Biology

14 pages, 620 KB

Open AccessArticle

Mercury Levels in Hair of Domestic and Wild Animals

by Carolina Fregonesi de Souza, Robson Carlos Antunes, Vinícius José Santos Lopes, Adriana de Barros, Arlei Rodrigues Bonet de Quadros, Ricardo Lopes Tortorela de Andrade and Julio Cesar de Souza

Biology 2025, 14(11), 1497; https://doi.org/10.3390/biology14111497 (registering DOI) - 27 Oct 2025

Abstract

This study quantified mercury (Hg) levels in the body hair of domestic and wild animals in four Brazilian states, Paraná, Mato Grosso do Sul, Goiás, and Minas Gerais, by analyzing 169 samples from sows, piglets, free-range pigs, and wild animals. The highest mean [...] Read more.

This study quantified mercury (Hg) levels in the body hair of domestic and wild animals in four Brazilian states, Paraná, Mato Grosso do Sul, Goiás, and Minas Gerais, by analyzing 169 samples from sows, piglets, free-range pigs, and wild animals. The highest mean Hg concentration (274.93 ± 48.14 µg/kg) was found in wild animals in the Pantanal (MSSilvestre, Mato Grosso do Sul), followed by Minas Gerais (245.09 ± 40.27 µg/kg) and Paraná (193.0 ± 42.45 µg/kg). Levels at the GO, MGM, MSLiv, and PRV sites were significantly lower (p ≤ 0.05), according to the Scott–Knott test. Statistical analysis using ANOVA indicated significant variation in Hg levels between locations (F = 2.36; p ≤ 0.05), with homogeneity of variance (Levene’s test, p = 0.1772). Animals raised in confinement had lower levels than wild animals, which, due to extensive movement and contact with diverse environments, exhibited greater bioaccumulation. Lactating sows showed greater sensitivity than piglets, demonstrating an effect of animal category on metal absorption. The main sources of mercury are anthropogenic activities, such as mining and industrial processes, responsible for the environmental release of the metal. Although the detected levels do not pose an immediate risk to animal health or meat quality, they highlight the need for continuous monitoring, given mercury’s ability to bioaccumulate and affect ecosystems and food security. This work contributes to the understanding of environmental exposure to mercury in Brazil, reinforcing the urgency of effective mitigation strategies to preserve biodiversity and public health. Full article

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14 pages, 1290 KB

Open AccessArticle

Seasonal Variation in Nocturnal Roost Timing and Diurnal Movement in Endangered Crested Ibis (Nipponia nippon): An Adaptation Strategy to Environmental Changes

by Wei Li, Dongping Liu, Yuhe Liao, Ke He and Chao Wang

Biology 2025, 14(11), 1496; https://doi.org/10.3390/biology14111496 (registering DOI) - 26 Oct 2025

Abstract

The living environment of birds exhibits seasonal variations, and winter cold and food shortages are key limiting factors influencing the survival rate of many bird species. However, most previous studies have focused on dynamic habitat changes, with relatively few investigating how changes in [...] Read more.

The living environment of birds exhibits seasonal variations, and winter cold and food shortages are key limiting factors influencing the survival rate of many bird species. However, most previous studies have focused on dynamic habitat changes, with relatively few investigating how changes in birds’ behavioral rhythms and ecological adaptability respond to seasonal fluctuations in the environment. The Crested Ibis (Nipponia nippon) is an endangered species, with winter food shortage being a critical factor constraining its population growth. Through 211 days of monitoring on the communal roosting behavior and GPS tracking of 19 individuals, this study aimed to clarify seasonal variations in their time allocation and activity levels, and reveal how Crested Ibises respond to environmental changes. During the wintering period, Crested Ibises departed nocturnal roosts earlier relative to sunrise and returned later relative to sunset, thereby utilizing more dawn and dusk time for foraging and increasing daylight utilization. GPS tracking data showed that both daily movement distance and activity levels of Crested Ibises during the wintering period were significantly lower than in other seasons—a pattern likely representing an adaptive strategy to cope with limited food resources, as it serves to minimize energy expenditure and enhance survival rates. Thus, these findings indicate that Crested Ibises adapt to wintering environmental changes through three seasonal behaviors: extending the dawn and dusk activity window, increasing daylight utilization, and reducing daily movement distance and activity levels. Full article

(This article belongs to the Special Issue Evolution, Genetics, and Conservation of Wildlife Respond to Environmental Changes)

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14 pages, 1037 KB

Open AccessArticle

Adulticidal Activity of the Insect Growth Regulators Methoprene and Cyromazine in House Flies (Musca domestica L.): Evidence from Feeding Trials

by Gökhan Erdoğan

Biology 2025, 14(11), 1495; https://doi.org/10.3390/biology14111495 (registering DOI) - 26 Oct 2025

Abstract

House flies (Musca domestica L.) are major vectors of numerous pathogens affecting both humans and animals. The global distribution of house flies has been steadily increasing the expansion of human settlements, increased waste production, and the growth of livestock farms established to [...] Read more.

House flies (Musca domestica L.) are major vectors of numerous pathogens affecting both humans and animals. The global distribution of house flies has been steadily increasing the expansion of human settlements, increased waste production, and the growth of livestock farms established to meet the demand for animal-derived products. Frequent exposure to intensive pesticide applications in agricultural and livestock areas has accelerated the development of insecticide resistance, posing a serious challenge to sustainable control efforts. The widespread and repeated use of conventional chemical insecticides has contributed to rapid resistance evolution in many populations worldwide. In this study, the acute toxic effects of two insect growth regulators (IGRs)—cyromazine and methoprene—commonly used in the larval stages of house flies were evaluated against adult flies. Treatments were applied (3 replicates) orally via 40% sugar-water solutions containing 1%, 5%, and 10% concentrations, and bioassays were conducted on eight distinct house fly populations. The results showed that cyromazine caused average adult mortalities of 76.35%, 81.00%, and 84.50% within 48 h, while methoprene produced 70.62%, 99.37%, and 100% mortality at the same concentrations. At 10%, methoprene achieved 100% mortality across all populations, whereas cyromazine induced mortality ranging from 44.28% to 100%. These findings suggest that IGRs can be effective alternatives to conventional insecticides and can be integrated into IPM/IVM programs to reduce chemical use and delay 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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18 pages, 4750 KB

Open AccessArticle

Polyamine Homeostasis and Morphophysiological Responses to Salinity in Dizygostemon riparius: An Endemic Species from Brazilian ‘Cerrado’ Biome

by Jordanya Ferreira Pinheiro, Sérgio Heitor Sousa Felipe, Irislene Cutrim Albuquerque, Vitória Karla de Oliveira Silva-Moraes, Givago Lopes Alves, Marion Nayon Braga Soares, Juliane Maciel Henschel, Laíse Trugilio Moreira Marinho, Claudete Santa-Catarina, Diego Silva Batista, Fábio Afonso Mazzei Moura de Assis Figueiredo, Fabrício de Oliveira Reis, Tiago Massi Ferraz, Aldilene da Silva Lima and Thais Roseli Corrêa

Biology 2025, 14(11), 1494; https://doi.org/10.3390/biology14111494 (registering DOI) - 25 Oct 2025

Abstract

Dizygostemon riparius is an endemic tropical Brazilian species whose physiological responses to salinity are poorly understood. This study evaluated the effects of NaCl (0, 50, and 100 mM) on in vitro-grown D. riparius by integrating growth, anatomical, photosynthetic, and biochemical analyses. Salinity significantly [...] Read more.

Dizygostemon riparius is an endemic tropical Brazilian species whose physiological responses to salinity are poorly understood. This study evaluated the effects of NaCl (0, 50, and 100 mM) on in vitro-grown D. riparius by integrating growth, anatomical, photosynthetic, and biochemical analyses. Salinity significantly reduced biomass and growth parameters, indicating impaired development. Photosystem II efficiency declined, as evidenced by decreases in the performance index and chlorophyll content, while anatomical changes such as epidermal thickening and reduced vascular bundles reflected structural adjustments under stress. At the biochemical level, salinity altered polyamine metabolism, with reductions in total free polyamines, suggesting potential limitations in defense mechanisms. Hyperhydricity observed under high salinity indicated a non-adaptive response. Overall, D. riparius displayed limited tolerance to salt stress, with physiological and biochemical impairments outweighing structural plasticity. This study provides the first data-driven characterization of salinity effects in this species and highlights the value of in vitro culture as a tool to investigate stress responses. Full article

(This article belongs to the Special Issue Advances in Tropical Plant Ecology and Physiology)

17 pages, 2103 KB

Open AccessArticle

A Sampling Method Considering Body Size for Detecting the Associated Microbes in Plankton Populations: A Case Study, Using the Bloom-Forming Cyanobacteria, Microcystis

by Lizhou Lin, Nanqin Gan, Licheng Huang, Lirong Song and Liang Zhao

Biology 2025, 14(11), 1493; https://doi.org/10.3390/biology14111493 (registering DOI) - 25 Oct 2025

Abstract

Accurately quantifying associated microbes is essential to understand the interactions between microplankton and their associated microbes. Most DNA-based methods, such as high-throughput sequencing, primarily assess the ratio of target objects to references in microplankton samples. However, simple random sampling (SRS) of individuals may [...] Read more.

Accurately quantifying associated microbes is essential to understand the interactions between microplankton and their associated microbes. Most DNA-based methods, such as high-throughput sequencing, primarily assess the ratio of target objects to references in microplankton samples. However, simple random sampling (SRS) of individuals may lead to deviations in quantifying these ratios at the population level if these characteristics are associated with the reference content of individuals. This study considered group analysis, which involves detecting k groups with n individuals in each group, as an alternative approach and used simulated data based on the detection of Microcystis populations to evaluate the accuracy of different sampling plans. Our results indicate that increasing the number of individuals in each group could reduce sampling bias and improve the accuracy of comparisons between populations. Group analysis could also minimize the impact of the detection limit. This study demonstrated that, when detection methods only provide the ratio of target objects to references, group analysis is more appropriate than SRS for characterizing microplankton populations. Group analysis can be used not only for detecting associated microbes but also for identifying ingested organisms or the biochemical composition of microplankton. Our results also demonstrate how in situ individual-level studies support ecological investigations. Full article

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

14 pages, 9999 KB

Open AccessArticle

Identification of HK3 as a Potential Key Biomarker in the Progression of Temporomandibular Joint Osteoarthritis via RNA Sequencing

by Ping Luo, Xueliang Lv, Wanting Wan and Hu Qiao

Biology 2025, 14(11), 1492; https://doi.org/10.3390/biology14111492 (registering DOI) - 25 Oct 2025

Abstract

The pathogenesis of temporomandibular joint osteoarthritis (TMJOA) is poorly understood. This study aims to identify key biomarkers involved in TMJOA progression and explore potential therapeutic drugs through transcriptome analysis. A rat TMJOA model was established by bilateral injection of monosodium iodoacetate (MIA) into [...] Read more.

The pathogenesis of temporomandibular joint osteoarthritis (TMJOA) is poorly understood. This study aims to identify key biomarkers involved in TMJOA progression and explore potential therapeutic drugs through transcriptome analysis. A rat TMJOA model was established by bilateral injection of monosodium iodoacetate (MIA) into the TMJ cavities. Model validation was conducted using hematoxylin-eosin (HE) and Safranin O-Fast Green (SO-FG) staining. Differentially expressed genes (DEGs) were identified through RNA sequencing. Key pathways were explored using Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Reactome pathway analyses. DEGs were clustered using MCODE analysis, and Hexokinase 3 (HK3) was identified as a key gene, which was further validated by qPCR. Potential drugs targeting HK3 were selected using the DGIdb database, and molecular docking was conducted to confirm drug-HK3 binding affinity. The TMJOA model was successfully established. RNA-seq analysis revealed 160 upregulated and 97 downregulated DEGs. KEGG, GO, and Reactome pathways analysis identified dysregulated pathways. The top five clusters of DEGs were identified, with HK3 emerging as the key gene. qPCR validation confirmed upregulated HK3 mRNA expression in TMJOA cartilage compared to the control group. Three drugs (MK8719, LY3372689, and Thiamet-G) targeting HK3 were identified through the Drug-Gene Interaction Database (DGIdb) screening, and molecular docking demonstrated high binding affinity between these drugs and HK3. This study suggests that HK3 may play a role in TMJOA progression and could serve as a potential biomarker for inflammatory progression in TMJOA. Targeting HK3 may offer new diagnostic and therapeutic strategies for TMJOA management. Full article

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24 pages, 2368 KB

Open AccessReview

Targeting C3a and C5a Signaling—A Game Changer for Cancer Therapy?

by Hunter Hudgins, Valeria Molina, Stanley Wiernicki, Kenneth Okwuegbe, Xiaodong Feng and Hongbin Wang

Biology 2025, 14(11), 1491; https://doi.org/10.3390/biology14111491 (registering DOI) - 25 Oct 2025

Abstract

Emerging evidence reveals a significant shift in understanding the complement system’s role in cancer, where activation of a complement within the tumor microenvironment (TME) fuels tumor growth and metastasis instead of suppressing it. Research highlights C3a and C5a anaphylatoxins as key drivers of [...] Read more.

Emerging evidence reveals a significant shift in understanding the complement system’s role in cancer, where activation of a complement within the tumor microenvironment (TME) fuels tumor growth and metastasis instead of suppressing it. Research highlights C3a and C5a anaphylatoxins as key drivers of cancer progression, showing that the blockade of their signaling pathways can inhibit tumor growth and metastasis. By interacting with immune cells in the TME, including tumor-associated macrophages (TAMs), T cells, and myeloid-derived suppressor cells, C3a and C5a promote immunosuppression, thereby driving cancer cell proliferation, angiogenesis, and metastasis. However, conflicting findings persist, despite growing evidence supporting the role of C3a and C5a in tumor progression and the potential therapeutic benefits of targeting pathological complement activation. This paper presents a systematic review of studies examining the activation of the complement system and the role of the C3a and C5a signaling pathways in the TME, focusing on their effects on tumor progression, their interactions with TME components, and the potential for targeting these signaling pathways to boost anti-tumor immune responses. Full article

(This article belongs to the Special Issue Signalling Pathways in Cancer and Disease)

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38 pages, 4620 KB

Open AccessReview

Modeling Glioblastoma for Translation: Strengths and Pitfalls of Preclinical Studies

by Concetta D’Antonio and Giovanna L. Liguori

Biology 2025, 14(11), 1490; https://doi.org/10.3390/biology14111490 (registering DOI) - 24 Oct 2025

Abstract

Glioblastoma (GB) is an extremely aggressive tumor for which effective therapy is still in its infancy. Although several candidate therapeutics have been identified in functional preclinical assays, clinical trials have not supported their effectiveness in GB patients. The poor clinical efficacy of the [...] Read more.

Glioblastoma (GB) is an extremely aggressive tumor for which effective therapy is still in its infancy. Although several candidate therapeutics have been identified in functional preclinical assays, clinical trials have not supported their effectiveness in GB patients. The poor clinical efficacy of the treatments can be attributed to the insufficient mimicry of GB in patients by the preclinical models used. In this review article, we provide a comprehensive overview of the available GB preclinical models, which are classified according to their origin (animal or human), species, type and modeling strategy (two- or three-dimensional cell culture, in vivo grafting or in silico modeling). Moreover, the article compares developing cutting-edge technologies, including GB-derived organoids, bioprinting, microfluidic devices, and their multimodal integration in GB-on-chip systems, which aim to replicate the GB microenvironment with high precision. In silico and in vivo approaches are also reviewed, including zebrafish transplantation models. The costs, benefits, applications and clinical relevance of each model system and/or modeling strategy are discussed in detail and compared. We highlight that the most appropriate, or combination of, GB preclinical models must be selected (or even customized) based on the specific aims and constraints of each study. Finally, to improve the reliability and translational relevance of GB research, we propose a practical roadmap that addresses critical challenges in preclinical assay development, ranging from short-term adjustments to long-term strategic planning. Full article

(This article belongs to the Section Cancer Biology)

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20 pages, 17856 KB

Open AccessArticle

Bioaccumulation of Lanthanum by Two Strains of Marine Diatoms Nanofrustulum shiloi and Halamphora kolbei

by Daria Sergeevna Balycheva, Anastasiia Andreevna Blaginina, Vyacheslav Nikolaevich Lishaev, Sergey Victorovich Kapranov, Ekaterina Sergeevna Miroshnichenko, Svetlana Nikolaevna Zheleznova, Mikhail Vitalievich Simokon and Vitaliy Ivanovich Ryabushko

Biology 2025, 14(11), 1489; https://doi.org/10.3390/biology14111489 (registering DOI) - 24 Oct 2025

Abstract

Bioaccumulation by diatoms, as the first stage of biomineralisation, has been widely studied for various metals, such as cadmium, copper, zinc, aluminium, gold, silver, etc. However, despite the fact that the mining and utilization of rare earth elements (REEs) are currently increasing, there [...] Read more.

Bioaccumulation by diatoms, as the first stage of biomineralisation, has been widely studied for various metals, such as cadmium, copper, zinc, aluminium, gold, silver, etc. However, despite the fact that the mining and utilization of rare earth elements (REEs) are currently increasing, there is almost no data on their bioaccumulation by diatoms. Therefore, the aim of this study was to determine the ability of diatoms to bioaccumulate REEs by the example of lanthanum (La), and to compare this ability for two marine diatoms Nanofrustulum shiloi and Halamphora kolbei. As a result of experiments on the cultivation of diatoms in nutrient media supplemented with La at concentrations of 10 mg·L⁻¹ and 50 mg·L⁻¹, energy-dispersive X-ray spectroscopy revealed the ability of diatoms to bioadsorb La on their frustule surface, as a first stage of its bioaccumulation. The high concentration of La (50 mg·L⁻¹) has a noticeable visual effect on the morphofunctional state of diatoms and causes a decrease in the rate of accumulation. The low concentration (10 mg·L⁻¹) promotes the hyperaccumulation of La by the diatom biomass as a whole, including both bioadsorption and bioabsorption within the cells. This resulted in an increase in La concentration in the biomass by nearly 2000-fold in H. kolbei (6.06 mg·g⁻¹) and by 1000-fold in N. shiloi (6.90 mg·g⁻¹). The results on La bioaccumulation by diatoms are significant for advancing methods to remediate aquatic environments contaminated with rare earth elements and for the bioindication purposes. Full article

(This article belongs to the Special Issue Metals in Biology (2nd Edition))

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14 pages, 2709 KB

Open AccessArticle

Transcriptome Analysis of the Pathogenic Mechanism of the Novel Pathogenic Fungus Bipolaris fujianensis in Chinese Fir (Cunninghamia lanceolata) Shoot Blight

by Bin Lin, Peiwen Yang, Ruifeng Luo, Ying Lu, Zhe Li, Menglan Shang, Wangdong Xu, Zihui Huang, Guanghong Liang and Qinghua Zhang

Biology 2025, 14(11), 1488; https://doi.org/10.3390/biology14111488 (registering DOI) - 24 Oct 2025

Abstract

Bipolaris fujianensis is a novel pathogenic species causing Chinese fir (Cunninghamia lanceolata) shoot blight (CFSB), first discovered in Nanping City, Fujian Province. However, its molecular pathogenic mechanisms remain largely unknown. Elucidating theses mechanisms has the potential of aiding future developments in [...] Read more.

Bipolaris fujianensis is a novel pathogenic species causing Chinese fir (Cunninghamia lanceolata) shoot blight (CFSB), first discovered in Nanping City, Fujian Province. However, its molecular pathogenic mechanisms remain largely unknown. Elucidating theses mechanisms has the potential of aiding future developments in disease management and resistance breeding in Chinese fir. In this regard, we examined the expression pattern of B. fujianensis grown on PDA (BGPDA), and during infection of Chinese fir at 24 h (BGCF-E), 48 h (BGCF-M), and 5 d (BGCF-L) post inoculation. Comparative transcriptome analysis identified 4133 differentially expressed genes (DEGs), including 1778 upregulated and 2355 downregulated in BGCF compared with BGPDA. During the infection process, Gene ontology (GO) enrichment analysis indicated that transporters and hydrolases in the molecular function categories play essential roles. Kyoto encyclopedia of genes and genomes (KEGG) analyses showed glycolysis/gluconeogenesis, carbon metabolism, and secondary metabolite biosynthesis were the major enriched pathways. Furthermore, this pathogen could produce diterpenoid toxin ophiobolin F, with cytochrome P450 and MFS transport proteins likely involved in its biosynthesis and transport predicted by RT-qPCR. Full article

(This article belongs to the Section Microbiology)

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21 pages, 2727 KB

Open AccessArticle

Explainable Artificial Intelligence for Ovarian Cancer: Biomarker Contributions in Ensemble Models

by Hasan Ucuzal and Mehmet Kıvrak

Biology 2025, 14(11), 1487; https://doi.org/10.3390/biology14111487 (registering DOI) - 24 Oct 2025

Abstract

Ovarian cancer’s high mortality is primarily due to late-stage diagnosis, underscoring the critical need for improved early detection tools. This study develops and validates explainable artificial intelligence (XAI) models to discriminate malignant from benign ovarian masses using readily available demographic and laboratory data. [...] Read more.

Ovarian cancer’s high mortality is primarily due to late-stage diagnosis, underscoring the critical need for improved early detection tools. This study develops and validates explainable artificial intelligence (XAI) models to discriminate malignant from benign ovarian masses using readily available demographic and laboratory data. A dataset of 309 patients (140 malignant, 169 benign) with 47 clinical parameters was analyzed. The Boruta algorithm selected 19 significant features, including tumor markers (CA125, HE4, CEA, CA19-9, AFP), hematological indices, liver function tests, and electrolytes. Five ensemble machine learning algorithms were optimized and evaluated using repeated stratified 5-fold cross-validation. The Gradient Boosting model achieved the highest performance with 88.99% (±3.2%) accuracy, 0.934 AUC-ROC, and 0.782 Matthews correlation coefficient. SHAP analysis identified HE4, CEA, globulin, CA125, and age as the most globally important features. Unlike black-box approaches, our XAI framework provides clinically interpretable decision pathways through LIME and SHAP visualizations, revealing how feature values push predictions toward malignancy or benignity. Partial dependence plots illustrated non-linear risk relationships, such as a sharp increase in malignancy probability with CA125 > 35 U/mL. This explainable approach demonstrates that ensemble models can achieve high diagnostic accuracy using routine lab data alone, performing comparably to established clinical indices while ensuring transparency and clinical plausibility. The integration of state-of-the-art XAI techniques highlights established biomarkers and reveals potential novel contributors like inflammatory and hepatic indices, offering a pragmatic, scalable triage tool to augment existing diagnostic pathways, particularly in resource-constrained settings. 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, 3223 KB

Open AccessArticle

Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (Rhinogobio ventralis)

by Jieming Chen, Xinhui Zhang, Yanping Li, Yunyun Lv, Xinxin You, Qiong Shi and Zhengyong Wen

Biology 2025, 14(11), 1486; https://doi.org/10.3390/biology14111486 (registering DOI) - 24 Oct 2025

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Abstract

As an economically important species endemic to the upper tributaries of Yangtze River in China, long-finned gudgeon fish (Rhinogobio ventralis) has been classified as endangered due to habitat destruction and population decline. In this study, we constructed a chromosome-level genome assembly [...] Read more.

As an economically important species endemic to the upper tributaries of Yangtze River in China, long-finned gudgeon fish (Rhinogobio ventralis) has been classified as endangered due to habitat destruction and population decline. In this study, we constructed a chromosome-level genome assembly of R. ventralis by integration of MGI, PacBio and Hi-C sequencing technologies. The final genome assembly was 1015.9 Mb in length (contig N50: 25.91 Mb; scaffold N50: 39.99 Mb), and 97.19% of the haplotypic genome sequences were anchored onto 25 chromosomes. Repetitive elements accounted for 51.00% of the entire genome assembly. A total of 23,220 protein-coding genes were predicted for the assembled genome, of which 99.79% were functionally annotated. Genome evaluation revealed 99.72% completeness for the genome assembly. Through genome-wide prediction of antimicrobial peptides (AMPs), we identified and localized 561 putative AMP-containing genes in the R. ventralis genome. These genes were further classified into 185 distinct functional categories based on public databases, with the top ten components of Penetratin (21.74%), Histone (5.70%), E6AP (4.09%), Scolopendin 1 (2.67%), D38 (2.31%), WBp-1 (2.13%), Defensin (2.13%), Claudin 1 (1.96%), Azurocidin (AZU1, 1.78%), and Ubiquitin (1.60%). Our data presented here provide a potential genetic resource for promoting fundamental research and wild population conservation of this endangered fish species. Full article

(This article belongs to the Special Issue Research Advances in Aquatic Omics)

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20 pages, 12030 KB

Open AccessArticle

Triploid Cyprinid Fish (TCF) Under Aeromonas sp. AS1-4 Infection: Metabolite Characteristics and In Vitro Assessment of Probiotic Potentials of Intestinal Enterobacter Strains

by Xu-Ying Kuang, Qin-Yang He, Zi-Xuan Fang, Zhuang-Wen Mao, Ming-Zhu Huang, Zi-Le Qin, Jie Peng, Yu-De Wang and Sheng-Wei Luo

Biology 2025, 14(11), 1485; https://doi.org/10.3390/biology14111485 (registering DOI) - 24 Oct 2025

Abstract

The majority of Aeromonas strains are opportunistic pathogens for both humans and animals, causing a variety of diseases and posing a considerable risk to their health. In the current study, triploid cyprinid fish (TCF) were infected with a novel pathogenic Aeromonas sp. AS1-4 [...] Read more.

The majority of Aeromonas strains are opportunistic pathogens for both humans and animals, causing a variety of diseases and posing a considerable risk to their health. In the current study, triploid cyprinid fish (TCF) were infected with a novel pathogenic Aeromonas sp. AS1-4 for pathological analysis. TCFs receiving Aeromonas sp. AS1-4 challenge exhibited oxidative damage in the liver and spleen, along with significant changes in immune-related gene expressions. Metabolomics assay indicated that strain AS1-4 challenge may exhibit a significant impact on metabolic processes of amino acids, with methylsuccinic acid (MSA) identified as vital biomarker. Following that, three potential probiotics designated Enterobacter strains fkY27-2, fkY84-1 and fkY84-4 were isolated from the intestine of TCFs, displaying excellent safety characteristics. In addition, intestinal Enterobacter strains exhibited multiple probiotic traits, including high degrees of hydrophobic activity, aggregation performance, biofilm-forming activity (BFA) and nutrient decomposing ability. Moreover, these probiotic isolates markedly coaggregated with Aeromonas sp. AS1-4 and Edwardsiella tarda 1l-4 and then suppressed their pathogenic biofilm-forming abilities, along with possessing robust antioxidant potential against various free radicals. These findings may provide valuable insights into metabolic response in fish post infection and health management in aquaculture. Full article

(This article belongs to the Special Issue Aquatic Economic Animal Breeding and Healthy Farming (2nd Edition))

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16 pages, 2060 KB

Open AccessArticle

StomachDB: An Integrated Multi-Omics Database for Gastric Diseases

by Gang Wang, Zhe Sun, Shiou Yih Lee, Mingyu Lai, Xiaojuan Wang and Sanqi An

Biology 2025, 14(11), 1484; https://doi.org/10.3390/biology14111484 (registering DOI) - 24 Oct 2025

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Abstract

Gastric diseases represent a significant challenge to global health. A comprehensive understanding of their complex molecular mechanisms, particularly the pathways of molecular progression in precancerous lesions, is essential for enhancing diagnosis and treatment. StomachDB, the first comprehensive multi-omics database dedicated to gastric diseases, [...] Read more.

Gastric diseases represent a significant challenge to global health. A comprehensive understanding of their complex molecular mechanisms, particularly the pathways of molecular progression in precancerous lesions, is essential for enhancing diagnosis and treatment. StomachDB, the first comprehensive multi-omics database dedicated to gastric diseases, has been developed to address these research needs. This database integrates 6 types of biological data: genomics, transcriptomics, emerging single-cell and spatial transcriptomics, proteomics, metabolomics, and therapeutic-related information. It encompasses 44 gastric-related pathologies, including various forms of gastric cancer, gastric ulcers, and gastritis, primarily involving humans and mice as model organisms. The database compiles approximately 2.5 million curated and standardized profiles, along with 268,394 disease-gene associations. The user-friendly analytics platform provides tools for browsing, querying, visualizing, and downloading data, facilitating systematic exploration of multi-omics features. This integrative approach addresses the limitations of single-omics analyses, such as data heterogeneity and insufficient analytical dimensions. Researchers can investigate the clinical significance of target genes (e.g., CDH1) across different omics levels and explore potential regulatory mechanisms. Furthermore, StomachDB emphasizes the discovery of therapeutic targets by cataloging interactions among chemical drugs, traditional herbal medicines, and probiotics. As an open-access resource, it serves as a powerful tool for studying complex biological interactions and regulatory mechanisms. Full article

(This article belongs to the Section Bioinformatics)

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17 pages, 38400 KB

Open AccessArticle

Chlorogenic Acid Alleviates Chronic Stress-Induced Ileal Oxidative Stress and Apoptosis in Rats by Influencing Intestinal Flora and Activating Nrf2 Pathway

by Wenjing Jiao, Haoyang Tan, Xin Cheng, Tianyuan Yang, Xuanpan Ding, Yaxin Ji, Haotian Yang, Jichen Sha, Guofeng Feng, Yuan Zhao and Honggang Fan

Biology 2025, 14(11), 1483; https://doi.org/10.3390/biology14111483 (registering DOI) - 24 Oct 2025

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Abstract

Background: Chronic stress is implicated in the pathogenesis of gastrointestinal disorders, with reactive oxygen species (ROS) contributing significantly. Chlorogenic acid (CGA), a polyphenolic compound, exhibits antioxidant properties. This study investigated whether CGA mitigates ROS-mediated oxidative stress and apoptosis in chronic stress-induced ileal injury. [...] Read more.

Background: Chronic stress is implicated in the pathogenesis of gastrointestinal disorders, with reactive oxygen species (ROS) contributing significantly. Chlorogenic acid (CGA), a polyphenolic compound, exhibits antioxidant properties. This study investigated whether CGA mitigates ROS-mediated oxidative stress and apoptosis in chronic stress-induced ileal injury. Methods: Rats were subjected to restraint stress for 21 days, with/without CGA (100 mg/kg, gavage). CGA’s mechanism was elucidated by assessing ileal flora, oxidative stress markers, apoptosis, structural changes, and the Nrf2 pathway. Results: CGA restored ileal structure, attenuated ROS and MDA levels, elevated GSH and SOD levels, and reduced apoptosis-associated proteins. CGA stabilized conformation bound to Keap1, deregulating Keap1’s negative regulation of Nrf2, thereby increasing Nrf2 and downstream protein expression (HO-1 and NQO1). Gut microbiota imbalance was corrected, with increased Lactobacillus abundance post-CGA intervention. Conclusions: CGA alleviates chronic stress-induced ileal oxidative stress and apoptosis, which relates closely to Nrf2 pathway activation and modulation of intestinal microflora. Full article

(This article belongs to the Section Microbiology)

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15 pages, 2772 KB

Open AccessArticle

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

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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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2 pages, 1001 KB

Open AccessCorrection

Correction: Le et al. Duplicated Genes on Homologous Chromosomes Decipher the Dominant Epistasis of the Fiberless Mutant in Cotton. Biology 2025, 14, 983

by Yu Le, Xingchen Xiong, Zhiyong Xu, Meilin Chen, Yuanxue Li, Chao Fu, Chunyuan You and Zhongxu Lin

Biology 2025, 14(11), 1481; https://doi.org/10.3390/biology14111481 - 24 Oct 2025

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Abstract

In the original publication [...] Full article

(This article belongs to the Special Issue Cotton: Genomics, Biotechnology and Molecular Breeding)

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23 pages, 2416 KB

Open AccessReview

The Biological Functions and Mode of Action of Transcription Factor ELF4: A Promising Target for Treating Intestinal Homeostasis Disorder-Related Diseases

by Linjiang Xie, Haixin Bai, Ziyi Bai, Lv Fu and Haitao Yu

Biology 2025, 14(11), 1480; https://doi.org/10.3390/biology14111480 - 23 Oct 2025

Viewed by 237

Abstract

Intestinal homeostasis disorders (IHDs), driven by food safety issues, pollution, and drug-resistant pathogens, threaten global health. Key factors in intestinal and metabolic diseases (like IBD, obesity, and liver disease) include barrier dysfunction, gut microbiota imbalance, and excessive immune activation. Transcription factors in intestinal [...] Read more.

Intestinal homeostasis disorders (IHDs), driven by food safety issues, pollution, and drug-resistant pathogens, threaten global health. Key factors in intestinal and metabolic diseases (like IBD, obesity, and liver disease) include barrier dysfunction, gut microbiota imbalance, and excessive immune activation. Transcription factors in intestinal epithelial cells are crucial regulators. ELF4, an ETS family transcription factor, plays vital roles in transcriptional regulation, impacting tumorigenesis, the DNA damage response, and the cell cycle. ELF4 deficiency exacerbates alcoholic liver disease (ALD). Significantly, ELF4 is a novel IFN-I transcription factor with antiviral capabilities. Its regulation of the type I IFN response offers new avenues for developing antiviral and anticancer strategies and managing IFN-induced autoimmune disorders. Thus, ELF4 emerges as a promising target for preventing and treating IHD-related diseases. Mechanistic studies could help identify diets or antimicrobials that activate intestinal ELF4 to combat pathogen/virus-induced intestinal diseases. Full article

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17 pages, 1993 KB

Open AccessArticle

Heavy Metal Contamination in Adaptogenic Herbal Dietary Supplements: Experimental, Assessment and Regulatory Safety Perspectives

by Agata Jasińska-Balwierz, Patrycja Krypel, Paweł Świsłowski, Małgorzata Rajfur, Radosław Balwierz and Wioletta Ochędzan-Siodłak

Biology 2025, 14(11), 1479; https://doi.org/10.3390/biology14111479 - 23 Oct 2025

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Abstract

While adaptogens are popular in dietary supplements for their health-promoting properties, their safety is compromised by the risk of heavy metal contamination, a threat amplified by inconsistent regulatory standards. This study aimed to assess the extent of heavy metal contamination in adaptogenic supplements [...] Read more.

While adaptogens are popular in dietary supplements for their health-promoting properties, their safety is compromised by the risk of heavy metal contamination, a threat amplified by inconsistent regulatory standards. This study aimed to assess the extent of heavy metal contamination in adaptogenic supplements on the Polish market and evaluate their compliance with international safety limits. Eleven commercially available supplements (tablets, powders, dried materials) containing Withania somnifera, Rhodiola rosea, Panax ginseng, and Schisandra chinensis were analyzed for lead (Pb), cadmium (Cd), mercury (Hg), nickel (Ni), and other elements using flame atomic absorption spectroscopy (FAAS) and mercury analysis (AMA 254). Results demonstrated widespread contamination, primarily with Pb and Ni. In processed forms (tablets and dried fruits), Pb concentrations exceeded permissible limits by up to 235%, while Ni levels were exceeded by up to 321%. Schisandra chinensis preparations showed the highest contamination levels. Furthermore, raw materials from India contained significantly higher Ni concentrations than those from China (p < 0.01). These findings reveal that a majority of the tested supplements fail to meet toxicological safety criteria, posing a significant health risk to consumers. This underscores a critical regulatory gap and highlights the urgent need for harmonized standards and stringent quality control for dietary supplements. Full article

(This article belongs to the Special Issue Exposure to Heavy Metals: Advances in Cytotoxicity and Genotoxicity)

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Open AccessArticle

Genome-Wide SNP Analysis Reveals the Unique Genetic Diversity Represented by Fat-Tailed Coarse-Wooled Sheep Breeds of Kazakhstan

by Kairat Dossybayev, Makpal Amandykova, Daniya Ualiyeva, Tilek Kapassuly, Altynay Kozhakhmet, Elena Ciani, Bakytzhan Bekmanov and Rauan Amzeyev

Biology 2025, 14(11), 1478; https://doi.org/10.3390/biology14111478 (registering DOI) - 23 Oct 2025

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Abstract

Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics [...] Read more.

Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts. Full article

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

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15 pages, 3308 KB

Open AccessArticle

Predicting the Potential Distribution of Galeruca daurica in Inner Mongolia Under Current and Future Climate Scenarios Using the MaxEnt Model

by Tian-Yu Xu, Xiao-Shuan Bai and MU Ren

Biology 2025, 14(11), 1477; https://doi.org/10.3390/biology14111477 - 23 Oct 2025

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Abstract

In the context of climate change and grassland degradation, the Inner Mongolia Autonomous Region, a key ecological barrier in Northern China, has faced recurrent outbreaks of the pest beetle Galeruca daurica. This study aims to project its potential geographic distribution under current [...] Read more.

In the context of climate change and grassland degradation, the Inner Mongolia Autonomous Region, a key ecological barrier in Northern China, has faced recurrent outbreaks of the pest beetle Galeruca daurica. This study aims to project its potential geographic distribution under current and future climate scenarios to support risk assessment and management strategies. Using the Maximum Entropy (MaxEnt) model with 122 occurrence records and environmental variables (climatic, topographic, and edaphic), we simulated habitat suitability under present conditions and future scenarios (SSP1-2.6, SSP2-4.5, and SSP5-8.5 for the 2050s and 2070s). The model performed excellently (AUC > 0.9), with key predictors being precipitation of the wettest month (39.6%), annual precipitation (24.0%), and annual temperature range (8.2%). Currently, about 44.9% of the region is suitable habitat, mainly in central–western arid and semi-arid areas. Future projections indicate a contraction in suitability, which is most pronounced under SSP2-4.5 (declining to 23.56% by the 2070s), along with a northward shift in the distribution centroid. These findings suggest that climate change will likely reduce and shift the suitable range of G. daurica, providing a scientific basis for early warning and targeted control in vulnerable grassland ecosystems. Full article

(This article belongs to the Special Issue Ecological Regulation of Forest and Grassland Pests)

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17 pages, 2651 KB

Open AccessArticle

Predicting Habitat Suitability and Range Dynamics of Three Ecologically Important Fish in East Asian Waters Under Projected Climate Change

by Ifeanyi Christopher Nneji, Winnie Wanjiku Mambo, Zhao Zheng, Segun Olayinka Oladipo, Hancheng Zhao, Wentao Lu, Lotanna Micah Nneji, Jianqing Lin and Wenhua Liu

Biology 2025, 14(11), 1476; https://doi.org/10.3390/biology14111476 - 23 Oct 2025

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Abstract

The vulnerability of ecologically important fish species to climate change underscores the need to predict shifts in their distributions and habitat suitability under future climate scenarios. In this study, we modeled the potential distribution ranges of three ecologically important fish species (Collichthys [...] Read more.

The vulnerability of ecologically important fish species to climate change underscores the need to predict shifts in their distributions and habitat suitability under future climate scenarios. In this study, we modeled the potential distribution ranges of three ecologically important fish species (Collichthys lucidus, Konosirus punctatus, and Clupanodon thrissa) across East Asia using a species distribution modeling framework under both current and projected future climate scenarios. Occurrence data were obtained from the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS), while environmental data were retrieved from the Bio-ORACLE database. Our models demonstrated high predictive performance (AUC > 0.88). Results showed that dissolved oxygen and salinity were the strongest bioclimatic predictors for C. lucidus, whereas chlorophyll and phosphate primarily shaped the distributions of K. punctatus and C. thrissa. Model projections indicated a decline in suitable habitats for C. lucidus, particularly under high-emission scenarios, and range expansions for K. punctatus and C. thrissa toward higher latitudes and nutrient-enriched waters. Highly suitable habitats were concentrated along coastlines within exclusive economic zones, exposing these species to significant anthropogenic pressures. Conservation gap analysis revealed that only 7%, 2%, and 6% of the distributional ranges of C. lucidus, C. thrissa, and K. punctatus, respectively, are currently encompassed by marine protected areas (MPAs). Our study further identified climatically stable regions that may act as climate refugia, particularly for C. lucidus in the Yellow and East China seas. Our findings highlight the urgent need for adaptive management, including the expansion and reconfiguration of MPAs, transboundary conservation initiatives, stronger regulation of exploitation, and increased public awareness to ensure the resilience of fisheries under future climate change. Full article

(This article belongs to the Section Marine Biology)

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16 pages, 1828 KB

Open AccessArticle

Heavy Metal Contamination and Risk Assessment in Soil–Wheat/Corn Systems near Metal Mining Areas in Northwestern China

by Shenghui Xu, Mingyang Yun, Yan Wang, Kaiwang Liu, Ao Wu, Shuning Li, Yanfang Su, Shengli Wang and Hongmei Kang

Biology 2025, 14(11), 1475; https://doi.org/10.3390/biology14111475 - 23 Oct 2025

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Abstract

Heavy metals in farmland soils pose severe threats to agricultural productivity and food safety. To investigate contamination in the soil–wheat/corn system, 24 sets of adjacent farmland soil, wheat, and corn plant samples were collected near metal smelting facilities in Jinchang City, a typical [...] Read more.

Heavy metals in farmland soils pose severe threats to agricultural productivity and food safety. To investigate contamination in the soil–wheat/corn system, 24 sets of adjacent farmland soil, wheat, and corn plant samples were collected near metal smelting facilities in Jinchang City, a typical urban oasis in northwestern China. Concentrations of Ni (nickel), Cu (copper), and Co (cobalt) were measured. Results indicated mean soil concentrations of 143.66 mg kg⁻¹ (Ni), 130.00 mg kg⁻¹ (Cu), and 24.04 mg kg⁻¹ (Co), all exceeding background values for Gansu Province, confirming that the sampling sites exhibit varying degrees of contamination with Ni, Cu, and Co. Correlation analyses revealed strong intermetal relationships (Ni, Cu, Co; p < 0.01), while spatial distribution patterns showed that Ni in wheat and corn grains closely mirrored soil Ni distribution. The bio-concentration factor (BCF) for wheat roots surpassed that of corn roots, highlighting wheat’s greater susceptibility to heavy metal uptake. Heavy metal levels in crop organs exceeded limits set by the Safety Guidelines for Feed Additives. Geo-accumulation indices and potential ecological risk assessments demonstrated substantial metal accumulation and varying ecological risks, with contamination levels ranked as Cu > Ni > Co. Non-carcinogenic hazard indices indicated elevated health risks for children consuming locally grown wheat and corn. This study provides a scientific foundation for crop rotation strategies and soil remediation in the region. Full article

(This article belongs to the Special Issue Biogeochemical Element Cycling in Plant–Soil Systems: Implications for Ecosystem Dynamics and Services)

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21 pages, 7755 KB

Open AccessArticle

Ecotone-Driven Vegetation Transitions Reshape Soil Nitrogen Cycling Functional Genes in Black Soils of Northeast China

by Junnan Ding, Yingjian Wang and Shaopeng Yu

Biology 2025, 14(11), 1474; https://doi.org/10.3390/biology14111474 - 23 Oct 2025

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Abstract

Forest–wetland ecotones are transitional ecosystems characterized by pronounced hydrological and biogeochemical heterogeneity, yet the microbial mechanisms regulating nutrient cycling in these zones remain insufficiently understood. This study investigated how vegetation transitions across a forest–wetland ecotone in the black-soil region of Northeast China shape [...] Read more.

Forest–wetland ecotones are transitional ecosystems characterized by pronounced hydrological and biogeochemical heterogeneity, yet the microbial mechanisms regulating nutrient cycling in these zones remain insufficiently understood. This study investigated how vegetation transitions across a forest–wetland ecotone in the black-soil region of Northeast China shape soil microbial communities and nitrogen–cycling functions. Soils were collected from four vegetation types: mixed forest (MF), coniferous forest (CF), wetland edge (WE), and natural wetland (NW). Quantitative PCR was used to quantify key nitrogen–cycling functional genes (nifH, amoA, amoB, norB, nosZ), and PICRUSt2 was applied to predict microbial functional potentials. Forest soils (MF and CF) exhibited higher microbial diversity, stronger network connectivity, and greater abundances of nifH and amoA, indicating enhanced nitrogen fixation and nitrification under oxic conditions. In contrast, wetland soils harbored denitrification-enriched communities with higher norB and nosZ abundances but lower diversity. The WE vegetation type acted as a functional hotspot where alternating oxic–anoxic conditions facilitated the coexistence of nitrifiers and denitrifiers, thereby enhancing carbon–nitrogen coupling and functional resilience. Redundancy and Mantel analyses identified soil organic carbon, total nitrogen, water content, and enzyme activities as major environmental drivers of microbial structural and functional variation. This study reveals that vegetation transitions reorganize microbial community assembly and nitrogen-cycling functions through hydrological and biogeochemical heterogeneity, providing mechanistic insights into nutrient turnover and ecological regulation in black-soil ecotones. Full article

(This article belongs to the Special Issue Wetland Ecosystems (2nd Edition))

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18 pages, 7066 KB

Open AccessArticle

Climate Change Enhances the Cultivation Potential of Ficus tikoua Bur. in China: Insights from Ensemble Modeling and Niche Analysis

by Mei Liu, Yutong Qin, Jian Yang, Xiaoyu Li, Fengli Zhu, Zhiliang Ma, Cong Zhao, Ruijun Su and Yan Chen

Biology 2025, 14(11), 1473; https://doi.org/10.3390/biology14111473 - 23 Oct 2025

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Abstract

Climate change is reshaping plant distribution and ecological adaptation worldwide. Ficus tikoua Bur., a perennial resource plant native to Southwest and South China, has not been systematically assessed for its future cultivation potential. In this study, we used the Biomod2 ensemble modeling framework, [...] Read more.

Climate change is reshaping plant distribution and ecological adaptation worldwide. Ficus tikoua Bur., a perennial resource plant native to Southwest and South China, has not been systematically assessed for its future cultivation potential. In this study, we used the Biomod2 ensemble modeling framework, integrating 12 algorithms with 469 occurrence records and 16 environmental variables, to predict the potential distribution and niche dynamics of F. tikoua under current and future climate scenarios (SSP126, SSP370, and SSP585). The ensemble model achieved high predictive accuracy based on multiple algorithms and cross-validation. The minimum temperature of the coldest month (bio6, 43.5%), maximum temperature of the warmest month (bio5, 25.0%), and annual precipitation (bio12, 10.3%) were identified as the dominant factors shaping its distribution. Model projections suggest that suitable habitats will generally expand northwestward, while contracting in the southeast. Core areas, such as the Yunnan–Guizhou Plateau and the Sichuan Basin, are predicted to remain highly stable. In contrast, southeastern marginal regions are likely to experience a decline in suitability due to intensified heat stress. Niche analyses further revealed strong niche conservatism (overlap D = 0.83–0.94), suggesting that the species maintains stable climatic tolerance and adapts primarily through range shifts rather than evolutionary change. This finding suggests limited adaptive flexibility in response to rapid warming. Overall, climate warming may enhance cultivation opportunities for F. tikoua at higher latitudes and elevations, while emphasizing the importance of protecting stable core habitats, planning climate adaptation corridors, and integrating this species into climate-resilient agroforestry strategies. These findings provide practical guidance for biodiversity conservation and land-use planning, offering a scientific basis for regional policy formulation under future climate change. Full article

(This article belongs to the Section Ecology)

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15 pages, 5026 KB

Open AccessArticle

Genetic Diversity of the Only Natural Population of Corylus avellana L. in Kazakhstan and Prospects for Its In Vitro Conservation

by Svetlana V. Kushnarenko, Madina Omasheva, Natalya Romadanova, Moldir Aralbayeva, Nazgul Rymkhanova, Ulzhan Manapkanova, Roberto Botta, Paola Ruffa, Nadia Valentini and Daniela Torello Marinoni

Biology 2025, 14(11), 1472; https://doi.org/10.3390/biology14111472 - 23 Oct 2025

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Abstract

Corylus avellana L. is a rare and endangered species in Kazakhstan, included in the national Red Book. The results of morphological and genetic characterization of the sole known natural population of C. avellana in the Western Kazakhstan region are presented in this study. [...] Read more.

Corylus avellana L. is a rare and endangered species in Kazakhstan, included in the national Red Book. The results of morphological and genetic characterization of the sole known natural population of C. avellana in the Western Kazakhstan region are presented in this study. Sixty wild accessions were evaluated based on tree and leaf morphological traits using standard descriptors in accordance with Bioversity International guidelines. Genetic diversity was assessed using ten nuclear simple sequence repeat (SSR) markers. A total of 120 alleles were detected across the nuclear loci, with the number of alleles per locus ranging from 9 to 16 and an average of 12. The mean effective number of alleles (Ne) per locus was 3.862. A high level of intraspecific polymorphism was observed, with an average observed heterozygosity (Ho) of 0.70. The population showed considerable genetic diversity, as highlighted by a mean Shannon’s diversity index of 1.526. STRUCTURE, PCoA, and phylogenetic analyses confirmed strong differentiation between the wild Kazakh population and the cultivated hazelnut germplasm. Due to the lack of viable seeds, in vitro conservation was initiated using vegetative shoots. A two-step disinfection protocol, involving Plant Preservative Mixture and mercuric chloride, significantly improved explant survival, enabling successful establishment of an aseptic in vitro collection. These findings highlight the urgent need for targeted conservation strategies and show the potential of biotechnological approaches for safeguarding Kazakhstan’s only natural C. avellana population. Full article

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

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27 pages, 3720 KB

Open AccessArticle

Reproductive Biology and Early Life History of the Apodid Sea Cucumber Chiridota laevis

by Sara Jobson, Jean-François Hamel and Annie Mercier

Biology 2025, 14(11), 1471; https://doi.org/10.3390/biology14111471 (registering DOI) - 22 Oct 2025

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Abstract

The apodid sea cucumber Chiridota laevis has been a documented member of endobenthic marine communities in northern waters for over a century and the rare studies available on its biology identify it as distinctive species and promising model for research. The present study [...] Read more.

The apodid sea cucumber Chiridota laevis has been a documented member of endobenthic marine communities in northern waters for over a century and the rare studies available on its biology identify it as distinctive species and promising model for research. The present study sought to elucidate fundamental aspects of its life history that remained unresolved. Adults were determined to be protandric, with individuals primarily demonstrating solely male or female gametes from winter (close to spawning) to the spring and summer months before undergoing a sex change in the fall months. Additionally, gametes of both sexes reached maturity synchronously in late winter (February to March). In mesocosms, free spawning occurred in February, as the temperature reached ~2.0 °C. The negatively buoyant eggs were encased in a sticky casing and fell to the sediment where they adhered to each other to form a mat on the muddy substratum. The realized fecundity was ~15,000 offspring. Development was lecithotrophic, demersal, and abbreviated, characterized by the absence of a pelagic larval stage. Embryos reached the gastrula stage after about 7 days post fertilization; the calcareous ring appeared at 6 weeks, and juveniles hatched from the sticky casing at 7 weeks, immediately becoming endobenthic. The size of late embryos and juveniles remained similar (~350 μm) until they began actively feeding at about 10 weeks of age. Feeding juveniles more than doubled in size in the first week (740 μm), reached 3.5 mm by year one, and measured up to 11 mm by year two. This growth rate suggests that it may take this species up to 7 years to reach adult size at ~24 mm contracted length. Full article

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14 pages, 1302 KB

Open AccessReview

Molecular and Physiological Mechanisms Underlying Submerged Germination in Rice

by Shuang Jia, Qianya Zhou, Shengqi Yuan, Yifeng Wang and Zhongchen Zhang

Biology 2025, 14(11), 1470; https://doi.org/10.3390/biology14111470 - 22 Oct 2025

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Abstract

Submergence during germination (SG) is a major constraint during sowing, severely limiting the promotion and application of direct-seeded rice. Recent studies have revealed the adaptive mechanisms by which rice responds to SG. At the physiological level, flood-tolerant varieties effectively maintain energy supply and [...] Read more.

Submergence during germination (SG) is a major constraint during sowing, severely limiting the promotion and application of direct-seeded rice. Recent studies have revealed the adaptive mechanisms by which rice responds to SG. At the physiological level, flood-tolerant varieties effectively maintain energy supply and cellular homeostasis by enhancing amylase activity, improving glycolysis and ethanolic fermentation efficiency, promoting embryo sheath elongation, and activating antioxidant enzyme systems; at the molecular level, multiple key genes and signalling pathways have been identified, including SUB1A, OsTPP7, OsGF14h, etc., participating in hypoxia perception, metabolic reprogramming, and hormone signal integration to regulate SG under flooding. In addition, the interactions among plant hormones, such as ethylene, gibberellin, abscisic acid, and cytokinin, also play key roles in the SG process. Future research should prioritize breeding strategies that pyramid multiple genes by integrating gene editing, whole-genome selection, and high-throughput phenotyping to improve seed germination under flood stress. Full article

(This article belongs to the Special Issue Molecular Basis of Seed Germination and Dormancy)

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19 pages, 1191 KB

Open AccessArticle

Assessing the Relationship Between the Flicker Test and Cognitive Performance

by Natalia D. Mankowska, Rita I. Sharma, Anna B. Marcinkowska, Jacek Kot and Pawel J. Winklewski

Biology 2025, 14(11), 1469; https://doi.org/10.3390/biology14111469 - 22 Oct 2025

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Abstract

An individual’s ability to process flickering light is expressed by critical flicker fusion frequency (CFFF), tested with the flicker test. CFFF is used to assess visual processing, arousal, and cognitive functioning, among other things, although it is unclear how it reflects these processes. [...] Read more.

An individual’s ability to process flickering light is expressed by critical flicker fusion frequency (CFFF), tested with the flicker test. CFFF is used to assess visual processing, arousal, and cognitive functioning, among other things, although it is unclear how it reflects these processes. Due to possible differences between CFFF values obtained in trials with increasing and decreasing frequency, it also remains questionable to use only averaged CFFF values in research. The main objective of the present study was to assess how CFFF is related to cognitive functions (attention, short-term and working memory, and executive functions), and psychomotor speed. The research objectives also included assessing the stability of CFFF and its variability with age and comparing CFFF between men and women. Thirty-six participants (17 women and 19 men) completed computerized cognitive tests (Simon and flanker tasks, the Corsi block-tapping task, and the digit span task) three times, along with the flicker test. We found that CFFF scores were stable across sessions but differed between fusion and flicker thresholds, with age significantly correlating only with the fusion frequency. Given that, we suggest that future studies analyze not only the averaged CFFF, but also examine flicker and fusion thresholds separately to better understand their distinct contributions. Our results also revealed generally weak correlations between CFFF and neuropsychological test scores, with significant associations found only in women, suggesting that CFFF may not be a reliable indicator of cognitive functioning. Full article

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20 pages, 3709 KB

Open AccessArticle

Isolation and Characterization of Chlorpyrifos-Degrading Gut Bacteria from Field-Collected Larvae of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)

by Ayatollah S. El-Zayat, Marwa N. Ahmed, Manar Sofy, Dalia E. El-Hefny, Nawal A. Alfuhaid, Dina El-Sayed, Hayam M. Fathy and Mona Awad

Biology 2025, 14(11), 1468; https://doi.org/10.3390/biology14111468 - 22 Oct 2025

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Abstract

Exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized that the gut microbiota associated with the field S. frugiperda population carries pesticide-degrading bacteria that would enhance the host’s ability to metabolize pesticides. Three strategies were implemented [...] Read more.

Exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized that the gut microbiota associated with the field S. frugiperda population carries pesticide-degrading bacteria that would enhance the host’s ability to metabolize pesticides. Three strategies were implemented to address this principle: (i) isolation and identification of chlorpyrifos-degrading gut bacteria from field-collected S. frugiperda larvae; (ii) evaluation of chlorpyrifos biodegradation capacity through in vitro assays; and (iii) assessment of the impact of specific bacterial taxa capable of degrading chlorpyrifos directly within the gut. In this study, we successfully isolated four chlorpyrifos-degrading gut bacterial isolates from a field-collected population of S. frugiperda. These isolates were identified using 16S rDNA sequencing as Klebsiella quasipneumoniae strain 60D (PP504878), Klebsiella pneumoniae strain 64D (PP504879), Klebsiella pneumoniae strain 66D (PP504880), and Klebsiella pneumoniae strain 71D (PP504881). In vitro chlorpyrifos degradation assays revealed that all isolates exhibited strong degradative capacities, with Klebsiella pneumoniae strain 64D achieving the highest degradation rate, 80.38%, after one day of inoculation. In contrast, in vivo chlorpyrifos biodegradation assessment demonstrated a clear protective effect of gut bacteria on host survival. Among the mono-associated groups, larvae colonized with Klebsiella pneumoniae strain 66D exhibited the most pronounced reduction in mortality by 19.16-fold compared to antibiotic-treated larvae following exposure to chlorpyrifos suspension. Full article

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