, Nayeon Kim, Ye Jin Park, Seungeun Cha, Young Sik Lee and Do-Hwan Lim

Biology 2025, 14(12), 1693; https://doi.org/10.3390/biology14121693 - 28 Nov 2025

Abstract

Cell growth control is a critical process underlying diverse biological events, including survival, development, tissue repair, and disease. Growth regulation is orchestrated by a combination of external and internal cues, involving a multitude of signaling pathways. Nevertheless, our comprehension of the regulation of [...] Read more.

Cell growth control is a critical process underlying diverse biological events, including survival, development, tissue repair, and disease. Growth regulation is orchestrated by a combination of external and internal cues, involving a multitude of signaling pathways. Nevertheless, our comprehension of the regulation of growth-associated signaling pathways is still incomplete. In this study, we discovered that microRNA miR-33 overexpression in Drosophila S2 cells resulted in a reduction in cell proliferation. This growth inhibition was attributed to the inactivation of ERK signaling, which is mediated through Ras64B, a direct target of miR-33-5p. In accordance with these observations in S2 cells, miR-33 inactivation in Drosophila wings led to an increase in cell number, while its overexpression resulted in a decrease. Notably, miR-33-induced wing reduction was associated with diminished ERK signaling, and this wing defect was rescued by co-expression of Ras64B or a constitutively active ERK variant. Consequently, these findings establish miR-33–Ras64B–ERK as a regulatory axis, providing new mechanistic insights into growth control in Drosophila. Full article

(This article belongs to the Special Issue Energy Metabolism, Genetics and Development in Drosophila)

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17 pages, 3448 KB

Open AccessArticle

Early Holocene Quantitative Summer Temperature Reconstructions in SE Lithuania Inferred from Chironomidae Data

by Neringa Gastevičienė, Gražyna Kluczynska and Vaida Šeirienė

Biology 2025, 14(12), 1692; https://doi.org/10.3390/biology14121692 - 27 Nov 2025

Abstract

Chironomid subfossils were analysed at the Čepkeliai palaeolake in southern Lithuania in order to reconstruct the environmental history of the site during the Early Holocene, paying particular attention to climate change. Mean July air temperatures were inferred using two different chironomid–climate calibration data [...] Read more.

Chironomid subfossils were analysed at the Čepkeliai palaeolake in southern Lithuania in order to reconstruct the environmental history of the site during the Early Holocene, paying particular attention to climate change. Mean July air temperatures were inferred using two different chironomid–climate calibration data sets. As currently no chironomid-based climate calibration set is available from Lithuania, calibration data sets from Fennoscandia, Finland, and Poland were used instead. Our reconstructions suggest that mean July temperatures varied between 13.2 °C and 18.5 °C during the Early Holocene, similar to present-day temperatures. Both reconstructions show a series of climatic events that occurred during the Early Holocene, including the Preboreal oscillation and the “10.2”, “9.2”, and “8.2” oscillations. The reconstruction results correlate well with those carried out simultaneously in neighbouring countries, providing valuable information for this period, as such studies are still rare in the Eastern Baltic region. Full article

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17 pages, 416 KB

Open AccessArticle

Effects of Bentonite, Zeolite, and Illite as Dietary Supplements for Pacific White Shrimp (Litopenaeus vannamei)

by Soohwan Kim, Seong-Mok Jeong, Hyun Mi Jung, Sara Lee, Seunghan Lee and Hyon-Sob Han

Biology 2025, 14(12), 1691; https://doi.org/10.3390/biology14121691 - 27 Nov 2025

Abstract

This study evaluated the effects of dietary supplementation with three silicate minerals (bentonite, zeolite, and illite) on the growth performance, whole-body composition, hematological and immune parameters, and apparent digestibility of Pacific white shrimp (Litopenaeus vannamei). Four isonitrogenous (35% crude protein) and [...] Read more.

This study evaluated the effects of dietary supplementation with three silicate minerals (bentonite, zeolite, and illite) on the growth performance, whole-body composition, hematological and immune parameters, and apparent digestibility of Pacific white shrimp (Litopenaeus vannamei). Four isonitrogenous (35% crude protein) and isoenergetic (17.0 MJ kg⁻¹) diets were formulated: a control (CON) and three experimental diets containing 5% bentonite (BE), zeolite (ZE), or illite (IL), in which an equivalent amount of starch was replaced. Juvenile shrimp specimens (initial weight: 0.02 g) were reared for nine weeks and assessed for growth performance, feed efficiency, survival, biochemical indices, immune responses, and apparent digestibility. Shrimp specimens fed the illite-supplemented diet exhibited significantly higher final body weight (5.95 ± 0.97 g), weight gain, specific growth rate, and protein efficiency ratio than the other groups (p < 0.05). The feed conversion ratios were significantly better in the IL (1.10 ± 0.03) and ZE (1.16 ± 0.02) groups than that in the BE (1.26 ± 0.05) and CON (1.32 ± 0.04) groups (p < 0.05). The whole-body crude protein content was significantly higher in the ZE and IL groups. Hemolymph glutamic-oxaloacetic transaminase (GOT) and glutamic-pyruvate transaminase (GPT) activities were significantly reduced in the ZE and IL groups, indicating improved hepatic health. Non-specific immune responses, including nitro blue tetrazolium (NBT), phenoloxidase (PO), glutathione peroxidase (GPx), and lysozyme activities, were most enhanced in shrimp fed the IL diet. Apparent crude protein digestibility peaked in the IL group (93.3 ± 0.70%) followed sequentially by the CON (87.3 ± 0.92%), BE (87.8 ± 0.88%), and ZE (89.1 ± 1.11%) groups (p < 0.05). These findings demonstrate that dietary supplementation with illite significantly improves the growth performance, feed efficiency, hepatic condition, innate immune response, and protein digestibility of L. vannamei. Illite appears to be a promising candidate for functional feed supplementation aimed at enhancing productivity and health in intensive shrimp aquaculture. Full article

(This article belongs to the Special Issue Aquatic Animal Nutrition and Feed)

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21 pages, 3569 KB

Open AccessArticle

Exploratory Single-Cell Transcriptomic Profiling Reveals Dysregulated Glial Populations and Pathways in Focal Cortical Dysplasia Epilepsy

by Chao Jiang, Qingyao Gao, Yan Zhao, Yiming You, Zhuojue Wang, Jian Wang, Guang Yang, Chuang Guo and Zhiqiang Cui

Biology 2025, 14(12), 1690; https://doi.org/10.3390/biology14121690 - 27 Nov 2025

Abstract

Background: Focal cortical dysplasia (FCD) is a prevalent cause of drug-resistant epilepsy, but a comprehensive understanding of its pathogenesis at a cellular resolution remains limited. Previous transcriptomic studies, often constrained by bulk tissue analysis, have been unable to dissect the cell-type-specific contributions to [...] Read more.

Background: Focal cortical dysplasia (FCD) is a prevalent cause of drug-resistant epilepsy, but a comprehensive understanding of its pathogenesis at a cellular resolution remains limited. Previous transcriptomic studies, often constrained by bulk tissue analysis, have been unable to dissect the cell-type-specific contributions to epileptogenesis. Methods: We performed scRNA-seq on cortical tissues from one surgical patient with FCD type II and one matched control. Cell clustering, annotation, and identification of differentially expressed genes (DEGs) were conducted using standard Seurat workflow. We focused on the molecular alterations in three major glial cell types: astrocytes, microglia, and oligodendrocytes. To functionally interpret the DEGs, we performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Results: Our profiling revealed a profoundly reconstituted cellular ecosystem in the FCD cortex. We found a marked expansion of microglia (65.57% vs. 47.02%; a ~39% relative increase) and astrocytes (10.98% vs. 4.11%; a ~167% relative increase), alongside a severe depletion of oligodendrocytes (8.12% vs. 30.63%; a ~73% relative decrease). Critically, a core set of 128 differentially expressed genes (DEGs) was shared across these glial populations, featuring consistent upregulation of RAC1 and downregulation of ATP5F1D, pointing to convergent pro-inflammatory and mitochondrial dysfunction pathways. Enrichment analyses further demonstrated a coordinated engagement of neuroinflammatory pathways, most notably IL-17 signaling. Subsequent cell–cell communication inference revealed a broad attenuation of intercellular signaling, with a 35% reduction in interaction numbers, indicating a breakdown of coordinated cellular crosstalk. Conclusions: This exploratory single-cell study provides preliminary evidence of a convergent glial pathology in FCD, characterized by shared molecular disruptions in inflammation and metabolism. Our findings highlight RAC1 and IL-17 signaling as potentially actionable pathways, warranting further investigation into their therapeutic potential for mitigating epileptogenesis in FCD. Full article

12 pages, 3800 KB

Open AccessArticle

Histone Deacetylase BpHST1 Regulates Plant Architecture and Photosynthesis in Birch

by Lili Hou, Baoxin Li, Mengyan Ge and Zhimin Zheng

Biology 2025, 14(12), 1689; https://doi.org/10.3390/biology14121689 - 27 Nov 2025

Abstract

(1) Background: Epigenetic mechanisms play a significant role in plant architecture. Histone deacetylases, as crucial epigenetic regulators, shape plant architecture by modifying chromatin structure and regulating gene expression. (2) Methods: This study combined bioinformatic identification of BpHST1 with its functional characterization in transgenic [...] Read more.

(1) Background: Epigenetic mechanisms play a significant role in plant architecture. Histone deacetylases, as crucial epigenetic regulators, shape plant architecture by modifying chromatin structure and regulating gene expression. (2) Methods: This study combined bioinformatic identification of BpHST1 with its functional characterization in transgenic birch overexpressing 35S::BpHST1::FLAG, including phenotypic and cytological analyses. The putative direct targets of BpHST1 were further identified by integrating RNA-seq and ChIP-seq data. (3) Results: Phylogenetic analysis revealed that the HST1 orthologs from birch and peach form a distinct clade, consistent with their high degree of protein sequence conservation. BpHST1 exhibited light-inducible and leaf-preferential expression, with transcript levels elevated under light versus dark conditions, enriched in leaves relative to roots, and promoter activity confirming this spatial patterning. Overexpression of BpHST1 significantly suppressed plant height, cell length, cell width, and photosynthetic capacity. Integrated RNA-seq and ChIP-seq analysis suggested that BpLHCA2 possible functions as a direct downstream target of BpHST1, mediating plant growth and development. (4) Conclusions: Our findings delineated the role of BpHST1 in regulating plant architecture through comprehensive expression and functional analyses, and identified a candidate target gene. This study provided a novel insight into the molecular mechanisms governing plant architecture and offers potential strategies for future epigenetic breeding. Full article

(This article belongs to the Collection Plant Epigenetics: Advancing Adaptation Strategies for Climate Change)

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21 pages, 3258 KB

Open AccessArticle

Acute Exercise Fatigue Impairs Cognitive Control: Neurophysiological Mechanisms Revealed by ERP and ERSP Analyses

by Shuqi Yao, Hongwei Lu, Longhai Zhang, Fujie Liu, Fuhai Ma and Aiping Chi

Biology 2025, 14(12), 1688; https://doi.org/10.3390/biology14121688 - 27 Nov 2025

Abstract

This study aimed to investigate the effects of acute exhaustion exercise on cognitive control in young men, a key higher cognitive function for goal-directed behavior. Although long-term regular exercise benefits cognition, the effects of acute exhaustion exercise on cognitive control and its neural [...] Read more.

This study aimed to investigate the effects of acute exhaustion exercise on cognitive control in young men, a key higher cognitive function for goal-directed behavior. Although long-term regular exercise benefits cognition, the effects of acute exhaustion exercise on cognitive control and its neural mechanisms are not fully understood. 35 male college students completed a Stroop task before and after exhaustion exercise on a cycle ergometer with incremental load. Electroencephalogram data were collected synchronously during the task. Behavioral measures (accuracy, reaction time), Event-Related Potential components (N2, P3 amplitudes and latencies), and Event-Related Spectral Perturbation (energy changes in theta, alpha, beta frequency bands) were analyzed. Results: Behavioral results showed that task accuracy only significantly decreased under the conflict condition (incongruent trials) following exhaustive exercise. ERP analysis revealed that the P3 amplitude at the anterior site (Fz) was significantly reduced post-exercise, but specifically for the incongruent condition, while the N2 amplitude demonstrated a more widespread enhancement. Time–frequency analysis found a significant decrease in alpha-band power over the parietal region after exercise. Theta and beta band activities were not significantly affected by exercise-induced fatigue. Conclusions: Acute exhaustive exercise did not impair early conflict monitoring functions (as indicated by stable N2 component and theta oscillations), but it compromised later higher-order cognitive processes related to attentional resource allocation and conflict resolution (manifested as reduced anterior P3 amplitude), accompanied by decreased efficiency in neural oscillatory activity associated with inhibitory control (reduced alpha power). This suggests that fatigue primarily affects the neural mechanisms of the “implementation” stage rather than the “monitoring” stage in the cognitive control cascade. Full article

(This article belongs to the Special Issue Mechanisms Underlying Neuronal Network Activity)

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17 pages, 1989 KB

Open AccessArticle

Optimal Dietary α-Starch Requirement and Its Effects on Growth and Metabolic Regulation in Chinese Hook Snout Carp (Opsariichthys bidens)

by Wenjing Cai, Xiaonian Luo, Jiao Li, Youjian Duan, Yong Wei, Yuxin Xing, Zongyun Hu and Chunyue Zhu

Biology 2025, 14(12), 1687; https://doi.org/10.3390/biology14121687 - 26 Nov 2025

Abstract

This study investigated the effects of dietary carbohydrate levels on growth performance, body composition, and hepatic expression of metabolic genes in Chinese hook snout carp (Opsariichthys bidens). Fish were fed five isonitrogenous diets with graded α-starch levels (8%, 14%, 20%, 26%, [...] Read more.

This study investigated the effects of dietary carbohydrate levels on growth performance, body composition, and hepatic expression of metabolic genes in Chinese hook snout carp (Opsariichthys bidens). Fish were fed five isonitrogenous diets with graded α-starch levels (8%, 14%, 20%, 26%, and 32%) for 56 days. The diet containing 14% α-starch significantly increased the weight gain rate (WGR) and specific growth rate (SGR) of O. bidens (p < 0.05). Both broken-line and polynomial regression analyses on WGR and SGR consistently indicated an optimal dietary α-starch level of approximately 14–17%. High carbohydrate diets significantly elevated plasma glucose, triglyceride, and cholesterol levels, as well as hepatosomatic and intraperitoneal fat indices. Gene expression analysis revealed that moderate carbohydrate intake upregulated lipoprotein lipase (lpl), hormone-sensitive lipase (hsl), and carnitine palmitoyltransferase 1 (cpt1) gene expressions, enhancing lipolysis and β-oxidation, whereas excessive carbohydrate intake (>26% α-starch) suppressed these pathways but strongly induced acc1 gene expressions, promoting lipogenesis. Additionally, glycogen metabolism genes (glycogen synthase (gys) and glycogen phosphorylase (pyg) and glycolysis-related phosphofructokinase (pfk) were responsive to carbohydrate supply, while oxidative metabolism gene cs was downregulated under excessive carbohydrate, implying reduced mitochondrial oxidative metabolism. Overall, O. bidens exhibited limited carbohydrate utilization, with optimal intake supporting growth and metabolic balance, whereas excessive intake redirected glucose toward glycogen and lipid accumulation, leading to metabolic imbalance. Full article

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28 pages, 14644 KB

Open AccessArticle

Genome-Wide Identification of the AP2/ERF Transcription Factor Family and Expression Analysis Under Selenium Stress in Cardamine hupingshanensis

by Nanrong Deng, Xixi Zeng, Jialin Liu, Shengcai Chen, Yanke Lu, Zhixin Xiang, Zhi Hou, Qiaoyu Tang and Yifeng Zhou

Biology 2025, 14(12), 1686; https://doi.org/10.3390/biology14121686 - 26 Nov 2025

Abstract

AP2/ERF (APETALA2/ethylene-responsive factor) is one of the largest plant transcription factor families, characterized by 1-2 AP2/ERF domains (≈60–70 amino acids) that regulate plant development and biotic/abiotic stress responses. This study presents the first genome-wide identification and characterization of the AP2/ERF family in the [...] Read more.

AP2/ERF (APETALA2/ethylene-responsive factor) is one of the largest plant transcription factor families, characterized by 1-2 AP2/ERF domains (≈60–70 amino acids) that regulate plant development and biotic/abiotic stress responses. This study presents the first genome-wide identification and characterization of the AP2/ERF family in the selenium (Se) hyperaccumulator Cardamine hupingshanensis via bioinformatics. A total of 230 AP2/ERF genes were identified, which were non-randomly distributed across 16 chromosomes. Their encoded proteins varied in length (126–623 aa), molecular mass (13.927–68.112 kDa), and isoelectric point (4.48–10.31). Phylogenetic analysis classified these genes into five conserved subfamilies (AP2, DREB, ERF, RAV, Soloist), consistent with other plant species. Intron distribution differed among subfamilies (42.17% of genes contained introns), and motif 1 was universally conserved. Promoter cis-element analysis revealed enrichment of hormone-, stress-, and growth-related elements, highlighting potential roles in abiotic stress responses (notably, light and abscisic acid signaling). Expression profiling under Se stress (100 μg Se/L and 80,000 μg Se/L) demonstrated tissue-specific, dose-dependent, and temporal dynamic patterns. This inaugural genome-wide investigation of C. hupingshanensis AP2/ERFs provides foundational datasets for deciphering regulatory networks governing growth and Se stress response in this Se hyperaccumulator plant. Full article

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17 pages, 3876 KB

Open AccessArticle

Prevalence, Risk Factors, and Genetic Evolution of Rat Hepatitis E Virus in Small Mammals from Southwestern Yunnan, China

by Ze Yang, Pei-Yu Han, Jun-Ying Zhao, Wei Kong, Yun Long, Song Wu, Li-Dong Zong, Chen-Jie He, Yu-Hong Chen, Wan-Chun Cao, Bo Wang and Yun-Zhi Zhang

Biology 2025, 14(12), 1685; https://doi.org/10.3390/biology14121685 - 26 Nov 2025

Abstract

Rat hepatitis E virus (rat HEV, Rocahepevirus genotype C1) represents a potential zoonotic threat, but its epidemiological and evolutionary characteristics in small mammals remain poorly understood, especially in regions with complex geography. Between 2022 and 2024, we collected 818 small mammals from seven [...] Read more.

Rat hepatitis E virus (rat HEV, Rocahepevirus genotype C1) represents a potential zoonotic threat, but its epidemiological and evolutionary characteristics in small mammals remain poorly understood, especially in regions with complex geography. Between 2022 and 2024, we collected 818 small mammals from seven border counties and cities in Yunnan, China. Rat HEV RNA was detected by RT-PCR, risk factors were assessed using binary logistic regression, and full genomes were sequenced for phylogenetic and molecular clock analysis. The overall prevalence of rat HEV was 6.23% (51/818), with significantly higher odds observed in Gengma and Heqing counties, in oriental house rat (Rattus tanezumi) and Chevrieri’s field mouse (Apodemus chevrieri), in residential habitats, and at mid-high altitudes (all p < 0.001). The 51 partial genomic sequences (RdRp gene) obtained in this study clustered within Rocahepevirus, forming two distinct subclades associated with host species. The two complete genomes, GS188 and GS197 from Rattus tanezumi, were classified as subtypes C1b and C1d, respectively. Bayesian analysis estimated that GS197 diverged from a closely related Rattus tanezumi-derived strain around 1998, while GS188 diverged from a lineage containing shrew and human strains around 1931. These findings reveal a relatively high prevalence and substantial genetic diversity of Rochepevirus in southwestern Yunnan, suggesting human-influenced transmission dynamics and a potential for cross-species infection. Full article

(This article belongs to the Special Issue Biology of Liver Diseases)

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18 pages, 5471 KB

Open AccessArticle

Comparative Analysis of Symbiotic Bacterial Diversity and Sublethal Effects of Nitenpyram Against Two Different Cotton Aphids

by Wenjie Li, Wei Cao, Xuanling Wei, Dongsheng Hu, Kailong Yuan, Renfu Zhang and Yongsheng Yao

Biology 2025, 14(12), 1684; https://doi.org/10.3390/biology14121684 - 26 Nov 2025

Abstract

Symbiotic bacteria in insects are known to play crucial roles in detoxification metabolism and adaptation to host plant secondary metabolites. In the cotton-growing region of Xinjiang, China, the Ap. gossypii and the Ac. gossypii exhibit significant differences in sensitivity or resistance to pesticides. [...] Read more.

Symbiotic bacteria in insects are known to play crucial roles in detoxification metabolism and adaptation to host plant secondary metabolites. In the cotton-growing region of Xinjiang, China, the Ap. gossypii and the Ac. gossypii exhibit significant differences in sensitivity or resistance to pesticides. However, whether their detoxification-related symbiotic bacteria change under insecticide stress remains unclear. This study assessed the toxicity of nitenpyram to both aphid species and the effects of LC₂₀ treatment on their growth, development, and reproduction. Bacterial community dynamics across generations (G0–G2) were analyzed by 16S rRNA gene amplicon sequencing. The LC₂₀ of nitenpyram reduced the longevity and fecundity of the parent generation in both species. In Ap. gossypii, the intrinsic rate of increase (r_m), net reproductive rate (R₀), and finite rate of increase (λ) increased in the G1–G2 generations, whereas these parameters significantly decreased in Ac. gossypii. By the G3 generation, biological parameters in both species showed no significant differences compared to the control. Nitenpyram disrupted the stability of symbiotic bacterial communities in both aphids. In Ac. gossypii, Sphingomonas, a genus with detoxification potential, was consistently suppressed in G1–G2, while the abundance of the primary symbiont Buchnera initially decreased sharply and subsequently recovered. In contrast, the bacterial community in Ap. gossypii remained largely stable. These findings indicate that sublethal concentrations of nitenpyram exert distinct transgenerational effects on the two aphid species and disrupt the stability of their symbiotic bacterial communities. Full article

(This article belongs to the Special Issue Feature Papers on Toxicology)

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19 pages, 2350 KB

Open AccessArticle

A Study on the Assembly Mechanisms of Shrub Communities in Coniferous and Broadleaved Forests—A Case Study of Jiangxi, China

by Yuxi Xue, Xiaoyue Guo, Wei Huang, Xiaohui Zhang, Yuxin Zhang, Yongxin Zhong, Xia Lin, Qi Zhang, Qitao Su and Yian Xiao

Biology 2025, 14(12), 1683; https://doi.org/10.3390/biology14121683 - 26 Nov 2025

Abstract

The ecological strategies of understory shrubs are critical for maintaining the structure and function of forest understory vegetation. Understanding the assembly mechanisms of these shrub communities is a central issue in modern ecology. To address this, our study was conducted in the typical [...] Read more.

The ecological strategies of understory shrubs are critical for maintaining the structure and function of forest understory vegetation. Understanding the assembly mechanisms of these shrub communities is a central issue in modern ecology. To address this, our study was conducted in the typical red soil regions of Jiangxi, China, focusing on secondary forests (including both broadleaved and coniferous types) of similar stand age. We aimed to assess the effects of various environmental factors—such as soil pH, total nitrogen content, bulk density, and understory temperature—along with tree-layer characteristics—including canopy closure, tree species richness, and diameter at breast height (DBH)—on the species composition, functional traits, and phylogenetic structure of the shrub layer. Results showed: One-way ANOVA revealed significant differences in functional traits between the two forest types. Specifically, leaf thickness, specific leaf area, and chlorophyll content were significantly higher in the coniferous forest, whereas leaf dry matter content was significantly lower compared to the broadleaved forest (p < 0.05). These results suggest that understory shrubs in the coniferous forest primarily adopt a resource-conservative strategy, while those in the broadleaved forest exhibit a resource-acquisitive strategy. Phylogenetic analysis further revealed that the phylogenetic diversity (PD) of coniferous forests was significantly lower than that of broadleaved forests (p < 0.05). The phylogenetic structure in coniferous forests showed a more clustered pattern (NTI > 0, NRI > 0), suggesting stronger environmental filtering. Diversity index analysis showed that the Chao1 index indicated a richer potential species pool in broadleaved forests (p < 0.05), while species distribution was more even in coniferous forests (p < 0.05). Random Forest model analysis identified the diameter at breast height (DBH) of trees as the most critical negative driver, while soil pH was the primary positive driver. Redundancy Analysis (RDA) confirmed that the community structure in coniferous forests was mainly driven by biotic competition pressure represented by DBH, whereas the structure in broadleaved forests was more closely associated with abiotic factors like soil total nitrogen and pH (R² = 0.29, p < 0.05). These environmental drivers, through strong environmental filtering, collectively resulted in a phylogenetically clustered pattern of shrub communities in both forest types. This study demonstrates that the assembly of understory shrub communities is a complex, multi-level process co-regulated by multiple factors, shaped by both the biotic pressure from the overstory structure and abiotic filtering from the soil environment. This finding deepens our understanding of the rules governing community assembly in forest ecosystems. Full article

(This article belongs to the Section Ecology)

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15 pages, 1707 KB

Open AccessArticle

A Dynamic Energy Budget Model for the Non-Continuous and Biphasic Growth of the Pond-Cultured Swimming Crab, Portunus trituberculatus

by Yi Jiang, Fan Lin, Jingyan Zhang, Ming Bao, Baoquan Gao, Jitao Li and Xianliang Meng

Biology 2025, 14(12), 1682; https://doi.org/10.3390/biology14121682 - 26 Nov 2025

Abstract

The swimming crab, Portunus trituberculatus, is an important mariculture crustacean species in China. To quantitatively characterize its discontinuous and biphasic growth under intensive aquaculture conditions, we developed a modified growth model based on the dynamic energy budget (DEB) theory. The model incorporates [...] Read more.

The swimming crab, Portunus trituberculatus, is an important mariculture crustacean species in China. To quantitatively characterize its discontinuous and biphasic growth under intensive aquaculture conditions, we developed a modified growth model based on the dynamic energy budget (DEB) theory. The model incorporates a discontinuous growth representation that explicitly accounts for the molting process. Molting events were parameterized using a threshold ratio (α), defined as the carbon weight-to-wet weight ratio, with stage-dependent critical values derived from laboratory experiments and published datasets. Laboratory experiments were designed to estimate the energy-budget-related parameters together with data from the literature. In addition, by introducing a feedback mechanism for the energy demand of ovarian development, a set of κ values was calibrated with data from the literature to reproduce the stage-specific growth determined by ovarian development. The model was validated with growth data from several published studies related to the growth of P. trituberculatus, as well as measurements from the aquaculture ponds. Multiple goodness-of-fit indices (R-square, modeling efficiency, and Theil’s inequality coefficient) confirmed that the modified DEB model accurately reproduced both wet weight and ovarian growth trajectories, along with the characteristic non-continuous pattern of molting-driven wet weight increase. The individual growth model can be a useful tool for optimizing the intensive culture practice of the swimming crab in the aquaculture ponds and assessing the environmental impact of crab aquaculture. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters (2nd Edition))

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