Biology

13 pages, 7339 KiB

Open AccessArticle

Unveiling Genomic Islands Hosting Antibiotic Resistance Genes and Virulence Genes in Foodborne Multidrug-Resistant Patho-Genic Proteus vulgaris

by Hongyang Zhang, Tao Wu and Haihua Ruan

Biology 2025, 14(7), 858; https://doi.org/10.3390/biology14070858 (registering DOI) - 15 Jul 2025

Abstract

Proteus vulgaris is an emerging multidrug-resistant (MDR) foodborne pathogen that poses a significant threat to food safety and public health, particularly in aquaculture systems where antibiotic use may drive resistance development. Despite its increasing clinical importance, the genomic mechanisms underlying antimicrobial resistance (AMR) [...] Read more.

Proteus vulgaris is an emerging multidrug-resistant (MDR) foodborne pathogen that poses a significant threat to food safety and public health, particularly in aquaculture systems where antibiotic use may drive resistance development. Despite its increasing clinical importance, the genomic mechanisms underlying antimicrobial resistance (AMR) and virulence transmission in foodborne Proteus vulgaris remain poorly understood, representing a critical knowledge gap in One Health frameworks. To investigate its AMR and virulence transmission mechanisms, we analyzed strain P3M from Penaeus vannamei intestines through genomic island (GI) prediction and comparative genomics. Our study provides the first comprehensive characterization of mobile genetic elements in aquaculture-derived Proteus vulgaris, identifying two virulence-associated GIs (GI12/GI15 containing 25/6 virulence genes) and three AMR-linked GIs (GI7/GI13/GI16 carrying 1/1/5 antibiotic resistance genes (ARGs)), along with a potentially mobile ARG cluster flanked by IS elements (tnpA-tnpB), suggesting horizontal gene transfer capability. These findings elucidate previously undocumented genomic mechanisms of AMR and virulence dissemination in Proteus vulgaris, establishing critical insights for developing One Health strategies to combat antimicrobial resistance and virulence in foodborne pathogens. Full article

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15 pages, 1797 KiB

Open AccessArticle

First Insights into Bioaccumulation Patterns in Different Tissues of the Greenland Shark Somniosus microcephalus from Kulusuk (Southeastern Greenland)

by Francesca Romana Reinero, Emilio Sperone, Samira Gallo, Donatella Barca, Francesco Luigi Leonetti, Gianni Giglio and Primo Micarelli

Biology 2025, 14(7), 857; https://doi.org/10.3390/biology14070857 (registering DOI) - 15 Jul 2025

Abstract

Marine environmental pollution has been rapidly increasing in Arctic waters, and the release and bioaccumulation of trace elements in Arctic marine species may pose significant risks to both ecosystem health and human well-being. As a top predator, the Greenland shark is an ideal [...] Read more.

Marine environmental pollution has been rapidly increasing in Arctic waters, and the release and bioaccumulation of trace elements in Arctic marine species may pose significant risks to both ecosystem health and human well-being. As a top predator, the Greenland shark is an ideal sentinel species for ecotoxicological studies in this region. In this study, trace element analyses were conducted on various tissues from two Greenland sharks—a male and a female—collected in Kulusuk (southeastern Greenland). Eleven trace elements (Mn55, Co59, Cu63, Zn64, As75, Se82, Rb85, Mo98, Ag107, Cd112, and Pb208) were measured in different skin samples from both specimens and in the muscle and fat of the female using an Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Principal Component Analyses (PCAs) revealed sex-related differences in skin bioaccumulation patterns, likely due to sampling of different skin regions. Notably, skin tissues from both sharks showed the highest concentration of trace elements, especially for As75 (9.39–41.13 ppm) and Zn64 (24.34–50.99 ppm) and with the exception of Ag107. These findings suggest that environmental exposure may play a more significant role than dietary intake in trace element accumulation in this area. This study represents the first investigation of trace element bioaccumulation in Greenland sharks from Kulusuk. While the results offer important preliminary insights into the species’ ecotoxicology, further research involving more specimens and tissues is needed to confirm these trends. These initial findings contribute to filling key data gaps and have implications for both environmental monitoring and public health within the Greenlandic community. Full article

(This article belongs to the Section Marine Biology)

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20 pages, 8662 KiB

Open AccessArticle

Analysis of Composition, Structure, and Driving Factors of Root-Associated Endophytic Bacterial Communities of the Chinese Medicinal Herb Glycyrrhiza

by Zhilin Zhang, Aifang Ma, Tao Zhang, Li Zhuang and Hanli Dang

Biology 2025, 14(7), 856; https://doi.org/10.3390/biology14070856 (registering DOI) - 15 Jul 2025

Abstract

The role of endophytic bacteria in the interaction between medicinal plants and microorganisms, secondary metabolite accumulation, plant nutrient changes, as well as their interactions with microbial communities, needs to be investigated in medicinal plants. In this study, 16S rRNA genes of endophytic bacterial [...] Read more.

The role of endophytic bacteria in the interaction between medicinal plants and microorganisms, secondary metabolite accumulation, plant nutrient changes, as well as their interactions with microbial communities, needs to be investigated in medicinal plants. In this study, 16S rRNA genes of endophytic bacterial communities in the root systems of three medicinal licorice species at different root depths (0–20, 20–40, and 40–60 cm) were sequenced using high-throughput sequencing technology, and their relationships with plant and soil factors were investigated. Our study indicated that the influence of Glycyrrhiza species on the structure of endophytic bacterial communities is significantly greater than that of root depth, and there are significant differences in the structure of endophytic bacterial communities at different sampling sites. At the phylum level, Proteobacteria and Actinobacteria are the dominant phylum. Functional gene prediction shows that functional genes related to metabolism dominate the endogenous bacterial community. Plant factors and soil physicochemical properties are important environmental drivers affecting the distribution of endophytic bacterial communities. This study will give new information on plant–soil–endophyte interactions and open up new possibilities for medicinal licorice development and use. Full article

(This article belongs to the Section Microbiology)

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13 pages, 1243 KiB

Open AccessArticle

Sex Differences in Human Myogenesis Following Testosterone Exposure

by Paolo Sgrò, Cristina Antinozzi, Guglielmo Duranti, Ivan Dimauro, Zsolt Radak and Luigi Di Luigi

Biology 2025, 14(7), 855; https://doi.org/10.3390/biology14070855 (registering DOI) - 14 Jul 2025

Abstract

Previous research has demonstrated sex-specific differences in muscle cells regarding sex hormone release and steroidogenic enzyme expression after testosterone exposure. The present study aims to elucidate sex-related differences in intracellular processes involved in myogenesis and regeneration. Neonatal 46XX and 46XY human primary skeletal [...] Read more.

Previous research has demonstrated sex-specific differences in muscle cells regarding sex hormone release and steroidogenic enzyme expression after testosterone exposure. The present study aims to elucidate sex-related differences in intracellular processes involved in myogenesis and regeneration. Neonatal 46XX and 46XY human primary skeletal muscle cells were treated with increasing doses of testosterone (0.5, 2, 5, 10, 32, and 100 nM) for 24 h. The molecular pathways involved in muscle metabolism and growth, as well as the release of myokines involved in satellite cell activation, were analyzed using western blot, real-time PCR, and a Luminex assay. The unpaired Student’s t-test and one-way ANOVA for repeated measures were used to determine significant variations within and between groups. An increase in the expression and release of MYF6, IGF-I, IGF-II, and CXCL1, as well as a decrease in GM-CSF, IL-9, and IL-12, was observed in 46XX cells. Conversely, testosterone up-regulated GM-CSF and CXCL1 in 46XY cells but did not affect the release of the other myokines. Preferential activation of the MAPK pathway was observed in 46XX cells, while the PI3K/AKT pathway was preferentially activated in 46XY cells. In conclusion, our findings demonstrate differential responses to androgen exposure in 46XX and 46XY cells, resulting in the activation of muscle cell growth and energy metabolic pathways in a sex-specific manner. Full article

(This article belongs to the Special Issue New Insights into Skeletal Muscle Metabolism in Pathological and Physiological Conditions)

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24 pages, 3598 KiB

Open AccessArticle

Comprehensive Analysis of the Complete Mitochondrial Genome of Paeonia ludlowii Reveals a Dual-Circular Structure and Extensive Inter-Organellar Gene Transfer

by Zhefei Zeng, Zhengyan Zhang, Ngawang Norbu, Ngawang Bonjor, Xin Tan, Shutong Zhang, Norzin Tso, Junwei Wang and La Qiong

Biology 2025, 14(7), 854; https://doi.org/10.3390/biology14070854 (registering DOI) - 14 Jul 2025

Abstract

Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first [...] Read more.

Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first complete assembly and comprehensive analysis of the P. ludlowii mitochondrial genome. Most remarkably, we discovered that the P. ludlowii mitogenome exhibits an atypical dual-circular structure, representing the first documented occurrence of this architectural feature within the genus Paeonia. The assembled genome spans 314,371 bp and encodes 42 tRNA genes, 3 rRNA genes, and 31 protein-coding genes, with a pronounced adenine–thymine bias. This multipartite genome structure is characterized by abundant repetitive elements (112 functionally annotated SSRs, 33 tandem repeats, and 945 dispersed repeats), which potentially drive genome rearrangements and facilitate adaptive evolution. Analyses of codon usage bias and nucleotide diversity revealed highly conserved gene expression regulation with limited variability. Phylogenetic reconstruction confirms that P. ludlowii, P. suffruticosa, and P. lactiflora form a monophyletic clade, reflecting close evolutionary relationships, while extensive syntenic collinearity with other Paeonia species underscores mitochondrial genome conservation at the genus level. Extensive inter-organellar gene transfer events, particularly from chloroplast to mitochondrion, suggest that such DNA exchanges enhance genetic diversity and promote environmental adaptation. The discovery of the dual-circular architecture provides novel insights into plant mitochondrial genome evolution and structural plasticity. This study elucidates the unique structural characteristics of the P. ludlowii mitochondrial genome and establishes a crucial genetic foundation for developing targeted conservation strategies and facilitating molecular-assisted breeding programs for this endangered species. Full article

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16 pages, 10651 KiB

Open AccessArticle

Impact of Amelogenesis Imperfecta on Junctional Epithelium Structure and Function

by Kevin Lin, Jake Ngu, Susu Uyen Le and Yan Zhang

Biology 2025, 14(7), 853; https://doi.org/10.3390/biology14070853 (registering DOI) - 14 Jul 2025

Abstract

The junctional epithelium, which lines the inner gingival surface, seals the gingival sulcus to block the infiltration of food debris and pathogens. The junctional epithelium is derived from the reduced enamel epithelium, consisting of late developmental stage ameloblasts and accessory cells. No prior [...] Read more.

The junctional epithelium, which lines the inner gingival surface, seals the gingival sulcus to block the infiltration of food debris and pathogens. The junctional epithelium is derived from the reduced enamel epithelium, consisting of late developmental stage ameloblasts and accessory cells. No prior studies have investigated whether defective ameloblast differentiation or enamel matrix formation affects junctional epithelium anatomy or function. Here, we examined the junctional epithelium in mice exhibiting amelogenesis imperfecta due to loss-of-function mutations in the major enamel matrix protein amelogenin (Amelx^−/−) or the critical enamel matrix protease KLK4 (Klk4^−/−). Histological analyses demonstrated altered morphology and cell layer thickness of the junctional epithelium in Amelx^−/− and Klk4^−/− mice as compared to wt. Immunohistochemistry revealed reduced ODAM, laminin 5, and integrin α6, all of which are critical for the adhesion of the junctional epithelium to the enamel in Amelx^−/− and Klk4^−/− mice. Furthermore, we observed altered cell–cell adhesion and increased permeability of Dextran-GFP through the mutants’ junctional epithelium, indicating defective barrier function. Reduced β-catenin and Ki67 at the base of the junctional epithelium in mutants suggest impaired mitotic activity and reduced capacity to replenish continuously desquamated epithelium. These findings highlight the essential role of normal amelogenesis in maintaining junctional epithelium homeostasis. Full article

(This article belongs to the Special Issue Understanding the Molecular Basis of Genetic Dental Diseases)

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55 pages, 2394 KiB

Open AccessFeature PaperReview

Salivaomic Biomarkers—An Innovative Approach to the Diagnosis, Treatment, and Prognosis of Oral Cancer

by Katarzyna Starska-Kowarska

Biology 2025, 14(7), 852; https://doi.org/10.3390/biology14070852 (registering DOI) - 13 Jul 2025

Abstract

(1) Background: Oral cancer (OC) is one of the most frequently diagnosed human cancers and remains a challenge for biologists and clinicians. More than 90% of OC cases are squamous cell carcinomas (OSCCs). Despite the use of modern diagnostic and prognostic methods, the [...] Read more.

(1) Background: Oral cancer (OC) is one of the most frequently diagnosed human cancers and remains a challenge for biologists and clinicians. More than 90% of OC cases are squamous cell carcinomas (OSCCs). Despite the use of modern diagnostic and prognostic methods, the 5-year survival rate remains unsatisfactory due to the late diagnosis of the neoplastic process and its resistance to treatment. This comprehensive review aims to present the latest literature data on the use and effectiveness of saliva as a non-invasive biomarker in patients with oral cancer. (2) Methods: The article reviews the current literature on the use of salivary omics biomarkers as an effective method in diagnosing and modifying treatment in patients with OSCC; the research corpus was acquired from the PubMed/Google/Scopus/Cochrane Library/Web of Science databases in accordance with the Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA 2020) guidelines. (3) Results: The identification of salivary omics biomarkers involved in carcinogenesis and neoplastic transformation may be a potential alternative to traditional invasive diagnostic methods. Saliva, being both an abundant reservoir of organic and inorganic components derived from epithelial cells as well as a cell-free environment, is becoming an interesting diagnostic material for studies in the field of proteomics, genomics, metagenomics, and metabolomics. (4) Conclusions: Saliva-based analysis is a modern and promising method for the early diagnosis and improvement of treatment outcomes in patients with OSCC and oral potentially malignant disorders (OPMDs), with high diagnostic, therapeutic, and prognostic potential. Full article

(This article belongs to the Special Issue New Sight in Cancer Genetics—2nd Edition)

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10 pages, 711 KiB

Open AccessBrief Report

High Variability in Human Sperm Membrane Potential over Time Can Limit Its Reliability as a Predictor in ART Outcomes

by Tomás J. Steeman, Carolina Baro Graf, Analia G. Novero, Mariano G. Buffone and Dario Krapf

Biology 2025, 14(7), 851; https://doi.org/10.3390/biology14070851 (registering DOI) - 12 Jul 2025

Abstract

Sperm membrane potential (Em) hyperpolarization during capacitation is a functional hallmark of fertilizing ability and has been proposed as a predictive biomarker for conventional in vitro fertilization (IVF) success. However, it is unclear whether Em remains stable across ejaculates over [...] Read more.

Sperm membrane potential (Em) hyperpolarization during capacitation is a functional hallmark of fertilizing ability and has been proposed as a predictive biomarker for conventional in vitro fertilization (IVF) success. However, it is unclear whether Em remains stable across ejaculates over time and can reliably guide assisted reproductive technology (ART) decisions in advance. Thus, we aimed to evaluate the temporal consistency of human sperm Em within individuals and assess its utility as a prognostic marker when measured days or weeks prior to IVF procedures. Em was assessed in capacitated and non-capacitated sperm from normospermic donors at three time points over 28 days, using a fluorometric assay. Capacitated values were compared to a −48.6 mV threshold previously associated with successful fertilization. Intra-donor Em variability and coefficients of variation (CV) were analyzed statistically. Our results showed that Em values exhibited significant intra-donor variability over time (p = 0.007), with approximately half of the donors crossing the −48.6 mV functional threshold across sessions. Capacitated sperm samples showed significantly greater variability than non-capacitated ones, with several donors exceeding a 30% CV cutoff. No consistent correlation was found between CV and mean Em values. While Em remains a promising functional marker when assessed on the day of IVF, its temporal variability undermines its reliability as a predictive tool for ART decisions made in advance. These findings underscore the importance of timing in functional sperm assessments and call for further studies to identify the physiological factors influencing Em stability. Full article

(This article belongs to the Section Cell Biology)

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12 pages, 3338 KiB

Open AccessArticle

Natural CCD2 Variants and RNA Interference for Boosting Crocin Biosynthesis in Tomato

by Elena Moreno-Giménez, Eduardo Parreño, Lucía Morote, Alberto José López Jiménez, Cristian Martínez Fajardo, Silvia Presa, Ángela Rubio-Moraga, Antonio Granell, Oussama Ahrazem and Lourdes Gómez-Gómez

Biology 2025, 14(7), 850; https://doi.org/10.3390/biology14070850 (registering DOI) - 12 Jul 2025

Abstract

Crocin biosynthesis involves a complex network of enzymes with biosynthetic and modifier enzymes, and the manipulation of these pathways holds promise for improving human health through the broad exploitation of these bioactive metabolites. Crocins play a significant role in human nutrition and health, [...] Read more.

Crocin biosynthesis involves a complex network of enzymes with biosynthetic and modifier enzymes, and the manipulation of these pathways holds promise for improving human health through the broad exploitation of these bioactive metabolites. Crocins play a significant role in human nutrition and health, as they exhibit antioxidant and anti-inflammatory activity. Plants that naturally accumulate high levels of crocins are scarce, and the production of crocins is highly limited by the characteristics of the crops and their yield. The CCD2 enzyme, initially identified in saffron, is responsible for converting zeaxanthin into crocetin, which is further modified to crocins by aldehyde dehydrogenases and glucosyltransferase enzymes. Crops like tomato fruits, which naturally contain high levels of carotenoids, offer valuable genetic resources for expanding synthetic biology tools. In an effort to explore CCD2 enzymes with improved activity, two CCD2 alleles from saffron and Crocosmia were introduced into tomato, together with a UGT gene. Furthermore, in order to increase the zeaxanthin pool in the fruit, an RNA interference construct was introduced to limit the conversion of zeaxanthin to violaxanthin. The expression of saffron CCD2, CsCCDD2L, led to the creation of transgenic tomatoes with significantly high crocins levels, reaching concentrations of 4.7 mg/g dry weight. The Crocosmia allele, CroCCD2, also resulted in high crocins levels, reaching a concentration of 2.1 mg/g dry weight. These findings underscore the importance of enzyme variants in synthetic biology, as they enable the development of crops rich in beneficial apocarotenoids. Full article

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

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18 pages, 2348 KiB

Open AccessArticle

Glucomannan Accumulation Induced by Exogenous Lanthanum in Amorphophallus konjac: Insights from a Comparative Transcriptome Analysis

by Xiaoxian Li, Zhouting Zeng, Siyi Zhu, Xirui Yang, Xiaobo Xuan and Zhenming Yu

Biology 2025, 14(7), 849; https://doi.org/10.3390/biology14070849 - 11 Jul 2025

Abstract

Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. [...] Read more.

Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. In this study, 20~80 mg L⁻¹ La significantly stimulated KGM accumulation compared with the control group. We performed a transcriptome analysis and found 21,047 differentially expressed genes (DEGs), predominantly enriched in carbohydrate and glycan metabolism pathways. A total of 48 DEGs were linked to KGM biosynthesis, with 20 genes (SuSy, INV1/3/5/6, HK1/2, FPK2, GPI3, PGM3, UGP2, GMPP1/4, CslA3~7, CslH2, and MSR1.2) showing significant positive correlations with KGM content. Interestingly, three key terminal pathway genes (UGP1, UGP3, and CslD3) exhibited strong upregulation (log2 fold change > 3). Seven DEGs were validated with qRT-PCR, aligning with the transcriptomic results. Furthermore, 12 hormone-responsive DEGs, including 4 ethylene-related genes (CTR1, EBF1/2, EIN3, and MPK6), 6 auxin-related genes (AUX/IAA1-3, SAUR1-2, and TIR1), and 2 gibberellin-related genes (DELLA1-2), were closely linked to KGM levels. Additionally, the transcription factors bHLH and AP2/ERF showed to be closely related to the biosynthesis of KGM. These results lay the foundation for a model wherein La (Ш) modulates KGM accumulation by coordinately regulating biosynthetic and hormonal pathways via specific transcription factors. Full article

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24 pages, 4222 KiB

Open AccessArticle

Transcriptome and Cellular Evidence of Depot-Specific Function in Beef Cattle Intramuscular, Subcutaneous, and Visceral Adipose Tissues

by Alexandra P. Tegeler, Hunter R. Ford, Jean Franco Fiallo-Diez, Tainara C. Michelotti, Bradley J. Johnson, Oscar J. Benitez, Dale R. Woerner and Clarissa Strieder-Barboza

Biology 2025, 14(7), 848; https://doi.org/10.3390/biology14070848 - 11 Jul 2025

Abstract

Deposition of intramuscular adipose tissue (IMAT) is the primary determinant for beef quality grade in the U.S. Accumulation of subcutaneous (SCAT) and visceral (VIAT) adipose tissue precedes that of IMAT and often leads to excessive adiposity in beef cattle. Approaches to increase marbling [...] Read more.

Deposition of intramuscular adipose tissue (IMAT) is the primary determinant for beef quality grade in the U.S. Accumulation of subcutaneous (SCAT) and visceral (VIAT) adipose tissue precedes that of IMAT and often leads to excessive adiposity in beef cattle. Approaches to increase marbling while limiting subcutaneous and visceral adiposity are limited. Our objective is to define the depot-specific transcriptome profile and adipocyte function in IMAT, SCAT, and VIAT in beef steers. Transcriptomics revealed the upregulation of adipogenic and lipogenic genes in SCAT and VIAT vs. IMAT. Functional transcriptome analysis demonstrated the activation of pathways for lipid metabolic processes and biosynthesis in SCAT, accompanied by increased preadipocyte proliferation, adipocyte size, and insulin responses of SCAT in vitro. While IMAT had a greater abundance of preadipocytes, they proliferated at a lower rate and differentiated into adipocytes that were smaller and less responsive to insulin compared to SCAT. The upregulation of extracellular matrix genes in IMAT suggests that fat accumulation may be limited by the muscle microenvironment. The activation of inflammatory and immune response pathways, combined with a higher abundance of immune cells, highlighted VIAT as an immune-responsive depot. Our findings reveal transcriptional and cellular profiles underlying fat deposition in SCAT, VIAT, and IMAT in beef cattle. Full article

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40 pages, 1029 KiB

Open AccessReview

Biotechnological Potential of Extremophiles: Environmental Solutions, Challenges, and Advancements

by Fabrizia Sepe, Ezia Costanzo, Elena Ionata and Loredana Marcolongo

Biology 2025, 14(7), 847; https://doi.org/10.3390/biology14070847 - 11 Jul 2025

Abstract

Extremophiles are microorganisms capable of living on Earth in ecological niches characterized by peculiar conditions, including extreme temperatures and/or pH, high salt concentrations, and the presence of heavy metals. The development of unique structural and functional adaptation strategies has stimulated an increasing scientific [...] Read more.

Extremophiles are microorganisms capable of living on Earth in ecological niches characterized by peculiar conditions, including extreme temperatures and/or pH, high salt concentrations, and the presence of heavy metals. The development of unique structural and functional adaptation strategies has stimulated an increasing scientific interest since their discovery. The importance of extremophiles lies in their exploitability in significant bioprocesses with several biotechnological applications and their role as a fundamental source of numerous high-value-added biomolecules. This review aims to examine the diversity and specificities of extremophilic archaea and bacteria, with particular emphasis on their potential applications and development in biotechnology and biomedicine. The use of extremophiles and their extremozymes has allowed applications in several fields, such as bioremediation, sustainable agriculture, the recovery of bioactive molecules for use in bioenergy, biomedicine, and nanoparticle production. The comprehension and exploitation of the complex molecular mechanisms that enable life in extreme environments represent a challenge to mitigate current climate change problems and to invest in sustainable development towards a green transition. Full article

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

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21 pages, 7490 KiB

Open AccessArticle

Exploring the Biocultural Nexus of Gastrodia elata in Zhaotong: A Pathway to Ecological Conservation and Economic Growth

by Yanxiao Fan, Menghua Tian, Defen Hu and Yong Xiong

Biology 2025, 14(7), 846; https://doi.org/10.3390/biology14070846 - 11 Jul 2025

Abstract

Gastrodia elata, known as Tianma in Chinese, is a valuable medicinal and nutritional resource. The favorable climate of Zhaotong City, Yunnan Province, China, facilitates its growth and nurtures rich biocultural diversity associated with Tianma in the region. Local people not only cultivate [...] Read more.

Gastrodia elata, known as Tianma in Chinese, is a valuable medicinal and nutritional resource. The favorable climate of Zhaotong City, Yunnan Province, China, facilitates its growth and nurtures rich biocultural diversity associated with Tianma in the region. Local people not only cultivate Tianma as a traditional crop but have also developed a series of traditional knowledge related to its cultivation, processing, medicinal use, and culinary applications. In this study, field surveys employing ethnobotanical methods were conducted in Yiliang County, Zhaotong City, from August 2020 to May 2024, focusing on Tianma. A total of 114 key informants participated in semi-structured interviews. The survey documented 23 species (and forms) from seven families related to Tianma cultivation. Among them, there were five Gastrodia resource taxa, including one original species, and four forms. These 23 species served as either target cultivated species, symbiotic fungi (promoting early-stage Gastrodia germination), or fungus-cultivating wood. The Fagaceae family, with 10 species, was the most dominant, as its dense, starch-rich wood decomposes slowly, providing Armillaria with a long-term, stable nutrient substrate. The cultural importance (CI) statistics revealed that Castanea mollissima, G. elata, G. elata f. flavida, G. elata f. glauca, G. elata f. viridis, and Xuehong Tianma (unknown form) exhibited relatively high CI values, indicating their crucial cultural significance and substantial value within the local community. In local communities, traditionally processed dried Tianma tubers are mainly used to treat cardiovascular diseases and also serve as a culinary ingredient, with its young shoots and tubers incorporated into dishes such as cold salads and stewed chicken. To protect the essential ecological conditions for Tianma, the local government has implemented forest conservation measures. The sustainable development of the Tianma industry has alleviated poverty, protected biodiversity, and promoted local economic growth. As a distinctive plateau specialty of Zhaotong, Tianma exemplifies how biocultural diversity contributes to ecosystem services and human well-being. This study underscores the importance of biocultural diversity in ecological conservation and the promotion of human welfare. Full article

(This article belongs to the Special Issue Young Researchers in Conservation Biology and Biodiversity)

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22 pages, 2749 KiB

Open AccessArticle

Genetic Diversity, Population Structure, and Historical Gene Flow Patterns of Nine Indigenous Greek Sheep Breeds

by Sofia Michailidou, Maria Kyritsi, Eleftherios Pavlou, Antiopi Tsoureki and Anagnostis Argiriou

Biology 2025, 14(7), 845; https://doi.org/10.3390/biology14070845 - 10 Jul 2025

Abstract

Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the F [...] Read more.

Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the F_IS inbreeding coefficient, and runs of homozygosity (ROH). The genetic differentiation of breeds was assessed using the F_ST index, whereas their population structure was analyzed using admixture and principal components analysis (PCA). Historical recombination patterns and genetic drift were evaluated based on linkage disequilibrium, effective population sizes, and gene flow analysis to reveal migration patterns. PCA revealed distinct clusters mostly separating mountainous, insular, and lowland breeds. The F_ST value was the lowest between Serres and Karagouniko breeds (0.050). Admixture analysis revealed a genetic substructure for Serres and Kalarritiko breeds, while Chios, followed by Katsika, demonstrated the highest within-breed genetic uniformity. ROH analysis revealed low levels of inbreeding for all breeds. Genetic introgression from both Anatolia and Eastern Europe has been evidenced for Greek sheep breeds. The results also revealed that Greek sheep breeds maintain adequate levels of genetic diversity, without signs of excessive inbreeding, and can serve as valuable resources for the conservation of local biodiversity. Full article

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

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24 pages, 3795 KiB

Open AccessArticle

Ecological Effects of Sargassum fusiforme Cultivation on Coastal Phytoplankton Community Structure and Water Quality: A Study Based on Microscopic Analysis

by Yurong Zhang, Rijin Jiang, Qingxi Han, Zimeng Li, Zhen Mao and Haifeng Jiao

Biology 2025, 14(7), 844; https://doi.org/10.3390/biology14070844 - 10 Jul 2025

Abstract

This study used microscopy-based quantitative enumeration to investigate the effects of large-scale Sargassum fusiforme cultivation on coastal water quality and phytoplankton communities. Data from April (cultivation period) and June (non-cultivation period) in 2018 and 2019 showed that cultivation increased pH and dissolved oxygen [...] Read more.

This study used microscopy-based quantitative enumeration to investigate the effects of large-scale Sargassum fusiforme cultivation on coastal water quality and phytoplankton communities. Data from April (cultivation period) and June (non-cultivation period) in 2018 and 2019 showed that cultivation increased pH and dissolved oxygen (DO). It also reduced nitrate–nitrogen (NO₃–N), nitrite–nitrogen (NO₂–N), phosphate–phosphorus (PO₄–P), total phosphorus (TP), and silicate–silicon (SiO₃–Si) concentrations. These changes indicate improved coastal water quality from S. fusiforme cultivation. Nutrient levels rose again during the non-cultivation period. This suggests that water purification decreased without cultivation. Cultivation also lowered the dominance of Skeletonema costatum. This led to a more diverse and stable phytoplankton community. Microscopic observation is valuable for quantifying larger phytoplankton species, and plays an important role in ecological monitoring. These findings provide insights for sustainable aquaculture and ecological restoration. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Aquatic Macrophytes and Algae—2nd Edition)

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26 pages, 1985 KiB

Open AccessReview

Stomatal and Non-Stomatal Leaf Traits for Enhanced Water Use Efficiency in Rice

by Yvonne Fernando, Mark Adams, Markus Kuhlmann and Vito Butardo Jr

Biology 2025, 14(7), 843; https://doi.org/10.3390/biology14070843 - 10 Jul 2025

Abstract

Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and [...] Read more.

Globally, rice cultivation consumes large amounts of fresh water, and urgent improvements in water use efficiency (WUE) are needed to ensure sustainable production, given increasing water scarcity. While stomatal traits have been a primary focus for enhancing WUE, complex interactions between stomatal and non-stomatal leaf traits remain poorly understood. In this review, we present an analysis of stomatal and non-stomatal leaf traits influencing WUE in rice. The data suggests that optimising stomatal density and size will be insufficient to maximise WUE because non-stomatal traits such as mesophyll conductance, leaf anatomy, and biochemical composition significantly modulate the relationship between stomatal conductance and the photosynthetic rate. Integrating recent advances in high-throughput phenotyping, multi-omics technologies, and crop modelling, we suggest that combinations of seemingly contradictory traits can enhance WUE without compromising yield potential. We propose a multi-trait breeding framework that leverages both stomatal and non-stomatal adaptations to develop rice varieties with superior WUE and climate resilience. This integrated approach provides a roadmap for accelerating the development of water-efficient rice cultivars, with broad implications for improving WUE in other crops. Full article

(This article belongs to the Special Issue Multi-omics Approaches in Agricultural Crops to Unravel Responses to Environmental Stresses and Advance Sustainable Agriculture)

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23 pages, 1028 KiB

Open AccessReview

Molecular and Genetic Pathogenesis of Oral Cancer: A Basis for Customized Diagnosis and Treatment

by Leonor Barroso, Pedro Veiga, Joana Barbosa Melo, Isabel Marques Carreira and Ilda Patrícia Ribeiro

Biology 2025, 14(7), 842; https://doi.org/10.3390/biology14070842 - 10 Jul 2025

Abstract

Oral cancer, the most common form of head and neck cancer, is worldwide a serious public health problem. Most patients present a locally advanced disease, and face poor prognosis, even with multimodality treatment. They may also develop second primary tumors in the entirety [...] Read more.

Oral cancer, the most common form of head and neck cancer, is worldwide a serious public health problem. Most patients present a locally advanced disease, and face poor prognosis, even with multimodality treatment. They may also develop second primary tumors in the entirety of their upper aerodigestive tract. The most altered signaling pathways are the PI3K/AKT/mTOR, TP53, RB, and the WNT/β-catenin pathways. Genomic and molecular cytogenetic analyses have revealed frequent losses at 3p, 8p, 9p, and 18q, along with gains at 3q, 7p, 8q, and 11q, and several genes frequently affected have been identified, such as TP53, CCND1, CTTN, CDKN2A, EGFR, HRAS, PI3K, ADAM9, MGAM, SIRPB1, and FAT1, among others. Various epigenetic alterations were also found, such as the global hypomethylation and hypermethylation of CDKN2A, APC, MGMT, PTEN, CDH1, TFP12, SOX17, GATA4, ECAD, MGMT, and DAPK. Several microRNAs are upregulated in oral cancer, including miR-21, miR-24, miR-31, miR-184, miR-211, miR-221, and miR-222, while others are downregulated, such as miR-203, miR-100, miR-200, miR-133a, miR-133b, miR-138, and miR-375. The knowledge of this molecular pathogenesis has not yet been translated into clinical practice, apart from the use of cetuximab, an EGFR antibody. Oral tumors are also genetically heterogenous and affect several pathways, which means that, due to the continuous evolution of these genetic alterations, a single biopsy is not sufficient to fully evaluate the most adequate molecular targets when more drugs become available. Liquid biopsies, either resorting to circulating tumor cells, extracellular vesicles or cell-free nucleic acids, have the potential to bypass this problem, and have potential prognostic and staging value. We critically review the current knowledge on the molecular, genetic and epigenetic alterations in oral cancer, as well as the applications and challenges of liquid biopsies in its diagnosis, follow-up, and prognostic stratification. Full article

(This article belongs to the Section Cancer Biology)

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19 pages, 4056 KiB

Open AccessArticle

Aerobiological Dynamics and Climatic Sensitivity of Airborne Pollen in Southeastern Türkiye: A Two-Year Assessment from Siirt

by Salih Akpınar

Biology 2025, 14(7), 841; https://doi.org/10.3390/biology14070841 - 10 Jul 2025

Abstract

This study investigates the composition, abundance, and seasonal variability of airborne pollen in Siirt, a transitional region between the Irano-Turanian and Mediterranean phytogeographical zones in southeastern Türkiye. The main objective was to assess pollen diversity and its relationship with meteorological parameters over a [...] Read more.

This study investigates the composition, abundance, and seasonal variability of airborne pollen in Siirt, a transitional region between the Irano-Turanian and Mediterranean phytogeographical zones in southeastern Türkiye. The main objective was to assess pollen diversity and its relationship with meteorological parameters over a two-year period (2022–2023). Airborne pollen was collected using a Hirst-type volumetric pollen and spore trap; a total of 18,666 pollen grains/m³ belonging to 37 taxa were identified. Of these, 70.67% originated from woody taxa and 29.33% from herbaceous taxa. Peak concentrations occurred in April, with the lowest levels in December. The dominant taxa, all exceeding 1% of the total, were Pinaceae (31.00%); Cupressaceae/Taxaceae (27.79%); Poaceae (18.42%); Moraceae (4.23%); Amaranthaceae (2.42%); Urticaceae (2.13%); Quercus (1.55%); Fabaceae (1.29%); and Rumex (1.02%). Spearman’s correlation analysis revealed significant relationships between daily pollen concentrations and meteorological variables such as temperature, humidity, precipitation, and wind speed. These findings highlight that both climatic conditions and the surrounding vegetation, shaped by regional land cover, play a crucial role in determining pollen dynamics. In conclusion, this study provides the first aerobiological baseline for Siirt and contributes valuable data for allergy-risk forecasting and long-term ecological monitoring in southeastern Türkiye. Full article

(This article belongs to the Section Plant Science)

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17 pages, 3082 KiB

Open AccessArticle

Full-Length Transcriptome Sequencing and hsp Gene Family Analysis Provide New Insights into the Stress Response Mechanisms of Mystus guttatus

by Lang Qin, Xueling Zhang, Yusen Li, Jun Shi, Yu Li, Yaoquan Han, Hui Luo, Dapeng Wang, Yong Lin and Hua Ye

Biology 2025, 14(7), 840; https://doi.org/10.3390/biology14070840 - 10 Jul 2025

Abstract

Mystus guttatus, a second-class protected species in China, has undergone severe population decline due to anthropogenic and environmental pressures, yet conservation efforts are hindered by limited genomic resources and a lack of mechanistic insights into its stress response systems. Here, the first [...] Read more.

Mystus guttatus, a second-class protected species in China, has undergone severe population decline due to anthropogenic and environmental pressures, yet conservation efforts are hindered by limited genomic resources and a lack of mechanistic insights into its stress response systems. Here, the first full-length transcriptome of M. guttatus was generated via SMRT sequencing. A total of 32,647 full-length transcripts were obtained, with an average length of 1783 bp. After structure and function annotation of full-length transcripts, 30,977 genes, 1670 transcription factors (TF), 918 alternative splicing (AS), and 11,830 simple sequence repeats (SSR) were identified. In order to further explore the stress resistance of M. guttatus, 93 genes belonging to the heat shock protein (HSP) family were identified and categorized into HSP70 and HSP90 subgroups. After phylogenetic analysis and selective stress analysis, it was discovered that the hsp family has suffered purifying selection and gene loss, potentially contributing to a decrease in the stress resilience and population of M. guttatus. Using protein interaction network and molecular docking tools, we observed the intricate interplay among HSPs and discovered HSP70-HOP-HSP90 interaction, which is an essential stress response mechanism. Our study sequenced the first full-length transcriptome of M. guttatus to enhance its genomic resources for its conservation and breeding and provide new insights into the future study of stress response mechanisms on M. guttatus. Full article

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