Biology

30 pages, 1393 KB

Open AccessReview

Bridging Neurobiology and Artificial Intelligence: A Narrative Review of Reviews on Advances in Cochlear and Auditory Neuroprostheses for Hearing Restoration

by Daniele Giansanti

Biology 2025, 14(9), 1309; https://doi.org/10.3390/biology14091309 - 22 Sep 2025

Viewed by 249

Abstract

Background: Hearing loss results from diverse biological insults along the auditory pathway, including sensory hair cell death, neural degeneration, and central auditory processing deficits. Implantable auditory neuroprostheses, such as cochlear and brainstem implants, aim to restore hearing by directly stimulating neural structures. Advances [...] Read more.

Background: Hearing loss results from diverse biological insults along the auditory pathway, including sensory hair cell death, neural degeneration, and central auditory processing deficits. Implantable auditory neuroprostheses, such as cochlear and brainstem implants, aim to restore hearing by directly stimulating neural structures. Advances in neurobiology and device technology underpin the development of more sophisticated implants tailored to the biological complexity of auditory dysfunction. Aim: This narrative review of reviews aims to map the integration of artificial intelligence (AI) in auditory neuroprosthetics, analyzing recent research trends, key thematic areas, and the opportunities and challenges of AI-enhanced devices. By synthesizing biological and computational perspectives, it seeks to guide future interdisciplinary efforts toward more adaptive and biologically informed hearing restoration solutions. Methods: This narrative review analyzed recent literature reviews from PubMed and Scopus (last 5 years), focusing on AI integration with auditory neuroprosthetics and related biological processes. Emphasis was placed on studies linking AI innovations to neural plasticity and device–nerve interactions, excluding purely computational works. The ANDJ (a standard narrative review checklist) checklist guided a transparent, rigorous narrative approach suited to this interdisciplinary, rapidly evolving field. Results and discussion: Eighteen recent review articles were analyzed, highlighting significant advancements in the integration of artificial intelligence with auditory neuroprosthetics, particularly cochlear implants. Established areas include predictive modeling, biologically inspired signal processing, and AI-assisted surgical planning, while emerging fields such as multisensory augmentation and remote care remain underexplored. Key limitations involve fragmented biological datasets, lack of standardized biomarkers, and regulatory challenges related to algorithm transparency and clinical application. This review emphasizes the urgent need for AI frameworks that deeply integrate biological and clinical insights, expanding focus beyond cochlear implants to other neuroprosthetic devices. To complement this overview, a targeted analysis of recent cutting-edge studies was also conducted, starting from the emerging gaps to capture the latest technological and biological innovations shaping the field. These findings guide future research toward more biologically meaningful, ethical, and clinically impactful solutions. Conclusions: This narrative review highlights progress in integrating AI with auditory neuroprosthetics, emphasizing the importance of biological foundations and interdisciplinary approaches. It also recognizes ongoing challenges such as data limitations and the need for clear ethical frameworks. Collaboration across fields is vital to foster innovation and improve patient care. Full article

(This article belongs to the Section Neuroscience)

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38 pages, 683 KB

Open AccessArticle

Mathematical Modeling of Population Dynamics of Pollinators: A Survey

by Fernando Huancas, Anibal Coronel, Esperanza Lozada and Jorge Torres

Biology 2025, 14(9), 1308; https://doi.org/10.3390/biology14091308 - 22 Sep 2025

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Abstract

In this paper, we develop a systematic review of the existing literature on the mathematical modeling of several aspects of pollinators. We selected the MathSciNet and Wos databases and performed a search for the words “pollinator” and “mathematical model”. This search yielded a [...] Read more.

In this paper, we develop a systematic review of the existing literature on the mathematical modeling of several aspects of pollinators. We selected the MathSciNet and Wos databases and performed a search for the words “pollinator” and “mathematical model”. This search yielded a total of 236 records. After a detailed screening process, we retained 107 publications deemed most relevant to the topic of mathematical modeling in pollinator systems. We conducted a bibliometric analysis and categorized the studies based on the mathematical approaches used as the central tool in the mathematical modeling and analysis. The mathematical theories used to obtain the mathematical models were ordinary differential equations, partial differential equations, graph theory, difference equations, delay differential equations, stochastic equations, numerical methods, and other types of theories, like fractional order differential equations. Meanwhile, the topics were positive bounded solutions, equilibrium and stability analysis, bifurcation analysis, optimal control, and numerical analysis. We summarized the research findings and identified some challenges that could inform the direction of future research, highlighting areas that will aid in the development of future research. Full article

(This article belongs to the Special Issue Pollination Biology)

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24 pages, 2725 KB

Open AccessArticle

Isolation, Identification, and Characterization of Novel Environmental Bacteria with Polyurethane-Degrading Activity

by Marta Muñoz-Martí, Virtudes Navarro Bañón, Mª Carmen García-Poyo, Carlos Castaño Forte, Josefina Garrido, Jose María Orts, Andrea Huguet, Jorge García-Hernández and María Ángeles Castillo

Biology 2025, 14(9), 1307; https://doi.org/10.3390/biology14091307 - 22 Sep 2025

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Abstract

Polyurethane (PU) is a widely used plastic material whose persistence in the environment entails a serious ecological challenge. This study aimed to isolate and characterize environmental bacteria capable of degrading PU, using Impranil DLN as a model substrate, and to investigate their enzymatic [...] Read more.

Polyurethane (PU) is a widely used plastic material whose persistence in the environment entails a serious ecological challenge. This study aimed to isolate and characterize environmental bacteria capable of degrading PU, using Impranil DLN as a model substrate, and to investigate their enzymatic mechanisms and phylogenetic relationships. A total of 31 bacterial isolates were obtained from four waste accumulation sites and taxonomically identified across 12 different genera using MALDI-TOF MS and 16S rRNA gene sequencing. This analysis revealed genera not previously reported as PU biodegraders, including Priesta, Dermacoccus, Gordonia, Micrococcus, Pseudarthrobacter, and Agromyces. The Bacillus cereus clade was the most prevalent group, followed by the Priestia megaterium clade and Achromobacter sp. Biodegradation assays revealed high variability among strains, with the most efficient degrading over 90% of Impranil DLN. Protease activity was the most frequently detected enzymatic function, followed by urease and esterase activities. However, no clear correlation was observed between enzymatic profiles and degradation efficiency. Selected strains were tested on polyether PU foam, revealing biodegradative activity, an uncommon observation for bacteria on such recalcitrant material. These findings contribute to our understanding of bacterial diversity and enzymatic mechanisms involved in PU biodegradation, as well as their potential applications in plastic waste bioremediation. Full article

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13 pages, 8472 KB

Open AccessArticle

Radiation-Induced EMT of Adipose-Derived Stem Cells in 3D Organotypic Culture via Notch Signaling Pathway

by Seon Jeong Choi, Meesun Kim, Kyung Tae Chung and Tae Gen Son

Biology 2025, 14(9), 1306; https://doi.org/10.3390/biology14091306 - 22 Sep 2025

Viewed by 172

Abstract

In our previous study, adipose-derived stem cells (ASCs) cultured in a three-dimensional (3D) organotypic system exhibited mesenchymal-to-epithelial transition (MET) features, including cobblestone morphology and increased expression of E-cadherin and CK18. In this study, we investigated whether ionizing radiation could reverse this phenotype via [...] Read more.

In our previous study, adipose-derived stem cells (ASCs) cultured in a three-dimensional (3D) organotypic system exhibited mesenchymal-to-epithelial transition (MET) features, including cobblestone morphology and increased expression of E-cadherin and CK18. In this study, we investigated whether ionizing radiation could reverse this phenotype via epithelial–mesenchymal transition (EMT) and examined the involvement of Notch signaling. Mouse ASCs were cultured in Matrigel-based 3D organotypic conditions and exposed to 8 Gy of γ-radiation, and EMT- and Notch-related gene and protein expression were assessed 96 h post-irradiation using ATP viability assays, RT-qPCR, and Western blotting. Exposure to 8 Gy significantly reduced cell viability in 2D ASCs to 49.50 ± 6.50% compared with 61.02 ± 5.77% in 3D organoids (p < 0.0001). Irradiated 3D organoids showed EMT-like changes, including an increase of ~2.5-fold in fibronectin and an increase of ~2.0-fold in Twist1 expression, while epithelial CK18 was modestly elevated. Notch signaling was concurrently activated, with Notch1 and Jagged1 increasing by more than twofold and Fra-1 being significantly upregulated. Pretreatment with 20 μM of the γ-secretase inhibitor (GSI) kept cell viability above 90% and suppressed radiation-induced fibronectin, Twist1, Notch1, and Jagged1 expression. These findings indicate that ionizing radiation promotes EMT in 3D-cultured ASCs and reverses prior epithelialization, with Notch signaling playing a key regulatory role. The 3D ASC organoid model may thus provide a physiologically relevant platform for investigating radiation-induced plasticity and potential antifibrotic interventions. Full article

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16 pages, 6003 KB

Open AccessArticle

Therapeutic Effects of Stem Cells from Human Exfoliated Deciduous Teeth and Their Conditioned Medium in Cisplatin-Induced Acute Kidney Injury: An In Vivo Study

by Ardeshir Talebi, Sahar Talebi, Sara Nikpoor, Nosrat Nourbakhsh, Hossein Talebi, Sareh Soroushzadeh, Miguel Gómez-Polo and Seyed Ali Mosaddad

Biology 2025, 14(9), 1305; https://doi.org/10.3390/biology14091305 - 22 Sep 2025

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Abstract

Background: Acute kidney injury (AKI) is a severe condition with high morbidity and mortality. Mesenchymal stem cells (MSCs) and their conditioned medium (MSCs-CM), containing extracellular vesicles (EVs), have shown therapeutic potential. This study evaluates the effects of stem cells from human exfoliated deciduous [...] Read more.

Background: Acute kidney injury (AKI) is a severe condition with high morbidity and mortality. Mesenchymal stem cells (MSCs) and their conditioned medium (MSCs-CM), containing extracellular vesicles (EVs), have shown therapeutic potential. This study evaluates the effects of stem cells from human exfoliated deciduous teeth (SHED) and their conditioned medium (SHED-CM) on cisplatin-induced AKI in an in vivo model. Methods: Male Wistar rats (n = 21) were randomly divided into three groups: a control group (cisplatin-induced AKI without intervention), a SHED group (receiving intraperitoneal SHED injections), and a SHED-CM group (receiving intraperitoneal SHED-CM injections). Kidney weight, urine parameters, histopathology, and injury scores were assessed. Results: SHED-CM treatment significantly improved renal function, with reduced kidney injury scores (1.42 ± 0.18 vs. 2.57 ± 0.23 in the control, p < 0.05). Kidney weight was lower in the SHED-CM group compared to the control (1.12 ± 0.05 g vs. 1.36 ± 0.07 g, p < 0.05). SHED-CM also significantly increased urine volume (2.41 ± 0.19 mL vs. 1.23 ± 0.14 mL in the control, p < 0.01) and reduced urinary protein concentration (27.3 ± 2.1 mg/dL vs. 48.5 ± 3.4 mg/dL in the control, p < 0.05). Histopathological analysis revealed reduced tubular necrosis and inflammation, with SHED-CM showing superior improvement over SHED. Conclusions: SHED-CM demonstrated superior therapeutic efficacy over SHED injection in mitigating cisplatin-induced AKI, likely due to extracellular vesicle-mediated paracrine effects. These findings support SHED-CM as a promising, non-invasive alternative for MSC-EV-based AKI therapy. Full article

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21 pages, 6273 KB

Open AccessArticle

The Bacterial Community Characteristics of Hippophae rhamnoides Subsp. sinensis Rousi in Different Distribution Areas of the Qinghai–Tibet Plateau and Their Responses to Habitat Factors

by Pei Gao, Guisheng Ye and Yuhua Ma

Biology 2025, 14(9), 1304; https://doi.org/10.3390/biology14091304 - 21 Sep 2025

Viewed by 208

Abstract

Investigating the compositional characteristics of rhizosphere soil bacterial communities of Chinese seabuckthorn across different distribution areas and their relationship with habitat factors holds significant value for the development and utilization of characteristic medicinal plant resources in the Qinghai–Tibet Plateau. This study targeted rhizosphere [...] Read more.

Investigating the compositional characteristics of rhizosphere soil bacterial communities of Chinese seabuckthorn across different distribution areas and their relationship with habitat factors holds significant value for the development and utilization of characteristic medicinal plant resources in the Qinghai–Tibet Plateau. This study targeted rhizosphere soil from 12 distribution areas of Chinese seabuckthorn on the Qinghai–Tibet Plateau. By integrating measurements of soil and climatic parameters with high-throughput sequencing and redundancy analysis (RDA), the research systematically elucidated the characteristics of rhizosphere bacterial communities and their environmental driving mechanisms. The results revealed that rhizosphere bacterial communities of Chinese seabuckthorn across all 12 distribution areas were dominated by Proteobacteria, Acidobacteriota, and Actinobacteriota. Among them, the R2 habitat exhibited the highest amplicon sequence variant counts (3496), while R1, R8, R9, and R12 habitats showed significantly lower counts. α/β diversity analysis revealed that Shannon, Ace, and Chao1 indices in R2 and R7 habitats were significantly higher than those in R1 and R8. Regarding community aggregation patterns, soil bacterial communities in R1, R9, and R12 habitats exhibited the highest aggregation, while those in R2 and R11 habitats showed relatively lower aggregation. Functional prediction demonstrated that Metabolism dominated across all distribution areas (50.40–52.02%), with the R11 habitat exhibiting exceptionally high metabolic function abundance (>9300). Clustering analysis partitioned the 12 habitats into two distinct groups: one comprising R2, R6, R7, R9, R10, and R11, and the other containing the remaining six habitats. Redundancy analysis (RDA) further clarified that habitat factors, including altitude, soil water content (SWC), east longitude (EAST), and pH, were key drivers shaping bacterial community structure. This study underscores the pivotal regulatory role of environmental factors in shaping rhizosphere microbial diversity, community structure, and functional profiles of Chinese seabuckthorn, thereby providing a valuable scientific foundation for the sustainable development of characteristic medicinal plant resources on the Qinghai–Tibet Plateau. Full article

(This article belongs to the Section Microbiology)

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19 pages, 2575 KB

Open AccessArticle

Biosensor-Based Comparison of Stress Responses in Qingtian Paddy Field Carp (Cyprinus carpio var. qingtianensis) and Xingguo Red Carp (Cyprinus carpio var. singuonensis) Under Acute Shallow Water Conditions

by Tengyu Liu, Rui Han, Yuhan Jiang, Jiamin Sun, Haiyun Wu and Qigen Liu

Biology 2025, 14(9), 1303; https://doi.org/10.3390/biology14091303 - 20 Sep 2025

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Abstract

The domestication of common carp in rice paddies (5–20 cm depth) is challenging, as the fish must withstand drastic fluctuations in temperature and dissolved oxygen, restricted movement, and bird predation without the option of diving. The effects of stress responses in different species [...] Read more.

The domestication of common carp in rice paddies (5–20 cm depth) is challenging, as the fish must withstand drastic fluctuations in temperature and dissolved oxygen, restricted movement, and bird predation without the option of diving. The effects of stress responses in different species of carp in shallow-water environments remain poorly understood, particularly with fluctuating water levels where real-time monitoring is challenging. This study employed a glucose biosensor system enabling real-time monitoring, together with biochemical analysis techniques capable of evaluating multiple physiological indicators, to investigate shallow-water adaptation in Qingtian paddy field carp and Xingguo red carp. Our results quantitatively reveal, for the first time, the differing physiological stress thresholds of the two carp strains under shallow water. The Qingtian paddy field carp exhibited a higher tolerance to shallow water and showed faster recovery from prolonged stress. Furthermore, the total cholesterol and triglyceride contents of Qingtian paddy field carp gradually increased with prolonged shallow-water stress, reflecting the activation of lipid metabolic pathways. These findings highlight the advantages of biosensor technology in aquatic stress research and a strong support of the core element of paddy domesticated carp in the Globally Important Agricultural Heritage Systems. Full article

(This article belongs to the Special Issue Metabolic and Stress Responses in Aquatic Animals)

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22 pages, 1516 KB

Open AccessArticle

Investigation of the Physiological and Antioxidant Properties of the Medicinal and Endemic Hypericum bilgehan-bilgilii Species Under Different Cultivation Methods

by Huseyin Turker

Biology 2025, 14(9), 1302; https://doi.org/10.3390/biology14091302 - 20 Sep 2025

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Abstract

Hypericum bilgehan bilgilii is a locally endemic species belonging to the genus Hypericum. Considering that the related plant has pharmacological and medicinal potential like other Hypericum species, this study has been conducted to determine its physiological and antioxidant activities. Plant extracts obtained [...] Read more.

Hypericum bilgehan bilgilii is a locally endemic species belonging to the genus Hypericum. Considering that the related plant has pharmacological and medicinal potential like other Hypericum species, this study has been conducted to determine its physiological and antioxidant activities. Plant extracts obtained through three different cultivation methods (wild, cultivated in a laboratory environment in peat, and cultivated using tissue culture methods) were used to determine physiological, biochemical, and antioxidant activity analyses. (The abbreviations for the cultivation methods are indicated as, respectively, W, in vivo in lab, in vitro in lab). In this study, the highest photosynthetic pigment content, total protein content, proline content, malondialdehyde (MDA) content, phenylalanine ammonium lyase (PAL) activity, antioxidant activity (2,2-Diphenyl-1-picryl hydrazyl radical scavenging activity, total phenolic content, carotenoid) values were determined for the first time in the in vitro in lab group in H. bilgehan bilgilii plants grown under three different cultivation methods. Superoxide dismutase (SOD) and catalase (CAT) enzyme activities were observed at the highest levels in the wild group. Based on these parameters, the physiological, biochemical, and antioxidant activities of the H. bilgehan bilgilii plant were studied for the first time under different cultivation conditions, producing new results. According to these results, it was determined that in vitro cultivated plants have higher physiological parameters and antioxidant content. This study has also demonstrated the significance of tissue culture, a biotechnological method, in enhancing bioactive compounds, and that in vitro cultures could be used as an alternative to traditional methods for producing larger quantities of bioactive compounds. In addition, establishing in vitro cultures for endemic, endangered, and medically significant species will enable the sustainable use of the local endemic species H. bilgehan-bilgilii, facilitate large-scale production of phytochemicals, and provide a valuable plant resource and information for future comprehensive phytochemical studies. Full article

(This article belongs to the Special Issue Nature's Pharmacy: Ethnobotanical Approaches to Medicinal Plant Research for the Discovery and Development of Potential Phytochemicals)

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13 pages, 1312 KB

Open AccessArticle

Provenance-Specific Height–Diameter Modeling for Chinese Fir: A Clustered Mixed-Effects Approach

by Xiangrong Wu, Yuhan Wang, Yanjuan Lyu, Wanrong Chen, Ming Li and Shuaichao Sun

Biology 2025, 14(9), 1301; https://doi.org/10.3390/biology14091301 - 20 Sep 2025

Viewed by 231

Abstract

Chinese fir is the predominant afforestation species in southern China, exhibiting distinct provenances due to long-term climatic adaptation. This study utilized data from four surveys conducted at different ages in a provenance trial forest at Zhangping Wuyi Forest Farm, Fujian Province, to classify [...] Read more.

Chinese fir is the predominant afforestation species in southern China, exhibiting distinct provenances due to long-term climatic adaptation. This study utilized data from four surveys conducted at different ages in a provenance trial forest at Zhangping Wuyi Forest Farm, Fujian Province, to classify Chinese fir provenances using cluster analysis based on growth metrics. The resulting clusters were integrated as random effects into height–diameter models. Model performance was enhanced by incorporating age parameters and validated through five-fold cross-validation. The findings reveal that: (1) the Logistic model best captured the fundamental height–diameter relationship of Chinese fir; (2) the inclusion of provenance-clustering random effects improved model fit and predictive accuracy, with height-based clustering outperforming other methods; (3) the addition of age parameters further refined the base models beyond the clustering effects, and the combination of both approaches achieved the highest precision. Among clustering techniques, height-based clustering surpassed combined height–diameter at breast height (DBH) clustering, while DBH-based clustering was the least effective. The developed models facilitate precise growth predictions for multi-provenance Chinese fir across extensive geographic ranges, offering a theoretical basis for provenance-specific management. Full article

(This article belongs to the Section Ecology)

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11 pages, 242 KB

Open AccessArticle

Upregulation of Placental Vitamin D Receptor Expression in Gestational Diabetes Is Not Directly Related to Vitamin D Concentration

by Marek Walkowiak, Małgorzata Jamka, Mateusz de Mezer, Jakub Żurawski, Paweł Gutaj and Ewa Wender-Ożegowska

Biology 2025, 14(9), 1300; https://doi.org/10.3390/biology14091300 - 20 Sep 2025

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Abstract

Vitamin D plays a key role in pregnancy beyond calcium–phosphate regulation, modulating immune responses and glucose metabolism via the vitamin D receptor (VDR). Placental expression may be altered in gestational diabetes mellitus (GDM). This study aimed to assess placental VDR expression in GDM [...] Read more.

Vitamin D plays a key role in pregnancy beyond calcium–phosphate regulation, modulating immune responses and glucose metabolism via the vitamin D receptor (VDR). Placental expression may be altered in gestational diabetes mellitus (GDM). This study aimed to assess placental VDR expression in GDM and evaluate its association with maternal vitamin D levels and clinical parameters. VDR expression in the placental tissue of 53 women with GDM and 26 healthy controls was assessed semi-quantitatively by immunohistochemistry. Maternal serum 25-hydroxyvitamin D (25(OH)D) levels, body mass index, weight gain, neonatal outcomes, and other variables were evaluated. Univariate and multivariate linear regression analyses were performed. VDR expression was significantly higher in the GDM group compared to controls (p = 0.0297 for mean, p = 0.0378 for median). No significant differences were observed in serum 25(OH)D concentrations between groups. Stepwise regression revealed that diabetes was the only independent predictor of VDR expression. Within the GDM subgroup, VDR expression was not associated with any clinical parameters, including maternal vitamin D status. Upregulated placental VDR in GDM may represent an adaptive response to metabolic stress. These findings suggest complex regulation of vitamin D signalling in diabetic pregnancies, warranting further investigation. Full article

(This article belongs to the Section Medical Biology)

23 pages, 4336 KB

Open AccessArticle

Characterization of the Complete Mitogenome of Polypedates braueri (Anura, Rhacophoridae, Polypedates) and Insights into the Phylogenetic Relationships of Rhacophoridae

by Simin Chen, Huiling Huang, Siqi Shan, Chengmin Li, Kaiyuan Huang, Xinyi Xu and Lichun Jiang

Biology 2025, 14(9), 1299; https://doi.org/10.3390/biology14091299 - 20 Sep 2025

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Abstract

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of [...] Read more.

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (O_L), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article

(This article belongs to the Special Issue Progress in Wildlife Conservation, Management and Biological Research)

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19 pages, 4885 KB

Open AccessArticle

Induction of Sustained Immunity Following Vaccination with Live Attenuated Trypanosoma cruzi Parasites Combined with Saponin-Based Adjuvants

by Brenda A. Zabala, María Elisa Vázquez, Daniela E. Barraza, Andrea C. Mesías, Federico Ramos, Alejandro Uncos, Iván S. Marcipar, Leonardo Acuña and Cecilia Pérez Brandán

Biology 2025, 14(9), 1298; https://doi.org/10.3390/biology14091298 - 20 Sep 2025

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Abstract

Chagas disease, caused by Trypanosoma cruzi, remains a major health concern in Latin America, particularly affecting low-income and rural communities. Among the many vaccine strategies explored, live attenuated parasites have shown the strongest ability to trigger protective immune responses. In this study, [...] Read more.

Chagas disease, caused by Trypanosoma cruzi, remains a major health concern in Latin America, particularly affecting low-income and rural communities. Among the many vaccine strategies explored, live attenuated parasites have shown the strongest ability to trigger protective immune responses. In this study, we investigated whether adding saponin-based adjuvants—Immunostimulant Particle Adjuvant (ISPA) and Quil-A—could improve the effectiveness and safety of a live parasite attenuated T. cruzi vaccine. Mice were vaccinated with a T. cruzi attenuated strain (TCC) alone or in combination with each adjuvant, and immunoglobulin G (IgG) subtypes in the serum of vaccinated mice, and interferon gamma (IFN-γ) and interleukin-10 (IL-10) in the supernatants of stimulated cells were measured at two weeks and twelve months post-vaccination. While protection levels were similar across all groups, the adjuvants assist in modulating the immune response over time: ISPA and Quil-A initially shifted antibody production toward IgG1 but later favored a balanced T_H1/T_H2 profile. ISPA also promoted long-term regulation through increased IL-10. Both adjuvants reduced tissue inflammation and enhanced clearance of vaccine-derived parasites. These findings suggest that while adjuvants may not boost protection directly, they significantly improve vaccine safety and immune quality, reinforcing their value in developing better vaccines for Chagas disease. Full article

(This article belongs to the Special Issue Hope for the Forgotten: Tackling Endemic Parasitic Diseases with New Tools and Ideas)

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16 pages, 4760 KB

Open AccessArticle

The Stone Moroko Pseudorasbora parva Altered the Composition and Stability of Sediment Microbial Communities Within the Chinese Mitten Crab (Eriocheir sinensis) Polyculture Pond

by Yiran Hou, Yun Bao, Rui Jia, Linjun Zhou, Lili Song, Baojuan Yang, Bing Li and Jian Zhu

Biology 2025, 14(9), 1297; https://doi.org/10.3390/biology14091297 - 19 Sep 2025

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Abstract

Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing [...] Read more.

Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing to assess the ecological impacts of two polyculture methods involving river crabs on sediment bacteria, fungi, and protists. One method involved polyculturing river crabs with mandarin fish, silver carp, and the stone moroko (SPC), and the other involved polyculturing river crabs with only mandarin fish and silver carp (SMC). The results showed that, compared to the SMC group, the SPC group remarkably increased the Chao1 index of bacterial communities in pond sediment and decreased the Pielou_J index of protists. The relative abundances of all fungal phyla and most dominant bacterial and protistan phyla (top 10 in relative abundance) in the SPC group were considerably different from those in the SMC group. In the co-occurrence networks of bacterial, fungal, and protistan communities, the numbers of edges and nodes were higher in the SPC group than in the SMC group, and the habitat niche breadth of bacterial community was also notably increased in the SPC group. The levels of total carbon (TC), total nitrogen (TN), and phosphates within pond sediment in the SPC group were obviously lower than those in the SMC group, and were significantly correlated with the microbial communities, with TC being identified as the primary contributor driving changes in the microbial communities. All the findings collectively demonstrate that the polyculture of river crabs with mandarin fish, silver carp, and the stone moroko enhances the stability of bacterial, fungal, and protistan communities in sediment and enhances resource utilization efficiency in aquaculture, thereby preventing the environmental risks associated with excessive nutrient accumulation in sediment. Polyculture systems integrating river crabs with mandarin fish, silver carp, and the stone moroko represent a sustainable aquaculture model with significant ecological benefits. Full article

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

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20 pages, 4824 KB

Open AccessArticle

Assembly and Analysis of the Complete Mitochondrial Genome of Eryngium foetidum L. (Apiaceae)

by Lihong Zhang, Wenhu Zhang, Yongjian Luo, Jun Liu, Qing Li and Qiongheng Liu

Biology 2025, 14(9), 1296; https://doi.org/10.3390/biology14091296 - 19 Sep 2025

Viewed by 346

Abstract

Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and [...] Read more.

Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and antimicrobial properties, showing great potential in medical and food applications. Additionally, its essential oil has substantial commercial value. Mitochondria play a crucial role as organelles within plant cells; however, the mitochondrial genome of E. foetidum remains underexplored. To fill this research gap, we conducted sequencing and assembly of the mitochondrial genome of E. foetidum, aiming to uncover its genetic mechanisms and evolutionary trajectories. Our investigation reveals that the mitochondrial genome of E. foetidum is a circular structure, similar to that of other species, with a length of 241,660 bp and a GC content of 45.35%, which is within the range observed in other organisms. This genome encodes 59 genes, comprising 37 protein-coding sequences, 18 tRNA genes, and 4 rRNA genes. Comparative analysis highlighted 16 homologous regions between the mitochondrial and chloroplast genomes, with the longest segment spanning 992 bp. By analyzing 37 protein-coding genes (PCGs), we identified 479 potential RNA editing sites, which induce the formation of stop codons in the nad3 and atp6 genes, as well as start codons in the ccmFC, atp8, nad4L, cox2, cox1, and nad7 genes. Meanwhile, the genome shows a preference for A/T bases and A/T-ending codons, with 32 codons having a relative synonymous codon usage (RSCU) value greater than 1. The codon usage bias is relatively weak and mainly influenced by natural selection. Most PCGs are under purifying selection (Ka/Ks < 1), while only a few genes, such as rps7 and matR, may be under positive selection. Phylogenetic analysis of mitochondrial PCGs from 21 species showed E. foetidum at the basal node of Apiaceae, consistent with the latest APG angiosperm classification and chloroplast genome-based phylogenetic relationships. In summary, our comprehensive characterization of the E. foetidum mitochondrial genome not only provides novel insights into its evolutionary history and genetic regulation but also establishes a critical genomic resource for future molecular breeding efforts targeting mitochondrial-associated traits in this economically important species. Full article

(This article belongs to the Section Genetics and Genomics)

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21 pages, 1693 KB

Open AccessReview

Selenium and Mammalian Uterine Health: A Comprehensive Review

by Ruoning Wu, Xiaohan Li, Zhaoming Li, Jilong Luo, Ziwei Zhang and Mengyao Guo

Biology 2025, 14(9), 1295; https://doi.org/10.3390/biology14091295 - 19 Sep 2025

Viewed by 387

Abstract

Selenium (Se) is an essential trace element for animals and plays an important role in maintaining various physiological functions. In recent years, more and more studies have focused on the relationship between selenium and mammalian uterus health. This review comprehensively summarizes the current [...] Read more.

Selenium (Se) is an essential trace element for animals and plays an important role in maintaining various physiological functions. In recent years, more and more studies have focused on the relationship between selenium and mammalian uterus health. This review comprehensively summarizes the current research progress in this field and introduces the physiological functions of selenium, including its antioxidant, anti-inflammatory, and immune regulatory functions. It also analyzed the role of selenium in uterine development, maintaining pregnancy, preventing and treating uterine diseases from multiple aspects. In addition, factors affecting animal selenium utilization and appropriate selenium supplementation strategies were also introduced. Understanding the relationship between selenium and animal uterine health is of great significance for improving animal reproductive performance, ensuring offspring health, and promoting sustainable development of the animal husbandry. Full article

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

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17 pages, 997 KB

Open AccessArticle

Gonadal Production and Quality in the Red Sea Urchin Mesocentrotus franciscanus Fed with Seaweed Devaleraea mollis and Ulva australis from a Land-Based Integrated Multi-Trophic Aquaculture (IMTA) System

by Matthew S. Elliott, Yuanzi Huo and Mark Drawbridge

Biology 2025, 14(9), 1294; https://doi.org/10.3390/biology14091294 - 19 Sep 2025

Viewed by 306

Abstract

Harvesting sea urchins from barrens and enhancing their gonads through aquaculture offers a promising way to convert low-value individuals into high-quality seafood. This study evaluated whether red sea urchins (Mesocentrotus franciscanus, RSUs) fed nutrient-enriched seaweeds produced in a land-based integrated multi-trophic [...] Read more.

Harvesting sea urchins from barrens and enhancing their gonads through aquaculture offers a promising way to convert low-value individuals into high-quality seafood. This study evaluated whether red sea urchins (Mesocentrotus franciscanus, RSUs) fed nutrient-enriched seaweeds produced in a land-based integrated multi-trophic aquaculture (IMTA) system could significantly improve gonad size and quality. Two seaweed species, Ulva australis and Devaleraea mollis, were grown in effluent from white seabass (Atractoscion nobilis) tanks and used to feed RSUs over an 8-week period. RSUs readily consumed both seaweeds, with measurable ingestion, fecal output, and absorption efficiency. We hypothesized that RSUs fed IMTA seaweed would exhibit increased gonadosomatic index and improved gonad quality. GSI significantly increased in both groups, from an initial 3.00 ± 0.50% (9.02 ± 1.80 g) to 4.64 ± 0.66% (23.04 ± 10.20 g) in the U. australis group and to 6.35 ± 1.30% (31.20 ± 7.20 g) in the D. mollis group. Gonad quality improved from “D” (unmarketable) to average “B” (high-quality) grade, based on color, firmness, and texture. These results demonstrate that RSUs collected from barrens can be enhanced into premium seafood using nutrient-enriched seaweeds. Integrating RSUs into land-based IMTA systems may increase aquaculture efficiency, reduce waste, and diversify seafood production in a sustainable and economically viable way. Full article

(This article belongs to the Section Marine Biology)

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17 pages, 2667 KB

Open AccessArticle

Comprehensive Analysis of TaNCED Gene Family in Wheat Vernalization Process

by Guoqing Cui and Hao Cheng

Biology 2025, 14(9), 1293; https://doi.org/10.3390/biology14091293 - 19 Sep 2025

Viewed by 268

Abstract

9-cis-epoxycarotenoid dioxygenases (NCEDs), serving as the rate-limiting enzymes in abscisic acid (ABA) biosynthesis, play a pivotal role in regulating plant growth and development, as well as responses to abiotic stresses. Despite their agronomic importance, the molecular dialog between ABA signaling and [...] Read more.

9-cis-epoxycarotenoid dioxygenases (NCEDs), serving as the rate-limiting enzymes in abscisic acid (ABA) biosynthesis, play a pivotal role in regulating plant growth and development, as well as responses to abiotic stresses. Despite their agronomic importance, the molecular dialog between ABA signaling and vernalization, a cold-induced switch from vegetative to reproductive growth in wheat, remains poorly characterized, particularly regarding the TaNCED gene family members. Here, we systematically identified 13 TaNCED members in hexaploid wheat, followed by multi-omics characterization encompassing physicochemical properties, exon–intron architectures, conserved catalytic domains, protein motifs, and cis-acting elements. By analyzing transcriptome data from vernalization treatments, we profiled the expression patterns of TaNCED genes during vernalization. Notably, TaNCED5-6A, TaNCED5-6B, and TaNCED5-6D exhibited significant upregulation in vernalized leaves and tiller buds, while maintaining basal expression in the shoot apical meristem, the site of floral induction. This tissue-specific expression pattern implicates their specialized role in mediating vernalization responses via ABA biosynthesis. Collectively, our findings provide novel insights into the regulatory mechanisms of ABA-mediated vernalization in wheat and offer valuable targets for vernalization efficiency in cereal breeding programs. Full article

(This article belongs to the Section Plant Science)

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17 pages, 10478 KB

Open AccessArticle

Urban Edge Predators: Wolf Spatial and Temporal Ecology at the Wildland–Urban Interface in Mongolia

by Jeff Dolphin, Maria Vittoria Mazzamuto, Gantulga Gankhuyag, Delgerchimeg Davaasuren, Bayaraa Munkhtsog, Ulam-Urnukh Bayanmunkh, Gansukh Sukhchuluun and John L. Koprowski

Biology 2025, 14(9), 1292; https://doi.org/10.3390/biology14091292 - 18 Sep 2025

Viewed by 334

Abstract

Mongolia’s rapidly expanding capital is encroaching on Bogd Khan Mountain, a UNESCO Biosphere Reserve and the oldest protected area in Eurasia. Gray wolves (Canis lupus) in this wildland–urban interface are locally near-threatened due to hunting, local beliefs, and human–wildlife conflict. In [...] Read more.

Mongolia’s rapidly expanding capital is encroaching on Bogd Khan Mountain, a UNESCO Biosphere Reserve and the oldest protected area in Eurasia. Gray wolves (Canis lupus) in this wildland–urban interface are locally near-threatened due to hunting, local beliefs, and human–wildlife conflict. In 2022 and 2023, we deployed 72 camera traps (11,539 trap nights) to investigate how wolves respond to overlapping pressures from free-ranging dogs, livestock, and human activity. Using a random habitat-stratified camera design and abundance modeling, we assessed diel activity and spatial co-occurrence. Wolves exhibited nocturnal and crepuscular activity, with the greatest temporal overlap with wild prey (wapiti: ∆⁴ = 0.73; Siberian roe deer: ∆⁴ = 0.79), moderate overlap with dogs (∆⁴ = 0.60) and horses (∆⁴ = 0.68), and minimal overlap with cattle (∆⁴ = 0.40) and people (∆⁴ = 0.43). Mean wolf abundance estimates ranged from λ = 0.91 (CI 95%, 0.05–1.77) in 2022 to λ = 1.52 (CI 95%, 0.44–3.53) in 2023. Wolves were more abundant at higher relative abundance of wild ungulates and in areas with more people. Wolves co-occurred with dogs at 11 sites and were more abundant in areas with a higher number of dogs. Our findings highlight the complex dynamics between wildlife, livestock, and human-associated disturbances at the wildland–urban interface, underscoring the need for integrated management strategies that address both ecological and human dimensions of conservation. Full article

(This article belongs to the Special Issue Biology, Ecology, Management and Conservation of Canidae)

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30 pages, 6286 KB

Open AccessArticle

Contrasting Assembly and Network Roles of Abundant and Rare Bacteria in Reservoir and Soil Habitats

by Cuixia Zhang, Haiming Li, Mengdi Li, Sihui Su, Han Xiao, Xiaodong Zhang and Qian Zhang

Biology 2025, 14(9), 1291; https://doi.org/10.3390/biology14091291 - 18 Sep 2025

Viewed by 329

Abstract

Reservoir water and the adjacent soil are ecologically interconnected yet distinct microhabitats in saline coastal wetland ecosystems, but direct comparisons of their bacterial community composition and assembly remain limited. Here, we integrated high-throughput 16S rRNA gene sequencing with statistical, null model, and network [...] Read more.

Reservoir water and the adjacent soil are ecologically interconnected yet distinct microhabitats in saline coastal wetland ecosystems, but direct comparisons of their bacterial community composition and assembly remain limited. Here, we integrated high-throughput 16S rRNA gene sequencing with statistical, null model, and network analyses to compare diversity patterns, assembly mechanisms, and interactions of abundant and rare bacterial taxa in both habitats. Soil communities exhibited greater taxonomic diversity but a lower overall abundance, while reservoir communities displayed a pronounced vertical stratification, in contrast to the more spatially uniform soil communities at the sampled scale. Key environmental drivers differed: salinity (reflecting the harsh saline context) and nutrient levels structured reservoir communities, whereas the nutrient availability and cation exchange capacity predominated in soils. Stochastic processes mainly governed the assembly of abundant taxa in both habitats, whereas deterministic selection more strongly structured rare taxa, especially in soils subject to harsh saline conditions. The co-occurrence network analysis revealed higher connectivity and modularity in soils, with moderate taxa acting as critical connectors between modules. In contrast, rare taxa played a pivotal role in sustaining network stability in the reservoir. Together, these findings demonstrate distinct, habitat-dependent assembly mechanisms and ecological roles of abundant and rare bacterial taxa in saline coastal wetland microhabitats, providing insights that can inform wetland conservation and ecosystem management. Full article

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

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26 pages, 2196 KB

Open AccessArticle

Morphofunctional Spaces from the Astragalus: Exploring Angular Excursions and Mechanical Efficiency in Caraguatypotherium munozi (Notoungulata, Mesotheriidae)

by Paul Medina-González

Biology 2025, 14(9), 1290; https://doi.org/10.3390/biology14091290 - 18 Sep 2025

Viewed by 911

Abstract

The astragalus is a key biomechanical link between the autopodium and limb in mammals, modulating stability and mobility during stance. Its morphology provides reliable proxies for inferring posture, body mass, and locomotor behavior in extinct taxa. Mesotheriids (Notoungulata, Mesotheriidae) have traditionally been regarded [...] Read more.

The astragalus is a key biomechanical link between the autopodium and limb in mammals, modulating stability and mobility during stance. Its morphology provides reliable proxies for inferring posture, body mass, and locomotor behavior in extinct taxa. Mesotheriids (Notoungulata, Mesotheriidae) have traditionally been regarded as fossorial generalists, yet their functional diversity remains poorly tested. The astragali of Caraguatypotherium munozi (Miocene, Chile) and Trachytherus spegazzinianus (early Miocene, Argentina) were analyzed, integrating osteological measurements and functional indices to explore their locomotor ecology. Principal component analyses were performed to compare their morphofunctional spaces with those of 38 extant terrestrial mammals grouped by posture, body mass, top speed, and locomotor habit. Total Angular Excursion (TAE) and Angular Efficiency Index (AEI) were estimated using a comparative dataset of 182 terrestrial mammals spanning 15 taxonomic orders, focused on stance-phase mechanics during comfortable locomotion. C. munozi shows a deeper trochlea and moderately expanded navicular facets, whereas T. spegazzinianus presents a shallower trochlea and narrower articular proportions. Despite these morphological differences, both species share broadly overlapping stance-phase kinematic ranges, reflecting a conserved plantigrade locomotor module optimized for stability and energy-efficient weight support. These findings challenge the view of mesotheriids as functionally uniform and highlight ecological diversification through subtle morphological adjustments within a constrained locomotor framework. Full article

(This article belongs to the Section Evolutionary Biology)

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26 pages, 2624 KB

Open AccessReview

The Dual Role of RASSF4 in Tumorigenesis: Mechanisms and Epigenetic Targeting Strategies

by Rui Tian, Yixin Wu, Wenbin Yuan, Lingli Tian, Rui Zhang, Hao Lyu, Shuai Xiao, Dong Guo, Qi Zhang, Declan William Ali, Marek Michalak, Cefan Zhou, Jingfeng Tang and Xing-Zhen Chen

Biology 2025, 14(9), 1289; https://doi.org/10.3390/biology14091289 - 18 Sep 2025

Viewed by 348

Abstract

RASSF4 is a key member of the Ras-associated domain family (RASSF) that exhibits dual functionality in tumorigenesis, playing critical yet context-dependent roles in various malignancies. Its expression is epigenetically regulated through promoter hypermethylation, histone modifications, and microRNAs including miR-155 and miR-196a-5p, which directly [...] Read more.

RASSF4 is a key member of the Ras-associated domain family (RASSF) that exhibits dual functionality in tumorigenesis, playing critical yet context-dependent roles in various malignancies. Its expression is epigenetically regulated through promoter hypermethylation, histone modifications, and microRNAs including miR-155 and miR-196a-5p, which directly target its 3′ untranslated region. In most cancers, such as non-small cell lung cancer (NSCLC) and gastric adenocarcinoma (GAC), RASSF4 acts as a tumor suppressor by inhibiting the RAS/MAPK pathway while activating the Hippo signaling cascade, ultimately inducing cell cycle arrest and apoptosis. Conversely, in aRMS, RASSF4 is upregulated by the PAX3-FOXO1 fusion oncoprotein and promotes tumor growth through MST1 inhibition and subsequent YAP activation. This review systematically analyzes current evidence regarding RASSF4’s complex regulatory mechanisms and clinical significance. We propose targeted therapeutic strategies including epigenetic reactivation, gene intervention, and combination therapies. Furthermore, we identify RASSF4 as a promising diagnostic biomarker and therapeutic target based on integrated mechanistic and clinical evidence. Future research should focus on elucidating context-dependent regulatory switches, developing targeted delivery systems, and validating clinical utility through prospective trials. Full article

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

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18 pages, 4063 KB

Open AccessArticle

Welander Distal Myopathy-Associated TIA1 E384K Mutation Disrupts Stress Granule Dynamics Under Distinct Stress Conditions

by Beatriz Ramos-Velasco, José Alcalde and José M. Izquierdo

Biology 2025, 14(9), 1288; https://doi.org/10.3390/biology14091288 - 18 Sep 2025

Viewed by 294

Abstract

Cellular stress triggers the formation of diverse RNA–protein aggregates, which can be associated with physiological responses, pathological conditions, or even detrimental outcomes. Under stress-induced proteostasis disruption, these RNA–protein assemblies are known as stress granules (SGs). Targeting such condensates—while sparing functional RNAs and proteins—remains [...] Read more.

Cellular stress triggers the formation of diverse RNA–protein aggregates, which can be associated with physiological responses, pathological conditions, or even detrimental outcomes. Under stress-induced proteostasis disruption, these RNA–protein assemblies are known as stress granules (SGs). Targeting such condensates—while sparing functional RNAs and proteins—remains a major therapeutic challenge in protein aggregation disorders such as myopathies and neuropathies. In this study, we investigated the cellular response to various stress conditions in the context of the TIA1 E384K mutation, a founder variant implicated in both Welander distal myopathy (WDM) and amyotrophic lateral sclerosis (ALS). Cells were exposed to different stressors, including proteotoxic, proteostatic, chemotoxic, and osmotic insults, and the behavior of TIA1-related SGs was analyzed. Our findings reveal a distinct yet conserved pattern in the dynamics of TIA1-dependent SG formation and clearance, influenced by the specific type of stressor and modulated by eIF2α Ser35 phosphorylation. These results indicate that the WDM-associated TIA1 mutation leads to aberrant SG dynamics across different stress conditions. Collectively, these observations support the idea that TIA1 E384K-associated SG dysregulation plays a role in WDM and ALS pathogenesis and underscores the importance of multiple stress contexts in disease progression. Full article

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14 pages, 6919 KB

Open AccessArticle

Branched Setae or Attached Macroalgae: A Case Study of an Exceptionally Preserved Brachiopod from the Early Cambrian Chengjiang Lagerstätte

by Yue Liang, Timothy P. Topper, Baopeng Song, Caibin Zhang, Oluwatoosin B. A. Agbaje, Lars E. Holmer and Zhifei Zhang

Biology 2025, 14(9), 1287; https://doi.org/10.3390/biology14091287 - 18 Sep 2025

Viewed by 640

Abstract

The remarkable conservation of soft tissues within Cambrian fossils has significantly enhanced our comprehension of the origins and evolutionary trajectories of animals, in addition to the progression of ecological intricacy. Here, we report an exceptionally preserved specimen of the lingulid brachiopod Xianshanella haikouensis [...] Read more.

The remarkable conservation of soft tissues within Cambrian fossils has significantly enhanced our comprehension of the origins and evolutionary trajectories of animals, in addition to the progression of ecological intricacy. Here, we report an exceptionally preserved specimen of the lingulid brachiopod Xianshanella haikouensis from the lower Cambrian Chengjiang Lagerstätte, exhibiting branched fringes along the distal ends of its marginal setae. These structures may represent either branched setae or attached macroalgae. The diameter of the branched fringes is slightly larger than that of the marginal setae, and they exhibit third- or fourth-order bifurcations, forming a complex structure comparable in length to the shell. Both the branched fringes and marginal setae are preserved as iron oxides, as revealed by SEM and Micro-XRF analyses, a characteristic preservation mode in Chengjiang fossils. The results of Micro-CT scanning suggest that these branched fringes are preserved along almost the entire distal end of marginal setae. Comparable branched fringes are reminiscent of those found in annelids, and such structural analogs between annelid and brachiopod setae support the homology of brachiopod and annelid setae, representing a lophotrochozoan synapomorphy. An alternative explanation involving attached macroalgae is proposed, given that branched setae have never been documented in either extinct or extant brachiopod taxa. If these structures represent macroalgae, this association could represent a mimicry strategy to deceive predators, although comparable macroalgal fossils remain undocumented in the Chengjiang Lagerstätte. Our research highlights the potential for brachiopod setae to serve roles in sensory function or ecological interactions, offering a new perspective on early animal adaptation and community dynamics. Full article

(This article belongs to the Section Evolutionary Biology)

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15 pages, 741 KB

Open AccessArticle

The Challenge of Lyme Borreliosis: Knowledge, Attitudes, and Practices in France

by Cynthia Philibert, Joana Ferrolho, Mark S. Gibson, Sérgio Ramalho de Sousa, Hugo Vilhena and Sofia Anastácio

Biology 2025, 14(9), 1286; https://doi.org/10.3390/biology14091286 - 17 Sep 2025

Viewed by 349

Abstract

Lyme borreliosis (LB), a zoonotic disease caused by Borrelia burgdorferi sensu lato and transmitted by Ixodes ricinus, is increasingly relevant in France, yet data on public awareness and prevention are limited. This cross-sectional study assessed the knowledge, attitudes, and practices (KAP) of [...] Read more.

Lyme borreliosis (LB), a zoonotic disease caused by Borrelia burgdorferi sensu lato and transmitted by Ixodes ricinus, is increasingly relevant in France, yet data on public awareness and prevention are limited. This cross-sectional study assessed the knowledge, attitudes, and practices (KAP) of companion-animal owners (CAOs) and veterinarians regarding LB. Online questionnaires were distributed between January and April 2023, yielding 159 valid CAO responses and 48 responses from veterinarians. Among owners, 95% reported outdoor access for their pets, 73.9% had observed ticks, and 88.8% used ectoparasiticides. However, only 16.4% reported LB vaccination, and just 38% recognized key canine clinical signs. Veterinarians frequently suspected LB (70%) but confirmed diagnoses less often (39.6%), relying mainly on clinical signs and the results of rapid tests. While prevention through antiparasitic use was common, communication between veterinarians and owners regarding LB was inconsistent. Despite this, most owners reported compliance with veterinary guidance. These findings reveal good preventive habits but identify knowledge gaps and underdiagnosis. Enhancing veterinary–client communication and promoting a One Health approach could improve LB prevention and control in France. Full article

(This article belongs to the Section Microbiology)

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16 pages, 3557 KB

Open AccessArticle

Mechanisms of Variation in Abdominal Adipose Color Among Male Kazakh Horses Through Non-Coding RNA Sequencing

by Yuhe Zhou, Xinkui Yao, Jun Meng, Jianwen Wang, Yaqi Zeng, Linling Li and Wanlu Ren

Biology 2025, 14(9), 1285; https://doi.org/10.3390/biology14091285 - 17 Sep 2025

Viewed by 253

Abstract

The Kazakh horse is a highly valuable indigenous Chinese breed known for its use in both milk and meat production. However, the mechanisms underlying color variation in the abdominal adipose tissue of this breed remain poorly understood. In this study, the sequencing of [...] Read more.

The Kazakh horse is a highly valuable indigenous Chinese breed known for its use in both milk and meat production. However, the mechanisms underlying color variation in the abdominal adipose tissue of this breed remain poorly understood. In this study, the sequencing of non-coding RNAs (ncRNAs) was conducted on abdominal adipose tissue of different colors from Kazakh horses, with the aim of investigating the molecular mechanisms responsible for this variation. A total of 205 differentially expressed long non-coding RNAs (DELncRNAs) including ENSECAG00000003836, ENSECAG00000017858, and ENSECAG00000035167; 52 differentially expressed microRNAs (DEmiRNAs) including miR-200-y and eca-miR-9a; and 559 differentially expressed circular RNAs (DEcircRNAs) including ZNF226 and ITPKC, were identified between Group W and Group Y. GO annotation and KEGG enrichment analyses of the DEGs revealed that these genes were primarily involved in biological processes such as chemical homeostasis (biological process, BP), intracellular components (cellular component, CC), and iron-sulfur cluster binding (molecular function, MF) as well as in metabolic pathways related to lipid biosynthesis and metabolism including vitamin B6 metabolism, tryptophan metabolism, and glycerolipid metabolism. The sequencing accuracy was further validated using reverse transcription quantitative PCR (RT-qPCR). This study identified key DEGs and signaling pathways associated with the color variation in adipose tissue of Kazakh horses and sheds light on the regulatory genes and biological processes involved. These findings provide a theoretical basis and research foundation for future studies on color variations in the adipose tissue of equine species. Full article

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14 pages, 1190 KB

Open AccessArticle

Effects of Inorganic Phosphorus-Solubilizing Bacteria on Rhizosphere Phosphorus Forms and Steroid Saponin Content of Paris polyphylla var. yunnanensis

by You Zhou, Yueheng Wang, Lingfeng Xu, Guoxin Lan, Dongqin Guo, Haizhu Zhang and Nong Zhou

Biology 2025, 14(9), 1284; https://doi.org/10.3390/biology14091284 - 17 Sep 2025

Viewed by 217

Abstract

To improve the phosphorus utilization efficiency and medicinal quality of the traditional Chinese medicinal herb Paris polyphylla var. yunnanensis, three inorganic phosphorus-solubilizing bacteria strains (Bacillus cereus Y1-1, Bacillus aryabhattai Z6-1, and Bacillus aryabhattai Z3-4) were inoculated individually and in combination into [...] Read more.

To improve the phosphorus utilization efficiency and medicinal quality of the traditional Chinese medicinal herb Paris polyphylla var. yunnanensis, three inorganic phosphorus-solubilizing bacteria strains (Bacillus cereus Y1-1, Bacillus aryabhattai Z6-1, and Bacillus aryabhattai Z3-4) were inoculated individually and in combination into the rhizosphere soil of Paris polyphylla var. yunnanensis in a greenhouse pot experiment. At the late growth stage, the contents of total and inorganic phosphorus in the rhizosphere soils, as well as the total phosphorus and six steroidal saponins in the plants, were measured. The proportion of inorganic phosphorus in rhizosphere soils of treatment groups increased by 9.83~30.43%. The content of effective phosphorus form Ca₂-P in the rhizosphere soils of treatment groups increased by 50.81~328.37%. Inoculation with B. aryabhattai (S2, S3, and S6) significantly increased total steroidal saponin content in plants by 9.14%, 10.64%, and 16.58%, respectively. An antagonistic effect was observed when multiple bacterial strains were inoculated together. Thus, mixed inoculation was less effective than single-strain inoculation in improving rhizosphere soil phosphorus structure. In conclusion, inoculation with inorganic phosphorus-solubilizing bacteria could enhance phosphorus availability in rhizosphere soil and improve medicinal quality of Paris polyphylla var. yunnanensis. These findings provide a basis for efficient phosphorus resource utilization and sustainable cultivation to enhance medicinal plant quality. Full article

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14 pages, 879 KB

Open AccessArticle

Earthworm Species from Diverse Ecological Groups Negatively Affect Enchytraeid Density in a Forest Ecosystem

by Kamil Karaban, Anita Kaliszewicz, Krassimira Ilieva-Makulec and Alexei V. Uvarov

Biology 2025, 14(9), 1283; https://doi.org/10.3390/biology14091283 - 17 Sep 2025

Viewed by 239

Abstract

Earthworms and enchytraeids are two very important groups of soil organisms that influence soil biology and ecology, as well as physicochemical processes occurring in the soil. The interactions within and between these major groups of soil fauna are currently among the most pressing [...] Read more.

Earthworms and enchytraeids are two very important groups of soil organisms that influence soil biology and ecology, as well as physicochemical processes occurring in the soil. The interactions within and between these major groups of soil fauna are currently among the most pressing topics in soil ecology and are still insufficiently understood. In a field mesocosm experiment, we examined the effects of the density of the following five key earthworm species in Central Europe: Dendrobaena octaedra, Lumbricus rubellus, L. terrestris, Aporrectodea caliginosa, and Allobophora chlorotica. These species were selected to represent the following three major ecological groups of lumbricids: epigeic, endogeic, and anecic. The mesocosm experiment examined the effect of these species across density gradients and at two soil profile horizons—litter and mineral soil—and at the entire soil profile within the mesocosm. This comprehensive and unique approach was used to compare the effects of earthworm density gradient on enchytraeid abundance under identical conditions in the forest soil. The results indicate that all studied species of earthworm negatively affected enchytraeid density. The strength of this effect depended on the earthworm species, earthworm density, and the level of the analyzed soil profile. Epigeic L. rubellus, endogeic Aporrectodea caliginosa, and anecic L. terrestris appeared to be the most effective. Higher earthworm density had a greater effect on the density of enchytraeids. The most significant results concerned the litter layer, where the density of enchytraeids was highest due to their natural occurrence. Our results provide new insights into the ecological relationships among key groups of soil fauna and can be a starting point for predicting changes caused by earthworms in newly occupied ecosystems. Full article

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20 pages, 10721 KB

Open AccessArticle

The Progressive Colonization of the Invasive Species Amphistegina lobifera on Pantelleria Island (Central Mediterranean, Sicily Channel)

by Claudia Cosentino and Antonio Caruso

Biology 2025, 14(9), 1282; https://doi.org/10.3390/biology14091282 - 17 Sep 2025

Viewed by 347

Abstract

Amphistegina lobifera, a symbiont-bearing benthic foraminifera native to the Indo-Pacific, is expanding its distribution range in the Mediterranean Sea due to ysian migration through the Suez Canal. This study investigates the colonization dynamics and ecological impact of A. lobifera on Pantelleria Island, [...] Read more.

Amphistegina lobifera, a symbiont-bearing benthic foraminifera native to the Indo-Pacific, is expanding its distribution range in the Mediterranean Sea due to ysian migration through the Suez Canal. This study investigates the colonization dynamics and ecological impact of A. lobifera on Pantelleria Island, which is located in the Central Mediterranean. Nine samples were collected from various substrates at different depths (−4 to −20 m) and analysed for composition, abundance, and ecological diversity. Results reveal a significant dominance of A. lobifera, especially in shallow unvegetated substrates, with relative abundances exceeding 50%. Conversely, more vegetated substrates host more diverse and balanced assemblages. Diversity indices are consistently lower where A. lobifera is dominant, indicating reduced biodiversity. Comparison with similar studies in Malta, Linosa, and Corfu confirms a 20% relative abundance threshold for A. lobifera as indicative of potential ecological imbalance. The results suggest that it represents a growing threat to native microbenthic biodiversity and reinforce its usefulness as a bioindicator species. Pantelleria represents a key transition zone for monitoring the dynamics of invasive species in the Mediterranean, and this study highlights the urgent need for long-term surveillance of benthic biodiversity. Full article

(This article belongs to the Special Issue Alien Marine Species in the Mediterranean Sea)

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15 pages, 2112 KB

Open AccessReview

HSP60 and SARS-CoV-2: Les Liaisons Dangereuses

by Adelaide Carista, Melania Ionelia Gratie, Francesco Cappello and Stefano Burgio

Biology 2025, 14(9), 1281; https://doi.org/10.3390/biology14091281 - 17 Sep 2025

Viewed by 243

Abstract

Heat shock protein 60 (Hsp60) plays a crucial role in cellular homeostasis and stress responses. Recent evidence highlights its involvement in COVID-19 pathophysiology, particularly in immune modulation, inflammation, and endothelial dysfunction. Extracellular Hsp60 can interact with Toll-like receptors, amplifying inflammatory responses and contributing [...] Read more.

Heat shock protein 60 (Hsp60) plays a crucial role in cellular homeostasis and stress responses. Recent evidence highlights its involvement in COVID-19 pathophysiology, particularly in immune modulation, inflammation, and endothelial dysfunction. Extracellular Hsp60 can interact with Toll-like receptors, amplifying inflammatory responses and contributing to cytokine storm and tissue damage. Additionally, since the presence of several common epitopes with SARS-CoV-2 proteins, its role in molecular mimicry suggests a potential link also to post-infectious autoimmune disorders. Hsp60 has also been implicated in endothelial damage and thromboembolic complications observed in severe COVID-19 cases. Beyond its pathogenic roles, Hsp60 could emerge as a potential biomarker for disease severity as well as a target for therapeutic strategies aimed at modulating immune responses. Finally, the structural similarity with SARS-CoV-2 proteins raises important considerations regarding both vaccine safety and the unexpected potential for anti-tumor immunity. This review critically examines the multifaceted roles of Hsp60 in COVID-19, specifically from a morpho-functional point of view, highlighting its implications in disease progression, post-viral complications, and therapeutic opportunities. Full article

(This article belongs to the Section Cell Biology)

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21 pages, 2253 KB

Open AccessArticle

Ferroptosis-Linked Six-Gene Panel Enables Machine Learning-Assisted Diagnosis and Therapeutic Guidance in Lung Adenocarcinoma

by Faris Alrumaihi

Biology 2025, 14(9), 1280; https://doi.org/10.3390/biology14091280 - 17 Sep 2025

Viewed by 277

Abstract

Lung adenocarcinoma (LUAD) remains the most common subtype of non-small-cell lung cancer and a major cause of cancer mortality, with many patients lacking actionable mutations or durable responses to targeted or immune therapies. Here, we report an integrative analysis of TCGA LUAD transcriptomes [...] Read more.

Lung adenocarcinoma (LUAD) remains the most common subtype of non-small-cell lung cancer and a major cause of cancer mortality, with many patients lacking actionable mutations or durable responses to targeted or immune therapies. Here, we report an integrative analysis of TCGA LUAD transcriptomes (n = 598) seeded from a curated ferroptosis gene catalogue, yielding a compact six-gene signature (AQP4, CDCA3, HJURP, KIF20A, PLK1, UHRF1) with diagnostic, prognostic, and therapeutic relevance. The signature was consistently dysregulated in tumours versus normal lung and stratified patients into high- and low-risk groups with distinct survival outcomes (log-rank p < 0.0001), outperforming conventional staging when incorporated into multivariable models. Across ten machine learning algorithms, the panel achieved near-perfect tumour-normal classification (AUC 0.99–1.00), highlighting its translational potential for early detection. Functional analyses linked the signature to cell-cycle, angiogenic, and immune modulation, while exploratory drug-gene correlations identified PLK1 and other candidates as potential therapeutic targets. Together, these findings establish a biologically anchored six-gene panel that complements existing mutation-based classifiers and provides a framework for advancing diagnostic precision, prognostic refinement, and biomarker-guided therapeutic strategies in LUAD. Full article

(This article belongs to the Special Issue Ferroptosis: Mechanisms and Human Disease)

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Biology, Volume 14, Issue 9 (September 2025) – 204 articles

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