Biology

12 pages, 3137 KB

Open AccessArticle

Genetic Diversity and Spawning Patterns of Small Yellow Croaker (Larimichthys polyactis) in a Large-Scale Pooling System

by Eun Soo Noh, Chun Mae Dong, Songhee Choi, Hyo Sun Jung, Jungwook Park, In Joon Hwang, Jung-Ha Kang and Yong-Woon Ryu

Biology 2026, 15(9), 734; https://doi.org/10.3390/biology15090734 - 6 May 2026

Viewed by 400

Abstract

Although mass-spawning pooling systems are widely used for small yellow croaker (Larimichthys polyactis) aquaculture, they often induce severe genetic bottlenecks driven by reproductive skew. This study evaluated cross-generational genetic diversity and spawning patterns to propose an optimal genetic management strategy. We [...] Read more.

Although mass-spawning pooling systems are widely used for small yellow croaker (Larimichthys polyactis) aquaculture, they often induce severe genetic bottlenecks driven by reproductive skew. This study evaluated cross-generational genetic diversity and spawning patterns to propose an optimal genetic management strategy. We analyzed 1049 adult broodstock and 950 juvenile offspring using nine microsatellite markers. To mitigate reproductive skew, fertilized eggs were collected via multi-time sampling (19 times) over a two-month spawning season and reared to the juvenile stage. Genetic diversity was highly conserved across generations, with expected heterozygosity maintained at 0.860 in the offspring. Parentage assignment succeeded for 96.2% of the offspring (914 individuals), revealing 802 unique families, of which 89.9% (721 families) were singletons. Also, 60.9% of the broodstock contributed to reproduction, exhibiting a right-skewed participation distribution. Importantly, comparisons with a short-term single-event collection control group demonstrated that our multi-time strategy effectively prevented drastic reductions in effective population size (N_e). These patterns highlight the species asynchronous spawning physiology and confirm that the strategy approximates random mating with minimal genetic drift. We suggest this long-term, multi-time egg collection method as an effective protocol for the sustainable genetic management of multiple-spawning marine fish. Full article

(This article belongs to the Section Marine and Freshwater Biology)

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29 pages, 1838 KB

Open AccessReview

Aging Theories and Prevention of Age-Related Diseases Using Phytocomplexes

by Marat R. Khanturin, Georgiy A. Demchenko, Laura U. Koibasova, Serik N. Abdreshov, Makpal A. Yessenova, Sofia K. Imankulova and Yerkenaz N. Akhatayeva

Biology 2026, 15(9), 733; https://doi.org/10.3390/biology15090733 - 6 May 2026

Viewed by 673

Abstract

Aging is a multifactorial biological process characterized by a progressive decline in functional capacity at the molecular, cellular, tissue, and organismal levels. The aim of this review is to summarize current concepts of aging mechanisms and the prevention of age-related pathologies from a [...] Read more.

Aging is a multifactorial biological process characterized by a progressive decline in functional capacity at the molecular, cellular, tissue, and organismal levels. The aim of this review is to summarize current concepts of aging mechanisms and the prevention of age-related pathologies from a lymphological perspective, taking into account contemporary literature data and the results of our own studies. Currently, two major concepts dominate in gerontology: programmed aging, which considers aging as a genetically determined process, and damage accumulation theories, which associate aging with the progressive accumulation of molecular and cellular damage. The hallmarks of aging include genomic instability, telomere shortening, epigenetic alterations, impaired proteostasis and macroautophagy, dysregulation of nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, dysbiosis, hormonal imbalance, and disturbances in interstitial humoral transport and lymphatic outflow. At the tissue and organ levels, impairment of lymphatic drainage is of particular importance, leading to interstitial fluid stagnation and the accumulation of toxic metabolites, which exacerbate cellular and subcellular dysfunction. Phytotherapeutic agents containing flavonoids, phenolic compounds, terpenoids, glycosides, polysaccharides, and other biologically active substances exhibit antioxidant, anti-inflammatory, and cytoprotective properties. They inhibit lipid peroxidation, reduce excessive nitric oxide production, and contribute to the restoration of interstitial humoral transport and lymphatic outflow. Interstitial humoral transport and the lymphatic system, together with renal mechanisms, play key roles in maintaining body fluid homeostasis. Targeted regulation of lymphatic system function may help reduce tissue congestion, maintain physiological homeostasis, and improve quality of life in the elderly. Full article

(This article belongs to the Section Physiology)

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18 pages, 3230 KB

Open AccessArticle

Rapalink-1 Attenuates Oxidative-Stress-Induced Senescence in Vascular Cells in Association with Reduced NF-κB and MAPK Signaling

by Jinliang You, Hongjun Liu, Dilaware Khan, Majeed Rana, Sihmehmet Sahan, Katharina Faust and Sajjad Muhammad

Biology 2026, 15(9), 732; https://doi.org/10.3390/biology15090732 - 6 May 2026

Viewed by 488

Abstract

Oxidative stress contributes to vascular dysfunction and senescence-associated changes through activation of inflammatory and stress-responsive signaling pathways. Although the mammalian target of rapamycin (mTOR) integrates metabolic and redox-related signals, its role in vascular stress responses remains incompletely understood. In this study, we investigated [...] Read more.

Oxidative stress contributes to vascular dysfunction and senescence-associated changes through activation of inflammatory and stress-responsive signaling pathways. Although the mammalian target of rapamycin (mTOR) integrates metabolic and redox-related signals, its role in vascular stress responses remains incompletely understood. In this study, we investigated the effects of Rapalink-1, an mTOR inhibitor, on H₂O₂-induced injury responses in human vascular endothelial cells (HUVECs) and vascular smooth muscle cells (SMCs). Oxidative stress-associated changes were assessed using oxidation-sensitive fluorescence, DNA damage markers (γ-H2AX and 8-OHDG), and senescence-associated readouts (SA-β-gal, Lamin B1, and p21). Senescence-associated secretory phenotype (SASP)-related factors were analyzed by qPCR and Western blot, and mTOR-, NF-κB-, and MAPK-related signaling was evaluated by Western blotting. H₂O₂ exposure reduced cell viability and increased oxidative stress-associated readouts, DNA damage markers, senescence-associated changes, and SASP-related factor expression in both HUVECs and SMCs. Rapalink-1 attenuated many of these responses, including oxidation-sensitive fluorescence, γ-H2AX and 8-OHDG staining, SA-β-gal positivity, Lamin B1 loss, p21 upregulation, and the expression of inflammatory and matrix-remodeling factors. These effects were accompanied by reduced phosphorylation of p65, p38, ERK1/2, S6, and 4EBP1. Overall, Rapalink-1 is associated with attenuation of oxidative stress-induced injury responses in vascular endothelial and smooth muscle cells, together with reduced NF-κB-, MAPK-, and mTOR-related signaling. These findings support further investigation of mTOR-targeted approaches in vascular aging and oxidative stress-related vascular dysfunction. Full article

(This article belongs to the Section Cell Biology)

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17 pages, 5030 KB

Open AccessArticle

Continuous Non-Invasive Monitoring of Hive Entrance Activity Reveals Honey Bee Colony Dynamics

by Cansu Özge Tozkar

Biology 2026, 15(9), 731; https://doi.org/10.3390/biology15090731 - 6 May 2026

Viewed by 516

Abstract

Honey bees are essential pollinators and ecological indicators, yet conventional monitoring approaches remain labor-intensive and limit the assessment of colony dynamics across biologically relevant time scales. Hive entrance activity, defined as the movement of bees entering and leaving the hive, serves as a [...] Read more.

Honey bees are essential pollinators and ecological indicators, yet conventional monitoring approaches remain labor-intensive and limit the assessment of colony dynamics across biologically relevant time scales. Hive entrance activity, defined as the movement of bees entering and leaving the hive, serves as a direct proxy for foraging effort, resource availability, and colony condition. However, manual observation is restricted in duration and resolution, constraining continuous evaluation of colony responses to environmental change. In this study, a non-invasive automated monitoring framework was developed to quantify hive entrance activity under diverse environmental conditions. The system integrates image-based detection, multi-object tracking, and direction-aware trajectory analysis to identify and quantify incoming and outgoing bees. Trained on 12,013 annotated images representing varied lighting conditions, backgrounds, and activity levels, the framework achieved high detection accuracy (mAP@50 = 0.96–0.98) and real-time processing capability. Video-based evaluations showed that frame-level detections can be translated into entrance and exit estimates, although counting accuracy varied with traffic density and occlusion. These findings demonstrate that automated monitoring enables continuous measurement of biologically meaningful indicators of colony dynamics. The proposed approach provides a scalable tool for investigating foraging activity, seasonal patterns, and colony responses to environmental stressors, supporting improved ecological assessment and pollinator conservation. Full article

(This article belongs to the Section Behavioural Biology)

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19 pages, 1554 KB

Open AccessReview

Conservation of Indigenous Pig Breeds in Vietnam: Genetic Characterization, Conservation Strategies, and Future Perspectives

by Thanh Van Nguyen, Nguyen Van Ba, Lan Doan Pham and Duy Ngoc Do

Biology 2026, 15(9), 730; https://doi.org/10.3390/biology15090730 - 5 May 2026

Viewed by 637

Abstract

Indigenous pig breeds in Vietnam represent an important genetic reservoir, offering traits adapted to local environments, cultural preferences, and disease resistance. However, rapid industrialization and the expansion of commercial breeds have endangered many indigenous populations. This review explores the trajectory of conservation efforts [...] Read more.

Indigenous pig breeds in Vietnam represent an important genetic reservoir, offering traits adapted to local environments, cultural preferences, and disease resistance. However, rapid industrialization and the expansion of commercial breeds have endangered many indigenous populations. This review explores the trajectory of conservation efforts for Vietnamese local pig breeds, from the early use of microsatellites and mitochondrial DNA to recent advances in SNP genotyping. Firstly, we summarize the key characteristics and values of 26 local breeds. Secondly, we highlight key findings on genetic diversity, population structure, and inbreeding levels across major breeds. In addition, we discuss challenges in the development of conservation breeding programs and national strategies, as well as challenges in data generation, infrastructure, and policy implementation and provide potential solutions for these challenges. This review provides the first integrated synthesis linking breed-level genetic evidence to practical conservation recommendations for indigenous pigs in Vietnam. By identifying the key breeds for conservation priority, such as Huong, Van Pa, Soc, ChuProng, Co Aluoi, and Lung Pu, as well as highlighting the exotic introgression in H’mong pig populations, this review might provide a resource for sustainable conservation and use of Vietnam’s rich pig genetic resources. Full article

(This article belongs to the Special Issue Feature Papers in 'Conservation Biology and Biodiversity' (2nd Edition))

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19 pages, 801 KB

Open AccessArticle

Thermophysiology and Locomotor Performance of the Andean Lizard Phymaturus williamsi: Vulnerable to Rising Temperatures?

by Ana E. Victorica Erostarbe, Franco Valdez Ovallez, José M. Sánchez, Yamila Méndez Osorio and Rodrigo Gómez Alés

Biology 2026, 15(9), 729; https://doi.org/10.3390/biology15090729 - 5 May 2026

Viewed by 590

Abstract

Ambient temperature strongly influences the physiology and performance of ectotherms, making it essential to understand their responses to thermal variation under climate change. We evaluated locomotor performance and thermal vulnerability in a population of Phymaturus williamsi from the Argentine Andes. Field measurements included [...] Read more.

Ambient temperature strongly influences the physiology and performance of ectotherms, making it essential to understand their responses to thermal variation under climate change. We evaluated locomotor performance and thermal vulnerability in a population of Phymaturus williamsi from the Argentine Andes. Field measurements included body (T_b) and operative temperatures (T_e), while laboratory analyses assessed preferred temperature (T_pref), thermoregulatory effectiveness, critical thermal limits, and thermal sensitivity of locomotion (endurance, sprint, and long runs). P. williamsi exhibited a preferred temperature higher than field body temperatures, together with high thermoregulatory effectiveness (E = 0.83) and a broad thermal tolerance range (TT = 35.41 °C). Optimal temperatures for locomotor performance were lower than T_pref, providing no support for the thermal coadaptation hypothesis. Despite low environmental thermal quality, individuals maintained body temperatures close to performance optima through effective behavioral thermoregulation. Thermal vulnerability indices indicated relatively high tolerance to projected warming scenarios. However, our results suggest that vulnerability to climate change is constrained more by the availability of suitable thermal microhabitats than by intrinsic physiological limits. We conclude that P. williamsi is a eurythermic and effective thermoregulator with thermally sensitive locomotor performance, whose persistence will depend on habitat structure and thermal heterogeneity. Full article

(This article belongs to the Special Issue Coping with Temperature Increase Induced by Climate Warming: Trends in Ectothermic Species—2nd Edition)

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21 pages, 3197 KB

Open AccessReview

Mesenchymal Stromal Cells at the Interface of Hemostasis and Immunothrombosis

by Luca Bonanni, Nicola Ferri and Paolo Simioni

Biology 2026, 15(9), 728; https://doi.org/10.3390/biology15090728 - 3 May 2026

Viewed by 614

Abstract

Mesenchymal stromal cells are increasingly used for their immunomodulatory and regenerative properties, yet their interaction with the hemostatic system remains incompletely understood. This review examines the mechanisms through which these cells influence coagulation within the broader framework of immunothrombosis. Evidence from in vitro [...] Read more.

Mesenchymal stromal cells are increasingly used for their immunomodulatory and regenerative properties, yet their interaction with the hemostatic system remains incompletely understood. This review examines the mechanisms through which these cells influence coagulation within the broader framework of immunothrombosis. Evidence from in vitro studies, animal models, and early clinical observations indicates that mesenchymal stromal cells can promote thrombin generation through tissue factor expression and phosphatidylserine exposure, while also engaging complement pathways, platelets, and innate immune responses. Counter-regulatory mechanisms, including adenosine-mediated platelet inhibition and immune reprogramming after cellular clearance, contribute to a context-dependent biological effect. Functional assays, rather than tissue factor expression alone, appear necessary to estimate the effective procoagulant potential of these products. Clinical data suggest that major thrombotic events remain uncommon, although subclinical activation of coagulation pathways may occur. The hemostatic impact of mesenchymal stromal cells depends on multiple variables, including cell source, dose, route of administration, and host inflammatory status. The available evidence supports a working model in which early coagulation and complement activation may be followed by immune modulation, supporting integrated strategies to optimise both safety and therapeutic efficacy. A central conclusion is that tissue factor, although mechanistically necessary for MSC-associated procoagulant activity, is not by itself an independent predictor of clinical thrombotic risk; the effective coagulation response also depends on phosphatidylserine exposure, membrane context, and host inflammatory conditions. Full article

(This article belongs to the Special Issue Novel Dynamics and Mechanisms of Stromal–Leukocyte Interactions in Tissue Inflammation, Immunity and Healing)

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16 pages, 2636 KB

Open AccessArticle

Identification of Genes Associated with Seed Weight and Development of Functional Markers for GmUBP15 in Glycine max

by Furui Wang, Huilong Hong, Zhihao Zhang, Jiangyuan Xu, Lili Yu, Suning Li, Yinghui Li and Lijuan Qiu

Biology 2026, 15(9), 727; https://doi.org/10.3390/biology15090727 - 2 May 2026

Viewed by 762

Abstract

Seed weight is a key agronomic trait determining soybean yield and quality, yet only a few of genes regulating this trait have been functionally characterized to date. In this study, we identified 155 homologous genes in the soybean genome through BLAST searches using [...] Read more.

Seed weight is a key agronomic trait determining soybean yield and quality, yet only a few of genes regulating this trait have been functionally characterized to date. In this study, we identified 155 homologous genes in the soybean genome through BLAST searches using 78 functionally validated rice grain weight-related genes as queries. Haplotype analysis prioritized 40 candidate genes exhibiting significant differences in seed weight between haplotypes. To further refine the candidate list, we integrated haplotype frequency analysis, expression–trait association mapping, and tissue-specific expression profiling, ultimately delineating eight key genes. Given the established role of ubiquitination in seed development, we focused on homologs of OsUBP15 and identified three candidate genes, GmUBP5, GmUBP11, and GmUBP33, that exhibited significant haplotype-dependent variation in seed weight. Subcellular localization assays confirmed their nuclear localization. Haplotype frequency analysis revealed that the superior haplotypes of these genes have been preferentially retained during modern breeding and are widely distributed across major soybean-producing regions. Leveraging non-synonymous SNP variants, we developed and validated robust KASP markers that efficiently discriminate germplasm with contrasting seed weight phenotypes. Collectively, our study provides not only high-confidence genetic targets and actionable molecular markers but also insights into pyramiding breeding strategies for improving seed weight in soybean. Full article

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19 pages, 1058 KB

Open AccessReview

Why Should a Genome Be Protected? Ethical, Legal, and Security Challenges in the Protection of Genomic Data

by Marlena Szalata, Mikołaj Danielewski, Karolina Wielgus and Ryszard Słomski

Biology 2026, 15(9), 726; https://doi.org/10.3390/biology15090726 - 2 May 2026

Viewed by 953

Abstract

Why should a genome be protected? Because it contains our most private data! A genome contains an organism’s set of genetic material (DNA and, in viruses, RNA), and it contains all genes and non-coding sequences. The structure of DNA was described by Watson [...] Read more.

Why should a genome be protected? Because it contains our most private data! A genome contains an organism’s set of genetic material (DNA and, in viruses, RNA), and it contains all genes and non-coding sequences. The structure of DNA was described by Watson and Crick in 1953, but the first studies were conducted a century earlier by Miescher, who described the structure and chemical composition of the nucleus. The first action aimed at securing the results of genetic research was the creation of databases for the results obtained using genetic fingerprinting technology. The discovery of the sequencing method and the introduction of the polymerase chain reaction laid the foundations for understanding the genome’s function. Automated DNA sequencing proved to be hundreds of times faster than traditional methods, thus reducing the cost and time of genome analyses. Thousands of genomic data points are stored in private and governmental databases. The security of patients’ genomic data must be ensured by protecting it from unauthorized use while, at the same time, enabling research for the sake of public health. The falling prices of genome sequencing and the increasing availability of commercial sequencing for the public could result in ethical problems and undermine the safety of personal information. Full article

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

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15 pages, 2480 KB

Open AccessArticle

Soil pH and Nitrogen Content Drive the Succession of RubisCO-Harboring Microbial Communities Across Picea asperata Plantation Ages

by Dehui Li, Yaodan Deng, Xiaohui Zhao, Qian Liao, Jialing Chen, Chaonan Li and Haijun Liao

Biology 2026, 15(9), 725; https://doi.org/10.3390/biology15090725 - 2 May 2026

Viewed by 685

Abstract

Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin–Benson–Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, [...] Read more.

Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin–Benson–Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, we investigated the community succession of microbes carrying the gene encoding RubisCO, a key enzyme in the CBB cycle, across a stand-age chronosequence in a Picea asperata plantation ecosystem. Our results revealed a progressive decrease in microbial α-diversity and a significant restructuring of community composition with increasing stand age, characterized by an enrichment of Proteobacteria and a concomitant depletion of Actinobacteria. While the Shannon–Wiener index was most strongly correlated with soil total nitrogen content, redundancy analysis identified soil pH as the predominant environmental driver of community turnover, a relationship that was found to be threshold-dependent, with substantial community shifts occurring in response to pH variations of 0.5 to 1.0 units. These findings suggest that sustaining the diversity of RubisCO-harboring microbes in older stands—a process potentially enhanced by soil nitrogen management—provides a viable strategy for augmenting the carbon sequestration capacity of managed forests through targeted microbiome regulation. Full article

(This article belongs to the Section Ecology)

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31 pages, 45064 KB

Open AccessArticle

The Role of Phytoplankton and Sediment Microbial Community on Sr, U, Pu, and Am Behavior in Freshwater Lake Dryazlo

by Marina Popova, Vasiliy Riabov, Nadezhda Popova, Grigoriy Artemiev and Alexey Safonov

Biology 2026, 15(9), 724; https://doi.org/10.3390/biology15090724 - 2 May 2026

Viewed by 597

Abstract

Radionuclide contamination of surface water bodies poses a significant environmental challenge, particularly for low-productivity dystrophic systems where natural self-purification capacity is limited. This study aimed to assess the potential of phytoplankton and bottom sediments as biogeochemical barriers for radionuclides. Laboratory modeling of ⁹⁰ [...] Read more.

Radionuclide contamination of surface water bodies poses a significant environmental challenge, particularly for low-productivity dystrophic systems where natural self-purification capacity is limited. This study aimed to assess the potential of phytoplankton and bottom sediments as biogeochemical barriers for radionuclides. Laboratory modeling of ⁹⁰Sr, ²³³U, ²³⁹Pu, and ²⁴¹Am accumulation was conducted using samples of Lake Dryazlo (Tver Oblast) water and bottom sediments as a representative dystrophic model system. Sorption onto phytoplankton biomass over a single growing season was estimated at 1.89 × 10⁴, 5.41 × 10⁴, 6.64 × 10⁴, and 4.04 × 10⁴ Bq g⁻¹ dry biomass for ⁹⁰Sr, ²³³U, ²³⁹Pu, and ²⁴¹Am, respectively. Actinide immobilization in bottom sediments depended on mineral composition and microbial community activity. Ammophos addition increased radionuclide removal from the liquid phase by 2–5-fold through enhanced phytoplankton productivity, and promoted actinide fixation via phosphate mineral phase formation and stimulation of anaerobic sulfur- and iron-cycling bacteria. These results demonstrate a viable biogeochemical barrier approach applicable to the decommissioning of radioactive waste storage ponds and remediation of radionuclide-contaminated water bodies. Full article

(This article belongs to the Section Marine and Freshwater Biology)

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35 pages, 6168 KB

Open AccessReview

Diabetic Peripheral Neuropathy: Mechanisms and Emerging Therapies

by Mohammed M. H. Albariqi, Ibrahim A. Alradwan, Saad M. Alqahtani, Majed A. Majrashi, Basem Jahz Almutiri, Amjad Jabaan and Sultan Alzahrani

Biology 2026, 15(9), 723; https://doi.org/10.3390/biology15090723 - 2 May 2026

Cited by 2 | Viewed by 1286

Abstract

Diabetic peripheral neuropathy (DPN) is a common and debilitating complication of diabetes mellitus which affects individuals with both type 1 and type 2 diabetes mellitus (T2DM), presenting with sensory loss, pain, and progressive nerve dysfunction. DPN pathogenesis is multifactorial: chronic hyperglycemia activates the [...] Read more.

Diabetic peripheral neuropathy (DPN) is a common and debilitating complication of diabetes mellitus which affects individuals with both type 1 and type 2 diabetes mellitus (T2DM), presenting with sensory loss, pain, and progressive nerve dysfunction. DPN pathogenesis is multifactorial: chronic hyperglycemia activates the polyol, hexosamine, and protein kinase C (PKC) pathways, increases advanced glycation end-products, and drives oxidative stress, mitochondrial dysfunction, inflammation, and impaired neurotrophic signaling. In addition to hyperglycemia-driven mechanisms, dyslipidemia and microvascular insufficiency exacerbate neural ischemia and metabolic stress. Recent mechanistic, animal, and associative human studies further implicate amyloidogenic toxicity, particularly from human islet amyloid polypeptide (hIAPP), as a plausible contributory factor in peripheral nerve degeneration in T2DM, linking protein misfolding and aggregation to axonal damage and demyelination in DPN. Despite increased understanding of these mechanisms, current treatments remain mainly symptomatic. Emerging therapeutic strategies, including antioxidants, anti-inflammatory agents, modulators of mitochondrial function, amyloid oligomer modulators, neurotrophic enhancers, and regenerative approaches such as stem cells and gene-based therapies, offer potential to modify disease progression. The strength of evidence across these methods varies, ranging from mechanistic and animal studies to early human research and, in some cases, randomized clinical trials. Therefore, although several candidates show potential to alter the disease, few have demonstrated consistent benefits on objective measures of nerve structure or function in large clinical trials. This review summarizes the key mechanisms driving DPN in T2DM and highlights promising therapeutic innovations poised for clinical translation. Full article

(This article belongs to the Special Issue Young Researchers in Neuroscience)

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26 pages, 16545 KB

Open AccessArticle

A Specimen-Based Comparative MicroCT–FEA Analysis of Vertebral Trabecular Bone Microarchitecture and Mechanical Response in Two South American Cervids: The Patagonian Huemul (Hippocamelus bisulcus) and the Southern Pudu (Pudu puda)

by Danae Tapia, Álvaro González, Fernando Vidal and Paulo Salinas

Biology 2026, 15(9), 722; https://doi.org/10.3390/biology15090722 - 2 May 2026

Viewed by 761

Abstract

The Patagonian huemul (Hippocamelus bisulcus) and the Southern pudu (Pudu puda) are native South American cervids that differ in body size, ecology, and conservation status. However, quantitative evidence linking vertebral trabecular microarchitecture with biomechanical behavior in these species remains [...] Read more.

The Patagonian huemul (Hippocamelus bisulcus) and the Southern pudu (Pudu puda) are native South American cervids that differ in body size, ecology, and conservation status. However, quantitative evidence linking vertebral trabecular microarchitecture with biomechanical behavior in these species remains scarce. This study aimed to comparatively characterize vertebral trabecular bone structure and its mechanical response using an integrative, non-destructive approach. Vertebral bodies from cervical, thoracic, and lumbar regions were analyzed using high-resolution micro-computed tomography to quantify structural parameters, followed by finite element analysis to estimate deformation and von Mises stress under standardized axial compression. Both specimens exhibited consistent regional variation, with cervical vertebrae showing lower density and organization, and thoracic–lumbar vertebrae displaying denser trabecular networks. The Southern pudu specimen appeared to present a more homogeneous microarchitecture and a relatively uniform mechanical response along the vertebral column. In contrast, the Patagonian huemul specimen tended to show greater structural heterogeneity, with apparently higher deformation and stress values, particularly in the cervical region. These findings suggest that trabecular organization may contribute to the differences in vertebral mechanical behavior observed between the analyzed specimens. This study provides a preliminary comparative baseline for understanding skeletal adaptation and structural vulnerability in South American cervid species. This exploratory analysis is based on single specimens per species and should be interpreted as preliminary evidence rather than population-level inference. Full article

(This article belongs to the Special Issue Bone Mechanics: From Cells to Organs to Function)

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17 pages, 2823 KB

Open AccessArticle

Feasibility of Elemental and Microstructural Differentiation of Land Snail Eggs from Bradybaena ravida and Cathaica fasciola

by Yiya Wang, Fengjiang Li, Siyi Peng, Jiujiang Zhao, Linghao Zhao, Yajie Dong, Dongyang Sun and Naiqin Wu

Biology 2026, 15(9), 721; https://doi.org/10.3390/biology15090721 - 2 May 2026

Viewed by 745

Abstract

Although species identification is crucial for land-snail eggs, limited effort has been made to identify the species responsible for producing the eggs. In this study, we used laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) to measure 54 elements in both the eggshells [...] Read more.

Although species identification is crucial for land-snail eggs, limited effort has been made to identify the species responsible for producing the eggs. In this study, we used laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) to measure 54 elements in both the eggshells and adult shells of Bradybaena ravida and Cathaica fasciola and we used scanning electron microscope (SEM) to analyze the microstructure of the eggshells of the two species. Our results reveal that while the concentrations of Sr, Na, Mg, P, and Ba in the adult shells of the two species are not distinct, they are distinct or partially distinct between their eggshells, indicating that these elements have the potential to differentiate the eggs of the two species. Moreover, the eggshells of C. fasciola exhibit a blocky morphology without cavities, whereas those of B. ravida, while also blocky, contain irregular cavities. These distinct elemental and microstructural characteristics enable the effective differentiation of the eggs of B. ravida and C. fasciola. Our study demonstrates the feasibility of a critical microscopic methodology for identifying land-snail eggs at the genus/species level, thereby facilitating deeper exploration of their value in understanding biological, climatic, and ecological changes. Full article

(This article belongs to the Section Ecology)

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15 pages, 2184 KB

Open AccessArticle

Effects of Topographic Variation on Soil Fungal Community Structure in a Podocarpus oleifolius D. Don Tree Plantation

by Lina Marcela Anacona-Finscué, Paola Torres-Andrade, Adriana Corrales, Adriana María Marín Velez and Jorge Andres Ramírez

Biology 2026, 15(9), 720; https://doi.org/10.3390/biology15090720 - 1 May 2026

Viewed by 826

Abstract

Soil fungal communities play a central role in nutrient cycling and ecosystem functioning in tropical montane forests, yet the relative influence of topographic heterogeneity and soil depth on their assembly remains poorly understood. This study evaluated the composition, diversity, and functional structure of [...] Read more.

Soil fungal communities play a central role in nutrient cycling and ecosystem functioning in tropical montane forests, yet the relative influence of topographic heterogeneity and soil depth on their assembly remains poorly understood. This study evaluated the composition, diversity, and functional structure of soil fungal communities associated with an experimental Podocarpus oleifolius plantation in the Colombian Andes. Using ITS2 rDNA sequencing, fungal assemblages were characterized from soil samples collected around ten trees distributed along a topographic gradient. For each tree, samples were collected at two soil depths (0–10 cm and 10–20 cm), yielding a total of 17 samples after quality control. Topographic variables derived from a digital elevation model were used to evaluate their influence on community structure. A total of 1875 Operational Taxonomic Units (OTUs) were detected, dominated by Ascomycota. No significant differences in alpha or beta diversity were observed between soil depths. In contrast, slope emerged as the strongest environmental driver of community composition. A high proportion of unassigned OTUs highlighted the presence of poorly characterized fungal diversity. These findings highlight the importance of incorporating fine-scale terrain heterogeneity into restoration strategies with native species and into future studies of soil microbial dynamics in tropical montane ecosystems. Full article

(This article belongs to the Section Ecology)

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22 pages, 2735 KB

Open AccessArticle

Grape Pomace Polyphenolic Extract Promotes Osteogenic Differentiation in Human Mesenchymal Stem Cells Through Activation of RUNX2 and NRF2 Transcription Factors: A Potential Natural Strategy for Osteoporosis Prevention

by Nadia Calabriso, Marika Massaro, Stefano Quarta, Luisa Siculella, Giuseppe Santarpino, Tiziano Verri, Carmela Gerardi, Giovanna Giovinazzo and Maria Annunziata Carluccio

Biology 2026, 15(9), 719; https://doi.org/10.3390/biology15090719 - 1 May 2026

Viewed by 691

Abstract

Osteoporosis is an age-related metabolic bone disorder characterized by an imbalance between bone resorption and formation. Natural polyphenols have gained attention as potential complementary strategies for its prevention. In this study, we investigated the effects of a sustainable, polyphenol-rich extract from red grape [...] Read more.

Osteoporosis is an age-related metabolic bone disorder characterized by an imbalance between bone resorption and formation. Natural polyphenols have gained attention as potential complementary strategies for its prevention. In this study, we investigated the effects of a sustainable, polyphenol-rich extract from red grape pomace (GPE) on human mesenchymal stem cell (MSC) fate and its underlying mechanisms of action. We found that GPE significantly promoted osteogenic differentiation while suppressing adipogenic differentiation in canonical bone marrow-derived MSCs (BMSCs). This biological effect was preserved in adipose tissue-derived MSCs (AdMSCs) obtained from elderly patients (>65 years) at high cardiovascular risk. Mechanistically, GPE downregulated adipogenic markers (PPARγ, CD36 and FABP4) and enhanced osteogenic markers (RUNX2, ALP, OSX, BMP-2, OPN, COL1A1 and OCN). Moreover, GPE activated NRF2-dependent redox signaling, as evidenced by increased NRF2 nuclear translocation and transcriptional activity. Accordingly, GPE treatment significantly upregulated, or consistently increased, the expression of multiple NRF2 target genes, including HO-1, GPX, CAT, GCLC, and NQO1. Importantly, pharmacological inhibition of NRF2 attenuated GPE-induced ALP activity, confirming NRF2 as a key mediator of its osteogenic effects. Overall, grape pomace-derived polyphenols act as upstream modulators of redox-sensitive and osteogenic transcription factors, rebalancing MSC differentiation toward osteogenesis and mitigating age-related bone fragility. Full article

(This article belongs to the Special Issue Osteoblast Differentiation in Health and Disease)

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14 pages, 3657 KB

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Taxonomic Variation in Coral Depletion at Orpheus Island (Inshore Great Barrier Reef, Australia) Linked to Unprecedented Rainfall and Hyposalinity

by Morgan S. Pratchett, Harrison Locke, Roemer Booij, Ewa Buczkowska, Raj H. Mathias, Jennifer Calcraft, Gideon Heller-Wagner, Scott F. Heron, Peter C. Doll and Mike J. McWilliam

Biology 2026, 15(9), 718; https://doi.org/10.3390/biology15090718 - 1 May 2026

Viewed by 920

Abstract

Acute disturbances caused by changing environmental conditions are increasingly affecting the structure and function of coral reef ecosystems. Notably, changing rainfall patterns are leading to increasing incidence of hyposalinity. This study explored interannual changes in the overall cover and composition of hard corals [...] Read more.

Acute disturbances caused by changing environmental conditions are increasingly affecting the structure and function of coral reef ecosystems. Notably, changing rainfall patterns are leading to increasing incidence of hyposalinity. This study explored interannual changes in the overall cover and composition of hard corals (order Scleractinia) in Pioneer Bay, Orpheus Island, which was subject to hyposalinity during unprecedented high rainfall in February 2025. Hard coral cover declined 66.60%, from 41.66% (±1.22 SE) in September 2024 to 13.92% (±0.92 SE) in October 2025, with coral loss mostly apparent on the reef flat and reef crest. Coral loss was not equally apportioned among different coral taxa (genera), possibly reflecting differential susceptibility to hyposalinity based on specific physiology and habitat associations. The most pronounced declines were recorded among Merulinidae, which were the predominant hard corals on the reef flat in 2024. Soft corals were similarly affected and exhibited major declines in abundance on the reef flat. Hyposalinity is rarely considered among the suite of climatic disturbances that impact on coral assemblages and reef ecosystems, but this research shows that the potential ecological effects are very extensive, adding to the diversity of acute disturbances that will influence the structure coral reef ecosystems in the Anthropocene. Full article

(This article belongs to the Special Issue Changing Coral Reef Biodiversity and Function in the Anthropocene)

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15 pages, 880 KB

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Repositioning of Fluoroquinolones: A New Approach in Antitumor Therapy

by Jeferson Ricardo da Silva, Jaqueline Barbosa de Souza, Lara Limeira de Oliveira, Luís André de Almeida Campos and Isabella Macário Ferro Cavalcanti

Biology 2026, 15(9), 717; https://doi.org/10.3390/biology15090717 - 30 Apr 2026

Viewed by 677

Abstract

Fluoroquinolones are known for their antibacterial properties, but recent research has revealed their potential to inhibit the growth and proliferation of cancer cells. Thus, this study aimed to emphasize the repositioning and potential of fluoroquinolones as possible therapeutic tools in the fight against [...] Read more.

Fluoroquinolones are known for their antibacterial properties, but recent research has revealed their potential to inhibit the growth and proliferation of cancer cells. Thus, this study aimed to emphasize the repositioning and potential of fluoroquinolones as possible therapeutic tools in the fight against cancer, opening up new perspectives for the field of oncology. Thus, this paper consists of a descriptive literature review of recent studies published between 2013 and 2023 on the use of fluoroquinolones in anticancer therapy. The results indicate that fluoroquinolones can interfere with the cell cycle, induce apoptosis and oxidative stress, and impact factors associated with tumorigenesis, such as the transcription of ectopic expression of SNAI1 for epithelial–mesenchymal transition. In addition, studies show that combining fluoroquinolones with other antineoplastic agents can increase their efficacy, and the possibility of encapsulating these drugs in controlled-release systems is also emerging as a promising antitumor strategy. In conclusion, repositioning fluoroquinolones in antitumor therapy presents an expanding field of research, offering new perspectives for cancer treatment. However, more studies are needed to fully elucidate their potential and establish effective clinical use protocols. Full article

(This article belongs to the Section Cancer Biology)

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26 pages, 61766 KB

Open AccessArticle

Quzhou Aurantii Fructus Extract Attenuates Idiopathic Pulmonary Fibrosis by Regulating Nrf2/HO-1 Axis

by Li Yu, Lixia Wang, Jinyao Zhang, Ruimin Sun, Siming Zhang, Ping Yin, Ying Chen, Guocan Chen, Yiping Ye, Haitong Wan, Yu He, Yunxiang Chen and Lijiang Zhang

Biology 2026, 15(9), 716; https://doi.org/10.3390/biology15090716 - 30 Apr 2026

Viewed by 820

Abstract

Recently, Quzhou Aurantii Fructus Extract (QAFE) was reported to exert anti-inflammatory effects on different types of respiratory diseases; however, it is yet to be determined whether it is effective in patients with idiopathic pulmonary fibrosis (IPF). The purpose of this study is to [...] Read more.

Recently, Quzhou Aurantii Fructus Extract (QAFE) was reported to exert anti-inflammatory effects on different types of respiratory diseases; however, it is yet to be determined whether it is effective in patients with idiopathic pulmonary fibrosis (IPF). The purpose of this study is to explore the capacity of QAFE to fight fibrotic disease, in particular how it works in relation to the regulation of the nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase 1 (HO-1) pathway. QAFE was made with Quzhou Fructus Aurantii (QAF), and the content of four flavonoids in the samples prepared was analyzed by high-performance liquid chromatography (HPLC). The therapeutic effect of QAFE was experimented by establishing IPF models in mice and in cells. Identification of the mechanism of QAFE in IPF through knockout or knockdown of the Nrf2 gene. The experiments suggest that QAFE has the potential to prevent IPF-induced inflammation, collagen deposition, oxidative stress, and apoptosis of cells. Silencing Nrf2 by knockdown or knockout is enough to prevent the capacity of QAFE to inhibit the process of inflammation, oxidative stress, and collagen deposition to cause more serious lung injury and HO-1 expression downregulation. QAFE is a potential new antifibrotic drug in IPF with an effect on the Nrf2/HO-1 pathway that reduces inflammation and oxidative stress. Full article

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12 pages, 2624 KB

Open AccessArticle

miRNA Sequencing and Differential Analysis of Testis in 1-Year-Old and 2-Year-Old Kazakh Horses

by Yuhe Zhou, Liuxiang Wen, Wanlu Ren, Mingyue Wen, Mengling Ming, Jianwen Wang, Jun Meng, Xinkui Yao and Yaqi Zeng

Biology 2026, 15(9), 715; https://doi.org/10.3390/biology15090715 - 30 Apr 2026

Viewed by 567

Abstract

The Kazakh horse represents a significant genetic resource within China’s equine population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for [...] Read more.

The Kazakh horse represents a significant genetic resource within China’s equine population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for the preservation of this breed and the advancement of the related industry. In this study, testicular tissues from 1-year-old (pre-pubertal) and 2-year-old (post-pubertal) Kazakh horses were analyzed. miRNA sequencing was conducted on tissues from these age groups, followed by bioinformatics analyses to elucidate the functions of differentially expressed miRNAs (DEmiRNAs). The reliability of the sequencing data was subsequently verified using RT-qPCR. Analysis revealed 165 differentially expressed miRNAs (DEmiRNAs) in the testicular tissues between the two age groups. Of these, 118 DEmiRNAs (e.g., eca-miR-206 and eca-miR-2483) were significantly up-regulated (p < 0.05), and 47 DEmiRNAs (e.g., eca-miR-196a and eca-miR-211) were significantly down-regulated (p < 0.05). These DEmiRNAs were mainly implicated in biological processes including lipid metabolism and signal transduction. Their predicted target genes are potentially involved in key reproductive processes, notably testicular development and spermatogenesis. This study identifies candidate miRNAs and potential regulatory pathways associated with sexual maturation in Kazakh horses, providing a preliminary molecular basis for future functional validation and improvement of equine reproductive performance. Full article

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

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20 pages, 15756 KB

Open AccessArticle

Evolutionary Tracing and Taxonomic Implications of the Mitochondrial Genome of Gephyrocharax atracaudatus (Meek and Hildebrand, 1912)

by Zhaowen Liu, Youkun Huang, Limin Yang, Jia Ye, Huiting Wu, Jiapan Pan, Chengtao Shan, Yudi Shan, Wenxi Wang, Junyi Wang, Zhuqing Feng and Siyu Chen

Biology 2026, 15(9), 714; https://doi.org/10.3390/biology15090714 - 30 Apr 2026

Viewed by 585

Abstract

Gephyrocharax atracaudatus is a rare freshwater fish in Panama. This study provides a comprehensive analysis of the mitochondrial genome of G. atracaudatus, highlighting its gene composition, codon usage, evolutionary pressures, and phylogenetic relationships. The findings reveal unique evolutionary patterns and divergence times [...] Read more.

Gephyrocharax atracaudatus is a rare freshwater fish in Panama. This study provides a comprehensive analysis of the mitochondrial genome of G. atracaudatus, highlighting its gene composition, codon usage, evolutionary pressures, and phylogenetic relationships. The findings reveal unique evolutionary patterns and divergence times of G. atracaudatus that enhance the understanding of the genetic diversity within Characiformes. The increasing availability of genomic data has prompted taxonomic revisions for numerous Characiformes species, encompassing corrections to species names, subfamily, and family classifications. This study reconfirmed the classification of G. atracaudatus as “Gephyrocharax, Stevardiinae, Stevardiidae, Characiformes”. A cross-analysis model for species differentiation and tracking was established using divergence time comparison and phylogenetic analysis. The results show that G. atracaudatus, Hyphessobrycon roseus and Pristella maxillaris converge on one branch, indicating that the genetic relationship may be the most similar, and it occurred approximately 90.45 Mya in the Cretaceous. This study establishes a robust model framework for understanding the evolution of G. atracaudatus, and correctly determines the biological classification status of G. atracaudatus, providing basic data support for clarifying the evolution mode of Characiformes. Full article

(This article belongs to the Special Issue Young Researchers in Conservation Biology and Biodiversity)

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20 pages, 7367 KB

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Impacts of Anthropogenic Activities and Climate Change on the Distribution Ranges of Five Tragopan Birds in China

by Jiming Cheng, Chao Zhang, Xingfu Yan, Xinyue Chen, Yingqun Feng, Furong Cai, Hongjin Yan, Shuqi Liu and Yonghong Luo

Biology 2026, 15(9), 713; https://doi.org/10.3390/biology15090713 - 30 Apr 2026

Viewed by 444

Abstract

Anthropogenic activities and environmental changes have exerted an increasingly high impact on the habitats of wild animals, especially endangered species. Researchers have paid attention to the effects of future climate change on wildlife habitats. However, the impact of climate change on the suitable [...] Read more.

Anthropogenic activities and environmental changes have exerted an increasingly high impact on the habitats of wild animals, especially endangered species. Researchers have paid attention to the effects of future climate change on wildlife habitats. However, the impact of climate change on the suitable habitats of Tragopan birds has rarely been reported. Here, we used the Maxent model to assess the influence of climate change on the geographical distribution of five Tragopan species. The results showed that the SSP585 scenario projected relatively favorable conditions, with the total area of suitable habitats expected to show an overall increasing trend over time. Centroid analysis revealed that the centroid gradually shifts toward lower latitudes and elevations due to climate warming. Environmental factor analysis showed that human-induced factors (particularly land use) are the main determinants affecting the habitat suitability of Tragopan birds. Notably, a comparison between dispersal velocity and biological velocity showed that despite the predicted gradual expansion of habitat area, Tragopan birds may be difficult to expand into the newly suitable habitat regions. We further emphasize that establishing ecological corridors and setting up new protected areas will have a more significant impact on conserving the Tragopan birds. Full article

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22 pages, 3862 KB

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Environmental Filtering of Bacterial Communities Driven by Pesticide Residue Profiles in the Almaty Region, Kazakhstan

by Lazzat Asylbekkyzy, Bekzhan D. Kossalbayev, Fiaz Ahmad, Jingjing Wang, Assemgul K. Sadvakasova, Meruyert O. Bauenova, Altynbek A. Abseyt and Dilnaz E. Zaletova

Biology 2026, 15(9), 712; https://doi.org/10.3390/biology15090712 - 30 Apr 2026

Viewed by 723

Abstract

Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use [...] Read more.

Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use agrochemicals on the structure and inferred functional potential of soil bacterial communities in the Almaty Region, Kazakhstan, using high-throughput 16S rRNA gene sequencing and GC–MS/MS analysis of 217 compounds. Results revealed a clear contrast between contamination regimes: modern organophosphate insecticides and herbicides, such as simazine (up to 32.3 mg kg⁻¹ at the Amangeldy site), were associated with lower alpha diversity (Shannon ≈ 3.03) and enrichment of copiotrophic taxa such as Pseudomonas and Sphingobium. In contrast, persistent OCP residues, such as p,p′-DDE (up to 1.43 mg kg⁻¹ at the Kyzylkairat site), were associated with higher diversity (Shannon ≈ 5.46) and enrichment of more stress-tolerant oligotrophic lineages, including Acidobacteria and Vicinamibacteraceae. Procrustes analysis supported significant concordance between pesticide profiles and taxonomic structure (M² = 0.286, p < 0.001), indicating that pesticide residue composition was strongly associated with bacterial community structure across the studied soils. The observed shift in community balance, particularly the relative increase in Pseudomonas versus Acidobacteria, is proposed as a candidate compositional indicator of ecosystem instability in semi-arid agricultural soils and may inform future remediation-oriented studies. Full article

(This article belongs to the Section Microbiology)

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33 pages, 26000 KB

Open AccessArticle

Ethnobotany and Medicinal Potential of Wild Edible Fruit Species in Kut Chum District, Yasothon Province, Thailand

by Tammanoon Jitpromma, Piyaporn Saensouk, Santi Watthana and Surapon Saensouk

Biology 2026, 15(9), 711; https://doi.org/10.3390/biology15090711 - 30 Apr 2026

Cited by 1 | Viewed by 630

Abstract

Wild edible fruits play an important role in supporting food security, nutrition, and traditional knowledge systems in rural communities, yet their diversity and uses remain insufficiently documented in many parts of Thailand. This study aimed to investigate the diversity, utilization, and ethnobotanical significance [...] Read more.

Wild edible fruits play an important role in supporting food security, nutrition, and traditional knowledge systems in rural communities, yet their diversity and uses remain insufficiently documented in many parts of Thailand. This study aimed to investigate the diversity, utilization, and ethnobotanical significance of wild edible fruit species in Kut Chum District, Yasothon Province. Ethnobotanical data were collected through semi-structured interviews and field surveys with local informants, and quantitative indices, including the Cultural Importance Index (CI), Fidelity Level (%FL), and Informant Consensus Factor (ICF), were applied to evaluate species significance and medicinal agreement. A total of 71 species belonging to 33 families were recorded, with most species consumed as fresh fruits and a subset used for medicinal purposes. Several species, such as Irvingia malayana Oliv. ex A.W.Benn., Phyllanthus emblica L., and Syzygium cumini (L.) Skeels exhibited high cultural importance, reflecting their key roles in local diets. High ICF values across therapeutic categories indicated strong consensus in ethnomedicinal knowledge. Additionally, 44 species not used medicinally in the study area were reported as medicinal in other regions, highlighting spatial variation in knowledge systems. These findings emphasize the importance of wild edible fruits as multifunctional resources contributing to food and nutritional security. Integrating culturally important species into conservation and sustainable use strategies may support biodiversity preservation and the continuity of traditional ecological knowledge. Full article

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

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15 pages, 2805 KB

Open AccessArticle

The Genome-Wide Identification and Expression Analysis of the AMT Gene Family in Foxtail Millet

by Mingge Han, Junliang Yan, Kang Zhao, Yang Zhang, Xiaojing Li, Mengyu Xue, Juwu Gong and Yajie Ma

Biology 2026, 15(9), 710; https://doi.org/10.3390/biology15090710 - 30 Apr 2026

Viewed by 434

Abstract

Ammonium transporters (AMTs) represent a class of proteins within the ammonium transporter domain, which play an important role in mediating the transmembrane transport of NH₄⁺ in plants. However, research on AMT genes in foxtail millet remains limited. In this study, members [...] Read more.

Ammonium transporters (AMTs) represent a class of proteins within the ammonium transporter domain, which play an important role in mediating the transmembrane transport of NH₄⁺ in plants. However, research on AMT genes in foxtail millet remains limited. In this study, members of the AMT gene family in foxtail millet were identified at the whole genome level through bioinformatic analysis. The gene structure, evolutionary relationships, chromosomal localization, interspecies collinearity, cis-acting elements, and expression patterns of SiAMT members were systematically analyzed. The results revealed that there were nine SiAMT family members in foxtail millet, with molecular weights ranging from 49.5 to 53.8 kDa. Phylogenetic analysis classified them into three groups, which were unevenly distributed across chromosomes. The analysis of promoter cis-acting elements identified multiple regulatory elements, including light-, anaerobic-, and hormone-responsive elements. Collinearity analysis showed that the divergence time of AMT family members in foxtail millet and rice was more recent compared to Arabidopsis thaliana. The expression levels of SiAMT members varied across different tissues of foxtail millet, with most SiAMT family members showing high expression in roots, while SiAMT7 was significantly expressed in leaves. qRT-PCR analysis showed that SiAMT1 was significantly down-regulated in roots, stems, and leaves under salt stress. This study provides a theoretical foundation for further investigation into the functions of the AMT gene family. Full article

(This article belongs to the Special Issue Plant Breeding: From Biology to Biotechnology)

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15 pages, 4192 KB

Open AccessArticle

Exploring the Phosphoregulatory Network of Human Sucrose Non-Fermenting 1-Related Kinase

by Vaishnavi Gopalakrishnan, Amal Fahma, Athira Perunelly Gopalakrishnan, Suhail Subair, Prathik Basthikoppa Shivamurthy, Rajesh Raju and Sowmya Soman

Biology 2026, 15(9), 709; https://doi.org/10.3390/biology15090709 - 30 Apr 2026

Viewed by 387

Abstract

Sucrose non-fermenting 1-related kinase (SNRK) is an understudied serine/threonine kinase of the CAMKL family, known for its role in metabolic regulation and cell signaling. Despite its emerging relevance in various biological processes and diseases, the phosphoregulatory landscape of human SNRK (valid substrates or [...] Read more.

Sucrose non-fermenting 1-related kinase (SNRK) is an understudied serine/threonine kinase of the CAMKL family, known for its role in metabolic regulation and cell signaling. Despite its emerging relevance in various biological processes and diseases, the phosphoregulatory landscape of human SNRK (valid substrates or role of its phosphosites) remains unexplored and demands robust, large-scale, data-oriented approaches to predict the potential substrates. A comprehensive analysis of global human phosphoproteomics datasets was performed to systematically identify class I phosphosites on SNRK, along with their predicted upstream kinases, potential downstream substrates, and coregulated phosphoproteins. Our analysis resulted in the identification of 33 dark SNRK phosphosites, of which 19 were differentially regulated across an array of experimental conditions. Among them, S518 and S569, outside their kinase domain, were the most frequently regulated and co-occurred phosphosites under diverse conditions. Notably, S569 is predicted as a candidate autophosphorylation site of SNRK. In these contexts, coregulation analysis of proteins and their phosphorylation sites suggested associations of phospho-SNRK in cell cycle progression, chromatin organization, and DNA replication. Uncovering candidate upstream kinases and potential substrates for prioritized validation, this study provides the first comprehensive phosphoproteomic map of SNRK, serving as a foundation for future investigations into its signaling network associations and therapeutic approaches. Full article

(This article belongs to the Section Bioinformatics)

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27 pages, 4488 KB

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A Neuro-Symbolic Bioinformatics Framework for Unlocking Chordate Physiological Dark Data and Validating Allometric Scaling

by Zhiyao Duan, Guihu Zhao, Changyun Li and Bo Liu

Biology 2026, 15(9), 708; https://doi.org/10.3390/biology15090708 - 30 Apr 2026

Viewed by 511

Abstract

Animal functional trait data are essential for macroecology, but massive datasets remain locked in unstructured scientific literature. Traditional manual extraction is inefficient, and general-purpose artificial intelligence (AI) systems struggle with complex biological tables and numerical accuracy. To address this bioinformatics challenge, we propose [...] Read more.

Animal functional trait data are essential for macroecology, but massive datasets remain locked in unstructured scientific literature. Traditional manual extraction is inefficient, and general-purpose artificial intelligence (AI) systems struggle with complex biological tables and numerical accuracy. To address this bioinformatics challenge, we propose a multimodal neuro-symbolic framework combining visual-language perception and code-based reasoning. This approach reconstructs complex document layouts and delegates biostatistical calculations, such as unit normalization and thermodynamic energy conversion, to an isolated programming environment to ensure mathematical and statistical consistency. By mining literature spanning 117 years, we constructed a high-fidelity physiological database for 1632 chordate species. Our method achieved a macro-averaged F1 score of 0.935 in extracting biophysical fields. External benchmarking against a curated mammalian trait database showed strong concordance for shared body-mass and metabolic-rate traits, while our database retained record-level provenance and physiological context. Furthermore, the extracted data reproduced classic allometric scaling relationships for basal metabolic rate and brain volume while preserving physiological adaptations, supporting the biological plausibility of the dataset. This study validates a reproducible bioinformatics pipeline that minimizes extraction artifacts and substantially reduces downstream mathematical and statistical conversion errors, while providing a scalable, complementary resource for building physiology-oriented trait databases from historical literature. Full article

(This article belongs to the Section Bioinformatics)

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31 pages, 4275 KB

Open AccessArticle

WCEDSAM: A Lightweight Multi-Scale Colonoscopy Polyp-Segmentation Network Combining Frequency-Domain Decomposition and Adaptive Feature Enhancement

by Lei Wang, Tongyu Wang, Sitong Liu, Zheng Chen, Jie Zhang, Cong Jin and Dexing Kong

Biology 2026, 15(9), 707; https://doi.org/10.3390/biology15090707 - 30 Apr 2026

Viewed by 471

Abstract

Colorectal cancer screening is challenged by variations in polyp morphology, indistinct polyp boundaries, and the high computational costs associated with current models. To address these issues, a lightweight medical image segmentation model, WCEDSAM, has been developed. WCEDSAM is based on a modified, compact [...] Read more.

Colorectal cancer screening is challenged by variations in polyp morphology, indistinct polyp boundaries, and the high computational costs associated with current models. To address these issues, a lightweight medical image segmentation model, WCEDSAM, has been developed. WCEDSAM is based on a modified, compact version of MedSAM, which incorporates a Wavelet Transform-based component to extract and separate overlapping features at the pixel level. Additionally, a DSConv-ECA module is positioned before the ViT encoder to capture local features efficiently while reducing parameter count and enhancing inter-channel communication. Experimental results demonstrate that WCEDSAM achieves top performance on five public datasets, including Kvasir-SEG and CVC-ClinicDB, with 15.38 million parameters, achieving mean Dice (mDice) scores of 0.9383 on Kvasir-SEG and 0.9376 on CVC-ClinicDB. Cross-domain evaluations yield mDice scores of 0.9189 on CVC-ColonDB, 0.8961 on CVC-300, and 0.7765 on ETIS datasets, respectively, substantially outperforming other methods such as UNet++ and TransUNet. Full article

(This article belongs to the Special Issue AI Deep Learning Approach to Study Biological Questions (2nd Edition))

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18 pages, 7304 KB

Open AccessArticle

Comparison of the Chemical Composition of Different Body-Color Phenotypes of Perinereis aibuhitensis (Grube, 1878) (Annelida, Nereididae)

by Huan Liu, Jiahao Liu, Chenchen Bian, Qiang Ma, Yuliang Wei, Mengqing Liang and Houguo Xu

Biology 2026, 15(9), 706; https://doi.org/10.3390/biology15090706 - 30 Apr 2026

Viewed by 505

Abstract

A comparative chemical analysis was conducted between P. aibuhitensis of orange and green body colors, evaluating their proximate composition, fatty acid profile, amino acid profile, astaxanthin content, lipidomic profile, and other biochemical parameters. Samples were categorized by body color into two groups, each [...] Read more.

A comparative chemical analysis was conducted between P. aibuhitensis of orange and green body colors, evaluating their proximate composition, fatty acid profile, amino acid profile, astaxanthin content, lipidomic profile, and other biochemical parameters. Samples were categorized by body color into two groups, each with ten biological replicates. The samples were collected from the same local polychaete farm. The results revealed that the green phenotype had significantly higher moisture content but lower crude protein, crude lipid, and ash content compared to the orange phenotype. The orange polychaete was characterized by significantly higher concentrations of 16:0 and saturated fatty acids (SFAs), whereas the green one exhibited higher contents of n-6 polyunsaturated fatty acids (n-6 PUFAs) and a higher PUFA/SFA ratio. Regarding free amino acids, the orange polychaete had significantly higher threonine content, while the green ones had significantly higher levels of valine, isoleucine, leucine, phenylalanine, glutamate, alanine, histidine and proline. Additionally, the astaxanthin content was significantly higher in the orange phenotype. The bile acid level was significantly higher in the green phenotype compared to the orange one, but no significant differences were observed in other biochemical parameters such as total protein, total cholesterol, and triglyceride content. The lipidomic analysis revealed that glycerophospholipids were the most abundant lipid class in both phenotypes, followed by glycerolipids and sphingolipids. A total of 65 differentially abundant lipid molecules were identified between the two groups. Compared to the orange polychaete, the green one had higher levels of 59 lipids (predominantly ceramides) and lower levels of six lipids, including three triglycerides, one monogalactosyldiacylglycerol, and two phosphatidylserines. In general, the orange P. aibuhitensis showed a favorable nutritional profile for aquafeed and human nutrition, whereas the green ones had potential for targeted health applications owing to its specific lipid composition. However, direct validating experiments are required. Full article

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18 pages, 4444 KB

Open AccessArticle

The Colorectal Cancer Glycocode: Tumour Sialylation Is Associated with an Immune-Excluded Phenotype and Distinct Therapeutic Signatures

by Abdulaziz Alfahed, Glowi Alasiri and Abdulrahman A. Alahmari

Biology 2026, 15(9), 705; https://doi.org/10.3390/biology15090705 - 30 Apr 2026

Viewed by 539

Abstract

Background: Tumour glycosylation regulates immune modulation and progression, but whether the CRC sialylome—the complete repertoire of sialylated glycans—defines a biologically distinct subtype remains unclear. We investigated how the “sugar code” shapes CRC biology, immunity, and therapeutic response. Methods: Transcriptomic data from three CRC [...] Read more.

Background: Tumour glycosylation regulates immune modulation and progression, but whether the CRC sialylome—the complete repertoire of sialylated glycans—defines a biologically distinct subtype remains unclear. We investigated how the “sugar code” shapes CRC biology, immunity, and therapeutic response. Methods: Transcriptomic data from three CRC cohorts (TCGA, Sidra-LUMC, and CPTAC-2; n = 988) were batch-corrected and integrated. Single-sample gene set enrichment analysis (ssGSEA) quantified sialyltransferase expression, sialic acid metabolism, EMT, MDR mechanisms, immune phenotypes, and Siglec-associated transcriptional signatures. GSEA, gene ontology enrichment analysis (GOEA), and drug ontology enrichment analysis (DOEA) characterised pathways and identified drug response-associated transcriptional signatures. Results: High sialylome activity defined a genomically stable but clinically advanced CRC subset enriched for left-sided tumours, mucinous histology, MSI, and BRAF mutations. At the transcriptional level, Sialyl-High tumours were associated with a mesenchymal, stromal-remodelling programme accompanied by reduced proliferative activity. They demonstrated enrichment of vesicular trafficking-related pathways alongside reduced representation of canonical efflux-associated programmes. Critically, the sialylome was associated with Siglec-related immune signatures, with sialylated glycan-related gene expression correlating with Siglec receptor expression (CD33 and SIGLEC7/9/10), consistent with an immune-inflamed yet structurally excluded microenvironment. DOEA identified selective enrichment of drug-response signatures related to sialic acid metabolism inhibitors (oseltamivir and Neu5Ac) and glycocalyx-disrupting agents (ginsenosides and soyasaponins). Conclusions: The CRC sialylome is associated with tumour phenotypic variation, including immune-excluded states linked to Siglec-associated transcriptional signatures and patterns consistent with non-canonical drug resistance programmes. These findings position the “sugar code” as a central organising principle in CRC and identify glycan-directed therapies as a promising strategy for the targeting of this aggressive subtype. Full article

(This article belongs to the Special Issue Decoding the Sugar Code: Understanding the Function of Glycans in Health and Disease)

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