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Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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16 pages, 1173 KB  
Article
Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2
by Lucas Bickmann, Matias Rodriguez, Xiaoyi Jiang and Wojciech Makałowski
Biology 2026, 15(1), 59; https://doi.org/10.3390/biology15010059 - 29 Dec 2025
Viewed by 675
Abstract
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes and play crucial roles in genome evolution, yet their diverse and complex sequences pose challenges for accurate classification. Existing tools often lack reliability in TE classification, limiting genomic analyses. Here, we present TEclass2, [...] Read more.
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes and play crucial roles in genome evolution, yet their diverse and complex sequences pose challenges for accurate classification. Existing tools often lack reliability in TE classification, limiting genomic analyses. Here, we present TEclass2, a software employing a deep learning approach based on a linear transformer architecture with k-mer tokenization and sequence-specific adaptations to classify TE consensus sequences into sixteen superfamilies. TEclass2 demonstrates improved classification performance and offers flexible model training on custom datasets. Accessible via a web interface with pre-trained models, TEclass2 facilitates rapid and reliable TE classification. These advancements provide a foundation for enhanced genomic annotation and support further bioinformatics research involving transposable elements. Full article
(This article belongs to the Special Issue AI Deep Learning Approach to Study Biological Questions (2nd Edition))
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16 pages, 961 KB  
Review
Biophysics of Bacterial Colonial Structures and the Occupancy of Microecological Spaces
by Fernando Baquero, Teresa M. Coque, Natalia Bastón-Paz and Ana Elena Pérez-Cobas
Biology 2026, 15(1), 56; https://doi.org/10.3390/biology15010056 - 28 Dec 2025
Viewed by 742
Abstract
The process of bacterial reproduction on surfaces conducive to growth forms colonies, which are defined as physical bodies with functional and environmental effects. This phenomenon can be conceptualized as transforming biological processes into physical phenomena. Large bacterial multicellular aggregates can be conceptualized as [...] Read more.
The process of bacterial reproduction on surfaces conducive to growth forms colonies, which are defined as physical bodies with functional and environmental effects. This phenomenon can be conceptualized as transforming biological processes into physical phenomena. Large bacterial multicellular aggregates can be conceptualized as physical entities, produced by “colonial organisms”, thereby transforming physics into biology. The formation of colonies requires surfaces, typically hydrogels or liquid–air interfaces, but also hard solid surfaces. Bacterial cell layers also contribute to the production of surfaces. Within a typical 3D-shaped, frequently domed colony, a variety of microcompartments form at the intersections of gradients that diffuse from its aerial and surface limits, leading to cellular functional diversity. This heterogeneity can lead to physical changes and fractures in the colony material, leading to the formation of fluid microchannels. The second primary type of colony is the 2D-shaped form that spreads over larger surfaces and is known as a biofilm. These physical structures possess significant water content, which is retained by a bacterial-excreted exopolymer. Biofilms are structurally organized as multilayer structures that can expand in the space through the lateral slippage of a more fluid overlayer on top of the surface-attached layer. The dissemination of biofilms may entail the integration of additional bacterial colonies, thereby giving rise to complex biofilms. The physical occupancy of microenvironments by colonies created on surfaces of higher organisms or on environmental surfaces exerts a significant influence on fluid mechanics and the functioning of organisms and ecosystems. In addition, colonies also contribute to the pathology of industrial constructions and devices, often leading to microbiologically influenced electrochemical corrosion, which results in material degradation. Full article
(This article belongs to the Section Biophysics)
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25 pages, 9003 KB  
Article
Steroidogenic Capacity of Ovarian Interstitial Tissue in the Koala (Phascolarctos cinereus): Morphological and Immunohistochemical Evidence
by Jackson Boyd, Stephen D. Johnston and Chiara Palmieri
Biology 2026, 15(1), 47; https://doi.org/10.3390/biology15010047 - 27 Dec 2025
Viewed by 417
Abstract
Ovarian interstitial tissue (IT) is a prominent but poorly characterised component of the koala ovary. This study analysed the morphology and immunohistochemical profile of IT in the koala ovary across different reproductive phases. Ovaries from ten sexually mature females were examined histologically and [...] Read more.
Ovarian interstitial tissue (IT) is a prominent but poorly characterised component of the koala ovary. This study analysed the morphology and immunohistochemical profile of IT in the koala ovary across different reproductive phases. Ovaries from ten sexually mature females were examined histologically and immunolabelled for aromatase, HSD3B2, HSD17B1, the follicle stimulating hormone receptor (FSHR), and the luteinizing hormone receptor (LHR). IT occurred as multifocal cortical aggregates composed of two distinct cell types. Large interstitial cells were polygonal with highly vacuolated and weakly eosinophilic cytoplasm and were morphologically consistent with a steroidogenic phenotype. Small interstitial cells were densely eosinophilic, non-vacuolated, and morphologically uniform across reproductive phases. Immunohistochemical analysis revealed that small interstitial cells exhibited the broadest expression of steroidogenic markers in the ovary, with coexpression of HSD3B2, HSD17B1, aromatase, FSHR, and LHR. In contrast, large interstitial cells exhibited comparatively limited enzyme and receptor expression. Staining intensity across all markers was strongest during the interoestrous phase, moderate in the proliferative phase, reduced in the luteal phase, and minimal or absent when the koalas were lactating, suggesting potential cyclical variation in IT function. Granulosa, theca and germinal epithelial cells showed variable expression of steroidogenic enzymes and gonadotropin receptors, indicating that ovarian steroidogenesis in the koala may be more heterogeneous than predicted by the classical two-cell, two-gonadotropin model. Together, these findings provide preliminary evidence for the steroidogenic capacity of ovarian IT in the koala, indicating that its activity varies across reproductive phases, and appear to suggest a unique cellular organisation compared to other mammals. As these results are based on morphology and immunohistochemistry alone, further functional studies are required to confirm the steroidogenic output and clarify the physiological significance of IT in this species. Full article
(This article belongs to the Special Issue Feature Papers on Developmental and Reproductive Biology)
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17 pages, 1493 KB  
Article
Expression Analysis of Hormone Receptor 38 (HR38) and Ecdysone-Induced Protein 75 (E75) Genes and Their Functional Implications in the Development of Heortia vitessoides Moore
by Na Liu, Hanyang Wang, Jiahe Liang, Zhiqiang Zhong and Tong Lin
Biology 2026, 15(1), 44; https://doi.org/10.3390/biology15010044 - 26 Dec 2025
Viewed by 464
Abstract
HR38 and E75 are early 20-hydroxyecdysone (20E)-responsive nuclear receptors that play important roles in insect molting and metamorphosis. Here, we cloned and characterized HvHR38 and HvE75 from Heortia vitessoides and analyzed their conserved domains and phylogenetic positions. Both genes exhibited distinct stage- and [...] Read more.
HR38 and E75 are early 20-hydroxyecdysone (20E)-responsive nuclear receptors that play important roles in insect molting and metamorphosis. Here, we cloned and characterized HvHR38 and HvE75 from Heortia vitessoides and analyzed their conserved domains and phylogenetic positions. Both genes exhibited distinct stage- and tissue-specific expression patterns closely associated with ecdysteroid-regulated developmental processes. Hormone-induction assays further demonstrated that the transcription of HvHR38 and HvE75 was strongly activated by 20E. RNA interference targeting either gene resulted in significant transcript knockdown, accompanied by incomplete molting, pupal deformities, and molting failure, ultimately leading to markedly reduced survival, with dsHvE75 causing the highest lethality. Collectively, these results suggest that HR38 and E75 function as key components of the early 20E-responsive transcriptional network involved in molting regulation, and highlight their potential as RNAi targets for species-specific and environmentally sustainable pest management. Full article
(This article belongs to the Section Developmental and Reproductive Biology)
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16 pages, 6280 KB  
Article
Allostery-Driven Substrate Gating in the Chlorothalonil Dehalogenase from Pseudomonas sp. CTN-3
by Grayson Gerlich, Judith Klein-Seetharaman and Richard C. Holz
Biology 2026, 15(1), 20; https://doi.org/10.3390/biology15010020 - 22 Dec 2025
Viewed by 381
Abstract
The catalytic mechanism of the Zn(II)-dependent chlorothalonil dehalogenase from Pseudomonas sp. CTN-3 (Chd) was examined using molecular dynamics (MD) simulations, Bayesian network analysis, and Markov state model analysis to quantify its motions. Chd selectively substitutes an aromatic chlorine-carbon bond in chlorothalonil (TPN; 2,4,5,6-tetrachloroisophtalonitrile) [...] Read more.
The catalytic mechanism of the Zn(II)-dependent chlorothalonil dehalogenase from Pseudomonas sp. CTN-3 (Chd) was examined using molecular dynamics (MD) simulations, Bayesian network analysis, and Markov state model analysis to quantify its motions. Chd selectively substitutes an aromatic chlorine-carbon bond in chlorothalonil (TPN; 2,4,5,6-tetrachloroisophtalonitrile) with an aromatic alcohol (4-hydroxytrichloro-isophthalonitrile; 4-OH-TPN). It is a homodimer with two solvent-accessible channels in each monomer, which are proposed to provide different routes for substrate and products to access/leave the catalytic Zn(II) site. Based on MD simulations, Chd exhibits allosteric behavior wherein a “Y”-shaped substrate channel exhibits a “flip flop” mechanism, where the “right” substrate channel opens to allow TPN to enter, after which it closes, followed by the “left” channel opening. The “right” channel then reopens, likely to allow the product, 4-OH-TPN, to leave the active site, but this reopening of the right channel drives the “left” channel to close. Coupled with the substrate channels alternately opening and closing, a corresponding possible Cl− channel opens and closes. Although the dynamics of this process are fast, Chd needs to overcome a 5 kT free-energy barrier for this transition and to relax after opening. Additionally, exposed “wing” residues, hydrophilic residues at the ends of protruding α-helices, act as allosteric indicators, signaling the complex allosteric motions required to open the substrate channel. We propose, for the first time, a dynamic mechanism that drives substrate binding and product release, providing new insight into Chd’s catalytic mechanism. Full article
(This article belongs to the Section Biophysics)
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13 pages, 909 KB  
Article
How Accurate Are Population Predictions? Wind Farms and Egyptian Vultures as a Case Study
by Miguel Ferrer, Jorge García-Macía, Mar Sánchez and Virginia Morandini
Biology 2025, 14(12), 1743; https://doi.org/10.3390/biology14121743 - 5 Dec 2025
Viewed by 489
Abstract
It is clear that scientists’ predictions must be rigorous and based on scientific evidence, but, even more, it is crucial to review scientific predictions after a reasonable time. However, predictions of published PVAs have rarely been contrasted with real populations’ trends over time. [...] Read more.
It is clear that scientists’ predictions must be rigorous and based on scientific evidence, but, even more, it is crucial to review scientific predictions after a reasonable time. However, predictions of published PVAs have rarely been contrasted with real populations’ trends over time. This is worrisome because this is the only way to keep learning and improve our ability to make more accurate predictions. In addition, conservation efforts can shift the initial predictions for the viability of threatened populations; thus, the evaluation of initial predictions becomes required over time. This is the case of the Egyptian vulture in Spain, where trajectories of real populations over the years differ from large-scale predictions. Its extinction in the Iberian Peninsula—due to mortality in wind farms, among other causes—was predicted by 2020, according to published viability analyses; yet, 14 years after this publication, not only did it not happen, but its national (and European) population remains stable and is even slightly increasing (+2.6%). These differences between predicted and observed trajectories of populations show the limitations of the simulations as a conservation tool and offer the opportunity to evaluate the used PVAs and the shortcomings that affected the assessment of the real trajectory of the species. With only four years of data available to simulate and generate 100-year predictions, along with the distribution and variance of mortality rates by collision in wind farms and an overestimation the number of pairs in risk areas, a clear relationship was assumed between predicted risk according to distances and the actual recorded mortality at wind farms, even though it is known that these are not closely related. Full article
(This article belongs to the Special Issue Advances in Wildlife Conservation and Habitat Management in the Anthropocene)
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22 pages, 10162 KB  
Article
Heterogeneous Lineages of DNA Transposons Encode a TET/JBP Dioxygenase in Fungi
by Kenji K. Kojima
Biology 2025, 14(12), 1741; https://doi.org/10.3390/biology14121741 - 4 Dec 2025
Viewed by 620
Abstract
Epigenetic DNA modification is a key component of the defense system against invading nucleic acids such as transposons. TET/JBP dioxygenases oxidize 5-methylcytosine and lead to its replacement by cytosine in mammals. Expansion of TET/JBP genes and their association with DNA transposons were previously [...] Read more.
Epigenetic DNA modification is a key component of the defense system against invading nucleic acids such as transposons. TET/JBP dioxygenases oxidize 5-methylcytosine and lead to its replacement by cytosine in mammals. Expansion of TET/JBP genes and their association with DNA transposons were previously reported in Basidiomycota fungi. In this study, a thorough bioinformatics investigation of TET/JBP genes revealed that diverse groups of DNA transposons have captured a TET/JBP dioxygenase in three lineages of fungi: Pucciniomycetes (rusts) and Agaricomycetes (mushrooms) in Basidiomycota, and Pezizomycetes (morels and truffles) in Ascomycota. TET/JBP genes encoded by DNA transposons can be classified into three types, designated as PU, AG, and PE here. The PU type is distributed in Pucciniomycetes and encoded by seven different lineages of DNA transposons (Dileera, hAT, Harbinger, IS3EU, EnSpm, ESTA, and Helitron). The AG type is distributed in Agaricomycetes, and encoded by two lineages of DNA transposons (Kyakuja and Zisupton). The PE type is distributed in Pezizomycetes and Agaricomycetes, and encoded by five lineages of DNA transposons (Zisupton, IS3EU, EnSpm, Plavaka, and Helitron). Phylogenetic analysis indicated several transmission events from certain DNA transposon lineage to another. These transposon-encoded TET/JBP dioxygenases likely contribute to the escape of transposons from the methylation-based silencing system in fungi. Full article
(This article belongs to the Section Genetics and Genomics)
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21 pages, 1554 KB  
Review
Gatekeepers of the Germ Line: How Mitochondria Shape Reproductive Evolution in Metazoans
by Yu-Tong Sun and Wan-Xi Yang
Biology 2025, 14(12), 1728; https://doi.org/10.3390/biology14121728 - 2 Dec 2025
Viewed by 848
Abstract
Mitochondria play essential roles for animal reproduction, influencing not only cellular energetics but also gamete quality, inheritance and evolutionary patterns. Currently, most research still focuses on chordates or mitochondrial diseases and their impact on the health of germ cells. However, few studies focus [...] Read more.
Mitochondria play essential roles for animal reproduction, influencing not only cellular energetics but also gamete quality, inheritance and evolutionary patterns. Currently, most research still focuses on chordates or mitochondrial diseases and their impact on the health of germ cells. However, few studies focus on integrative synthesis that connect comparative morphology, inheritance mechanisms and evolutionary theory. In this review, we integrate cross-phyla evidence to explore two interconnected dimensions: the fate of mitochondria during gametogenesis and the strategy shaping their evolution. We compare mitochondrial morphology, distribution, and metabolic strategies in gametogenesis, revealing how these traits align with reproductive modes and ecological adaptations. Then we further discuss how mitochondrial genome evolution, bottleneck effects and mito-nuclear coevolution contribute to germline stability and maternal inheritance. Special attention is given to exceptional systems such as Doubly Uniparental Inheritance (DUI) in bivalves, which challenges conventional mode of strictly maternal transmission and illuminates the flexibility of mito-nuclear evolution. Altogether, these perspectives highlight mitochondria as gatekeepers and evolutionary recorders in the reproductive systems across metazoans, providing a unifying framework for future research across ecology, evolution and molecular biology. Full article
(This article belongs to the Section Developmental and Reproductive Biology)
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30 pages, 8473 KB  
Article
A Squirrel’s Guide to the Olive Galaxy: Tree-Level Determinants of Den-Site Selection in the Persian Squirrel within Traditional Mediterranean Olive Groves
by Yiannis G. Zevgolis, Efstratios Kamatsos, Apostolos Christopoulos, Christina Valeta, Eleni Rekouti, Christos Xagoraris, George P. Mitsainas, Petros Lymberakis, Dionisios Youlatos and Panayiotis G. Dimitrakopoulos
Biology 2025, 14(12), 1676; https://doi.org/10.3390/biology14121676 - 25 Nov 2025
Viewed by 1419
Abstract
Traditional centennial olive groves represent ecologically valuable agroecosystems that support both biodiversity and cultural heritage across Mediterranean landscapes. On Lesvos Island, Greece, which marks the westernmost limit of the Persian squirrel (Sciurus anomalus) distribution, these centennial olive trees serve as essential [...] Read more.
Traditional centennial olive groves represent ecologically valuable agroecosystems that support both biodiversity and cultural heritage across Mediterranean landscapes. On Lesvos Island, Greece, which marks the westernmost limit of the Persian squirrel (Sciurus anomalus) distribution, these centennial olive trees serve as essential nesting resources for this regionally Vulnerable species. However, the tree-level mechanisms determining den-site suitability remain insufficiently understood. We examined 288 centennial olive trees, including 36 with confirmed dens, integrating structural, physiological, and thermal metrics to identify the attributes influencing den occupancy. Our results showed that squirrels consistently selected older and taller olives with broad crowns and high photosynthetic activity, indicating a preference for vigorous, architecturally complex trees that provide stable microclimatic conditions. Infrared thermography revealed that occupied trees exhibited lower trunk temperature asymmetries and stronger thermal buffering capacity, highlighting the role of microclimatic stability in den-site selection. Overall, our findings show that den-site selection in S. anomalus is shaped by the interplay of structural maturity, physiological performance, and thermal coherence. By linking tree function to den-site suitability, our work advances a mechanistic understanding of microhabitat selection and emphasizes the importance of centennial olive trees as biophysical refugia within traditional Mediterranean agroecosystems. Full article
(This article belongs to the Special Issue Young Researchers in Ecology)
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17 pages, 5897 KB  
Article
3D Breast Cancer Spheroids Reveal Architecture-Dependent HER2 Expression and Signaling
by Pietro Arnaldi, Valentina Delli Zotti, Grazia Bellese, Maria Cristina Gagliani, Paola Orecchia, Patrizio Castagnola and Katia Cortese
Biology 2025, 14(12), 1654; https://doi.org/10.3390/biology14121654 - 24 Nov 2025
Viewed by 1126
Abstract
Background: Three-dimensional (3D) culture systems offer a physiologically relevant alternative to monolayers for studying tumor organization, signaling, and drug response. HER2-positive breast cancers (BCa) account for 15–30% of BCa cases and benefit from HER2-targeted therapies, yet predictive in vitro models remain limited. Objective: [...] Read more.
Background: Three-dimensional (3D) culture systems offer a physiologically relevant alternative to monolayers for studying tumor organization, signaling, and drug response. HER2-positive breast cancers (BCa) account for 15–30% of BCa cases and benefit from HER2-targeted therapies, yet predictive in vitro models remain limited. Objective: To generate and compare 3D spheroids from two HER2+ BCa cell lines, SKBR3 and BT474, and investigate how 3D architecture influences HER2 distribution, intracellular signaling, and cellular organization. Methods: Spheroids were reproducibly generated from SKBR3 and BT474 cells and analyzed after 4 days of culture. Cell viability was evaluated using live/dead staining, HER2 distribution was assessed by confocal microscopy and quantified on cryosections, and protein expression/phosphorylation was measured by Western blotting. Epithelial and EMT markers were visualized by immunofluorescence, and ultrastructural features were examined by transmission electron microscopy (TEM). Results: Both cell lines formed viable spheroids with distinct architectures: SKBR3 spheroids were loose and heterogeneous, whereas BT474 spheroids were compact and highly spherical. Confocal and cryosection imaging showed consistent membrane HER2 localization with a progressive signal decrease toward the core of the spheroids, more pronounced in BT474. Western blotting revealed divergent HER2 expression and AKT phosphorylation: SKBR3 spheroids displayed increased HER2 but reduced pAKT, while BT474 spheroids showed reduced HER2 and pAKT levels. EpCAM and E-cadherin staining revealed cell line-specific epithelial organization, and TEM demonstrated differences in intercellular spacing and mitochondrial morphology, reflecting spheroid compactness. Conclusions: 3D architecture profoundly influences HER2 distribution, signaling, and structural organization in HER2+ BCa spheroids. This model provides a robust platform for investigating architecture-dependent molecular processes, with potential applications in drug response, receptor trafficking, and targeted therapy evaluation. Full article
(This article belongs to the Special Issue Ultrastructure and Function in In Vitro Cancer Models: From Morphology to Mechanism)
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26 pages, 659 KB  
Review
Towards a Research Programme Aiming at Causes and Consequences of Reticulate Evolution
by Christoph Oberprieler
Biology 2025, 14(11), 1601; https://doi.org/10.3390/biology14111601 - 15 Nov 2025
Cited by 1 | Viewed by 1430
Abstract
Evolution is reticulate. Reticulation increases diversity and complexity on the different levels of the evolutionary hierarchy. In addition to the tendency for diversity and complexity to increase in unchecked evolutionary systems by ongoing divergence (‘Zero-Force Evolutionary Law’, ‘Biology’s First Law’), reticulate evolution, therefore, [...] Read more.
Evolution is reticulate. Reticulation increases diversity and complexity on the different levels of the evolutionary hierarchy. In addition to the tendency for diversity and complexity to increase in unchecked evolutionary systems by ongoing divergence (‘Zero-Force Evolutionary Law’, ‘Biology’s First Law’), reticulate evolution, therefore, acts as a second mechanism for the establishment of evolutionary novelty and the rise in biodiversity and biocomplexity (‘Biology’s Second Law’). This provides the raw material for subsequent diversity-confining drift and selection processes. In order to fully appreciate reticulation processes as part of an updated paradigm of evolutionary biology, a research programme on the topic should encompass the identification of the fundamental evolutionary entities as vertices and the study of the relationships among these vertices as edges in the resulting network architectures. Additionally, along with surveys on the underlying determinants, this will lead to the study of emergent boundary conditions for reticulations and for the porosity of evolutionary entities. Finally, the programme should address the question whether there are equilibrium conditions between the complete fusion and complete isolation of evolutionary entities (‘Goldilocks Zones’) that foster reticulate evolution. As tools in this research programme, machine learning and modelling approaches, along with methods in the field of network reconstruction, transcriptomics, epigenetics, and karyology, are identified. Full article
(This article belongs to the Section Evolutionary Biology)
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15 pages, 4226 KB  
Article
Loss of βENaC Prevents Hepatic Steatosis but Promotes Abdominal Fat Deposition Associated with a High-Fat Diet
by Madison Hamby, Elizabeth Barr, Seth Lirette and Heather A. Drummond
Biology 2025, 14(11), 1558; https://doi.org/10.3390/biology14111558 - 6 Nov 2025
Viewed by 528
Abstract
Background: Degenerin proteins, such as Acid-Sensing Ion Channel 2 (ASIC2) and β Epithelial Na+ Channel (βENaC), have been implicated in cardiovascular function. We previously demonstrated that mice lacking normal levels of βENaC and ASIC2 are protected from diet-induced obesity, metabolic disruption, and [...] Read more.
Background: Degenerin proteins, such as Acid-Sensing Ion Channel 2 (ASIC2) and β Epithelial Na+ Channel (βENaC), have been implicated in cardiovascular function. We previously demonstrated that mice lacking normal levels of βENaC and ASIC2 are protected from diet-induced obesity, metabolic disruption, and hepatic steatosis. Methods: To investigate the specific role of βENaC proteins in the progression of metabolic disease, we examined the impact of a high-fat diet (HFD) in the βENaC hypomorph mouse model (βMUT). Body composition and metabolic and behavioral phenotypes were examined in male and female and βMUT and WT mice (n = 6–14/group) fed a normal chow diet (NFD) from weaning until 16 weeks of age, then a 60% kcal-fat diet for 5 weeks. Results: Compared to WT mice, βMUT male mice have reduced lean and total body mass. No remarkable differences in energy expenditure, motor activity, or food consumption patterns were detected. HFD-fed male βMUT mice exhibited reduced liver fat content (mass and Oil Red O staining) yet increased abdominal fat depots. HFD-fed female βMUT mice exhibited lower heart mass. Conclusions: These novel findings suggest a role for βENaC in the maintenance of metabolic homeostasis and adipose tissue distribution. Full article
(This article belongs to the Special Issue Animal Models of Metabolic Diseases)
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19 pages, 14541 KB  
Article
Pan-Mitogenome Construction, Intraspecific Variation, and Adaptive Evolution of the Plant Pathogenic Fungus Claviceps purpurea
by Mingliang Ding, Rui Hu, Jinlong Jia, Cuiyuan Wei, Yongzhen Cui, Hefa Liao, Zhuliang Yang, Jianwei Guo, Zhanhong Ma and Yuanbing Wang
Biology 2025, 14(11), 1548; https://doi.org/10.3390/biology14111548 - 4 Nov 2025
Viewed by 767
Abstract
Claviceps purpurea is a specialized phytopathogenic fungus that infects grasses and produces pharmacologically active compounds, attracting considerable interest in genomic research. In this study, we assembled and annotated the complete mitogenomes of 15 C. purpurea strains isolated from different host plants, including seven [...] Read more.
Claviceps purpurea is a specialized phytopathogenic fungus that infects grasses and produces pharmacologically active compounds, attracting considerable interest in genomic research. In this study, we assembled and annotated the complete mitogenomes of 15 C. purpurea strains isolated from different host plants, including seven newly sequenced isolates from China. Analysis of the C. purpurea pan-mitogenome demonstrated that the accessory regions, with an average proportion of 48.23%, are the main contributor to mitogenome variation. Analysis of the 14 protein-coding genes revealed Ka/Ks ratios below 1, indicating strong purifying selection. Notably, the atp9 gene was absent in all strains, suggesting a potential adaptive gene loss. Structural variations were predominantly located in the intergenic region between rns and rnl. Phylogenetic analysis based on concatenated mitochondrial genes placed Claviceps as most closely related to the genus Epichloë. The 15 C. purpurea strains grouped into five well-supported subclades, with Chinese and non-Chinese isolates forming distinct lineages. Among these, the Chinese strains ACCC 37001 and KUNCC 11030 represented the earliest diverging lineages. This study elucidates the intraspecific variation and evolutionary patterns of the mitogenome in C. purpurea and highlights the value of mitogenome in resolving phylogenetic relationships. Full article
(This article belongs to the Section Microbiology)
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27 pages, 5435 KB  
Article
Zebrafish (Danio rerio) Embryo–Larvae as a Biosensor for Water Quality Assessment
by María Santos-Villadangos, Vanesa Robles and David G. Valcarce
Biology 2025, 14(11), 1533; https://doi.org/10.3390/biology14111533 - 31 Oct 2025
Viewed by 1261
Abstract
Wastewater treatment plants (WWTPs) play a key role in the protection of the environment and public health by reducing the levels of pollutants released into the water. Here, we evaluate the quality of water obtained from two key points of the treatment process [...] Read more.
Wastewater treatment plants (WWTPs) play a key role in the protection of the environment and public health by reducing the levels of pollutants released into the water. Here, we evaluate the quality of water obtained from two key points of the treatment process of a municipal WWTP (León, Spain) using zebrafish (Danio rerio) embryos and larvae as sentinels. Three experimental groups were established: (1) “Control” (CTRL) maintained in embryo medium, (2) “Influent” (I) exposed to influent water before the secondary (biological) treatment (concentrations: I-100% and I-75%), and (3) “Effluent” (E) exposed to effluent water from the secondary treatment (concentrations: E-100% and E-75%). Our results confirmed that survival was subtly affected in I-100% and E-100%, as well as the hatching rate in the effluent. Larvae exposed to both experimental conditions also presented a higher rate of malformations, affecting biometry and showing reduced embryo motility, with the exception of E-75%. The I-100% condition also caused reduced heartbeat, reduced fin regeneration, and a higher number of delocalized primordial germ cells. I-100%-exposed larvae showed dysregulation of four genes (foxm1l, cenpf3b, hoxc6a, and ddit3) out of the 19 studied. Effluent dilution mitigated the observed effects, and the model proved to be an effective additional test for wastewater treatment plants. Full article
(This article belongs to the Section Biotechnology)
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27 pages, 6823 KB  
Article
Programmed Genome Elimination Is Evolutionarily Conserved Across Pelophylax Hybrids—As Evidenced by P. grafi Hybridogenetic Reproduction
by Anna Dudzik, Beata Rozenblut-Kościsty, Dmitrij Dedukh, Pierre-André Crochet, Lukáš Choleva, Monika Przewłocka-Kosmala, Zuzanna Stryczak, Maria Ogielska and Magdalena Chmielewska
Biology 2025, 14(11), 1526; https://doi.org/10.3390/biology14111526 - 30 Oct 2025
Cited by 1 | Viewed by 939
Abstract
Gametogenesis is a fundamental biological process that ensures both genetic recombination and the continuity of successive generations. Interspecific hybrids can reproduce through modified mechanisms, such as hybridogenesis, by transmitting clonal, unrecombined genomes of only one of the parental species via their gametes. Pelophylax [...] Read more.
Gametogenesis is a fundamental biological process that ensures both genetic recombination and the continuity of successive generations. Interspecific hybrids can reproduce through modified mechanisms, such as hybridogenesis, by transmitting clonal, unrecombined genomes of only one of the parental species via their gametes. Pelophylax grafi (RP) is a natural hybrid frog composed of mixed genomes (subgenomes) of two related species, Pelophylax perezi (P) and Pelophylax ridibundus (R), and coexists in populations with P. perezi. This study tested the involvement of programmed genome elimination in gamete production of P. grafi, providing new insight into reproductive mechanisms of hybrid vertebrates. Using comparative genomic hybridization (CGH) and fluorescent in situ hybridization (FISH), we examined the genomic constitution of germline cells in tadpoles and adult male and female P. grafi. Controlled crosses between P. perezi and P. grafi produced F1 hybrid tadpoles, whose genotypes confirmed that P. grafi parents transmitted the R subgenome through their gametes. In the early germline cells (gonocytes) of these tadpoles, P chromosomes were selectively eliminated via micronuclei formation during interphase. The occasional presence of the R genome and mixed R/P genome micronuclei suggests variability and imperfect fidelity in the elimination process. In adult hybrids, the majority of diplotene oocytes, spermatogonial stem cells (SSC) and spermatocytes carried R subgenomes. We demonstrated that programmed genome rearrangement in Pelophylax hybrids is an evolutionarily conserved mechanism underlying this unique reproductive strategy. Full article
(This article belongs to the Section Developmental and Reproductive Biology)
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29 pages, 5404 KB  
Article
The Human Omental Adipose Depot Mitigates Inflammation, Immune Response, and Oxidative Stress Pathways in Response to Injury via Its Secretome
by Meredith Krause-Hauch, Rekha S. Patel, Bangmei Wang, Brianna Jones, Paul Albear and Niketa A. Patel
Biology 2025, 14(11), 1509; https://doi.org/10.3390/biology14111509 - 28 Oct 2025
Cited by 1 | Viewed by 862
Abstract
Human intraperitoneal omental adipose tissue, part of the visceral adipose depots, surrounds the abdominal organs and has functions distinct from the subcutaneous adipose depots. In the clinical setting, it is observed that the omentum is beneficial to combat internal sources of inflammation, oxidative [...] Read more.
Human intraperitoneal omental adipose tissue, part of the visceral adipose depots, surrounds the abdominal organs and has functions distinct from the subcutaneous adipose depots. In the clinical setting, it is observed that the omentum is beneficial to combat internal sources of inflammation, oxidative stress, and injury-related stress. However, the molecular mechanisms involved in these functions are not fully understood. We previously demonstrated that adipose stem cells derived from human omental adipose tissue (om-hASCs) secrete exosomes (exos). We and others have extensively evaluated the subcutaneous adipose depot-derived exosomes; however, the role of adipose stem cells derived from the human omental depot (om-hASCs) remains less known. In this study, we postulated that exosomes from om-hASCs (om-hASCexos) drive the repair ability of the omentum to heal organs after internal injury and insults. First, we characterized the om-hASCexos using a proteomic analysis which identified the distinct cargo. Using in vitro injury models, we show that om-hASCexos significantly improve cell migration and proliferation, while decreasing oxidative stress and inflammation. To study acute in vivo healing, a rat wound model was evaluated. Om-hASCexos significantly improved the healing rate of injuries. RNAseq revealed that om-hASCexo treatment acts upon pathways associated with lipid and fatty acid metabolism, apoptosis, immune response, and cell differentiation. The pathway analysis indicated that om-hASCexos significantly regulate the expression of Clec5a and Trem1 in the immune response pathway. Overall, we demonstrate the singular properties of om-hASCexos that are distinct from other sources of hASC. Thus, this study provides an understanding of the unique ability of the omental adipose depot to combat internal injuries. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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15 pages, 2772 KB  
Article
Perinatal Fluoxetine Exposure Has No Major Effect on Myelin-Associated Glycoprotein and Myelin Basic Protein Levels in Auditory Brain Regions
by Joëlle D. Jagersma, Marije Visser, Sonja J. Pyott, Eelke M.S. Snoeren and Jocelien D.A. Olivier
Biology 2025, 14(11), 1482; https://doi.org/10.3390/biology14111482 - 24 Oct 2025
Viewed by 2501
Abstract
Hearing loss and serotonergic dysfunction both impact social and cognitive behaviors, yet their neurobiological interplay remains poorly understood. This study investigated whether perinatal fluoxetine exposure alters myelination in (auditory) brain regions during development. Female Wistar rats received 10 mg/kg fluoxetine from gestational day [...] Read more.
Hearing loss and serotonergic dysfunction both impact social and cognitive behaviors, yet their neurobiological interplay remains poorly understood. This study investigated whether perinatal fluoxetine exposure alters myelination in (auditory) brain regions during development. Female Wistar rats received 10 mg/kg fluoxetine from gestational day 1 until postnatal day (PND)21. Brain tissue was collected from male offspring at PND21 and PND35. Myelination was assessed via immunohistochemical analysis of Myelin-Associated Glycoprotein (MAG) and Myelin Basic Protein (MBP) in the auditory cortex, inferior colliculus, and corpus callosum. MAG+ cell counts, MBP+ area, and MBP fluorescence intensity were quantified. No major effects of fluoxetine were observed on myelin markers in any brain region or developmental stage. However, changes in myelination emerged between PND21 and PND35. MAG+ cell density declined in the inferior colliculus but remained stable in the auditory cortex. MBP+ area decreased over time in both the corpus callosum and auditory cortex, while MBP fluorescence intensity increased in the corpus callosum. These results suggest that myelination changes between PND21 and PND35 are region- and age-dependent and not altered by fluoxetine. These findings highlight the dynamic nature of postnatal myelination and suggest that serotonergic alterations alone may be insufficient to disrupt structural maturation in auditory regions. Full article
(This article belongs to the Special Issue Pathophysiology of Hearing Loss)
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14 pages, 420 KB  
Review
Catalyzing Protein Folding by Chaperones
by Zijue Huang and Scott Horowitz
Biology 2025, 14(10), 1450; https://doi.org/10.3390/biology14101450 - 20 Oct 2025
Viewed by 1897
Abstract
Protein folding is a fundamental process essential for cellular growth and health, yet it is also susceptible to errors that can result in misfolding and disease. This literature review explores the current knowledge of the roles of different factors on protein folding in [...] Read more.
Protein folding is a fundamental process essential for cellular growth and health, yet it is also susceptible to errors that can result in misfolding and disease. This literature review explores the current knowledge of the roles of different factors on protein folding in the cell. We examine the cellular proteostasis network, with a focus on the catalytic actions of prolyl isomerases and molecular chaperones (including RNA G-quadruplexes), which collaborate to guide newly synthesized polypeptides toward their native structures and prevent aggregation. By integrating structural and biochemical insights, this review highlights the current understanding and ongoing questions regarding how chaperones can improve folding times of proteins to physiological pertinent rates. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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17 pages, 1432 KB  
Review
Polarized Macrophages and Their Exosomes: Implications for Autoimmune and Immune-Mediated Diseases
by Vincent G. Yuan
Biology 2025, 14(10), 1371; https://doi.org/10.3390/biology14101371 - 8 Oct 2025
Cited by 1 | Viewed by 1977
Abstract
Autoimmune diseases result from dysregulated immune responses that mistakenly attack the body’s own tissues, causing chronic inflammation and progressive damage. Macrophages, with their remarkable plasticity, play key roles in both promoting and resolving inflammation, with pro-inflammatory M1 and anti-inflammatory M2 states shaping disease [...] Read more.
Autoimmune diseases result from dysregulated immune responses that mistakenly attack the body’s own tissues, causing chronic inflammation and progressive damage. Macrophages, with their remarkable plasticity, play key roles in both promoting and resolving inflammation, with pro-inflammatory M1 and anti-inflammatory M2 states shaping disease outcomes. Macrophage-derived exosomes have emerged as important mediators of intercellular communication, reflecting the functional state of their parent cells while influencing recipient cell behavior. Exosomes from M1 macrophages amplify inflammation through cytokines and microRNAs, whereas M2-derived exosomes support tissue repair and immune regulation. Studies in rheumatoid arthritis, lupus, multiple sclerosis, inflammatory bowel disease, type 1 diabetes, and psoriasis highlight their dual roles in pathology and resolution. In addition, macrophage exosomes can be engineered to deliver targeted therapeutic molecules, offering cell-free interventions with advantages in specificity, biocompatibility, and immunomodulation. This review summarizes current insights into macrophage-derived exosomes, their role in autoimmune pathogenesis, and emerging strategies to harness their therapeutic potential, highlighting their promise as precision-guided treatments for autoimmune diseases. Full article
(This article belongs to the Special Issue Pathophysiology of Chronic Inflammatory Diseases)
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18 pages, 1190 KB  
Review
Liver Progenitor Cells: Cellular Origins, Plasticity, and Signaling Pathways in Liver Regeneration
by Jinsol Han, Ahyeon Sung, Hayeong Jeong and Youngmi Jung
Biology 2025, 14(10), 1361; https://doi.org/10.3390/biology14101361 - 4 Oct 2025
Cited by 1 | Viewed by 2083
Abstract
The liver has a notable regenerative capacity, primarily through hepatocyte proliferation. However, when this process is impaired—due to severe and/or chronic injury—liver progenitor cells (LPCs) serve as a facultative reserve to restore hepatic function. LPCs, which are a bipotent and heterogeneous population located [...] Read more.
The liver has a notable regenerative capacity, primarily through hepatocyte proliferation. However, when this process is impaired—due to severe and/or chronic injury—liver progenitor cells (LPCs) serve as a facultative reserve to restore hepatic function. LPCs, which are a bipotent and heterogeneous population located near the canals of Hering, can differentiate into hepatocytes and cholangiocytes. Recent evidence suggests that LPCs may originate from mature hepatic cells—such as hepatocytes, cholangiocytes, and hepatic stellate cells—through dedifferentiation under specific injury conditions. Cellular plasticity in the liver is governed by complex signaling networks that regulate LPC activation, maintenance, and lineage commitment. However, the precise cellular origin of LPCs and the mechanisms driving their activation remain incompletely defined. Therefore, this review aims to synthesize current insights into LPC biology and emphasize their diverse cellular origins, functional roles in liver regeneration, and the key signaling pathways involved. A deeper understanding of LPC dynamics may ultimately guide the development of novel therapeutic strategies to enhance liver regeneration in chronic liver disease. Full article
(This article belongs to the Section Cell Biology)
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26 pages, 1067 KB  
Review
Borrelial Diseases Across Eurasia
by Serena Bergamo, Giusto Trevisan, Maurizio Ruscio and Serena Bonin
Biology 2025, 14(10), 1357; https://doi.org/10.3390/biology14101357 - 3 Oct 2025
Cited by 5 | Viewed by 1961
Abstract
This comprehensive review explores the distribution, diversity, and epidemiology of tick-borne borrelioses across Eurasia, focusing on Lyme borreliosis (LB) and other Borrelia-related infections. The genus Borrelia is categorized into three major groups, the Lyme Group (LG), the Relapsing Fever Group (RFG), and the [...] Read more.
This comprehensive review explores the distribution, diversity, and epidemiology of tick-borne borrelioses across Eurasia, focusing on Lyme borreliosis (LB) and other Borrelia-related infections. The genus Borrelia is categorized into three major groups, the Lyme Group (LG), the Relapsing Fever Group (RFG), and the Echidna–Reptile Group (REPG), each with distinct vectors, reservoirs, and pathogenic profiles. LB, caused by Borrelia burgdorferi sensu lato, is highly endemic in Europe and is increasingly reported in Asia, although it is underdiagnosed in Southeast Asia due to limited surveillance. This review details the ecological dynamics of tick vectors—primarily Ixodes spp.—and their vertebrate hosts, emphasizing the role of migratory birds and climate change in disease spread. It also highlights the presence of relapsing fever Borrelia species transmitted by soft ticks (Ornithodoros spp.) and the emergence of novel species such as Borrelia miyamotoi (RFG) and Borrelia turcica (REPG). This study underscores the need for harmonized surveillance systems, improved diagnostic tools, and integrated public health strategies to address the growing threat of borreliosis in Eurasia. Full article
(This article belongs to the Section Ecology)
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14 pages, 1461 KB  
Article
Body Design or Behavior? What Explains the Performance of Slender-Billed Gulls (Chroicocephalus genei) Feeding on Brine Shrimp (Artemia sp.) in Salt Pans?
by Maud de Saint Seine, Lyse Hannier, Vincent Bels, Nicolas Schtickzelle and Michel Baguette
Biology 2025, 14(10), 1331; https://doi.org/10.3390/biology14101331 - 26 Sep 2025
Cited by 1 | Viewed by 669
Abstract
(1) Background: Understanding the evolution of the form–function relationship requires identifying the selection pressures acting on individuals. The paradigm of Arnold provides a useful framework to infer how the natural selection acting on phenotypic traits can modulate individual fitness. Despite the theoretical advance, [...] Read more.
(1) Background: Understanding the evolution of the form–function relationship requires identifying the selection pressures acting on individuals. The paradigm of Arnold provides a useful framework to infer how the natural selection acting on phenotypic traits can modulate individual fitness. Despite the theoretical advance, experimental studies of individual performances that explicitly address form, i.e., the phenotypic integration of functional morphology (body design and mechanics) and of behavior, are still rare. (2) Methods: Slender-billed gull food acquisition behaviors were video recorded in the salt pans of Salin de Giraud, Camargue, where brine shrimp are their main prey. We averaged the food intake rate over 21 individuals. We computed the mean hourly energy intake of an average gull by multiplying the mean hourly prey intake rate by the weight and energy content of a brine shrimp. We used this mean hourly energy intake to investigate the time needed by an average slender-billed gull individual to acquire the energy required to achieve their daily field metabolic rate. We computed the food metabolic rate of slender-billed gulls by using the model of Dunn et al. In addition, using slow-motion video sequences, we perform a functional and integrative analysis of three performances associated with food acquisition behaviors, i.e., locomotion, food capture, and food transport. (3) Results: We demonstrate that the energy assimilated by this performance is sufficient to cover less than 6 h of an adult gull’s metabolic food rate during its breeding season. We show that brine shrimp capture by gulls does not involve the use of specialized morphological structures but rather involves a particular behavioral sequence that invariably associates a mode of locomotion, a mode of capture and a mode of transport of the prey from the beak to the pharynx. The comparison of this sequence to the register of food acquisition behaviors used by other Charadriiformes reveals its similarity with behaviors that are used by two shorebird species (Phalaropus fulicarius and P. lobatus) also feeding on prey captured from saltwater surfaces. (4) Conclusions: Altogether, our study supports (1) a causal chain in which performance results from the interaction between morphological structures and behaviors and (2) the idea that the performance peak of a realized phenotype can be reached by using the best combination of behaviors, either by convergent evolution or by their conservation among those available in a phylogenetically determined register. Full article
(This article belongs to the Special Issue The Future of Marine Megafauna)
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30 pages, 6286 KB  
Article
Contrasting Assembly and Network Roles of Abundant and Rare Bacteria in Reservoir and Soil Habitats
by Cuixia Zhang, Haiming Li, Mengdi Li, Sihui Su, Han Xiao, Xiaodong Zhang and Qian Zhang
Biology 2025, 14(9), 1291; https://doi.org/10.3390/biology14091291 - 18 Sep 2025
Viewed by 3713
Abstract
Reservoir water and the adjacent soil are ecologically interconnected yet distinct microhabitats in saline coastal wetland ecosystems, but direct comparisons of their bacterial community composition and assembly remain limited. Here, we integrated high-throughput 16S rRNA gene sequencing with statistical, null model, and network [...] Read more.
Reservoir water and the adjacent soil are ecologically interconnected yet distinct microhabitats in saline coastal wetland ecosystems, but direct comparisons of their bacterial community composition and assembly remain limited. Here, we integrated high-throughput 16S rRNA gene sequencing with statistical, null model, and network analyses to compare diversity patterns, assembly mechanisms, and interactions of abundant and rare bacterial taxa in both habitats. Soil communities exhibited greater taxonomic diversity but a lower overall abundance, while reservoir communities displayed a pronounced vertical stratification, in contrast to the more spatially uniform soil communities at the sampled scale. Key environmental drivers differed: salinity (reflecting the harsh saline context) and nutrient levels structured reservoir communities, whereas the nutrient availability and cation exchange capacity predominated in soils. Stochastic processes mainly governed the assembly of abundant taxa in both habitats, whereas deterministic selection more strongly structured rare taxa, especially in soils subject to harsh saline conditions. The co-occurrence network analysis revealed higher connectivity and modularity in soils, with moderate taxa acting as critical connectors between modules. In contrast, rare taxa played a pivotal role in sustaining network stability in the reservoir. Together, these findings demonstrate distinct, habitat-dependent assembly mechanisms and ecological roles of abundant and rare bacterial taxa in saline coastal wetland microhabitats, providing insights that can inform wetland conservation and ecosystem management. Full article
(This article belongs to the Special Issue Wetland Ecosystems (2nd Edition))
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16 pages, 301 KB  
Review
Focus on Cognitive Enhancement: A Narrative Overview of Nootropics and “Smart Drug” Use and Misuse
by Fabrizio Schifano, Stefania Bonaccorso, Davide Arillotta, John Martin Corkery, Giuseppe Floresta, Gabriele Duccio Papanti Pelletier and Amira Guirguis
Biology 2025, 14(9), 1244; https://doi.org/10.3390/biology14091244 - 11 Sep 2025
Viewed by 21013
Abstract
Whilst “nootropics” are meant to treat a range of medical disorder-related cognitive impairments, the typically healthy “smart drugs” user ingests a range of drugs/molecules to achieve improved mental performance. Given the increasing levels of related concerns, this study aimed to provide an overview [...] Read more.
Whilst “nootropics” are meant to treat a range of medical disorder-related cognitive impairments, the typically healthy “smart drugs” user ingests a range of drugs/molecules to achieve improved mental performance. Given the increasing levels of related concerns, this study aimed to provide an overview of the clinical pharmacological issues relating to both the most popular nootropics and the vast range of drugs that are being used as putative cognitive enhancers/smart drugs. In terms of the cognitive decline associated with neurological degenerative disorders, a significant variation in research methodology was observed. Therefore, the overall usefulness of these pharmaceuticals in various central nervous system disorders as supplements/adjuvant therapy needs to be better established before their widespread use can be recommended. The most popular smart drugs, self-administered to cope with high-perceived stress and academic/work-related pressure, were methylphenidate, modafinil, amphetamine-based compounds, and psychedelics. At present, however, there are relevant levels of uncertainty in terms of smart drugs’ effectiveness in improving executive functions. Addressing the health harms associated with cognitive enhancers’ intake remains challenging due to the lack of updated and contextualized epidemiological data. In particular, there appears to be a range of clinical concerns relating to the non-prescribed intake of stimulant smart drugs by otherwise healthy individuals. Enhanced training for prescribers, pharmacists, and healthcare professionals can strengthen monitoring and early intervention efforts. Full article
(This article belongs to the Section Neuroscience)
30 pages, 5556 KB  
Article
Dysregulation of Protein Kinase CaMKI Leads to Autism-Related Phenotypes in Synaptic Connectivity, Sleep, Sociality, and Aging-Dependent Degeneration in Drosophila
by Claudia Gualtieri, Zachary M. Smith, Abby Cruz, Ziam Khan, Conor Jenkins, Ketu Mishra-Gorur and Fernando J. Vonhoff
Biology 2025, 14(9), 1228; https://doi.org/10.3390/biology14091228 - 9 Sep 2025
Viewed by 1607
Abstract
Autism spectrum disorder (ASD) encompasses a range of conditions, primarily marked by deficits in social behaviors, along with several comorbidities such as sleep abnormalities and motor dysfunction. Recent studies have identified genetic risk factors associated with ASD, including the CAMK4 (calcium/calmodulin-dependent protein kinase [...] Read more.
Autism spectrum disorder (ASD) encompasses a range of conditions, primarily marked by deficits in social behaviors, along with several comorbidities such as sleep abnormalities and motor dysfunction. Recent studies have identified genetic risk factors associated with ASD, including the CAMK4 (calcium/calmodulin-dependent protein kinase 4). However, the molecular mechanisms linking CAMK4 dysregulation and ASD-associated phenotypes remain poorly understood. Here, we used Drosophila melanogaster as a model system to investigate ASD-associated phenotypes in flies with dysregulated CaMKI, the fly homolog of mammalian CAMK4. We show that CaMKI manipulations affect sleep, circadian rhythmicity, and social behavior. Consistent with the higher prevalence of dementia observed in autistic patients, we also observed a significantly enhanced behavioral decline in motor performance and dendritic degeneration in flies expressing RNAi-based CaMKI knockdown in flight motoneurons, suggesting a link between developmental and degenerative processes. As aberrant synaptic pruning is hypothesized to underlie the synaptic phenotypes observed in brains of autistic patients, we examined synaptic phenotypes following CaMKI manipulations using the larval neuromuscular junction (NMJ) and observed miswiring phenotypes suggesting aberrant synaptic refinement. We performed shotgun mass-spectrometry proteomics and identified various molecular candidates, particularly molecules involved in cytoskeleton regulation and chemorepulsion, likely to regulate the phenotypes described here. Thus, our results suggest that CaMKI plays a role in developmental processes and influences aging-dependent degenerative processes, possibly providing mechanistic insight into the genetic basis of ASD etiology and the development of effective treatments. Full article
(This article belongs to the Special Issue Unveiling Novel Gene Functions: Mechanisms, Evolution and Applications)
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17 pages, 551 KB  
Review
Stabilin-1 in Tumor-Associated Macrophages: A Potential Therapeutic Target in Cancer Immunotherapy
by Jampa Lhamo Gurung, Raju Lama Tamang, Lepakshe Madduri, Robert G. Bennett, Edward N. Harris, Paul W. Denton and Benita McVicker
Biology 2025, 14(9), 1198; https://doi.org/10.3390/biology14091198 - 5 Sep 2025
Cited by 2 | Viewed by 2563
Abstract
Stabilin-1 (STAB1) is a multifunctional scavenger receptor expressed by endothelial cells of the liver, spleen, lymph nodes, bone marrow and a subset of macrophages. STAB1 interacts with different ligands and modulates a wide range of functions including cell trafficking, endocytosis, homeostasis, angiogenesis, and [...] Read more.
Stabilin-1 (STAB1) is a multifunctional scavenger receptor expressed by endothelial cells of the liver, spleen, lymph nodes, bone marrow and a subset of macrophages. STAB1 interacts with different ligands and modulates a wide range of functions including cell trafficking, endocytosis, homeostasis, angiogenesis, and tumor vascularization. The role of STAB1 in cancer progression and metastasis first became evident in Stab1 knockout (KO) mice, which developed smaller primary tumors and metastatic foci for some cancers. To date, various clinical cohorts and preclinical rodent studies have shown that STAB1 inhibition is associated with elevated anti-tumor T-cell responses. Moreover, human trials using anti-STAB1 antibody treatment indicate a shift towards immune activation and the potential to overcome cancer treatment resistance experienced with other immunotherapies. Although the role of STAB1 in cancer development and metastasis remains to be defined, STAB1 signaling in tumor-associated macrophages and downstream immune modulation are thought to be crucial mechanisms. Herein, we discuss the role of STAB1 in tumor-associated macrophages in relationship to disease progression and patient outcome. Full article
(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)
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22 pages, 2866 KB  
Article
Metagenomic Analysis Revealed Significant Changes in the Beef Cattle Rectum Microbiome Under Fescue Toxicosis
by Gastón F. Alfaro, Yihang Zhou, Wenqi Cao, Yue Zhang, Soren P. Rodning, Russell B. Muntifering, Wilmer J. Pacheco, Sonia J. Moisá and Xu Wang
Biology 2025, 14(9), 1197; https://doi.org/10.3390/biology14091197 - 5 Sep 2025
Cited by 1 | Viewed by 1376
Abstract
Tall fescue toxicosis, caused by ingestion of endophyte-infected tall fescue (Lolium arundinaceum), impairs growth and reproduction in beef cattle and results in over USD 3 billion annual loss to the U.S. livestock industry. While the effects on host metabolism and rumen [...] Read more.
Tall fescue toxicosis, caused by ingestion of endophyte-infected tall fescue (Lolium arundinaceum), impairs growth and reproduction in beef cattle and results in over USD 3 billion annual loss to the U.S. livestock industry. While the effects on host metabolism and rumen function have been described, the impact on the rectal microbiome remains poorly understood. In this study, we performed whole-genome shotgun metagenomic sequencing on fecal samples collected before and after a 30-day toxic fescue seed supplementation from eight pregnant Angus × Simmental cows and heifers. We generated 157 Gbp of sequencing data in 16 metagenomes, and assembled 13.1 Gbp de novo microbial contigs, identifying 22 million non-redundant microbial genes from the cattle rectum microbiome. Fescue toxicosis significantly reduced alpha diversity (p < 0.01) and altered beta diversity (PERMANOVA p < 0.01), indicating microbial dysbiosis. We discovered significant enrichment of 31 bacterial species post-treatment, including multiple core rumen taxa. Ruminococcaceae bacterium P7 showed an average of 16-fold increase in fecal abundance (p < 0.01), making it the top-featured species in linear discriminant analysis. Functional pathway analysis revealed a shift from energy metabolism to antimicrobial resistance and DNA replication following toxic seed consumption. Comparative analysis showed increased representation of core rumen taxa in rectal microbiota post-treatment, suggesting disrupted rumen function. These findings demonstrate that fescue toxicosis alters both the composition and functional landscape of the hindgut microbiota. Ruminococcaceae bacterium P7 emerges as a promising biomarker for monitoring fescue toxicosis through non-invasive fecal sampling, with potential applications in herd-level diagnostics and mitigation strategies. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease (2nd Edition))
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20 pages, 2100 KB  
Article
Mutational Analysis Reveals Functional Roles of METTL16 Domains and Residues
by Kurtis Breger, Ian P. Schowe, Noah A. Springer, Nathan J. O’Leary, Agnieszka Ruszkowska, Carlos Resende and Jessica A. Brown
Biology 2025, 14(9), 1145; https://doi.org/10.3390/biology14091145 - 29 Aug 2025
Viewed by 1200
Abstract
Human methyltransferase-like protein 16 (METTL16) installs N6-methyladenosine on U6 small nuclear RNA (snRNA) and other RNAs. Multiple X-ray crystal structures of METTL16 have been published; however, we do not yet fully understand the structure–function relationships of specific residues. We designed 38 [...] Read more.
Human methyltransferase-like protein 16 (METTL16) installs N6-methyladenosine on U6 small nuclear RNA (snRNA) and other RNAs. Multiple X-ray crystal structures of METTL16 have been published; however, we do not yet fully understand the structure–function relationships of specific residues. We designed 38 mutants, including seven cancer-associated mutants, and used electrophoretic mobility shift assays and single-turnover kinetic assays to better understand the functional roles of specific domains and amino acid residues in binding to U6 snRNA, formation of the METTL16•U6 snRNA•S-adenosylmethionine (SAM) complex, and the rate of methylation. While point mutations in the methyltransferase domain mildly weaken the binding of METTL16 to U6 snRNA, the C-terminal vertebrate conserved regions (VCRs), particularly the arginine-rich region (R382 to R388), mediate cooperative binding and contribute more to RNA binding. All METTL16 K-loop mutants displayed tighter SAM binding, suggesting that the K-loop blocks SAM binding. In addition, residues E133 and F227 are critical for stabilizing SAM binding. Mutations in the 184NPPF187 catalytic core and R282A abolished methyltransferase activity. Two METTL16 somatic cancer-associated mutants (G110C and R241Dfs*2) displayed reduced methylation activity. This mutational analysis expands our understanding of how specific domains and residues contribute to substrate-binding activity and methylation of U6 snRNA catalyzed by METTL16. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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15 pages, 772 KB  
Review
Mutational Signatures in Radiation-Induced Cancer: A Review of Experimental Animal and Human Studies
by Kazuhiro Daino, Chizuru Tsuruoka, Atsuko Ishikawa, Shizuko Kakinuma and Tatsuhiko Imaoka
Biology 2025, 14(9), 1142; https://doi.org/10.3390/biology14091142 - 29 Aug 2025
Cited by 2 | Viewed by 2876
Abstract
Ionizing radiation can damage DNA, leading to mutations, and is a risk factor for cancer. Based on the assumption that all radiation exposure poses a risk in linear proportion to its dose, ionizing radiation is considered a non-threshold carcinogen. However, most epidemiological studies [...] Read more.
Ionizing radiation can damage DNA, leading to mutations, and is a risk factor for cancer. Based on the assumption that all radiation exposure poses a risk in linear proportion to its dose, ionizing radiation is considered a non-threshold carcinogen. However, most epidemiological studies have had insufficient statistical power to detect excess cancer risks from low-dose radiation exposure. Therefore, research is needed to identify radiation signatures that distinguish radiation-induced cancers from spontaneously developed cancers. In rodent cancer models, interstitial chromosomal deletions of specific tumor-suppressor gene loci are characteristically found in cancers from irradiated animals. In humans, a high frequency of small deletions and chromosome rearrangements, such as large deletions, inversions, and translocations, has also been reported in second cancers that develop in patients who received radiotherapy and in thyroid cancers diagnosed in residents after the Chornobyl accident. These genomic alterations are likely to be generated as a consequence of the processing of radiation-induced DNA double-strand breaks. Particularly, chromosome rearrangements that occur at loci directly linked to tumor formation after ionizing-radiation exposure are potentially useful as biomarkers and as therapeutic targets for radiation-induced cancer. Here we provide an overview of the radiation-induced mutational signatures observed in animal and human cancers. Full article
(This article belongs to the Special Issue Radiation and Biology: Investigating Cellular, Organismal, and Environmental Responses)
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22 pages, 1926 KB  
Review
Biological Sequence Representation Methods and Recent Advances: A Review
by Hongwei Zhang, Yan Shi, Yapeng Wang, Xu Yang, Kefeng Li, Sio-Kei Im and Yu Han
Biology 2025, 14(9), 1137; https://doi.org/10.3390/biology14091137 - 27 Aug 2025
Cited by 2 | Viewed by 2333
Abstract
Biological-sequence representation methods are pivotal for advancing machine learning in computational biology, transforming nucleotide and protein sequences into formats that enhance predictive modeling and downstream task performance. This review categorizes these methods into three developmental stages: computational-based, word embedding-based, and large language model [...] Read more.
Biological-sequence representation methods are pivotal for advancing machine learning in computational biology, transforming nucleotide and protein sequences into formats that enhance predictive modeling and downstream task performance. This review categorizes these methods into three developmental stages: computational-based, word embedding-based, and large language model (LLM)-based, detailing their principles, applications, and limitations. Computational-based methods, such as k-mer counting and position-specific scoring matrices (PSSM), extract statistical and evolutionary patterns to support tasks like motif discovery and protein–protein interaction prediction. Word embedding-based approaches, including Word2Vec and GloVe, capture contextual relationships, enabling robust sequence classification and regulatory element identification. Advanced LLM-based methods, leveraging Transformer architectures like ESM3 and RNAErnie, model long-range dependencies for RNA structure prediction and cross-modal analysis, achieving superior accuracy. However, challenges persist, including computational complexity, sensitivity to data quality, and limited interpretability of high-dimensional embeddings. Future directions prioritize integrating multimodal data (e.g., sequences, structures, and functional annotations), employing sparse attention mechanisms to enhance efficiency, and leveraging explainable AI to bridge embeddings with biological insights. These advancements promise transformative applications in drug discovery, disease prediction, and genomics, empowering computational biology with robust, interpretable tools. Full article
(This article belongs to the Special Issue Machine Learning Applications in Biology—2nd Edition)
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18 pages, 1463 KB  
Article
Hypoxia-Driven Extracellular Vesicles Promote Pro-Metastatic Signalling in LNCaP Cells via Wnt and EMT Pathways
by Melissa Santos, Khansa Bukhari, Irem Peker-Eyüboğlu, Igor Kraev, Dafydd Alwyn Dart, Sigrun Lange and Pinar Uysal-Onganer
Biology 2025, 14(9), 1135; https://doi.org/10.3390/biology14091135 - 27 Aug 2025
Viewed by 1560
Abstract
Prostate cancer (PCa) progression is shaped by the tumour microenvironment, where hypoxia promotes aggressiveness and contributes to therapy resistance. Extracellular vesicles (EVs), secreted under hypoxia, can deliver modified bioactive cargo that reprograms recipient cells. This study examined whether EVs from hypoxia-conditioned metastatic PCa [...] Read more.
Prostate cancer (PCa) progression is shaped by the tumour microenvironment, where hypoxia promotes aggressiveness and contributes to therapy resistance. Extracellular vesicles (EVs), secreted under hypoxia, can deliver modified bioactive cargo that reprograms recipient cells. This study examined whether EVs from hypoxia-conditioned metastatic PCa cells enhance malignant traits in cancerous and non-tumorigenic prostate cell lines via Wnt signalling and epithelial–mesenchymal transition (EMT). EVs from PC3 cells cultured under hypoxia (1% O2) or normoxia (21% O2) as control were applied to LNCaP (low metastatic potential) and PNT2 (non-tumorigenic) cells. PC3 hypoxia-derived EVs increased HIF-1α, upregulated mesenchymal markers (Vimentin, N-cadherin) and Wnt-related genes (Wnt3A, Wnt5A, Fzd7), and suppressed the epithelial marker E-cadherin. Functional assessment showed that LNCaP cells treated with PC3 hypoxia EVs showed greater motility and invasiveness, and PNT2 cells displayed transcriptomic reprogramming. These findings show that hypoxia-driven EVs can propagate pro-metastatic signalling in less aggressive and normal prostate cells. The findings highlight EVs as a potential therapeutic target in PCa progression. Full article
(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)
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29 pages, 2190 KB  
Review
The Sublethal Effects of Neonicotinoids on Honeybees
by Zunair Ahsan, Zhijia Wu, Zheguang Lin, Ting Ji and Kang Wang
Biology 2025, 14(8), 1076; https://doi.org/10.3390/biology14081076 - 18 Aug 2025
Cited by 5 | Viewed by 6153
Abstract
Honeybees (Apis mellifera) are indispensable pollinators vital to global biodiversity, ecosystem stability, and agricultural productivity, and they promote over 35% of food crops and 75% of flowering plants. Yet, they are in unprecedented decline, partly as a result of neonicotinoid pesticide [...] Read more.
Honeybees (Apis mellifera) are indispensable pollinators vital to global biodiversity, ecosystem stability, and agricultural productivity, and they promote over 35% of food crops and 75% of flowering plants. Yet, they are in unprecedented decline, partly as a result of neonicotinoid pesticide use elsewhere. These effects on honey bee health are synthesized in this paper through molecular, physiological, and behavioral data showing that sublethal effects of neonicotinoids impair honey bee health. As neurotoxic insecticides that target nicotinic acetylcholine receptors (nAChRs), these insecticides interfere with neurotransmission and underlie cognitive impairment, immune suppression, and oxidative stress. Developmental toxicity is manifested in larvae as retarded growth, reduced feeding, and increased death; queen and drone reproduction are impaired, lowering colony viability. As a result, adult bees have shortened lives and erratic foraging, are further disoriented, and experience impaired navigation, communication, and resource collection. Together, these effects cascade to reduced brood care, thermoregulatory failure, and heretofore unrecognized increased susceptibility to pathogens, increasing the probability of colony collapse at the colony level. Contaminants such as pesticides may cause pollinator exposure and, in turn, may cause their population to be undermined if they are not mitigated; therefore, urgent mitigation strategies, including integrated pest management (IPM), regulatory reforms, and adoption of biopesticides, are needed to mitigate pollinator exposure. The focus of this review lies in the ecological necessity of restructuring how agriculture is managed to simultaneously meet food security and the conservation of honeybee health, the linchpin of global ecosystems. Full article
(This article belongs to the Special Issue Insecticide Resistance: Molecular Mechanisms and Ecological Implications)
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25 pages, 2027 KB  
Review
Mapping Multi-Modal Fatigue in Elite Soccer Through Sweat-Omics Perspectives: A Narrative Review
by Moses Gnanasigamani, Ersan Arslan, Yusuf Soylu, Bulent Kilit and Paweł Chmura
Biology 2025, 14(8), 1069; https://doi.org/10.3390/biology14081069 - 16 Aug 2025
Cited by 3 | Viewed by 2274
Abstract
Fatigue in elite soccer is a multifaceted phenomenon involving physical, metabolic, psychological, and neuromuscular stressors that accumulate over training and competition. Traditional monitoring tools, while informative, are often invasive, impractical during play, or fail to provide real-time insights. This narrative review synthesizes sweat-based [...] Read more.
Fatigue in elite soccer is a multifaceted phenomenon involving physical, metabolic, psychological, and neuromuscular stressors that accumulate over training and competition. Traditional monitoring tools, while informative, are often invasive, impractical during play, or fail to provide real-time insights. This narrative review synthesizes sweat-based biomarkers linked to fatigue in elite soccer, with a focus on multi-modal domains (neuromuscular, metabolic, inflammatory, psychological). Using an integrative approach, we reviewed studies published across databases including PubMed, Scopus, and Web of Science that evaluate sweat biomarkers of different types of fatigue in soccer. We identified key candidates—lactate, sodium, cortisol, IL-6, and hypoxanthine—and evaluated their potential in non-invasive monitoring. Youth-specific and female populations remain underrepresented. We also assessed each biomarker’s technological maturity using a sweat-specific Technology Readiness Level (TRL) framework. Based on these findings, we propose a translational framework for practitioners and outline priorities for future research and validation in real-world sport settings. Full article
(This article belongs to the Section Physiology)
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17 pages, 551 KB  
Review
The Genetics and Evolution of Human Pigmentation
by Dorra Guermazi and Elie Saliba
Biology 2025, 14(8), 1026; https://doi.org/10.3390/biology14081026 - 10 Aug 2025
Cited by 3 | Viewed by 12709
Abstract
Human skin pigmentation is one of the most visible and variable traits among populations and has been shaped primarily by natural selection in response to ultraviolet (UV) radiation. This review synthesizes the current understanding of the genetic and evolutionary mechanisms that underlie pigmentation [...] Read more.
Human skin pigmentation is one of the most visible and variable traits among populations and has been shaped primarily by natural selection in response to ultraviolet (UV) radiation. This review synthesizes the current understanding of the genetic and evolutionary mechanisms that underlie pigmentation differences across the globe. The roles of key pigmentation-related genes, such as MC1R, SLC24A5, TYR, and OCA2, are examined in terms of how different versions of these genes have been favored in different UV environments to balance the need for photoprotection and vitamin-D synthesis. Evidence of convergent evolution in lighter skin pigmentation is explored among populations in Europe and East Asia, along with the relatively stable presence of darker pigmentation alleles in equatorial regions. We also highlight how recent research has integrated ecological, anthropological, and genomic data to paint a fuller picture of these adaptive patterns. Finally, we discuss the biomedical implications of these evolutionary processes, including how historical adaptations influence current differences in skin cancer risk, vitamin-D metabolism, and pigmentary disorders. By tracing the evolutionary history of skin color, this review emphasizes the intricate interplay between our genetics, environment, and health. Full article
(This article belongs to the Section Evolutionary Biology)
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30 pages, 2475 KB  
Review
Trans-Scale Insights into Variability in Radiation Cancer Risk Across Tissues, Individuals, and Species
by Tatsuhiko Imaoka
Biology 2025, 14(8), 1025; https://doi.org/10.3390/biology14081025 - 9 Aug 2025
Cited by 1 | Viewed by 2099
Abstract
Diversity is evident in various aspects of life and the human population. The current radiological protection system considers the diversity in disease susceptibility and incorporates some of it to provide a unified risk model for the human population. This paper focuses on variability [...] Read more.
Diversity is evident in various aspects of life and the human population. The current radiological protection system considers the diversity in disease susceptibility and incorporates some of it to provide a unified risk model for the human population. This paper focuses on variability in cancer risk among cells/tissues, individuals, and animal species. At the cell/tissue level, radiation cancer risk per unit dose varies among tissues, as indicated by epidemiological and animal studies. This variation is most likely due to the epigenetics of cells. At the individual level, radiation risks vary considerably depending on physiological, environmental, and genetic factors. At the species level, epidemiology is considered the most relevant source of radiological information, and limitations have been recognized in extrapolating animal data to human risks. A recent study demonstrated a fundamental relationship between cancer risk and somatic mutation rate in humans and mice. This relationship could lead to a new extrapolation method, which could be used to protect a wider range of species, including humans and other mammals. Thus, considering diversity in radiation cancer risk provides insight into the underlying aspects of radiobiology of radiological protection. Full article
(This article belongs to the Special Issue Radiation and Biology: Investigating Cellular, Organismal, and Environmental Responses)
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16 pages, 4615 KB  
Article
Daily Variation in the Feeding Activity of Pacific Crown-of-Thorns Starfish (Acanthaster cf. solaris)
by Josie F. Chandler, Deborah Burn, Will F. Figueira, Peter C. Doll, Abby Johandes, Agustina Piccaluga and Morgan S. Pratchett
Biology 2025, 14(8), 1001; https://doi.org/10.3390/biology14081001 - 5 Aug 2025
Cited by 3 | Viewed by 1516
Abstract
The ecological impact of crown-of-thorns starfish (CoTS; Acanthaster spp.) on coral reefs is intrinsically linked to their feeding behaviour. Management thresholds designed to mitigate coral loss driven by elevated densities of crown-of-thorns starfish rely on accurate estimates of individual feeding rates. In this [...] Read more.
The ecological impact of crown-of-thorns starfish (CoTS; Acanthaster spp.) on coral reefs is intrinsically linked to their feeding behaviour. Management thresholds designed to mitigate coral loss driven by elevated densities of crown-of-thorns starfish rely on accurate estimates of individual feeding rates. In this study, structure-from-motion photogrammetry and intensive tracking of adult Pacific CoTS over an extended survey period were used to generate three-dimensional, high-resolution estimates of daily feeding rates. Our findings revealed substantial variation in the areal extent of coral consumed, both across consecutive days and among individuals. Notably, CoTS did not feed consistently; feeding occurred on 65% of observation days, with 2–3 days periods of inactivity common. Despite this variability, mean daily feeding rates aligned with previous studies (1.35 coral colonies d−1; 198.4 cm2 day−1 planar area, and 998.83 cm2 day−1 three-dimensional surface area). Across all tracked individuals (n = 8), feeding was recorded on 17 coral genera; however, Acropora alone accounted for 51% of colonies consumed and contributed 82% of the total three-dimensional surface area ingested during the survey period. This highlights the disproportionately large feeding yield derived from Acropora-dominated diets and raises important questions about how future declines in Acropora cover may impact CoTS feeding success and energetic intake. Full article
(This article belongs to the Section Marine and Freshwater Biology)
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19 pages, 3755 KB  
Review
In Vivo Shadows and In Vitro Light: The Early Embryological Journey Amid Endometriosis
by Grzegorz Mrugacz, Aleksandra Mospinek, Maria Modrzyńska-Olejniczak, Bartłomiej Byczkowski, Ewelina Radaj and Piotr Olcha
Biology 2025, 14(8), 957; https://doi.org/10.3390/biology14080957 - 29 Jul 2025
Viewed by 1204
Abstract
Endometriosis significantly impacts fertility through complex mechanisms. These include chronic inflammation, oxidative stress, and anatomical distortion. These mechanisms impair oocyte quality, embryo development, and implantation. While in vivo challenges persist, in vitro fertilization (IVF) offers a controlled environment to overcome some barriers. A [...] Read more.
Endometriosis significantly impacts fertility through complex mechanisms. These include chronic inflammation, oxidative stress, and anatomical distortion. These mechanisms impair oocyte quality, embryo development, and implantation. While in vivo challenges persist, in vitro fertilization (IVF) offers a controlled environment to overcome some barriers. A systematic review of evidence is presented for (1) endometriosis-associated oocyte dysfunction, (2) conflicting IVF outcomes, and (3) innovative strategies. Significant medical advancements have been made. However, gaps remain in personalized prognosis and targeted therapies. Emerging tools, specifically AI-driven embryo selection, single-cell omics, and immunomodulation, are promising for improving outcomes. Hence, a patient-centered approach, balancing science with personalized care, is essential to navigate endometriosis-related infertility. Full article
(This article belongs to the Section Medical Biology)
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31 pages, 3043 KB  
Article
Physiological and Phytochemical Responses of Calendula officinalis L. to End-of-Day Red/Far-Red and Green Light
by Luisa F. Lozano-Castellanos, Giuseppina Pennisi, Luis Manuel Navas-Gracia, Francesco Orsini, Eva Sánchez-Hernández, Pablo Martín-Ramos and Adriana Correa-Guimaraes
Biology 2025, 14(8), 935; https://doi.org/10.3390/biology14080935 - 24 Jul 2025
Cited by 1 | Viewed by 1851
Abstract
Calendula officinalis L. is a widely used medicinal plant whose secondary metabolism and morphology are influenced by light. This study evaluated the effects of 2 and 4 h end-of-day (EOD) red/far-red (R:FR) and green (G) light on the growth, physiology, and phytochemical profile [...] Read more.
Calendula officinalis L. is a widely used medicinal plant whose secondary metabolism and morphology are influenced by light. This study evaluated the effects of 2 and 4 h end-of-day (EOD) red/far-red (R:FR) and green (G) light on the growth, physiology, and phytochemical profile of hydroponically grown C. officinalis under a constant red/blue light background, compared with a red/blue control without EOD treatment. Morphological, physiological (gas exchange, chlorophyll fluorescence), biochemical (chlorophyll, anthocyanin), and chemical composition (attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and Gas Chromatography-Mass Spectrometry (GC-MS)) were evaluated. EOD G 2 h enhanced photosynthetic pigments, anthocyanins, and biomass, while control plants showed higher phenolic content. EOD R:FR induced stem elongation but reduced pigment and metabolite accumulation. GC-MS revealed organ-specific metabolic specialization, with flowers displaying greater chemical diversity than leaves. EOD G favored sesquiterpene diversity in flowers, while EOD R:FR increased nitrogen-containing compounds and unsaturated fatty acids. Vibrational data supported these shifts, with spectral signatures of esters, phenolics, and lipid-related structures. Bioactive compounds, including α-cadinol and carboxylic acids, were identified across treatments. These findings demonstrate that EOD light modulates physiological and metabolic traits in C. officinalis, highlighting EOD G as an enhancer of biomass and phytochemical richness for pharmaceutical applications under controlled conditions. Full article
(This article belongs to the Special Issue Physiological, Biochemical, and Molecular Response in Plants under Light-Emitting Diode (LED) Treatment (Volume II))
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17 pages, 2253 KB  
Article
Sexual Dimorphism in the Skeletal Morphology of Asian Elephants (Elephas maximus): A Preliminary Morphometric Study of Skull, Scapula, and Pelvis
by Piyamat Kongtueng, Promporn Piboon, Sarisa Klinhom, Intorn Aunsan, Nontanan Tongser, Taweepoke Angkawanish, Korakot Nganvongpanit and Burin Boonsri
Biology 2025, 14(8), 933; https://doi.org/10.3390/biology14080933 - 24 Jul 2025
Cited by 1 | Viewed by 1991
Abstract
Background: Sexual dimorphism in Asian elephants (Elephas maximus) is evident in external features, but skeletal differences remain underexplored. This study aimed to examine the skull, scapula, and pelvis using traditional morphometric methods to assess sex-related variation. Methods: Eleven skeletal specimens were [...] Read more.
Background: Sexual dimorphism in Asian elephants (Elephas maximus) is evident in external features, but skeletal differences remain underexplored. This study aimed to examine the skull, scapula, and pelvis using traditional morphometric methods to assess sex-related variation. Methods: Eleven skeletal specimens were analyzed, including nine skulls, eleven pelves, and eighteen scapulae. Linear measurements were obtained using measuring tape and calipers. Statistical analyses included Mann–Whitney U tests, Pearson’s correlation, and logistic regression for sex prediction. Results: No significant differences were found in skull measurements between sexes. However, the pelvis and scapula exhibited notable variation. Significant pelvic parameters included pelvic girdle length (p = 0.024), symphysis length (p = 0.012), and pubis shaft perimeter (p = 0.048). Scapular differences were observed in diagonal breadth, mediolateral width, and spine length. Logistic regression using pelvic measurements yielded 100% accuracy for female classification and 66.67% for males, with an overall prediction accuracy of 90.91%. Conclusions: The pelvis demonstrated the highest reliability for sex determination. These findings enhance the anatomical understanding of Asian elephants and support applications in conservation, forensic science, and population studies. Future research with larger sample sizes and advanced imaging may improve the precision of morphometric sex prediction models. Full article
(This article belongs to the Special Issue Recent Advances in Animal Anatomy)
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29 pages, 9335 KB  
Review
Plant Disease Suppressiveness Enhancement via Soil Health Management
by Chinmayee Priyadarshini, Rattan Lal, Pu Yuan, Wenshan Liu, Ashna Adhikari, Santosh Bhandari and Ye Xia
Biology 2025, 14(8), 924; https://doi.org/10.3390/biology14080924 - 23 Jul 2025
Cited by 6 | Viewed by 3879
Abstract
Managing soil-borne pathogens and diseases in plants is particularly challenging because the pathogens that cause them can persist in the soil for extended periods, often resulting in repeated crop damage in affected areas. These destructive diseases compromise plant health by weakening the root [...] Read more.
Managing soil-borne pathogens and diseases in plants is particularly challenging because the pathogens that cause them can persist in the soil for extended periods, often resulting in repeated crop damage in affected areas. These destructive diseases compromise plant health by weakening the root systems, which makes the plants more susceptible to environmental stress and nutritional deficiencies. Every year in the United States, a whopping $9.6 million is allocated to reverse the harmful effects of pesticides on humans, plants, animals, and the environment. On the contrary, disease-suppressive soils offer an effective strategy for controlling pathogens while ensuring the least contamination of the environment. These soils can be managed by both conventional and advanced methods, such as reduced tillage, crop rotation, organic amendments, nanoparticles, omics approaches, and biofumigation. However, these soils can be local in nature, and their properties might be disrupted by common agricultural practices like tillage and agro-chemical application. This review synthesizes the concepts and mechanisms of disease suppression in soils and explores the ways that can be improved through the management of soil health for enhanced plant health and yield. Full article
(This article belongs to the Special Issue Advances in Research on Diseases of Plants (2nd Edition))
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9 pages, 2281 KB  
Communication
Characterization of Small Extracellular Vesicles Isolated from Aurelia aurita
by Aldona Dobrzycka-Krahel, Aleksandra Steć, Grzegorz S. Czyrski, Andrea Heinz and Szymon Dziomba
Biology 2025, 14(8), 922; https://doi.org/10.3390/biology14080922 - 23 Jul 2025
Viewed by 1085
Abstract
A moon jellyfish (Aurelia aurita) is a representative of the phylum Cnidaria, commonly found in the northern seas of the globe. The regenerative abilities of cnidarians have recently been associated with extracellular vesicles (EVs) secreted by these organisms. In this study, [...] Read more.
A moon jellyfish (Aurelia aurita) is a representative of the phylum Cnidaria, commonly found in the northern seas of the globe. The regenerative abilities of cnidarians have recently been associated with extracellular vesicles (EVs) secreted by these organisms. In this study, a method for the isolation of EVs from the oral arms of A. aurita is presented. The methodology includes differential centrifugation, size-exclusion chromatography, and ultrafiltration. The isolates were characterized with tunable resistive pulse sensing, cryogenic transmission electron microscopy, capillary electrophoresis (CE), and electrophoretic light scattering (ELS). Small (<150 nm in diameter) EVs were abundant in the isolates. The EVs were found to carry nucleic acids, indicating their role in signaling. Additionally, the difference in zeta potential values measured with ELS and CE indicates high glycation in the vesicles analyzed. Although the method developed was effective in isolating EVs from small sample volumes (0.5 mL), the EV yield was insufficient for omics analysis. Thus, the scaling up of the isolation process is required for comprehensive biochemical analysis and biological activity assessment in A. aurita-derived EVs. Full article
(This article belongs to the Section Marine and Freshwater Biology)
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20 pages, 6280 KB  
Article
The V5-Epitope Tag for Cell Engineering and Its Use in Immunohistochemistry and Quantitative Flow Cytometry
by Katja Fritschle, Marion Mielke, Olga J. Seelbach, Ulrike Mühlthaler, Milica Živanić, Tarik Bozoglu, Sarah Dötsch, Linda Warmuth, Dirk H. Busch, Arne Skerra, Christian Kupatt, Wolfgang A. Weber, Richard E. Randall, Katja Steiger and Volker Morath
Biology 2025, 14(7), 890; https://doi.org/10.3390/biology14070890 - 20 Jul 2025
Cited by 1 | Viewed by 2440
Abstract
Synthetic biology has fundamentally advanced cell engineering and helped to develop effective therapeutics such as chimeric antigen receptor (CAR)-T cells. For these applications, the detection, localization, and quantification of heterologous fusion proteins assembled from interchangeable building blocks is of high importance. The V5 [...] Read more.
Synthetic biology has fundamentally advanced cell engineering and helped to develop effective therapeutics such as chimeric antigen receptor (CAR)-T cells. For these applications, the detection, localization, and quantification of heterologous fusion proteins assembled from interchangeable building blocks is of high importance. The V5 tag, a 14-residue epitope tag, offers promising characteristics for these applications but has only rarely been used in this context. Thus, we have systematically evaluated the murine anti-V5 tag antibody mu_SV5-Pk1 as well as its humanized version, hu_SV5-Pk1, to analyze cells expressing V5-tagged receptors in samples from various in vitro and in vivo experiments. We found that the V5 tag signal on cells is affected by certain fixation and detachment reagents. Immunohistochemistry (IHC) on formalin-fixed paraffin-embedded (FFPE) mouse tissue samples was performed to sensitively detect cells in tissue. We improved IHC by applying the hu_SV5-Pk1 monoclonal antibody (mAb) to avoid cross-reactivity within and unspecific background signals arising on fixed mouse tissue. Conversely, the absence of unspecific binding by the mu_SV5-Pk1 mAb was evaluated on 46 human normal or cancer tissues. Our findings present a robust toolbox for utilizing the V5 tag and cognate antibodies in synthetic biology applications. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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14 pages, 2425 KB  
Review
Immunological Factors in Recurrent Pregnancy Loss: Mechanisms, Controversies, and Emerging Therapies
by Efthalia Moustakli, Anastasios Potiris, Athanasios Zikopoulos, Eirini Drakaki, Ioannis Arkoulis, Charikleia Skentou, Ioannis Tsakiridis, Themistoklis Dagklis, Peter Drakakis and Sofoklis Stavros
Biology 2025, 14(7), 877; https://doi.org/10.3390/biology14070877 - 17 Jul 2025
Cited by 7 | Viewed by 4313
Abstract
Immunological factors have gained growing recognition as key contributors to recurrent pregnancy loss (RPL) after in vitro fertilization (IVF), representing a major challenge in reproductive medicine. RPL affects approximately 1–2% of women trying to conceive naturally and up to 10–15% of those undergoing [...] Read more.
Immunological factors have gained growing recognition as key contributors to recurrent pregnancy loss (RPL) after in vitro fertilization (IVF), representing a major challenge in reproductive medicine. RPL affects approximately 1–2% of women trying to conceive naturally and up to 10–15% of those undergoing IVF, where overall success rates remain around 30–40% per cycle. An imbalance in maternal immunological tolerance toward the semi-allogeneic fetus during pregnancy may lead to miscarriage and implantation failure. IVF-related ovarian stimulation and embryo modification offer additional immunological complications that can exacerbate existing immune dysregulation. Recent advances in reproductive immunology have significantly deepened our understanding of the immune mechanisms underlying RPL following IVF, particularly highlighting the roles of regulatory T cells (T regs), natural killer cells, cytokine dysregulation, and disruptions in maternal–fetal immune tolerance. In order to better customize therapies, this evaluation incorporates recently discovered immunological biomarkers and groups patients according to unique immune profiles. Beyond conventional treatments like intralipid therapy and intravenous immunoglobulin, it also examines new immunomodulatory medications that target certain immune pathways, such as precision immunotherapies and novel cytokine modulators. We also discuss the debates over immunological diagnostics and therapies, such as intralipid therapy, intravenous immunoglobulin, corticosteroids, and anticoagulants. The heterogeneity of patient immune profiles combined with a lack of strong evidence highlights the imperative for precision medicine to improve therapeutic consistency. Novel indicators for tailored immunotherapy and emerging treatments that target particular immune pathways have encouraging opportunities to increase pregnancy success rates. Improving management approaches requires that future research prioritize large-scale clinical trials and the development of standardized immunological assessments. This review addresses the immunological factors in RPL during IVF, emphasizing underlying mechanisms, ongoing controversies, and novel therapeutic approaches to inform researchers and clinicians. Full article
(This article belongs to the Section Immunology)
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14 pages, 8113 KB  
Article
Cellular and Matrix Organisation of the Human Aortic Valve Interleaflet Triangles
by Najma Latif, Padmini Sarathchandra, Albaraa Al-Holy, Sanida Vaz, Adrian H. Chester and Magdi H. Yacoub
Biology 2025, 14(7), 863; https://doi.org/10.3390/biology14070863 - 16 Jul 2025
Viewed by 1240
Abstract
(1) Background: The sophisticated function of the aortic root relies on the coordinated movement of its constituent components. This study examines the extracellular components of the interleaflet triangles (ILTs) and characterises the cells that are present within this region of the aortic root. [...] Read more.
(1) Background: The sophisticated function of the aortic root relies on the coordinated movement of its constituent components. This study examines the extracellular components of the interleaflet triangles (ILTs) and characterises the cells that are present within this region of the aortic root. (2) Methods: A total of 10 human aortic valves and 6 porcine aortic valves were processed for immunohistochemical staining, scanning, and transmission electron microscopy. (3) Results: The three ILTs differed in size and macroscopic appearance. Each triangle comprised up to five distinct layers of tissue: an innermost endothelial layer, an inner elastin-rich layer, a thicker outer layer comprising densely packed layers of collagen and glycosaminoglycans, and an outer layer of intermingled myocardial and adipose tissue. A band of cells near the luminal surfaces of all ILTs expressed smooth muscle cell α-actin with variable expression of smooth muscle myosin heavy chain. In all the ILTs, there was evidence of neurofilament staining, indicating the presence of nerve fibres. (4) Conclusions: Each ILT is unique in its structure and organisation, with differing amounts of elastin and collagen, as well as myocardial, adipose, and fibrous content. The ILTs contain multiple cell types in varying abundance. Functional studies are required to determine the role of the different cells and their organisation in contributing to the sophisticated, dynamic behaviour of the aortic root. Full article
(This article belongs to the Section Cell Biology)
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15 pages, 1797 KB  
Article
First Insights into Bioaccumulation Patterns in Different Tissues of the Greenland Shark Somniosus microcephalus from Kulusuk (Southeastern Greenland)
by Francesca Romana Reinero, Emilio Sperone, Samira Gallo, Donatella Barca, Francesco Luigi Leonetti, Gianni Giglio and Primo Micarelli
Biology 2025, 14(7), 857; https://doi.org/10.3390/biology14070857 - 15 Jul 2025
Cited by 1 | Viewed by 1778
Abstract
Marine environmental pollution has been rapidly increasing in Arctic waters, and the release and bioaccumulation of trace elements in Arctic marine species may pose significant risks to both ecosystem health and human well-being. As a top predator, the Greenland shark is an ideal [...] Read more.
Marine environmental pollution has been rapidly increasing in Arctic waters, and the release and bioaccumulation of trace elements in Arctic marine species may pose significant risks to both ecosystem health and human well-being. As a top predator, the Greenland shark is an ideal sentinel species for ecotoxicological studies in this region. In this study, trace element analyses were conducted on various tissues from two Greenland sharks—a male and a female—collected in Kulusuk (southeastern Greenland). Eleven trace elements (Mn55, Co59, Cu63, Zn64, As75, Se82, Rb85, Mo98, Ag107, Cd112, and Pb208) were measured in different skin samples from both specimens and in the muscle and fat of the female using an Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Principal Component Analyses (PCAs) revealed sex-related differences in skin bioaccumulation patterns, likely due to sampling of different skin regions. Notably, skin tissues from both sharks showed the highest concentration of trace elements, especially for As75 (9.39–41.13 ppm) and Zn64 (24.34–50.99 ppm) and with the exception of Ag107. These findings suggest that environmental exposure may play a more significant role than dietary intake in trace element accumulation in this area. This study represents the first investigation of trace element bioaccumulation in Greenland sharks from Kulusuk. While the results offer important preliminary insights into the species’ ecotoxicology, further research involving more specimens and tissues is needed to confirm these trends. These initial findings contribute to filling key data gaps and have implications for both environmental monitoring and public health within the Greenlandic community. Full article
(This article belongs to the Section Marine and Freshwater Biology)
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13 pages, 1243 KB  
Article
Sex Differences in Human Myogenesis Following Testosterone Exposure
by Paolo Sgrò, Cristina Antinozzi, Guglielmo Duranti, Ivan Dimauro, Zsolt Radak and Luigi Di Luigi
Biology 2025, 14(7), 855; https://doi.org/10.3390/biology14070855 - 14 Jul 2025
Viewed by 1389
Abstract
Previous research has demonstrated sex-specific differences in muscle cells regarding sex hormone release and steroidogenic enzyme expression after testosterone exposure. The present study aims to elucidate sex-related differences in intracellular processes involved in myogenesis and regeneration. Neonatal 46XX and 46XY human primary skeletal [...] Read more.
Previous research has demonstrated sex-specific differences in muscle cells regarding sex hormone release and steroidogenic enzyme expression after testosterone exposure. The present study aims to elucidate sex-related differences in intracellular processes involved in myogenesis and regeneration. Neonatal 46XX and 46XY human primary skeletal muscle cells were treated with increasing doses of testosterone (0.5, 2, 5, 10, 32, and 100 nM) for 24 h. The molecular pathways involved in muscle metabolism and growth, as well as the release of myokines involved in satellite cell activation, were analyzed using western blot, real-time PCR, and a Luminex assay. The unpaired Student’s t-test and one-way ANOVA for repeated measures were used to determine significant variations within and between groups. An increase in the expression and release of MYF6, IGF-I, IGF-II, and CXCL1, as well as a decrease in GM-CSF, IL-9, and IL-12, was observed in 46XX cells. Conversely, testosterone up-regulated GM-CSF and CXCL1 in 46XY cells but did not affect the release of the other myokines. Preferential activation of the MAPK pathway was observed in 46XX cells, while the PI3K/AKT pathway was preferentially activated in 46XY cells. In conclusion, our findings demonstrate differential responses to androgen exposure in 46XX and 46XY cells, resulting in the activation of muscle cell growth and energy metabolic pathways in a sex-specific manner. Full article
(This article belongs to the Special Issue New Insights into Skeletal Muscle Metabolism in Pathological and Physiological Conditions)
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16 pages, 10651 KB  
Article
Impact of Amelogenesis Imperfecta on Junctional Epithelium Structure and Function
by Kevin Lin, Jake Ngu, Susu Uyen Le and Yan Zhang
Biology 2025, 14(7), 853; https://doi.org/10.3390/biology14070853 - 14 Jul 2025
Viewed by 2696
Abstract
The junctional epithelium, which lines the inner gingival surface, seals the gingival sulcus to block the infiltration of food debris and pathogens. The junctional epithelium is derived from the reduced enamel epithelium, consisting of late developmental stage ameloblasts and accessory cells. No prior [...] Read more.
The junctional epithelium, which lines the inner gingival surface, seals the gingival sulcus to block the infiltration of food debris and pathogens. The junctional epithelium is derived from the reduced enamel epithelium, consisting of late developmental stage ameloblasts and accessory cells. No prior studies have investigated whether defective ameloblast differentiation or enamel matrix formation affects junctional epithelium anatomy or function. Here, we examined the junctional epithelium in mice exhibiting amelogenesis imperfecta due to loss-of-function mutations in the major enamel matrix protein amelogenin (Amelx−/−) or the critical enamel matrix protease KLK4 (Klk4−/−). Histological analyses demonstrated altered morphology and cell layer thickness of the junctional epithelium in Amelx−/− and Klk4−/− mice as compared to wt. Immunohistochemistry revealed reduced ODAM, laminin 5, and integrin α6, all of which are critical for the adhesion of the junctional epithelium to the enamel in Amelx−/− and Klk4−/− mice. Furthermore, we observed altered cell–cell adhesion and increased permeability of Dextran-GFP through the mutants’ junctional epithelium, indicating defective barrier function. Reduced β-catenin and Ki67 at the base of the junctional epithelium in mutants suggest impaired mitotic activity and reduced capacity to replenish continuously desquamated epithelium. These findings highlight the essential role of normal amelogenesis in maintaining junctional epithelium homeostasis. Full article
(This article belongs to the Special Issue Understanding the Molecular Basis of Genetic Dental Diseases)
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55 pages, 2394 KB  
Review
Salivaomic Biomarkers—An Innovative Approach to the Diagnosis, Treatment, and Prognosis of Oral Cancer
by Katarzyna Starska-Kowarska
Biology 2025, 14(7), 852; https://doi.org/10.3390/biology14070852 - 13 Jul 2025
Cited by 2 | Viewed by 5053
Abstract
(1) Background: Oral cancer (OC) is one of the most frequently diagnosed human cancers and remains a challenge for biologists and clinicians. More than 90% of OC cases are squamous cell carcinomas (OSCCs). Despite the use of modern diagnostic and prognostic methods, the [...] Read more.
(1) Background: Oral cancer (OC) is one of the most frequently diagnosed human cancers and remains a challenge for biologists and clinicians. More than 90% of OC cases are squamous cell carcinomas (OSCCs). Despite the use of modern diagnostic and prognostic methods, the 5-year survival rate remains unsatisfactory due to the late diagnosis of the neoplastic process and its resistance to treatment. This comprehensive review aims to present the latest literature data on the use and effectiveness of saliva as a non-invasive biomarker in patients with oral cancer. (2) Methods: The article reviews the current literature on the use of salivary omics biomarkers as an effective method in diagnosing and modifying treatment in patients with OSCC; the research corpus was acquired from the PubMed/Google/Scopus/Cochrane Library/Web of Science databases in accordance with the Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA 2020) guidelines. (3) Results: The identification of salivary omics biomarkers involved in carcinogenesis and neoplastic transformation may be a potential alternative to traditional invasive diagnostic methods. Saliva, being both an abundant reservoir of organic and inorganic components derived from epithelial cells as well as a cell-free environment, is becoming an interesting diagnostic material for studies in the field of proteomics, genomics, metagenomics, and metabolomics. (4) Conclusions: Saliva-based analysis is a modern and promising method for the early diagnosis and improvement of treatment outcomes in patients with OSCC and oral potentially malignant disorders (OPMDs), with high diagnostic, therapeutic, and prognostic potential. Full article
(This article belongs to the Special Issue New Insights in Cancer Genetics—2nd Edition)
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40 pages, 1029 KB  
Review
Biotechnological Potential of Extremophiles: Environmental Solutions, Challenges, and Advancements
by Fabrizia Sepe, Ezia Costanzo, Elena Ionata and Loredana Marcolongo
Biology 2025, 14(7), 847; https://doi.org/10.3390/biology14070847 - 11 Jul 2025
Cited by 13 | Viewed by 7068
Abstract
Extremophiles are microorganisms capable of living on Earth in ecological niches characterized by peculiar conditions, including extreme temperatures and/or pH, high salt concentrations, and the presence of heavy metals. The development of unique structural and functional adaptation strategies has stimulated an increasing scientific [...] Read more.
Extremophiles are microorganisms capable of living on Earth in ecological niches characterized by peculiar conditions, including extreme temperatures and/or pH, high salt concentrations, and the presence of heavy metals. The development of unique structural and functional adaptation strategies has stimulated an increasing scientific interest since their discovery. The importance of extremophiles lies in their exploitability in significant bioprocesses with several biotechnological applications and their role as a fundamental source of numerous high-value-added biomolecules. This review aims to examine the diversity and specificities of extremophilic archaea and bacteria, with particular emphasis on their potential applications and development in biotechnology and biomedicine. The use of extremophiles and their extremozymes has allowed applications in several fields, such as bioremediation, sustainable agriculture, the recovery of bioactive molecules for use in bioenergy, biomedicine, and nanoparticle production. The comprehension and exploitation of the complex molecular mechanisms that enable life in extreme environments represent a challenge to mitigate current climate change problems and to invest in sustainable development towards a green transition. Full article
(This article belongs to the Special Issue Adaptation of Living Species to Environmental Stress)
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26 pages, 1985 KB  
Review
Stomatal and Non-Stomatal Leaf Traits for Enhanced Water Use Efficiency in Rice
by Yvonne Fernando, Mark Adams, Markus Kuhlmann and Vito Butardo Jr
Biology 2025, 14(7), 843; https://doi.org/10.3390/biology14070843 - 10 Jul 2025
Cited by 6 | Viewed by 4549
Abstract
Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and [...] Read more.
Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and non-stomatal leaf traits remain poorly understood. In this review, we present an analysis of stomatal and non-stomatal leaf traits influencing WUE in rice. The data suggests that optimising stomatal density and size will be insufficient to maximise WUE because non-stomatal traits such as mesophyll conductance, leaf anatomy, and biochemical composition significantly modulate the relationship between stomatal conductance and the photosynthetic rate. Integrating recent advances in high-throughput phenotyping, multi-omics technologies, and crop modelling, we suggest that combinations of seemingly contradictory traits can enhance WUE without compromising yield potential. We propose a multi-trait breeding framework that leverages both stomatal and non-stomatal adaptations to develop rice varieties with superior WUE and climate resilience. This integrated approach provides a roadmap for accelerating the development of water-efficient rice cultivars, with broad implications for improving WUE in other crops. Full article
(This article belongs to the Special Issue Multi-omics Approaches in Agricultural Crops to Unravel Responses to Environmental Stresses and Advance Sustainable Agriculture)
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