Biology

13 pages, 3435 KB

Open AccessArticle

Genetic Diversity, Genetic Structure and Demographic History of the Leaf Beetle Platycorynus peregrinus (Herbst, 1783) (Coleoptera: Chrysomelidae) from Thailand

by Satakoon Kaewmungkoon, Nakorn Pradit, Warayutt Pilap, Salakjit Ninlaphay, Takan Chatiwong, Jatupon Saijuntha, Chavanut Jaroenchaiwattanachote, Wittaya Tawong, Warong Suksavate, Pairot Pramual, Chairat Tantrawatpan and Weerachai Saijuntha

Biology 2025, 14(9), 1266; https://doi.org/10.3390/biology14091266 (registering DOI) - 13 Sep 2025

Abstract

Platycorynus peregrinus (Herbst, 1783) is a leaf beetle of agricultural importance, yet its genetic diversity and population structure remain poorly understood. We analyzed mitochondrial cytochrome c oxidase subunit I (COI) sequences from 147 individuals across 19 populations in Thailand. Forty-five haplotypes [...] Read more.

Platycorynus peregrinus (Herbst, 1783) is a leaf beetle of agricultural importance, yet its genetic diversity and population structure remain poorly understood. We analyzed mitochondrial cytochrome c oxidase subunit I (COI) sequences from 147 individuals across 19 populations in Thailand. Forty-five haplotypes were identified, showing high haplotype diversity (0.942) and moderate nucleotide diversity (0.00562). Significant genetic differentiation (Φ_ST = 0.0000–0.7857) was strongly associated with geographical distance, and this population structure was further supported by AMOVA (F_CT = 0.21925, p < 0.001). Neutrality tests and mismatch distribution analyses revealed signals of population expansion, alongside evidence of localized differentiation. The substantial genetic variability observed suggests high dispersal ability and possible cryptic lineages. These insights not only advance understanding of the evolutionary dynamics of P. peregrinus but also provide valuable guidance for developing sustainable pest management strategies. Full article

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

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16 pages, 3149 KB

Open AccessArticle

Integrated miRNA-mRNA Atlas Reveals Temperature-Graded Brain Neuroendocrine Adaptation to Cold Stress in Silvery Pomfret (Pampus argenteus)

by Danqing Yin and Xianhui Ning

Biology 2025, 14(9), 1265; https://doi.org/10.3390/biology14091265 (registering DOI) - 13 Sep 2025

Abstract

Temperature stress is a major cause of mortality in aquaculture, yet the molecular mechanisms underlying cold adaptation in commercially important fish such as the silver pomfret (Pampus argenteus) remain poorly understood. In this study, we used integrated miRNA and mRNA transcriptomics [...] Read more.

Temperature stress is a major cause of mortality in aquaculture, yet the molecular mechanisms underlying cold adaptation in commercially important fish such as the silver pomfret (Pampus argenteus) remain poorly understood. In this study, we used integrated miRNA and mRNA transcriptomics to analyze brain tissue responses of silver pomfret under gradient cold exposure conditions (28 °C control, 18 °C moderate, 13 °C extreme). We identified 85 differentially expressed miRNAs (DEmiRs), with 22 altered under moderate cold and 68 altered in extreme cold, demonstrating that miRNA regulatory activity intensifies with decreasing temperature. Combined miRNA target prediction and expression correlation analysis revealed 8 and 247 differentially expressed target genes (DETGs), which formed cold-adaptive regulatory networks with corresponding DEmiRs. Functional analysis showed enrichment of pathways related to circadian rhythm (e.g., PER targeted by miR-429-y and miR-181-z), immunity (e.g., JUN-miR-10545-x cluster), and endocrine function (e.g., NHERF1-miR-181-z). Notably, miR-181-z was identified as a central regulatory hub, interacting with 13.2% nodes in BE network. Our study provides the first comprehensive miRNA-mRNA network resource for cold stress response in silver pomfret, offering valuable molecular biomarkers for breeding cold-resilient strains and enhancing sustainable aquaculture practices. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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31 pages, 21438 KB

Open AccessArticle

Ethnobotanical Heritage of Edible Plants Species in Mueang District, Yasothon Province, Northeastern Thailand

by Piyaporn Saensouk, Surapon Saensouk, Thawatphong Boonma, Yuefeng Zhang, Lingling Lv and Tammanoon Jitpromma

Biology 2025, 14(9), 1264; https://doi.org/10.3390/biology14091264 (registering DOI) - 13 Sep 2025

Abstract

Traditional knowledge of edible plants is essential for food security, nutrition, and cultural identity in rural communities, yet many regions, including Mueang District, Yasothon Province (MY), remain underexplored in ethnobotanical studies. The lack of systematic documentation of local plant diversity and uses in [...] Read more.

Traditional knowledge of edible plants is essential for food security, nutrition, and cultural identity in rural communities, yet many regions, including Mueang District, Yasothon Province (MY), remain underexplored in ethnobotanical studies. The lack of systematic documentation of local plant diversity and uses in MY presents a significant gap in understanding how these resources contribute to the sustainability of local food systems. This study addresses this gap by providing a comprehensive ethnobotanical survey of edible plants in Mueang District, Northeastern Thailand. Documenting 170 species across 60 families, the study reveals a rich plant diversity reflecting a dynamic interplay of native and introduced species, as well as cultivated and wild-harvested resources that sustain local food security, nutrition, and cultural traditions. Fabaceae emerged as the most species-rich family, while staple cereals such as Oryza sativa L. and Zea mays L. dominate use-value rankings. Quantitative indices, including Species Use Value (SUV), Relative Frequency of Citation (RFC), Cultural Food Significance Index (CFSI), and Fidelity Level (%FL), elucidate nuanced patterns of plant utilization, highlighting multifunctional species that bridge food and medicine. High cultural consensus on key medicinal plants underscores the deep integration of traditional healthcare within local food systems. The diversity of edible plant uses—from beverages and condiments to medicinal foods—illustrates adaptive strategies that enhance dietary diversity and ecological resilience. These findings contribute to the understanding of biocultural diversity and underscore the importance of conserving both plant biodiversity and indigenous knowledge to promote sustainable, locally adapted food systems. The study also identifies priority species for future pharmacological and agronomic research to support climate-resilient food sovereignty. Full article

17 pages, 2205 KB

Open AccessArticle

Contribution to the Knowledge of Leontodon Sect. Asterothrix (Cass.) Ball in Italy and on the Balkan Peninsula

by Fabio Conti, Luca Bracchetti, Marco Dorfner, Ramona Schöpf, Nadine Benda and Christoph Oberprieler

Biology 2025, 14(9), 1263; https://doi.org/10.3390/biology14091263 (registering DOI) - 12 Sep 2025

Abstract

In order to better understand the Leontodon crispus group within L. sect. Asterothrix, we collected specimens belonging to this group during several journeys to the Apennines and the Balkan Peninsula, especially to Croatia, Albania, and Greece. In the present contribution, Leontodon biscutellifolius is [...] Read more.

In order to better understand the Leontodon crispus group within L. sect. Asterothrix, we collected specimens belonging to this group during several journeys to the Apennines and the Balkan Peninsula, especially to Croatia, Albania, and Greece. In the present contribution, Leontodon biscutellifolius is lectotypified; the locus classicus of this taxon is located in the Abruzzo Mts (central Italy). As a consequence, the taxon is confirmed for the Italian flora (central and southern Apennines) and a new combination on variety rank is proposed: L. crispus var. biscutellifolius. Plants from the Balkan Peninsula, currently named L. biscutellifolius, were compared from a morphological point of view with the Apennines populations. Balkan populations show denser indumentum on the leaves, usually consisting of 4-fid hair vs. usually 3-fid hairs in the Apennines. Additionally, the ray number of marginal hairs on the external involucral bracts was found to be 3–5 in the Apennines vs. 4–6 in the Balkan Peninsula accessions. Morphological variation was found to be in correspondence with a variation in genetic respects based on DNA-based fingerprinting (AFLPseq). The oldest subspecific name that can be used for Greek and Albanian populations is L. crispus subsp. asper. A morphologically and genetically deviating population from Southern Pindus (Greece) is described here as L. hellenicus subsp. valeriae. Full article

(This article belongs to the Section Plant Science)

29 pages, 1088 KB

Open AccessArticle

Expression Dynamics of Neurotransmitter System Genes in Early Sea Urchin Embryos: Insights from a Four-Species Comparative Transcriptome Analysis

by Yuri B. Shmukler, Nina M. Alyoshina, Yulia O. Nikishina and Denis A. Nikishin

Biology 2025, 14(9), 1262; https://doi.org/10.3390/biology14091262 (registering DOI) - 12 Sep 2025

Abstract

Transmitters such as serotonin, dopamine, noradrenaline, and acetylcholine act as regulators or triggers of numerous processes in the early embryo, including in sea urchins. However, the identity of these mechanisms relative to mature nervous systems remains controversial. The aim of this study was [...] Read more.

Transmitters such as serotonin, dopamine, noradrenaline, and acetylcholine act as regulators or triggers of numerous processes in the early embryo, including in sea urchins. However, the identity of these mechanisms relative to mature nervous systems remains controversial. The aim of this study was to comprehensively characterize the transcriptomic basis of these as well as glutamatergic, GABAergic and histaminergic systems by comparing publicly available RNA-Seq data across four sea urchin species (Mesocentrotus franciscanus, Lytechinus variegatus, Paracentrotus lividus, Strongylocentrotus purpuratus) during early development (egg to early gastrula). Transcript abundance was normalized using the geometric mean of housekeeping genes (GHG) to facilitate comparative analysis and to use the universal significance threshold. We detected mRNA transcripts encoding numerous components (enzymes, receptors, transporters) for all seven transmitter systems from the earliest stages, suggesting a complex signaling potential prior to neurogenesis. The expression of multiple mRNAs of receptors for the same transmitter indirectly supports our earlier notion of the possibility of simultaneous regulation of different processes by this transmitter even in the single-cell embryo. Notably, transcripts for key synthesis enzymes (TPH, DBH) were often low, indicating limited de novo synthesis, while transcripts for degradation enzymes (MAO, AChE) were abundant. Consistent expression across species was observed for specific receptors such as HTR6, D1-like dopamine, β-adrenergic receptors and the α7 subunit of nicotinic AChR. However, the expression profiles of many components, particularly glutamatergic receptors and metabolic enzymes, showed considerable interspecies variability. These findings indicate that multiple transmitter systems are transcriptionally represented early in development, suggesting substantial molecular overlap with mature systems, while the diversity between species points to possible evolutionary plasticity. This comparative transcriptomic dataset provides a basis for targeted functional studies of the role and interactions of these pre-nervous transmitter pathways in orchestrating embryogenesis. Full article

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

21 pages, 1781 KB

Open AccessArticle

Time-Restricted Feeding Affects Energy Metabolism in Lactating Striped Hamsters (Cricetulus barabensis, Cricetidae, Rodentia)

by Wenting Li, Xinyuan Dong, Jiachen He, Xiaojie Jin, Binxin Yin, Tingbei Bo and Jing Wen

Biology 2025, 14(9), 1261; https://doi.org/10.3390/biology14091261 - 12 Sep 2025

Abstract

Lactation is a critical period in which mothers generally increase food intake and metabolism to meet high energy demands. In the present study, we examined the effect of time-restricted feeding (TRF) on lactating striped hamsters. On the day of litter birth, lactating females [...] Read more.

Lactation is a critical period in which mothers generally increase food intake and metabolism to meet high energy demands. In the present study, we examined the effect of time-restricted feeding (TRF) on lactating striped hamsters. On the day of litter birth, lactating females were assigned into 3 experimental groups that experienced 24-h ad lib feeding (Con), 12-h daytime feeding (DF), or 12-h nighttime feeding (NF). A group of non-lactating females with 24-h feeding (NL) served as an additional control. Our data show that lactating females had increased food intake, oxygen consumption, and small intestine mass but a decreased level of circulating melatonin, compared to the NL females. However, TRF manipulation significantly reduced the mother’s food intake, the pup’s body mass, and survival rate. In addition, TRF had some phase-specific (i.e., DF vs. NF) effects on facilitating body mass loss, decreasing CART, AgRP, and POMC gene expression in the hypothalamus, and increasing abundance in Desulfobacterota and Actinobacteriota in the gut microbiota of lactating females. Together, our data illustrate adaptive changes of lactating hamsters under TRF conditions, and highlight the importance of food access and dietary rhythm regulation in maternal and offspring health, development, and reproductive success. These findings not only expand our understanding of lactation biology and ecological feeding strategies but also highlight the significance of regular dietary patterns for lactating individuals, with particular emphasis on shift workers and other populations with irregular daily schedules. Full article

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20 pages, 8036 KB

Open AccessArticle

Leaf Nitrogen Allocation Trade-Offs Promote Efficient Utilization of Different Nitrogen Forms in Hemarthria altissima

by Nan Xu, Xiaowei Wei, Ju Zhang, Mingyue Sun, Jinwei Zhang, Zihao Zhao and Xuechen Yang

Biology 2025, 14(9), 1260; https://doi.org/10.3390/biology14091260 - 12 Sep 2025

Abstract

The sharp increase in atmospheric nitrogen deposition has had profound effects on nitrogen availability and the photosynthetic capacity of terrestrial plants. Consequently, understanding the intricate trade-off between nitrogen sources and their allocation within leaves is essential for unraveling the photosynthetic responses of grassland [...] Read more.

The sharp increase in atmospheric nitrogen deposition has had profound effects on nitrogen availability and the photosynthetic capacity of terrestrial plants. Consequently, understanding the intricate trade-off between nitrogen sources and their allocation within leaves is essential for unraveling the photosynthetic responses of grassland ecosystems to nitrogen deposition. In a series of field experiments, the effects of different nitrogen forms (ammonium and nitrate nitrogen) on nitrogen assimilation and allocation in the C₄ plant Hemarthria altissima were thoroughly investigated. Towards the end of the growing season, H. altissima was observed to exhibit high photosynthetic efficiency. Ammonium nitrogen treatment notably enhanced photosynthetic nitrogen use efficiency (PNUE) by modifying the nitrogen allocation within the leaf’s photosynthetic apparatus and leaf area, leading to a significant improvement in photosynthetic efficiency and biomass accumulation. Under ammonium nitrogen treatment, H. altissima directed more nitrogen toward its carboxylation process and other protein-related functions to increase carboxylation efficiency, thereby facilitating the accumulation of photosynthetic products. In contrast, under nitrate nitrogen treatment, the plant balanced growth and light absorption by allocating nitrogen to leaf light-capturing proteins. The application of both ammonium and nitrate nitrogen resulted in increased nitrogen content in the soil, as ammonium nitrogen is converted to nitrate nitrogen through nitrification. The net photosynthetic rate (A_n), nitrogen allocation to photosynthetic components (N_psn), and chlorophyll content per unit area (Chl_area) were all significantly and positively correlated with photosynthetic nitrogen use efficiency (PNUE). Notably, under the sole NH₄⁺ treatment, nitrogen allocation to the photosynthetic components increased, which enhanced the NPQ and ETR in H. altissima leaves. These findings suggest that H. altissima preferentially utilizes ammonium nitrogen from the soil, optimizing its PNUE and biomass accumulation through a strategic allocation of nitrogen within its leaves. Further investigation is needed to explore how these nitrogen allocation strategies may vary under different environmental conditions and how they influence ecosystem-level productivity. 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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18 pages, 4537 KB

Open AccessArticle

Study of FOXL2 Regulation on Ovarian Function in Chlamys farreri Through Comparative ChIP-Seq and Transcriptome Analysis Using RNA Interference

by Xiaoling Liu, Han Yun, Yan Xing, Shuo Wang, Xueying Zhou and Jianbai Zhang

Biology 2025, 14(9), 1259; https://doi.org/10.3390/biology14091259 - 12 Sep 2025

Abstract

FOXL2 (forkhead box protein L2) is a transcription factor, its function and regulatory mechanism have been mainly studied in mammals; related research on marine invertebrates is still insufficient. It was found that oogenesis was affected, and even a small number of cells resembling [...] Read more.

FOXL2 (forkhead box protein L2) is a transcription factor, its function and regulatory mechanism have been mainly studied in mammals; related research on marine invertebrates is still insufficient. It was found that oogenesis was affected, and even a small number of cells resembling spermatogonial morphology appeared in C. farreri ovaries after the FOXL2 was knocked down through RNA interference (RNAi) technology in our laboratory previously. Based on previous research, this paper conducted transcriptome sequencing and differential expression analysis on the ovarian tissues between the experimental group (post-RNAi) and the control group (pre-RNAi) of C. farreri, and used recombinant C. farreri FOXL2 protein for antibody production in Chromatin Immunoprecipitation Sequencing (ChIP seq) experiments to comprehensively analyze the pathways and key genes regulated by FOXL2 during oogenesis. The results showed that in the RNAi experimental group, 389 genes were upregulated, and 1615 genes were downregulated. Among the differentially expressed genes (DEGs), the differential genes related to gender or gonadal development are relatively concentrated in physiological processes such as steroid hormone synthesis, spermatogenesis, gonadal development, and ovarian function maintenance, as well as the FoxO and estrogen signaling pathways. Combining transcriptome and ChIP-seq data, it was found that there were some genes related to sex gonadal development among genes which were directly regulated by FOXL2, such as Wnt4, SIRT1, HSD17B8, GABABR1, KRAS, NOTCH1, HSD11B1, cPLA2, ADCY9, IP3R1, PLCB4, and Wnt1. This study lays the foundation for a deeper understanding of the FOXL2′s specific regulatory mechanism during oogenesis in scallops as a transcription factor. Full article

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21 pages, 1140 KB

Open AccessArticle

Gasdermin-Mediated Pyroptosis in Hidradenitis Suppurativa: Molecular Insights and Therapeutic Implications

by Kinga Tyczyńska, Piotr K. Krajewski, Aleksandra Sójka, Danuta Nowicka-Suszko, Iwona Bednarz-Misa, Mariusz Fleszar, Małgorzata Krzystek-Korpacka and Jacek C. Szepietowski

Biology 2025, 14(9), 1258; https://doi.org/10.3390/biology14091258 - 12 Sep 2025

Abstract

Hidradenitis suppurativa (HS) is a debilitating inflammatory skin condition with unclear underlying mechanisms. Recent studies suggest pyroptosis, a highly inflammatory form of programmed cell death, could significantly contribute to the disease process. This study aimed to investigate the roles of gasdermin D (GSDMD) [...] Read more.

Hidradenitis suppurativa (HS) is a debilitating inflammatory skin condition with unclear underlying mechanisms. Recent studies suggest pyroptosis, a highly inflammatory form of programmed cell death, could significantly contribute to the disease process. This study aimed to investigate the roles of gasdermin D (GSDMD) and gasdermin E (GSDME), two key mediators of pyroptosis, in HS pathogenesis. Serum and skin samples from HS patients and healthy individuals were analyzed. Serum gasdermin D levels were significantly elevated in HS patients, although gasdermin E showed no significant difference compared to controls. Skin tissue analysis revealed increased expression of both GSDMD and GSDME in inflamed HS lesions compared to unaffected skin from the same patients and healthy control skin. However, these molecules did not correlate directly with disease severity. Interestingly, systemic metabolic markers showed some associations with gasdermin expression, suggesting potential connections between systemic health and inflammation in HS. These findings confirm a critical role of gasdermins in HS-related inflammation and identify pyroptosis as a promising therapeutic target. Further exploration of these pathways could yield valuable treatment strategies for managing this challenging skin condition. Full article

(This article belongs to the Special Issue Biology and Function of Inflammasomes)

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19 pages, 7149 KB

Open AccessArticle

Whole-Genome Analysis of a Novel Multidrug-Resistant Escherichia coli Strain from Dairy Calves in Northeast China: Mechanisms of Antibiotic Resistance and Biofilm Formation

by Xuanpan Ding, Qiuyue An, Huijie Kang, Siyao Li, Shuai Zhang, Haotian Yang, Xinyi Dou, Yaxin Ji, Yuan Zhao and Honggang Fan

Biology 2025, 14(9), 1257; https://doi.org/10.3390/biology14091257 - 12 Sep 2025

Abstract

The use of antibiotics is so widespread in animal husbandry, but negligent management and lack of policies often lead to the massive use of antibiotics on farms. In this study, we collected cases of epidemic calf diarrhea in northeastern China and isolated a [...] Read more.

The use of antibiotics is so widespread in animal husbandry, but negligent management and lack of policies often lead to the massive use of antibiotics on farms. In this study, we collected cases of epidemic calf diarrhea in northeastern China and isolated a new strain of multidrug-resistant Escherichia coli (MDR-E. coli). In order to explore the information of this pathogen in detail, we used whole-genome sequencing to determine the genome sequence, and explored in detail the resistance, pathogenicity, genetic evolution and other biological processes of the strain through bioinformatics analysis. The results showed that the E. coli isolated in this study was a new multidrug-resistant strain with a large number of drug resistance genes (77) and virulence genes (84), including a circular chromosome and five circular plasmids, which are basically impossible to treat by currently commonly used antibiotics. The findings of this study suggest that the prolonged misuse of antibiotics in agricultural settings may contribute to the development of antibiotic-resistant strains of E. coli. This, in turn, has the potential to trigger outbreaks of antibiotic-resistant bacterial diarrhea, leading to substantial economic losses and posing significant public health risks. These results underscore the necessity for the judicious use of antibiotics and will inform the development of pertinent policies and regulations. Full article

(This article belongs to the Section Microbiology)

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17 pages, 1935 KB

Open AccessArticle

Chromosomal Instability and Periodontal Disease in Idiopathic Infertility: Evidence of a Possible Association

by Cristina-Crenguţa Albu, Ştefan-Dimitrie Albu, Claudia Florina Bogdan-Andreescu, Cristian-Viorel Poalelungi, Constantin Marian Damian, Alexandru Burcea, Andreea-Mariana Bănățeanu, Emin Cadar, Dan Alexandru Slăvescu and Anca Daniela Brăila

Biology 2025, 14(9), 1256; https://doi.org/10.3390/biology14091256 - 12 Sep 2025

Abstract

Background: Chromosomal instability (CIN) may underlie a subset of idiopathic infertility, and chronic periodontitis could contribute to genomic fragility. We tested whether periodontal status is associated with cytogenetic instability in adults with idiopathic infertility. Methods: This was a cross-sectional study of 60 adults [...] Read more.

Background: Chromosomal instability (CIN) may underlie a subset of idiopathic infertility, and chronic periodontitis could contribute to genomic fragility. We tested whether periodontal status is associated with cytogenetic instability in adults with idiopathic infertility. Methods: This was a cross-sectional study of 60 adults aged 20–40 years, comprising idiopathic infertility (n = 30) and fertile controls (n = 30), each with 18 women and 12 men. Significant exclusions included systemic inflammatory disease, pregnancy/lactation, recent antibiotics/NSAIDs, and periodontal therapy within 6 months. Periodontal examination recorded probing depth (PD), clinical attachment loss (CAL), and bleeding on probing (BOP). Cytogenetic testing used mitomycin C-induced chromosomal breakage to derive the Breakage Index (BI); CIN was defined as BI ≥ 4.0. Analyses compared infertile with CIN (n = 19), infertile without CIN (n = 11), and controls (n = 30). Results: Infertile participants with CIN had a higher periodontitis burden compared to infertile participants without CIN and to controls (moderate–severe: 89.5% vs. 54.5% vs. 26.7%); mean BI also differed (5.2 ± 0.9 vs. 1.3 ± 0.5 vs. 0.4 ± 0.2). Periodontal measures followed the same gradient, with greater CAL and PD in CIN-positive infertility. Conclusions: In idiopathic infertility, CIN was cross-sectionally associated with more severe periodontitis, and the BI correlated with CAL, PD, and BOP. Causality cannot be inferred and residual confounding cannot be excluded. Periodontal screening is a feasible adjunct that may help identify a modifiable inflammatory burden; prospective and interventional studies are warranted. Full article

(This article belongs to the Section Medical Biology)

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19 pages, 2079 KB

Open AccessArticle

Decapod Crustaceans in a Transitional River System: Insights from the Ribeira de Iguape Ecoregion, Brazil

by Esthephany Konesuk Santos Miranda, Maria Rosa Roque Santana Gomes, Luis Carlos Ferreira de Almeida and Giovana Bertini

Biology 2025, 14(9), 1255; https://doi.org/10.3390/biology14091255 - 12 Sep 2025

Abstract

Freshwater ecosystems are essential for biodiversity conservation but face increasing threats from human activities. This study assessed the species richness, diversity, and spatial and temporal distribution of decapod crustaceans (Caridea and Brachyura) in the lower Ribeira de Iguape River, southeastern Brazil, a globally [...] Read more.

Freshwater ecosystems are essential for biodiversity conservation but face increasing threats from human activities. This study assessed the species richness, diversity, and spatial and temporal distribution of decapod crustaceans (Caridea and Brachyura) in the lower Ribeira de Iguape River, southeastern Brazil, a globally recognized freshwater ecoregion. Monthly sampling took place over one year at three sites using both active and passive capture methods. Environmental parameters were measured in the field, and multivariate analyses (correspondence analysis, PERMANOVA, and multiple regression) were applied to explore species–environment relationships and community structure. A total of 42,897 individuals were recorded, including eight Caridea and four Brachyura species. Carideans accounted for over 97 percent of the total, with Potimirim spp. and Macrobrachium acanthurus as the most abundant. The site nearest the river mouth showed the highest species richness and diversity, likely due to its transitional characteristics and moderate salinity variation. Environmental variables such as dissolved oxygen and salinity influenced species occurrence, although biological interactions may also contribute. Seasonal changes in abundance appeared most evident during winter and spring, driven by shifts in dominant taxa. The presence of the non-native Macrobrachium rosenbergii suggests early establishment and reinforces the need for long-term ecological monitoring in transitional freshwater environments. Full article

(This article belongs to the Section Ecology)

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17 pages, 3724 KB

Open AccessArticle

Whole Transcriptome Sequencing and Differential Analysis of Testes in Pre- and Post-Sexual Maturity Bactrian Camels (Camelus bactrianus)

by Xiaokang Chang, Xinkui Yao, Jun Meng, Jianwen Wang, Yaqi Zeng, Linling Li and Wanlu Ren

Biology 2025, 14(9), 1254; https://doi.org/10.3390/biology14091254 - 12 Sep 2025

Abstract

Testicular development in male animals is a conserved and highly regulated biological process. Investigating the molecular mechanisms underlying testicular development in Junggar Bactrian camels is essential for gaining a deeper understanding of this process in the species. This study selected testicular tissue from [...] Read more.

Testicular development in male animals is a conserved and highly regulated biological process. Investigating the molecular mechanisms underlying testicular development in Junggar Bactrian camels is essential for gaining a deeper understanding of this process in the species. This study selected testicular tissue from the Junggar Bactrian camel at pre-sexual maturity (G3 group, n = 4, 3 years old) and post-sexual maturity (G5 group, n = 4, 5 years old) for whole transcriptome sequencing and bioinformatics analysis. We identified differentially expressed mRNA (DEmRNA), including KPNA2 and LRRC46; differentially expressed LncRNA (DELncRNA), including LOC123613926 and LOC123613624; and differentially expressed miRNA (DEmiRNA), including eca-miR-196a and eca-miR-183. Additionally, we also identified 87 currently unnamed DEmiRNAs, which are of practical value for future research on the Junggar Bactrian camel testicular development and spermatogenesis. GO and KEGG enrichment analyses showed that DERNA are mainly involved in functions and processes such as protein binding (MF), protein import into nucleus (BP), and extracellular space (CC), as well as signaling pathways such as Insulin, FoxO, MAPK, and PI3K-Akt. Subsequently, we predicted some DEmiRNAs and DELncRNAs association with DEmRNAs, and constructed the competitive endogenous RNA (ceRNA) regulatory network. Finally, we randomly selected 10 DERNAs for RT-qPCR validation, and the transcriptome results were consistent with the RT-qPCR results, indicating that the sequencing results were true and reliable. In conclusion, this study analyzed the differential expression of mRNA, LncRNA, and miRNA in Junggar Bactrian camels before and after sexual maturity, providing data references for future studies related to testicular development and spermatogenesis. Full article

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13 pages, 20320 KB

Open AccessArticle

Mucus Secretion as a Defensive Mechanism in the Freshwater Flatworm Stenostomum sphagnetorum Against the Ciliate Predator Coleps hirtus

by Gabriele Achille, Santosh Kumar, Daizy Bharti, Graziano Guella, Claudio Ortenzi and Federico Buonanno

Biology 2025, 14(9), 1253; https://doi.org/10.3390/biology14091253 - 12 Sep 2025

Abstract

This study investigates the defensive mechanisms employed by the freshwater flatworm Stenostomum sphagnetorum against the predatory ciliate, Coleps hirtus. Focusing on the role of the glandular secretions produced by S. sphagnetorum, the research demonstrates that the flatworm secretes mucus that acts [...] Read more.

This study investigates the defensive mechanisms employed by the freshwater flatworm Stenostomum sphagnetorum against the predatory ciliate, Coleps hirtus. Focusing on the role of the glandular secretions produced by S. sphagnetorum, the research demonstrates that the flatworm secretes mucus that acts as a barrier, disrupting predator attack. In particular, we show that: (1) S. sphagnetorum specimens artificially deprived of glandular secretions are significantly more susceptible to predation by C. hirtus than untreated specimens; (2) the secretion-deprived organisms consistently exhibit a significantly greater sensitivity to the main toxins employed by C. hirtus for predation, relative to untreated counterparts; (3) the characterization of the glandular secretion indicates that the mucus contains both neutral and acidic glycosaminoglycans, along with protein components, suggesting a complex chemical composition that may contribute to its protective function. Full article

(This article belongs to the Section Zoology)

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13 pages, 2631 KB

Open AccessArticle

Comparison of the Biological Response of a Head and Neck Carcinoma and a Glioblastoma Cell Line Under Neutron Irradiation with BPA Administration

by Patricia Álvarez-Rodríguez, Cristina Méndez-Malagón, Maribel Porras-Quesada, María Pedrosa-Rivera, Ulli Köster, Ignacio Porras, Javier Praena, Rocío Estrada, Leonor Pérez-Fuentes, Juan Luis Osorio-Ceballos, Carmen Ruiz-Ruiz, Lucie Sancey and María José Ruiz-Magaña

Biology 2025, 14(9), 1252; https://doi.org/10.3390/biology14091252 - 12 Sep 2025

Abstract

Background and objective: In Boron Neutron Capture Therapy, treatment planning is based on a weighted dose in which dose components are weighted with different biological effectiveness (RBE) factors. The most important one for the tumor dose is the compound dependent biological effectiveness (CBE) [...] Read more.

Background and objective: In Boron Neutron Capture Therapy, treatment planning is based on a weighted dose in which dose components are weighted with different biological effectiveness (RBE) factors. The most important one for the tumor dose is the compound dependent biological effectiveness (CBE) factor which weighs the boron dose. This was established for brain tumors from radiobiological experiments and has been extrapolated to the more recent application of BNCT to head and neck cancers. The purpose of this work is to study the validity of this assumption. Methods: Two cell lines, CAL-33 (head and neck squamous cell carcinoma) and A172 (Glioblastoma Multiforme), were irradiated with a very pure thermal-equivalent neutron beam after BPA incubation, and the surviving fraction of cells after irradiation was determined by clonogenicity assays. Results: The Compound Biological Effectiveness of both cell lines is similar, although for head and neck carcinoma, 10% higher values are systematically found. In addition to this, radiobiological coefficients for the different dose components (photon, neutron and boron) of BNCT in both cell lines are provided. Full article

(This article belongs to the Section Cancer Biology)

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15 pages, 1025 KB

Open AccessArticle

Droplet Digital PCR Assay for Detection and Quantification of ‘Candidatus Phytoplasma solani’ in Grapevine Samples

by Lucia Landi, Sergio Murolo and Gianfranco Romanazzi

Biology 2025, 14(9), 1251; https://doi.org/10.3390/biology14091251 - 11 Sep 2025

Abstract

‘Candidatus Phytoplasma solani’ is the causal agent of the Bois noir (BN), affecting grapevine worldwide. The complex epidemiology of BN, which involves multiple ‘Ca. P. solani’ host plants and insect vectors, as well as the occurrence of recovery (loss of [...] Read more.

‘Candidatus Phytoplasma solani’ is the causal agent of the Bois noir (BN), affecting grapevine worldwide. The complex epidemiology of BN, which involves multiple ‘Ca. P. solani’ host plants and insect vectors, as well as the occurrence of recovery (loss of symptoms on grapevine canopy), makes disease investigations and containment in vineyards difficult. To achieve early detection of ‘Ca. P. solani’, a droplet digital PCR (ddPCR)-based approach and quantitative (q)PCR assay were compared, testing specific primers based on the elongation factor Tu (tuf) gene using SYBR Green chemistry. The regression curve analysis of the ddPCR assay showed good linearity. Compared with the qPCR method, the sensitivity of ddPCR improved about 10-fold. The analysis of grapevine roots spiked with serial dilutions of ‘Ca P. solani’. PCR tuf fragments showed that qPCR was inhibited, while ddPCR was not affected. Testing 66 grapevine samples from 50 grapevine plants, the ddPCR provided superior diagnostic performance compared to qPCR in roots of symptomatic plants (75% detected by ddPCR, 41.6% by qPCR), roots of recovered plants (58.8% detected by ddPCR, 25% by qPCR), and asymptomatic leaf tissues from recovered plants (75% detected by ddPCR, 25% by qPCR). The ddPCR analysis allowed us to detect ‘Ca. P. solani’ on 40% of leaf samples from recovered plants and 20% of roots from asymptomatic plants. No differences among ddPCR and qPCR were found in detecting phytoplasma on symptomatic leaf samples. The ddPCR assay allowed the absolute quantification of ‘Ca. P. solani’ in complex matrices, such as roots, and when low titer of phytoplasma is present. Full article

(This article belongs to the Section Plant Science)

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17 pages, 1183 KB

Open AccessArticle

Comparative Study of Hirudins and Encoding Genes in Hirudo nipponia and Hirudo tianjinensis

by Jingjing Yin, Zichao Liu, Yunfei Yu, Anping Wang, Zuhao Huang, Lizhou Tang, Fang Zhao and Gonghua Lin

Biology 2025, 14(9), 1250; https://doi.org/10.3390/biology14091250 - 11 Sep 2025

Abstract

This study systematically compared the genetic characteristics and functional activities of hirudins and their encoding genes between Hirudo nipponia (Hnip1–3) and Hirudo tianjinensis (Htia1–3) through bioinformatics analysis, recombinant protein eukaryotic expression, and activity assays. The results revealed 42 nucleotide variation sites and 27 [...] Read more.

This study systematically compared the genetic characteristics and functional activities of hirudins and their encoding genes between Hirudo nipponia (Hnip1–3) and Hirudo tianjinensis (Htia1–3) through bioinformatics analysis, recombinant protein eukaryotic expression, and activity assays. The results revealed 42 nucleotide variation sites and 27 amino acid variation sites across both species. All six genes were expressed and significant pairwise differences between genes were detected within each species. All hirudins were identified as secretory proteins, with Hnip2, Hnip3, and Htia1 showing higher docking scores with thrombin. Four recombinant proteins (Hnip1, Hnip2, Htia1, and Htia2) exhibited antithrombin activity, with Hnip1 displaying the strongest activity. No significant differences were observed in the sequence variation, gene expression, physicochemical properties, predicted three-dimensional structures, or antithrombin activity of hirudins between the two leech species. This may stem from substantial heterogeneity in the genetic makeup and functional characteristics of distinct hirudins within each species, ultimately reducing the statistical power of these interspecific comparisons. Integrating gene expression profiles with recombinant protein activity assessments revealed that H. nipponia hirudins exhibit superior antithrombotic potency compared to those of H. tianjinensis. This study establishes a theoretical foundation for medicinal leech resource development and provides critical data for innovative antithrombotic drug discovery. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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11 pages, 1289 KB

Open AccessArticle

Biofilm Formation by Rice Rhizosphere Nitrogen-Fixing Microorganisms and Its Effect on Rice Growth Promotion

by Jae-Hyeon Oh, Eunhee Kim and Mihyun Cho

Biology 2025, 14(9), 1249; https://doi.org/10.3390/biology14091249 - 11 Sep 2025

Abstract

Excessive nitrogen fertilizer use contributes to environmental pollution and undermines agricultural sustainability. Enhancing symbiotic interactions between rice and nitrogen-fixing microorganisms offers a promising strategy to potentially improve nitrogen use efficiency (NUE). This study investigates the role of rice root exudates in promoting biofilm [...] Read more.

Excessive nitrogen fertilizer use contributes to environmental pollution and undermines agricultural sustainability. Enhancing symbiotic interactions between rice and nitrogen-fixing microorganisms offers a promising strategy to potentially improve nitrogen use efficiency (NUE). This study investigates the role of rice root exudates in promoting biofilm formation by nitrogen-fixing microbes to enhance nitrogen fixation. Nine nitrogen-fixing microbial strains were evaluated for biofilm formation in response to flavone and apigenin treatments, with Gluconacetobacter diazotrophicus KACC 12358 serving as the reference strain. The most responsive strain was selected, and a library of 1597 natural compounds was screened to identify those that promote biofilm formation in both the selected and reference strains. A. indigens KACC 11682 exhibited the highest biofilm-forming capacity, with apigenin treatment showing an OD595 value approximately 1.4 times higher than the DMSO control. Screening identified 68 compounds that enhanced biofilm formation by more than 500% compared to the control. Among them, eight compounds induced strong biofilm formation (O.D. > 2.0) in A. indigens. Cardamomin, a chalconoid flavonoid, emerged as one of the most effective compounds, showing a 245% increase in biofilm formation. Growth promotion assays showed that A. indigens increased rice fresh weight by approximately 128% compared to untreated controls. This study demonstrates the potential of rice root exudate-derived compounds to promote beneficial symbiosis with nitrogen-fixing microbes. These findings offer a novel approach that may contribute to enhancing rice NUE. Future research will focus on evaluating the long-term effects of these compounds and microorganisms, assessing their applicability in real agricultural settings, and conducting further validation across various rice cultivars. Full article

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19 pages, 4024 KB

Open AccessArticle

Overexpression of LIM Homeodomain Gene Arrowhead Induces Pleiotropic Developmental Alterations in the Silkworm, Bombyx mori

by Nur Fazleen Binti Idris, Chunping Hou, Zhongyi Liu, Lulu Liu, Chunyan Yang, Zongmeng Yang, Hai Hu, Fangyin Dai and Xiaoling Tong

Biology 2025, 14(9), 1248; https://doi.org/10.3390/biology14091248 - 11 Sep 2025

Abstract

LIM homeodomain (LIM-HD) is a versatile family of transcription factors that act as master regulators in various developmental processes of eukaryotes, and one of the LIM-HD encoded genes is the arrowhead (AWH). In silkworm Bombyx mori, the Arrowhead gene ( [...] Read more.

LIM homeodomain (LIM-HD) is a versatile family of transcription factors that act as master regulators in various developmental processes of eukaryotes, and one of the LIM-HD encoded genes is the arrowhead (AWH). In silkworm Bombyx mori, the Arrowhead gene (BmAWH) functions as a key component activating all three fibroin genes in the silk glands of B. mori, but the potential pleiotropic effects of BmAWH on various tissues of the silkworm is yet to be discovered. The objective of this study is to investigate the functional role of a BmAWH gene in the B. mori (Dazao) developmental process, using the piggyBac-based transgene technique. The size of transgenic line silk glands have become smaller, resulting in the reduction in whole cocoon weight, cocoon shell weight, and cocoon–shell ratio. Overexpression of BmAWH has induced significant changes in juvenile hormone levels in female larvae at the fifth instar larval stage. Female reproductive defects (reduction in fecundity rate, abnormal egg morphology) were observed. In addition, transgenic line larvae exhibit the complete disappearance of larval body patterns and color (melanin pigmentation). Since the LIM-HD protein functions to orchestrate complex developmental programs, this study may shed light on evolutionary adaptations and the divergence of insect gene functions. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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