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Biology

Biology is an international, peer-reviewed, open access journal of biological sciences, published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) and Federation of European Laboratory Animal Science Associations (FELASA) are affiliated with Biology and their members receive discounts on the article processing charges.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, and other databases.
Journal Rank: JCR - Q1 (Biology) / CiteScore - Q1 (General Agricultural and Biological Sciences)
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 17.4 days after submission; acceptance to publication is undertaken in 2.5 days (median values for papers published in this journal in the first half of 2025).
Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.

Impact Factor: 3.5 (2024); 5-Year Impact Factor: 4.0 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2079-7737

Latest Articles

17 pages, 946 KB

Open AccessReview

An Emerging Role for OGDHL: From Mitochondrial Energy Metabolism to Neurodevelopmental Disorders

by Xian Liu, Guicheng Zhang, Decai Yu and Junhai Han

Biology 2025, 14(12), 1777; https://doi.org/10.3390/biology14121777 (registering DOI) - 12 Dec 2025

The oxoglutarate dehydrogenase-like (OGDHL) gene encodes a brain-enriched, rate-limiting enzyme in the tricarboxylic acid cycle, playing an essential role in mitochondrial energy metabolism. Mutations in OGDHL are linked to a broad spectrum of neurodevelopmental disorders, characterized by developmental delay, intellectual disability, epilepsy, corpus [...] Read more.

The oxoglutarate dehydrogenase-like (OGDHL) gene encodes a brain-enriched, rate-limiting enzyme in the tricarboxylic acid cycle, playing an essential role in mitochondrial energy metabolism. Mutations in OGDHL are linked to a broad spectrum of neurodevelopmental disorders, characterized by developmental delay, intellectual disability, epilepsy, corpus callosum dysgenesis, and sensory deficits. This mini-review systematically summarizes the discovery, structural features, and molecular functions of OGDHL, and provides a comprehensive catalog of all reported pathogenic mutations and their clinical phenotypes. By linking mitochondrial energy metabolism and neural pathogenesis, this work positions OGDHL as a potential key regulator in neural development and function. Ultimately, this review aims to advance further research on OGDHL in the nervous system, enhance the understanding of metabolic regulation in neurodevelopment, and lay the groundwork for elucidating the mechanisms underlying OGDHL-related neurological diseases. Full article

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15 pages, 6994 KB

Open AccessArticle

Repetitive DNA Dynamics, Phylogenetic Relationships and Divergence Times in Andean Ctenomys (Rodentia: Ctenomyidae)

by Rodrigo A. Vargas, Ronie E. Haro, Camilla Bruno Di-Nizo and Elkin Y. Suárez-Villota

Biology 2025, 14(12), 1776; https://doi.org/10.3390/biology14121776 - 12 Dec 2025

The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in two parapatric Andean species from Chile: Ctenomys maulinus brunneus (2n = 26; [...] Read more.

The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in two parapatric Andean species from Chile: Ctenomys maulinus brunneus (2n = 26; FNa = 48) and Ctenomys sp. (2n = 28; FNa = 50). Self-genomic in situ hybridization (Self-GISH), whole comparative genomic hybridization (W-CGH), and fluorescent in situ hybridization (FISH) using a telomeric probe were performed. Phylogenetic relationships and divergence times based on cytochrome b sequences helped infer the direction and timing of cytogenetic changes. Self-GISH revealed the absence of highly repetitive sequences in four chromosome pairs of C. m. brunneus and nine in Ctenomys sp. W-CGH showed no differential expansion of species-specific repeats, suggesting no recent major sequence turnover. FISH detected signals exclusively in telomeres. Phylogenetic analyses indicate that C. m. maulinus (2n = 26) diverged from the clade formed by C. m. brunneus and Ctenomys sp. during the Late Pleistocene, supporting, together with cytogenetic data, a loss of repetitive sequences associated with fission events from 2n = 26 to 28. These findings highlight the evolutionary significance of repetitive DNA and reinforce Ctenomys as a model for studying chromosomal evolution. Full article

(This article belongs to the Section Evolutionary Biology)

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21 pages, 20704 KB

Open AccessArticle

Structural Adaptations to Saline Stress: Histomorphological Changes in the Osmoregulatory and Metabolic Organs of Perca schrenkii Under Acute and Chronic Challenges

by Guanping Xing, Kaipeng Zhang, Shixin Gao, Yichao Hao, Zhulan Nie, Jie Wei, Tao Ai, Shijing Zhang, Jiasong Zhang and Zhaohua Huang

Biology 2025, 14(12), 1775; https://doi.org/10.3390/biology14121775 - 11 Dec 2025

The escalating scarcity of freshwater resources necessitates the utilization of alternative saline waters for sustainable aquaculture. Perca schrenkii, an endemic fish from the Ili River basin, demonstrates considerable potential for cultivation in chloride-type saline–alkaline waters: its 96 h acute salinity tolerance is [...] Read more.

The escalating scarcity of freshwater resources necessitates the utilization of alternative saline waters for sustainable aquaculture. Perca schrenkii, an endemic fish from the Ili River basin, demonstrates considerable potential for cultivation in chloride-type saline–alkaline waters: its 96 h acute salinity tolerance is higher than that of freshwater populations of its congeneric Perca fluviatilis. This study systematically investigated the histomorphological responses of its key osmoregulatory and metabolic organs—gill, kidney, intestine, and liver—under acute (12–14 ppt for 96 h) and chronic (3–7 ppt for 60 days) salinity stress. Acute exposure induced dose- and time-dependent structural damage, including lamellar fusion in gills, glomerular reduction in kidneys, mucosal atrophy in intestines, and hepatocellular swelling. In contrast, chronic acclimation revealed active remodeling, such as lamellar shortening, renal tubular dilation, intestinal muscularis thickening, and biphasic hepatocyte adjustments. A hierarchical framework of structural adaptation was proposed, delineating Safe (≤3 ppt), Acclimation (5 ppt), Tolerance (7 ppt), and Lethal (≥13 ppt) zones. These findings elucidate the structural basis of salinity tolerance in Perca schrenkii and provide practical morphological indicators for assessing fish health in saline aquaculture. Full article

(This article belongs to the Special Issue Adaptation of Living Species to Environmental Stress)

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28 pages, 10595 KB

Open AccessArticle

Genome-Wide Discovery and Characterization of the Auxin Response Factor (ARF) Gene Family in Avicennia marina That Regulates Phytohormone Levels and Responds to Salt and Auxin Treatments

by Quaid Hussain, Muhammad Azhar Hussain, Yingying Li, Qi Zhang, Chenjing Shang, Mostafa A. Abdel-Maksoud, Salman Alrokayan and Abdulaziz Alamri

Biology 2025, 14(12), 1774; https://doi.org/10.3390/biology14121774 - 11 Dec 2025

Auxin response factors (ARFs) are crucial components of auxin signaling, playing a vital role in plant growth, development, hormone regulation, and stress responses. Salinity influences plant growth and development; however, Avicennia marina exhibits remarkable salt tolerance. This study analyzed Avicennia marina ARF genes [...] Read more.

Auxin response factors (ARFs) are crucial components of auxin signaling, playing a vital role in plant growth, development, hormone regulation, and stress responses. Salinity influences plant growth and development; however, Avicennia marina exhibits remarkable salt tolerance. This study analyzed Avicennia marina ARF genes (AmARFs) and their roles in responding to salt and indole-3-acetic acid (IAA) stress. The results indicated that across 5–15 days, endogenous IAA and abscisic acid (ABA) levels in A. marina leaves showed significant, time-dependent changes under salt and IAA treatments, with IAA fluctuating around 2.0–3.3 µg g⁻¹ FW and ABA rising sharply under combined high-salt + IAA conditions (AS25), reaching up to ~25 µg g⁻¹ FW (p < 0.05). This is the first genome-wide identification of 41 ARF genes in Avicennia marina with expression responses to combined salt and auxin treatments. We identified 41 AmARF genes spread across 23 chromosomes. These genes are divided into four groups according to their phylogenetic relationships. Their coding regions encode amino acids from 361 to 1264, and the number of exons varies from 2 to an unspecified upper limit of 25. Examining these gene promoters revealed various hormone- and stress-response elements, with each gene containing distinct response elements. Sixteen miRNAs can inhibit various ARF genes, while protein–protein interactions and 3D structures offered valuable insights into AmARF proteins. GO enrichment analysis revealed that all 41 AmARFs are involved in the auxin-activated signaling pathway and are also involved in cell division. According to the expression experiments, 11 randomly selected genes showed predominantly upregulation in response to salt and IAA stressors compared with controls. These findings extend our understanding of the functional roles of AmARFs in stress responses. The systematic annotation of AmARF family genes offers candidate genes for future functional validation, which may help elucidate the precise roles of AmARFs in stress responses. Full article

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

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17 pages, 2382 KB

Open AccessArticle

The Synergistic Effect of Sodium Hypochlorite (NaClO) and Organosilicone Adjuvant Enhances the Inhibition and Oxidative Damage in Cladophora sp.

by Liangjie Zhao, Chenxi Tan, Yongtao Tang, Zhen Zhang, Liangxin Guo, Gaoyou Yao, Qihu Dai, Yongxu Cheng and Chen Qian

Biology 2025, 14(12), 1773; https://doi.org/10.3390/biology14121773 - 11 Dec 2025

Cladophora-dominated filamentous algal blooms constitute a growing threat to aquatic ecosystem stability and aquaculture operations. This study systematically evaluated the algicidal efficacy of sodium hypochlorite (NaClO), both individually and in combination with an organosilicone adjuvant, against Cladophora sp., with particular focus on [...] Read more.

Cladophora-dominated filamentous algal blooms constitute a growing threat to aquatic ecosystem stability and aquaculture operations. This study systematically evaluated the algicidal efficacy of sodium hypochlorite (NaClO), both individually and in combination with an organosilicone adjuvant, against Cladophora sp., with particular focus on induced oxidative damage mechanisms. Results demonstrated that NaClO exhibited a dose- and time-dependent inhibitory effect, achieving ≥90% inhibition at 1.20 mmol L⁻¹ within 48 h and >99% by 120 h, significantly surpassing the efficacy of lower concentrations (0.40 mmol L⁻¹) (p < 0.05). Physiological assessment revealed that 1.20 mmol L⁻¹ NaClO significantly suppressed total antioxidant capacity (T-AOC) after 96 h (p < 0.05). Notably, synergistic enhancement was observed with adjuvant co-application: at 0.40 mmol L⁻¹ NaClO, superoxide dismutase (SOD) activity reached its minimum with 0.33 ppm organosilicone adjuvant, showing significant reduction compared to higher adjuvant concentrations (p < 0.05). Furthermore, combinations of 0.80 and 1.20 mmol L⁻¹ with organosilicone adjuvant consistently maintained inhibition rates ≥ 94% across all sampling intervals, achieving control efficacy equivalent to 2.00 and 2.40 mmol L⁻¹ NaClO alone within 48 h. These findings demonstrate that NaClO supplemented with low-dose organosilicone adjuvant constitutes a promising and efficient strategy for mitigating Cladophora blooms. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Harmful Algae)

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27 pages, 2290 KB

Open AccessFeature PaperReview

Major Plant-Based Compounds for the Prevention and Treatment of Melanoma—A Mini Review

by Isabella Kirshteyn, Megha Srivastav, Karen Grace, Victoria Cescato and Ajay Bommareddy

Biology 2025, 14(12), 1772; https://doi.org/10.3390/biology14121772 - 11 Dec 2025

Melanoma, particularly the malignant type owing to its aggressive metastatic potential, is one of the most severe cancers. When detected early, the cure rate of melanoma is very promising and has a higher 5-year survival rate. However, it becomes very difficult to treat [...] Read more.

Melanoma, particularly the malignant type owing to its aggressive metastatic potential, is one of the most severe cancers. When detected early, the cure rate of melanoma is very promising and has a higher 5-year survival rate. However, it becomes very difficult to treat when it has spread to deeper layers of the skin and to other parts of the body. Despite the reduced mortality, the incidence of melanoma is on the rise due to exposure to various environmental factors, particularly UV radiation without protection. Naturally occurring dietary agents have been studied for their antitumor and chemopreventive potential against the development of various cancers including melanoma. The current review is aimed at compiling developments in the past ten years surrounding their preclinical and clinical relevance in the treatment and prevention of malignant melanoma. Various cellular pathways modulated by these phytochemicals are also examined to provide a comprehensive overview of their mechanisms involved in reducing tumor burden. Specifically, the review focuses on the most consumed foods across the world that are rich in such phytochemicals including curcumin, sulforaphane, resveratrol, quercetin and epigallocatechin gallate (EGCG) and their potential against the development of melanoma. Full article

(This article belongs to the Special Issue Plant Natural Products: Mechanisms of Action for Promoting Health)

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22 pages, 5865 KB

Open AccessArticle

Contrasting La Crosse Virus Lineage III Vector Competency in Two Geographical Populations of Aedes triseriatus and Aedes albopictus Mosquitoes

by Lindsey R. Faw, Philip M. Armstrong, Sally L. Paulson and Gillian Eastwood

Biology 2025, 14(12), 1771; https://doi.org/10.3390/biology14121771 - 11 Dec 2025

La Crosse virus (LACV) is a mosquito-borne virus (family Peribunyaviridae) that can result in severe human infection in children under sixteen. Historically, LACV comprised two lineages, predominantly in the Midwest and Appalachian regions of the US. In 2005, a virus of a [...] Read more.

La Crosse virus (LACV) is a mosquito-borne virus (family Peribunyaviridae) that can result in severe human infection in children under sixteen. Historically, LACV comprised two lineages, predominantly in the Midwest and Appalachian regions of the US. In 2005, a virus of a third lineage was detected in the Northeast; however, this and subsequently isolated strains of lineage III have not, to date, been implicated in human disease. One hypothesis for this discrepancy is that vector mosquitoes have a reduced vector competency for LACV lineage III, thus preventing horizontal transmission and clinical cases. Here, we utilized two mosquito species, Aedes triseriatus, the native vector, and Aedes albopictus, an invasive potential vector, each from both a historic LACV range (Virginia) and from the region of lineage III (Connecticut). Utilizing oral feeding and intrathoracic inoculation methods of viral exposure, rates of LACV infection, dissemination, and transmission (proxied via salivary secretion) and capability for vertical transmission (proxied via virus-positive ovaries) were determined by harvesting mosquito bodies, legs, saliva, and ovaries, respectively. Overall, we did not detect consistent differences in transmission between any lineage, species, or state of origin, at day 14 post-infection. However, we highlight the transmission potential of LACV lineage III in all mosquito populations tested here, representing the first evidence of lineage III competency in Aedes triseriatus and Aedes albopictus, indicating the potential for human disease. We thus suggest that the absence of human cases of LACV lineage III is not modulated by a lack of vector competency in mosquitoes. Full article

(This article belongs to the Special Issue Arthropods as Vectors of Human and Animal Pathogens: Vector Ecology and Disease Transmission)

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Graphical abstract

12 pages, 853 KB

Open AccessCommunication

Targeted NanoBiT Screening Identifies a Novel Interaction Between SNAPIN and Influenza A Virus M1 Protein

by Xiaoxuan Zhang, Huanhuan Wang, Conghui Zhao, Wenjun Shi, Faxin Wen, Haoxi Qiang, Sha Liu, Peilin Li, Xinhui Chen, Chunping Zhang, Jiacheng Huang, Yang Wang, Ziyi Zhang and Shujie Ma

Biology 2025, 14(12), 1770; https://doi.org/10.3390/biology14121770 - 11 Dec 2025

Influenza A virus (IAV) poses a significant threat due to its rapid evolution through gene mutations and reassortments. Understanding host–virus protein interactions is vital for developing countermeasures. In this study, we developed a live-cell screening platform using the NanoBiT system for rapid discovery [...] Read more.

Influenza A virus (IAV) poses a significant threat due to its rapid evolution through gene mutations and reassortments. Understanding host–virus protein interactions is vital for developing countermeasures. In this study, we developed a live-cell screening platform using the NanoBiT system for rapid discovery of host–virus protein–protein interactions (PPIs). Novel interactions between the host factor SNAPIN and the viral M1, M2 and NS2 were identified using this system. We confirmed the platform’s reliability by validating the SNAPIN-M1 interaction using independent methods including co-immunoprecipitation (Co-IP) and glutathione S-transferase (GST) pull-down assays. These results demonstrate the robustness of the PPI screening system and provide a basis for studying the role of SNAPIN in regulating IAV replication. Full article

(This article belongs to the Special Issue Zoonotic Diseases)

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18 pages, 15862 KB

Open AccessArticle

The WRKY Transcription Factor GmWRKY40 Enhances Soybean Resistance to Phytophthora sojae via the Jasmonic Acid Pathway

by Hong Gao, Chuanzhong Zhang, Gengpu Zhang, Fengcai Guo, Yan Sun, Xin Fang, Xiaoyu Chen, Kexin Ma, Xiran Wang, Kexin Li, Jiapeng Tong, Junjiang Wu, Pengfei Xu and Shuzhen Zhang

Biology 2025, 14(12), 1769; https://doi.org/10.3390/biology14121769 - 11 Dec 2025

Phytophthora root and stem rot is a destructive soybean disease worldwide, and thus improving soybean resistance to P. sojae is a major breeding target. However, the complex regulatory networks governing host defense remain unclear. Our previous study showed that GmWRKY40 positively regulates resistance [...] Read more.

Phytophthora root and stem rot is a destructive soybean disease worldwide, and thus improving soybean resistance to P. sojae is a major breeding target. However, the complex regulatory networks governing host defense remain unclear. Our previous study showed that GmWRKY40 positively regulates resistance of soybean to P. sojae. Here, to explore its molecular mechanism, we found that GmWRKY40 is induced by P. sojae in resistant cultivars and that the protein localizes in nucleus. RNA-seq and metabolomic analyses revealed that GmWRKY40 modulates the jasmonate (JA) signaling pathway. We then found that GmWRKY40 directly suppresses the key JA repressor GmJAZ1 by binding to the promoter. This leads to higher endogenous JA levels, and the overall state of enhanced resistance is also characterized by elevated SOD and POD antioxidant enzyme activity. Furthermore, we demonstrated that GmWRKY40 interacts with GmWRKY36, a transcription factor identified as a negative regulator of P. sojae infection in this research. Taken together, our study delineates a novel regulatory module where GmWRKY40 enhances resistance to P. sojae through a dual mechanism: activating the JA pathway by repressing its suppressor GmJAZ1, and engaging in a potentially antagonistic interaction with the negative regulator GmWRKY36, ultimately enhancing soybean resistance to P. sojae. Full article

(This article belongs to the Special Issue Advances in Research on Diseases of Plants (2nd Edition))

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19 pages, 1578 KB

Open AccessArticle

Spatial Exposure Responses of Malaria Vectors to Eucalyptus grandis (W. Hill ex Maiden) and Cymbopogon citratus (DC.) Stapf Essential Oils

by Martha A. Kaddumukasa, Norah M. Mutekanga, Faisal Kula, Charles Batume and Agapitus B. Kato

Biology 2025, 14(12), 1768; https://doi.org/10.3390/biology14121768 - 11 Dec 2025

Background: Recently, the use of volatile compounds as spatial repellents have received special attention as a promising strategy for adult An. gambiae s.l control. Anopheles gambiae s.l is a primary vector of malaria, an arthropod-borne disease of global significance. Current strategies for controlling [...] Read more.

Background: Recently, the use of volatile compounds as spatial repellents have received special attention as a promising strategy for adult An. gambiae s.l control. Anopheles gambiae s.l is a primary vector of malaria, an arthropod-borne disease of global significance. Current strategies for controlling mosquitoes heavily rely on vector control methods. Understanding the responses of these vectors to volatile compounds will be helpful in the formulation of repellants or attractants for control vector populations. This study was conducted in Nwoya district, Uganda, one of the high-malaria-transmission areas in the northern part of Uganda, as one of the ways of reducing contact between the parasite, vector, and malaria outbreak. Materials and Methods: In this study, a laboratory-reared female An. gambiae Kisumu strain from Uganda Virus Research Institute (UVRI) insectaries were used to examine spatial behavior responses of An. gambiae to selected EOs of Eucalyptus grandis and Cymbopogon citratus. Spatial activity responses were measured using a Y-tube olfactometer under controlled conditions using three replicates in various concentrations of the tested EOs. These oils were extracted by steam distillation and the main constituents identified using gas chromatography–mass spectrometry. Results: Mosquito response curves indicating effective repellency concentrations are reported, as well as the gas chromatography–mass spectrophotometry analysis results. For Eucalyptus grandis, the two components with the highest composition were L-α terpineol and Eucalyptol, while those for Cymbopogon citratus were Lavandulol, methyl ether, and citral. Other components had a percentage composition less than five but they might play a big role in repellent activity against mosquito species. Conclusions: The mosquito repellency results in this study indicate that Eucalyptus grandis and Cymbopogon citratus EOs could be used as mosquito repellents, providing more evidence that natural products have promising lead compounds for further development of botanical spatial repellents. Further characterization of EOs and testing on mosquito behavior related to the prevention of malaria and other vector-borne diseases will promote innovation in vector control and provide new vector control tools that are needed in this era of insecticide resistance. Full article

(This article belongs to the Special Issue Arthropods as Vectors of Human and Animal Pathogens: Vector Ecology and Disease Transmission)

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27 pages, 9956 KB

Open AccessArticle

Watching the South China Sea—Portiodora (Iridaceae), a New Genus for Iris speculatrix Based on Comprehensive Evidence: The Contribution of Taxonomic Resolution to Biodiversity Conservation

by Manuel B. Crespo, Mario Martínez-Azorín and Evgeny V. Mavrodiev

Biology 2025, 14(12), 1767; https://doi.org/10.3390/biology14121767 - 11 Dec 2025

Iris speculatrix was described from plants collected in Hong Kong and is accepted to extend through southeastern China. The species is scheduled under the Forestry Regulations and is regarded as endangered (EN) according to the IUCN categories. This enigmatic plant exhibits multiple morphological [...] Read more.

Iris speculatrix was described from plants collected in Hong Kong and is accepted to extend through southeastern China. The species is scheduled under the Forestry Regulations and is regarded as endangered (EN) according to the IUCN categories. This enigmatic plant exhibits multiple morphological connections to other congeners, and was classified in contrasting groups such as the “Chinenses” or the “Ensatae” irises. Molecular work placed it as an isolated lineage sister to the beardless/uncrested subgroup of the so-called “Xiphion s.l. clade”. In this contribution, we integrate molecular analyses, including the plastid sequence data of I. speculatrix, together with a re-evaluation of morphological, ecological, karyological, chorological and phylogenetic data on the Hong Kong plant, to describe the new genus Portiodora. Three-taxon statement analysis was employed as a primary analytical tool, helping to clarify phylogenetic relationships and support the recognition of Portiodora. Two new combinations are established, and an identification key is presented for the “Iris-flower clade”. Relationships to other Chinese taxa often related to P. speculatrix, such as I. grijsii, I. cavaleriei and I. fujianensis are discussed, and their inclusion in Portiodora is not favoured based on the available data. Furthermore, the contribution of taxonomic resolution to biodiversity conservation is discussed. Full article

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28 pages, 13047 KB

Open AccessArticle

Two New Species of the Taxonomically Ambiguous Mongolodiaptomus birulai Group from Southwestern China and Southeast Asia (Crustacea, Copepoda, Calanoida, Diaptomidae)

by Rachada Chaicharoen and Laorsri Sanoamuang

Biology 2025, 14(12), 1766; https://doi.org/10.3390/biology14121766 - 10 Dec 2025

Currently, the synonymy of the two morphologically analogous copepod species, Mongolodiaptomus birulai (Rylov, 1922) and M. formosanus Kiefer, 1937, remains doubtful. While examining the detailed morphology of diaptomid copepods from China, Cambodia, and Vietnam, we came across two undescribed species whose morphology is [...] Read more.

Currently, the synonymy of the two morphologically analogous copepod species, Mongolodiaptomus birulai (Rylov, 1922) and M. formosanus Kiefer, 1937, remains doubtful. While examining the detailed morphology of diaptomid copepods from China, Cambodia, and Vietnam, we came across two undescribed species whose morphology is closely similar to that of M. birulai from Northeast China and M. formosanus from Taiwan. In this paper, descriptions of M. parabirulai sp. nov. from Yunnan, Southwestern China, and M. longiserratus sp. nov. from Cambodia and Vietnam are presented. The first new species, M. parabirulai sp. nov., can be distinguished from its congeners in the male P5 by it having the distal outer portion of the second right exopod produce a wing-shaped expansion and its strongly robust left and right basis. The second new species, M. longiserratus sp. nov., can be differentiated by the following characteristics in the male: the spiniform process on segment 20 of the right antennule is longer than that of segment 21 and has a serrate outer margin, and the right P5 basis has two (longitudinal and semicircular) hyaline lamellae. Furthermore, the status of M. birulai and M. formosanus is reviewed and recommended. Full article

(This article belongs to the Special Issue Biodiversity, Conservation, and Application of Crustaceans)

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19 pages, 3633 KB

Open AccessArticle

Single-Cell Mapping of Genetic Risk Across Ten Respiratory Diseases

by Miao Zhou and Chao Xue

Biology 2025, 14(12), 1765; https://doi.org/10.3390/biology14121765 - 10 Dec 2025

Understanding how genetic risk variants contribute to respiratory diseases requires mapping genome-wide association study (GWAS) signals to disease-relevant cell types and states within the human lung. Here, we integrated GWAS summary statistics for ten major respiratory diseases, including asthma, COPD, idiopathic pulmonary fibrosis [...] Read more.

Understanding how genetic risk variants contribute to respiratory diseases requires mapping genome-wide association study (GWAS) signals to disease-relevant cell types and states within the human lung. Here, we integrated GWAS summary statistics for ten major respiratory diseases, including asthma, COPD, idiopathic pulmonary fibrosis (IPF), COVID-19, and lung cancer, using a large-scale single-cell transcriptomic dataset of more than 523,000 cells from the Human Lung Cell Atlas. Applying the single-cell Disease Relevance Score (scDRS) framework, we systematically identified shared and disease-specific cellular associations across four major compartments, namely epithelial, immune, endothelial, and stromal. We found that alveolar type II (AT2) cells represent a central susceptibility hub for asthma, COPD, and COVID-19, whereas disease-specific risk enrichment was observed in subpopulations such as CCL3⁺ alveolar macrophages in COVID-19 and adventitial fibroblasts in asthma. Importantly, subclustering revealed substantial heterogeneity within cell types, with distinct transcriptional programs underlying differential disease associations. For example, AT2 subclusters exhibited divergent susceptibility patterns to asthma versus COVID-19, reflecting immune-interacting versus antiviral states. Our results provide a systematic single-cell framework for linking genetic risk to the cellular architecture of the human lung and uncover both shared and disease-specific mechanisms underlying respiratory disease susceptibility. Full article

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21 pages, 4695 KB

Open AccessArticle

A Graph-Based Deep Learning Framework with Gating and Omics-Linked Attention for Multi-Omics Integration and Biomarker Discovery

by Zhanpeng Huang, Yutao Deng, Jinyuan Liu and Zhaohan Cai

Biology 2025, 14(12), 1764; https://doi.org/10.3390/biology14121764 - 10 Dec 2025

Integration of multi-omics data provides a comprehensive perspective on complex biological systems, facilitating advances in disease classification and biomarker discovery. However, the heterogeneity and high dimensionality of omics data present significant analytical challenges. To achieve effective and interpretable multi-omics integration, we propose a [...] Read more.

Integration of multi-omics data provides a comprehensive perspective on complex biological systems, facilitating advances in disease classification and biomarker discovery. However, the heterogeneity and high dimensionality of omics data present significant analytical challenges. To achieve effective and interpretable multi-omics integration, we propose a novel deep learning framework named MOGOLA(Multi-Omics integration by Gating and Omics-Linked Attention). MOGOLA consists of three core components: (1) A hybrid graph learning module that integrates Graph Convolutional Networks and Graph Attention Networks for intra-omics feature extraction. (2) A gating and confidence mechanism that adaptively weighs feature importance across different omics types. (3) A cross-omics attention-based fusion module that captures inter-omics relationships. Comprehensive evaluations on four benchmark datasets (BRCA, KIPAN, ROSMAP, and LGG) demonstrate that MOGOLA consistently outperforms eleven state-of-the-art approaches. Ablation studies further validate the contribution of each module, while biomarkers identification highlight the framework’s clinical potential. These results show that MOGOLA is a robust and interpretable approach for multi-omics data integration and a contribution to advances in computational biology and precision medicine. Full article

(This article belongs to the Special Issue Advancing Translational Science Using Bioinformatics and Big Data-Driven Approaches)

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15 pages, 927 KB

Open AccessArticle

UV-B Resistance in Artemia: A Comparative Analysis Across Altitudinal Gradients, Development Stages, and Reproductive Modes

by Jiawei Xu, Cheng Ma, Bingheng Chen, Yunhao Guo, Malik Qammar, Yingguo Gan, Xiaoqi Yu and Zhichao Wang

Biology 2025, 14(12), 1763; https://doi.org/10.3390/biology14121763 - 10 Dec 2025

The Artemia exhibit broad environmental adaptability and distinct reproductive modes, making them ideal for studying stress tolerance. Solar UV-B radiation poses a threat to aquatic organisms; however, for Artemia—a key aquatic organism characterized by a wide altitudinal distribution range and unique reproductive [...] Read more.

The Artemia exhibit broad environmental adaptability and distinct reproductive modes, making them ideal for studying stress tolerance. Solar UV-B radiation poses a threat to aquatic organisms; however, for Artemia—a key aquatic organism characterized by a wide altitudinal distribution range and unique reproductive modes—it remains unclear how their UV-B resistance varies with altitudinal gradients, developmental stages, and reproductive modes. Here, we evaluated six Artemia species/lineages (three bisexual species, three parthenogenetic lineages) from 113 to 4700 m altitude across three developmental stages (embryo, nauplius, adult) under gradient UV-B doses. Key results: (1) UV-B resistance showed a dose-dependent positive correlation with altitude, especially under high-dose UV-B (6.4 kJ·m⁻², R² = 0.72, p < 0.01); (2) Adults had the highest resistance, while nauplii were the most vulnerable; (3) Bisexual species had 41–57% higher adult survival rates than parthenogenetic lineages at similar altitudes, but parthenogenetic lineages showed higher embryo relative hatching rates. These findings clarify the adaptive traits of Artemia in response to UV-B stress. Full article

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

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Open AccessArticle

Comparative Transcriptomics as a Key to Understanding the Adaptation Mechanisms of Baikal Sculpins to the Deep-Water Habitat

by Yulia P. Sapozhnikova, Anastasiya G. Koroleva, Tuyana V. Sidorova, Evgenia A. Vakhteeva, Alexander A. Epifantsev, Sergey A. Potapov, Vera M. Yakhnenko, Lyubov V. Sukhanova, Sergei V. Kirilchik, Tatyana V. Butina, Ivan A. Nebesnykh and Igor V. Khanaev

Biology 2025, 14(12), 1762; https://doi.org/10.3390/biology14121762 - 9 Dec 2025

Understanding the molecular mechanisms that enable vertebrate adaptation to deep-water environments remains a central goal in evolutionary biology. This study used comparative transcriptomics of skeletal muscle tissue to investigate these mechanisms in four endemic sculpin fish species (Cottoidei) from Lake Baikal, which inhabit [...] Read more.

Understanding the molecular mechanisms that enable vertebrate adaptation to deep-water environments remains a central goal in evolutionary biology. This study used comparative transcriptomics of skeletal muscle tissue to investigate these mechanisms in four endemic sculpin fish species (Cottoidei) from Lake Baikal, which inhabit different depth niches ranging from pelagic to benthic-abyssal zones up to 1642 m. Pelagic species showed increased activity in genes involved in sarcomere structure, calcium handling, and motor proteins, indicating adaptations for sustained locomotion. In contrast, deep-benthic specialists showed enrichment in pathways for glycolytic metabolism, proteasome function, and ubiquitination, reflecting adaptations for energy efficiency and protein homeostasis in a high-pressure environment. We conclude that the colonization of the Baikal abyssal zone by sculpins relies on a suite of shared molecular mechanisms, with distinct ecological pressures driving specific transcriptional changes in motility, metabolic strategy, and cellular integrity. This study provides a systems-level model for deep-water adaptation in vertebrates. Full article

(This article belongs to the Special Issue Living Resources of the Deep Sea: Biological Profiles and Environmental Linkages)

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20 pages, 2265 KB

Open AccessArticle

Effects of Bamboo Expansion on Soil Enzyme Activity and Its Stoichiometric Ratios in Karst Broad-Leaved Forests

by Long Tong, Qingping Zeng, Lijie Chen, Xiaoying Zeng, Ling Shen, Fengling Gan, Minglan Liang, Lixia Chen, Xiaoyan Zhang and Lianghua Qi

Biology 2025, 14(12), 1761; https://doi.org/10.3390/biology14121761 - 9 Dec 2025

The expansion ratio of bamboo forests has significantly influenced soil nutrient cycling in broad-leaved forests through alterations in vegetation composition. However, the extent to which varying expansion ratios of bamboo within broad-leaved forest areas (MRB) affect soil enzyme activities and stoichiometric ratio in [...] Read more.

The expansion ratio of bamboo forests has significantly influenced soil nutrient cycling in broad-leaved forests through alterations in vegetation composition. However, the extent to which varying expansion ratios of bamboo within broad-leaved forest areas (MRB) affect soil enzyme activities and stoichiometric ratio in karst regions with yellow limestone soil remains poorly understood. Therefore, we examined five MRB levels (<20%, 20–40%, 40–60%, 60–80%, and >80%) and three soil depths (0–20 cm, 20–40 cm, and 40–60 cm) to analyze variations in soil microbial resource limitation within a field experiment conducted in a karst region. The results revealed showed that root morphology was significantly less developed at both low (<20%) and high (≥80%) expansion ratios than at moderate expansion ratios (40–60%) and exhibited a decreasing trend with increasing soil depth. The soil TC (46.43 g·kg⁻¹), SOC (80.05 g·kg⁻¹) and N:P (0.96) reached their highest values in the 40–60% MRB, whereas the pH (4.61), BD (0.42 g·cm⁻³), AN (20.28 g·kg⁻¹) and C:N (45.51) were lowest at 0–20 cm. Moreover, the CBH and the E_C:N ratio at 40–60 cm depth in the 0–20% MRB were significantly 2.64 and 1.31 times greater than those at 0–20 cm depth in the 40–60% MRB. Mantel and structural equation modeling (SEM) analyses revealed that soil enzyme activity and stoichiometric ratios are indirectly influenced by soil bulk density (β = −0.156) and root characteristics (β = −0.630). Overall, both C and P limitations are present at the lowest MRB (<20%), whereas other MRB ranges exhibit only P limitation without C limitation. Our results highlight that soil nutrient availability in karst regions of Southwest China is influenced by vegetation structure. These findings provide a scientific foundation for achieving the green and sustainable management of bamboo forests within broad-leaved forest ecosystems. Full article

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17 pages, 2732 KB

Open AccessArticle

A Novel Mitochondrial Genome Resource for the Endemic Fish Gymnodiptychus integrigymnatus and Insights into the Phylogenetic Relationships of Schizothoracinae

by Yanping Li, Yawen Luo, Yunyun Lv, Yangjia Ou, Ruilin Zhang and Renyi Zhang

Biology 2025, 14(12), 1760; https://doi.org/10.3390/biology14121760 - 9 Dec 2025

Gymnodiptychus integrigymnatus is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of G. integrigymnatus. The complete mitochondrial genome of one individual of G. integrigymnatus was sequenced using the Illumina HiSeq [...] Read more.

Gymnodiptychus integrigymnatus is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of G. integrigymnatus. The complete mitochondrial genome of one individual of G. integrigymnatus was sequenced using the Illumina HiSeq X Ten sequencing platform and comprehensively characterized. The mitochondrial genome was 16,714 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a typical control region. The genome composition showed a positive A + T skew (0.029) and a negative G + C skew (−0.198). All tRNAs were predicted to form typical cloverleaf secondary structures, except for tRNA-Ser (GCT), which lacked the DHU stem. Phylogenetic reconstruction based on 13 PCGs revealed that the subfamily Schizothoracinae was not a monophyletic group. Two major clades were identified within this subfamily: one comprising primitive taxa (Percocypris, Aspiorhynchus, and Schizothorax) and the other consisting of specialized and highly specialized groups. Gymnodiptychus integrigymnatus was distinct from both its congeners and the specialized clade and was instead recovered within a highly specialized group of the Schizothoracinae subfamily. This study offers novel perspectives on the taxonomy and phylogenetic relationships within the Schizothoracinae subfamily, with a specific focus on G. integrigymnatus, thereby enhancing the understanding of the systematics and phylogeny of the Schizothoracinae subfamily. Full article

(This article belongs to the Section Evolutionary Biology)

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20 pages, 19118 KB

Open AccessArticle

Metabolomics and Transcriptomics Analyses Uncover the Potential of Flavonoids in Response to Saline–Alkali Stress in Codonopsis pilosula

by Jinhua Liu, Yongqing Wan, Xiaowei Sun, Wenting Su and Kaixia Li

Biology 2025, 14(12), 1759; https://doi.org/10.3390/biology14121759 - 9 Dec 2025

Codonopsis pilosula (Cp) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline–alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline–alkali stress response mechanism of Cp’s flavonoids is unknown. This study [...] Read more.

Codonopsis pilosula (Cp) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline–alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline–alkali stress response mechanism of Cp’s flavonoids is unknown. This study carried out saline–alkali stress treatments in Cp, collected samples from roots, stems, and leaves, and conducted physiological, biochemical, transcriptomic, and metabolomic tests. Phenotypic observations showed varying degrees of saline–alkali stress effects on different organs of Cp. Physiological tests revealed inconsistent antioxidant indicator changes across organs. Metabolomic and transcriptomic analyses revealed that, compared to roots and stems, leaves contained the highest number of differentially accumulated metabolites (DAMs) related to flavonoids, reaching up to 23, and harbored the most differentially expressed flavonoid-related genes, with up to 54; the roots treated with NaHCO₃ contained up to 14 types of flavonoids, while the leaves treated with NaHCO₃ contained up to 20 types of differentially expressed flavonoid-related genes; additionally, flavonoid pathway genes, including CHS, CHI, and bHLH transcription factors, might have responded to saline–alkali stress by modulating the production of flavonoid compounds such as Cyanidin and Galangin. This study preliminarily elucidated the molecular mechanisms of flavonoid response to saline–alkali stress in Cp, providing a theoretical basis for flavonoid exploitation, molecular breeding, and cultivation area expansion. Full article

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

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22 pages, 8311 KB

Open AccessArticle

Promoter Hypomethylation Unleashes HMGA1 to Orchestrate Immune Evasion and Therapy Resistance Across Cancers

by Iram Shahzadi, Taswar Ahsan, Shoaib Anwaar, Wajid Zaman and Houjun Xia

Biology 2025, 14(12), 1758; https://doi.org/10.3390/biology14121758 - 9 Dec 2025

High mobility group A1 (HMGA1) is a chromatin-associated protein that regulates transcription and drives cancer progression. In this pan-cancer study, we analyzed multi-omics data to comprehensively characterize HMGA1’s expression patterns, prognostic significance, epigenetic regulation, and immunotherapy roles. We found that HMGA1 was markedly [...] Read more.

High mobility group A1 (HMGA1) is a chromatin-associated protein that regulates transcription and drives cancer progression. In this pan-cancer study, we analyzed multi-omics data to comprehensively characterize HMGA1’s expression patterns, prognostic significance, epigenetic regulation, and immunotherapy roles. We found that HMGA1 was markedly upregulated in most cancers, mainly driven by promoter hypomethylation and copy number alterations. Elevated HMGA1 expression was consistently associated with unfavorable patient survival, stemness features, and the activation of oncogenic signaling pathways. Crucially, HMGA1 expression correlated with an immune-excluded tumor microenvironment, characterized by suppressed stromal and immune scores. Even in tumors with immune infiltration, high HMGA1 predicted poor prognosis, likely mediated by enhanced regulatory T-cell (Treg) recruitment and impaired effector immune function. Moreover, HMGA1 levels were positively correlated with tumor mutational burden (TMB), and microsatellite instability (MSI), and immunotherapy-related checkpoints including PD-1, CTLA-4, and TIGIT. Drug sensitivity analysis further revealed that HMGA1 predicted resistance to AKT inhibitors, which was experimentally validated in breast cancer cells treated with Capivasertib. Collectively, our findings establish HMGA1 as a pivotal oncogenic regulator and a promising biomarker for prognosis and for guiding strategies in immunotherapy and overcoming targeted therapy resistance. Full article

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