Biology

15 pages, 3646 KiB

Open AccessArticle

Changes in the Distribution Range of the Genus Cardiocrinum in China Under Climate Change and Human Activities

by Yuxin Zhang, Shujian Zhang, Haiyan Xiao, Heng Li, Da Liao, Yuxi Xue, Xinyi Huang, Qitao Su and Yian Xiao

Biology 2025, 14(5), 581; https://doi.org/10.3390/biology14050581 - 21 May 2025

Abstract

Cardiocrinum are perennial herbaceous plants of the Liliaceae family with high ornamental, nutritional, and medicinal value. However, critical knowledge gaps remain regarding the following: (1) the fine-scale habitat preferences of Cardiocrinum; (2) the key ecological drivers influencing their growth and distribution. The [...] Read more.

Cardiocrinum are perennial herbaceous plants of the Liliaceae family with high ornamental, nutritional, and medicinal value. However, critical knowledge gaps remain regarding the following: (1) the fine-scale habitat preferences of Cardiocrinum; (2) the key ecological drivers influencing their growth and distribution. The MaxEnt software 3.4.1 was used to simulate the current and future suitable habitats of Cardiocrinum, evaluate the impacts of environmental changes on its distribution, and determine the distribution changes under climate change scenarios. The AUC value of the model used in the current study was >0.98, which indicates that the model had good accuracy. The results show that as a typical understory herb, precipitation in the warmest quarter (bio18) and temperature seasonality (bio04) are the main factors affecting the distribution of Cardiocrinum. In addition, Cardiocrinum giganteum and Cardiocrinum giganteum var. yunnanense are also affected by slope and human activity. Under the SSP126, SSP245, and SSP585 climate scenarios, the suitable habitat areas of Cardiocrinum cathayanum and C. giganteum showed an increasing trend. The suitable habitat area of C. giganteum var. yunnanense increased under the SSP126 climate scenario; however, it substantially declined in SSP245 and SSP585 scenarios. The distribution area of Cardiocrinum shifted to higher latitudes. The centroid of C. cathayanum shifted more than 5 degrees of latitude during SSP585 2081s, while the centroid of C. giganteum and C. giganteum var. yunnanense did not shift more than 2 degrees of latitude. In addition, the centroid longitudes of C. giganteum and C. giganteum var. yunnanense shifted westward under the three climate scenarios. There is ecological niche differentiation among C. cathayanum and others, whilst C. giganteum and C. giganteum var. yunnanense have overlapping ecological niches. In the future, we will strengthen the protection of wild Cardiocrinum resources in accordance with environmental factors and suitable habitats for Cardiocrinum. Full article

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16 pages, 2895 KiB

Open AccessArticle

Genome-Wide-Association-Analysis-Based Identification of Genetic Loci and Candidate Genes Associated with Cold Germination in Sweet Corn

by Changjin Wang, Yulin Yu, Jie Liu, Ahmad Rizwan, Zain Abbas, Haibing Yu and Xinxin Cheng

Biology 2025, 14(5), 580; https://doi.org/10.3390/biology14050580 - 21 May 2025

Abstract

Sweet corn is highly susceptible to low temperatures, especially during seed germination, which severely affects plant growth and crop yield. This study used 100 sweet corn micro-core germplasms to evaluate two key germination traits under cold stress: seed storage material utilization efficiency (SRUE) [...] Read more.

Sweet corn is highly susceptible to low temperatures, especially during seed germination, which severely affects plant growth and crop yield. This study used 100 sweet corn micro-core germplasms to evaluate two key germination traits under cold stress: seed storage material utilization efficiency (SRUE) and mobilization weight (WMSR). To investigate the genetic basis of cold germination in sweet corn, we selected the BLINK model for GWAS due to its ability to minimize false positives. A total of nine SNPs were found to be significantly associated with cold germination. These SNPs explained between 9.8% and 17.2% of the phenotypic variance (PVE). Within the confidence interval, 63 functionally annotated genes were identified. Fourteen candidate genes associated with cold germination were identified through GO functional analysis and the functional expression of homologous genes. A literature analysis indicated that these genes are primarily involved in seed germination, cold tolerance, and responses to other abiotic stresses. These findings enhance our understanding of the genetic and molecular mechanisms underlying cold germination, establishing a theoretical foundation for breeding cold-tolerant sweet corn varieties. Full article

(This article belongs to the Section Plant Science)

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20 pages, 8218 KiB

Open AccessArticle

Integrative Transcriptomic Profiling Identifies TNF and IL1B as Candidate Key Early-Response Genes in Macrophages Infected with Smooth Brucella Using a Comprehensive Bioinformatic Approach

by Xiaoyu Yang and Qiang Chen

Biology 2025, 14(5), 579; https://doi.org/10.3390/biology14050579 - 21 May 2025

Abstract

Smooth Brucella are the main pathogenic bacteria that threaten human health and food safety. The early stage of smooth Brucella and macrophage interaction is an important phase, and smooth Brucella species elicit a dramatic transcriptional response in infected macrophages. However, the key transcriptional [...] Read more.

Smooth Brucella are the main pathogenic bacteria that threaten human health and food safety. The early stage of smooth Brucella and macrophage interaction is an important phase, and smooth Brucella species elicit a dramatic transcriptional response in infected macrophages. However, the key transcriptional events are still obscure. This study aimed to identify key candidate response pathways and genes in macrophages infected with smooth Brucella at the early interaction stage. Three gene expression profiles including GSE21117, GSE5202, and GSE8385 were retrieved from the NCBI GEO database, and were integrated using comprehensive bioinformatics methods including gene set enrichment analysis, differentially expressed gene analysis, protein and protein interaction (PPI) network construction, and transcription factor prediction. The results showed that 16 up-regulated and 22 down-regulated pathways were identified, including six up-regulated immune-related pathways. A total of 41 up-regulated and four down-regulated genes were identified, and a PPI network including 31 nodes and 134 edges was constructed based on the interactive information of 45 dysregulated genes. A highly correlated module comprising 19 nodes and 103 edges was identified based on the topological features of the whole PPI network. Seven centrality analyses revealed that Tnf and Il1b were essential genes in the highly correlated module, and that the two essential genes were simultaneously enriched in eight significantly up-regulated pathways (including two immune-related pathways). Bcl3 was predicted as a transcription factor in the highly correlated module, and may play regulatory roles in the transcription of Tnf and Il1b genes. The present study identified Tnf and IL1b as candidate key response genes in infected macrophages at the early stage of smooth Brucella and macrophage interaction, which contributes to a deeper understanding of the early key transcriptional events in macrophages infected with smooth Brucella species. Full article

(This article belongs to the Special Issue Zoonotic Diseases)

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21 pages, 2608 KiB

Open AccessArticle

Phytoplankton Structure and Ecological Niche Differentiation of Dominant Species in Tahe Bay, China

by Yanrong Zhang, Zengqiang Yin, Yinghai Du, Xiangxu Wei, Yikai Lan, Quan Yu, Yan Wang, Tao Tian, Lei Chen and Jun Yang

Biology 2025, 14(5), 578; https://doi.org/10.3390/biology14050578 - 21 May 2025

Abstract

Phytoplankton serve as crucial producers in marine ecosystems, and their community composition and populations’ dispersion directly or indirectly influence the productivity of marine waters via the trophic cascade effect within the food chain. A survey was undertaken in September 2021 and March, April, [...] Read more.

Phytoplankton serve as crucial producers in marine ecosystems, and their community composition and populations’ dispersion directly or indirectly influence the productivity of marine waters via the trophic cascade effect within the food chain. A survey was undertaken in September 2021 and March, April, and November 2022 to examine the phytoplankton structure and the environmental variables influencing ecological niche differentiation in the waters of Tahe Bay in Lushun, Dalian city, China. The findings indicated that there are 83 species representing forty-one genera and six phyla, with an annual mean abundance of 22.13 × 10⁴ ind·m⁻³, predominantly represented by Bacillariophyta (65 species, constituting 78.31% of the total species). The phytoplankton richness indices varied from 0.83 to 4.99, diversity indices ranged from 2.03 to 2.80, and evenness indices spanned from 0.28 to 0.84. Pearson’s correlation between phytoplankton abundance and community diversity with environmental parameters, including water temperature, salinity, pH, DO, NH₃-N, and NO₃-N, was substantial in Tahe Bay’s waters. The dominant species, comprising 20 species across three phyla, primarily include broad-niche species, with Paralia sulcata being the most prevalent species, except during summer. The extent of ecological niche overlap among the dominant species varied by season, exhibiting 40.0% severe overlap in September 2021, 100.0% severe overlap in March 2022, 93.0% severe overlap in April 2022, and 58.0% severe overlap in November 2022. The findings of redundancy analysis (RDA) and canonical correspondence analysis (CCA) revealed that COD, water temperature, NO₃-N, DIP, NO₂-N, and NH₃-N are the primary environmental variables influencing the ecological niche differentiation of dominant species of phytoplankton. The results of the study elucidate the alteration rules of dominant species and the stability of the community structure of the phytoplankton community in this sea area, thereby offering a theoretical foundation for the scientific assessment of the ecological health of the area and the sustainable utilization of marine biological resources. Full article

(This article belongs to the Special Issue Global Fisheries Resources, Fisheries, and Carbon-Sink Fisheries)

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16 pages, 3478 KiB

Open AccessArticle

The Population Density, Interspecific Territoriality, and Philopatry of Shrikes (Laniidae) and Bushshrikes (Malaconotidae) in a Mosaic of Natural and Human-Modified Acacia Savanna

by Grzegorz Kopij

Biology 2025, 14(5), 577; https://doi.org/10.3390/biology14050577 - 20 May 2025

Abstract

In avian behavioural and spatial ecology, issues related to population density, territoriality, and philopatry are especially important. These are often interrelated. The aim of this study was to analyse these behaviours in shrikes inhabiting an acacia savanna in northern Namibia (400 ha). Population [...] Read more.

In avian behavioural and spatial ecology, issues related to population density, territoriality, and philopatry are especially important. These are often interrelated. The aim of this study was to analyse these behaviours in shrikes inhabiting an acacia savanna in northern Namibia (400 ha). Population densities of one shrike and four bushshrike species were studied by means of the territory mapping method. About half of the study area had been modified by humans into cultivated fields, orchards, sport fields, and human settlements. This study was conducted in 2012/2013, 2017/2018, and 2019/2020. The most common species were the Black-backed Puffback (2.5 pairs/100 ha) and Crimson-breasted Shrike (1.9); the least common were the Southern White-crowned Shrike (0.8) and Brubru (1.0). Statistics for the Brown-crowned Tchagra indicated a density of 1.5 pairs/100 ha. While the density of the Brown-crowned Tchagra and Brubru remained stable over the years, the population densities of the Black-backed Shrike, Crimson-breasted Shrike, and Southern White-crowned Shrike showed a remarkable increase over the years 2012–2020. All bushshrike species showed a preference for patches of natural savanna vegetation. This was especially evident in the Crimson-breasted Shrike and the Brubru. However, the Southern White-crowned Shrike from the shrike family did not show this preference. The presented studies showed marked interspecific differences in territoriality and philopatry. Furthermore, even within the same species, marked temporal differences were shown in population density, probably also in philopatry. Within families, these behaviours may shape both resource competition and mate competition, while between families, these behaviours only shape resource competition. Full article

(This article belongs to the Special Issue Bird Biology and Conservation)

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18 pages, 2559 KiB

Open AccessArticle

Unveiling Prophage Diversity and Host Interactions in Liberibacter: Genomic Insights for Phage Therapy Against Citrus Huanglongbing

by Hui Yin, Jiaxing Wan, Siyu Zhang, Zhuozhuo Wu, Wanshan Zhang and Yuxia Gao

Biology 2025, 14(5), 576; https://doi.org/10.3390/biology14050576 - 20 May 2025

Abstract

HLB is a severe and devastating disease affecting citrus plants, for which no cure is currently available. The pathogen CLas is an unculturable, phloem-limited α-proteobacterium associated with HLB. Phages, known for their ability to directly lyse pathogenic bacteria, have been widely recognized as [...] Read more.

HLB is a severe and devastating disease affecting citrus plants, for which no cure is currently available. The pathogen CLas is an unculturable, phloem-limited α-proteobacterium associated with HLB. Phages, known for their ability to directly lyse pathogenic bacteria, have been widely recognized as effective control agents in both medical and agricultural fields. In this study, we identified 191 prophages across 48 Liberibacter genomes using comparative genomics and phylogenetic methods. These prophages were classified into 17 distinct types, with 13 novel types, named NF1 to NF13. Diversity analysis revealed that the number of prophages per genome ranged from one to eight, with an average of four. Annotation showed that the genome sizes of NF1–NF13 ranged from 10,160 bp to 72,736 bp, with an average size of 27,616 bp, containing between 7 and 66 genes (average: 27 genes). Further functional enrichment of the sequences within 5 kb upstream and downstream of the integration site identified six main aspects, involving four core biological processes: genome structure modification, gene expression regulation, stress response activation, and metabolic pathway modulation. It is speculated that the insertion of the prophage significantly impacts the host. Six virulence factors, including carB, clpC, flhA, algW, rffG, and IlpA, were identified in the prophages. Interestingly, prophages containing carB or clpC are predominantly found in CLas, which may contribute to the global colonization of CLas. Notably, among the 35 identified Type 4 prophages, 19 were found to be active. Type 4 is the only active prophage type, making it a promising candidate for developing phage therapy against CLas. This study is significant for a deeper understanding of the diversity of Liberibacter and the interactions between prophages and their hosts. Full article

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16 pages, 2783 KiB

Open AccessArticle

Transdermal Semaglutide Administration in Mice: Reduces Body Weight by Suppressing Appetite and Enhancing Metabolic Rate

by Wenjing Li, Ruilin Cai, Binxin Yin, Yingying Zhou, Xinyuan Dong, Wenting Li and Jing Wen

Biology 2025, 14(5), 575; https://doi.org/10.3390/biology14050575 - 20 May 2025

Abstract

Background: Semaglutide is a glucagon-like peptide-1 (GLP-1) receptor agonist that shows significant efficacy in treating obesity. However, its associated side effects, including poor patient compliance and gastrointestinal inflammation, are concerning and may be largely attributed to its administration methods (e.g., injection vs. oral) [...] Read more.

Background: Semaglutide is a glucagon-like peptide-1 (GLP-1) receptor agonist that shows significant efficacy in treating obesity. However, its associated side effects, including poor patient compliance and gastrointestinal inflammation, are concerning and may be largely attributed to its administration methods (e.g., injection vs. oral) and the pronounced fluctuations in systemic drug concentrations. To address these challenges, we investigated an innovative drug delivery system (Transdermal Drug Delivery System, TDDS) designed to maintain therapeutic efficacy while improving patient adherence. Results: Both transdermal and injection treatments of semaglutide decreased body weight, carcass weight, blood glucose, and triglyceride levels in male mice compared with the vehicle-treated control group. In addition, transdermal semaglutide in mice reduced the expression of feeding neuropeptides and the mass of the digestive tract, but increased brown adipose tissue (BAT) mass, metabolic rate, and physical activity, compared with the semaglutide injection group. Additionally, transdermal semaglutide had anxiolytic effects on behavior and did not alter tissue pathology in mice. Conclusion: Compared with the injection paradigm, transdermal semaglutide treatment achieved superior weight loss results in two possible ways: It may reduce energy intake by decreasing the expression of feeding neuropeptides and reducing the weight of the digestive tract. It may also facilitate energy expenditure by enhancing physical activity and increasing BAT mass to boost the metabolic rate. Transdermal semaglutide treatment also has an anxiolytic effect on behavior. Together, our data suggest that TDDS treatment of GLP-1RA may have superior clinical safety and sustainability, providing a novel, efficient, and low-risk obesity treatment. Full article

(This article belongs to the Special Issue Animal Models of Metabolic Diseases)

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17 pages, 7269 KiB

Open AccessArticle

Integrated miRNA–mRNA Profiling of C2C12 Myoblasts Indicates Regulatory Interactions Involved in Proliferation and Differentiation

by Xiaolong Chang and Junwu Ma

Biology 2025, 14(5), 574; https://doi.org/10.3390/biology14050574 - 20 May 2025

Abstract

Myogenesis is a complex biological process regulated by multiple factors. This study systematically revealed the dynamic changes of gene expression and its regulatory network in C2C12 myoblasts during proliferation and differentiation stages by integrating transcriptome and miRNA-omics data. The analysis results showed that [...] Read more.

Myogenesis is a complex biological process regulated by multiple factors. This study systematically revealed the dynamic changes of gene expression and its regulatory network in C2C12 myoblasts during proliferation and differentiation stages by integrating transcriptome and miRNA-omics data. The analysis results showed that in the early stage of proliferation, gene expression showed significant fluctuations, and key cell cycle and DNA replication-related genes were closely associated with specific miRNAs (miR-486a-5p, miR-486b-5p, and miR-351-5p), suggesting that these miRNAs play an important role in regulating cell proliferation. In the differentiation stage, the activation of key myogenic transcription factors and signaling pathways, such as MAPK and PI3K-Akt, synergizes with miRNA regulation to promote the myogenic program. In addition, we found that genes such as IGF1 and Dio2 were continuously upregulated during differentiation, and IGF1 might be regulated by multiple miRNAs during this process. This study provides key molecular insights for a deeper understanding of muscle development and regeneration. Full article

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23 pages, 3126 KiB

Open AccessArticle

The LIFE STREAMS Project for the Recovery of the Native Mediterranean Trout in Six Italian Pilot Areas: Planning and Adoption of Conservation Actions

by Antonella Carosi, Lorenzo Talarico, Claudia Greco, Antonia Vecchiotti, Susanna D’Antoni, Alessandro Longobardi, Stefano Macchio, Marco Carafa, Paolo Casula, Antonio Perfetti, Paola Amprimo, Alessandro Rossetti, Federico Morandi, Davide Alberti, Pietro Serroni, Stefano Raimondi, Diego Mattioli, Nadia Mucci and Massimo Lorenzoni

Biology 2025, 14(5), 573; https://doi.org/10.3390/biology14050573 - 20 May 2025

Abstract

The Mediterranean trout (currently referred to as Salmo ghigii for Corsican and Italian-native populations) is listed as Endangered in the IUCN Red List, due to fragmented distribution and declining populations across its whole range, and is included in Annex II of the European [...] Read more.

The Mediterranean trout (currently referred to as Salmo ghigii for Corsican and Italian-native populations) is listed as Endangered in the IUCN Red List, due to fragmented distribution and declining populations across its whole range, and is included in Annex II of the European Habitat Directive. The widespread genome introgression from the invasive Atlantic trout (Salmo trutta), overexploitation, and habitat alterations represent major threats to the persistence of native populations. The LIFE18NAT/IT/000931 STREAMS project aims to enhance conservation status of Mediterranean trout in 6 Italian pilot areas (Maiella, Sibillini Mountains, Casentino Forests and Pollino National Parks, Montemarcello-Magra-Vara Regional Park, and Sardinia with five sites of the Natura 2000 Network), and in 19 transferability areas covering almost the whole Italian species range. To achieve this, the following conservation strategies were implemented: (i) the identification of residual native populations; (ii) eradication of entirely Atlantic-exotic populations and removal of hybrids in admixed populations; (iii) restocking/reintroduction of native populations; (iv) monitoring/improving the Mediterranean trout habitats quality; (v) production of the “Guidelines for the conservation and management of native Mediterranean trout and its habitat”; and (vi) the prevention of illegal stocking. Here, we present the project rationale, major outcomes on demographic and genetic characterization of wild populations, and summary results from conservation actions. Full article

(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)

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24 pages, 2686 KiB

Open AccessArticle

Predicting Treatment Outcomes in Glioblastoma: A Risk Score Model for TMZ Resistance and Immune Checkpoint Inhibition

by Nazareno Gonzalez, Melanie Perez Küper, Matias Garcia Fallit, Alejandro J. Nicola Candia, Jorge A. Peña Agudelo, Maicol Suarez Velandia, Ana Clara Romero, Guillermo Agustin Videla-Richardson and Marianela Candolfi

Biology 2025, 14(5), 572; https://doi.org/10.3390/biology14050572 - 20 May 2025

Abstract

Glioblastoma (GBM) presents significant therapeutic challenges due to its invasive nature and resistance to standard chemotherapy, i.e., temozolomide (TMZ). This study aimed to identify gene signatures that predict poor TMZ response and high PD−L1/PD−1 tumor expression, and explore potential sensitivity to alternative drugs. [...] Read more.

Glioblastoma (GBM) presents significant therapeutic challenges due to its invasive nature and resistance to standard chemotherapy, i.e., temozolomide (TMZ). This study aimed to identify gene signatures that predict poor TMZ response and high PD−L1/PD−1 tumor expression, and explore potential sensitivity to alternative drugs. We analyzed The Cancer Genome Atlas (TCGA) biopsy data to identify differentially expressed genes (DEGs) linked to these characteristics. Among 33 upregulated DEGs, 5 were significantly correlated with overall survival. A risk score model was built using these 5 DEGs, classifying patients into low-, medium-, and high-risk groups. We assessed immune cell infiltration, immunosuppressive mediators, and epithelial–mesenchymal transition (EMT) markers in each group using correlation analysis, Gene Set Enrichment Analysis (GSEA), and machine learning. The model demonstrated strong predictive power, with high-risk patients exhibiting poorer survival and increased immune infiltration. GSEA revealed upregulation of immune and EMT-related pathways in high-risk patients. Our analyses suggest that high-risk patients may exhibit limited response to PD−1 inhibitors, but could show sensitivity to etoposide and paclitaxel. This risk score model provides a valuable tool for guiding therapeutic decisions and identifying alternative chemotherapy options to enable the development of personalized and cost-effective treatments for GBM patients. Full article

(This article belongs to the Special Issue Immune Microenvironment and Molecular Mechanism of Glioma)

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14 pages, 1595 KiB

Open AccessArticle

Light/Dark Cycle Lighting Influences Growth and Energy Use Efficiency of Hydroponic Lettuces in an LED Plant Factory

by Wen Li, Luming Zhong, Xiang Ji, Jun Wang and Dongxian He

Biology 2025, 14(5), 571; https://doi.org/10.3390/biology14050571 - 20 May 2025

Abstract

The alterable light/dark cycle in a plant factory with artificial lighting eliminates the traditional concept of day and night in nature. Adjusting the light/dark cycle to closely align with the inherent circadian rhythm of plants can enhance biomass accumulation. In this study, we [...] Read more.

The alterable light/dark cycle in a plant factory with artificial lighting eliminates the traditional concept of day and night in nature. Adjusting the light/dark cycle to closely align with the inherent circadian rhythm of plants can enhance biomass accumulation. In this study, we examined the effects of different light/dark cycles on the photosynthetic performance, growth, and energy use efficiency of two hydroponic lettuce cultivars (Lactuca sativa L. cv. ‘Frillice’ and ‘Crunchy’). The lettuces were subjected to four light/dark cycle treatments—16 h light/8 h dark (L₁₆D₈, as control), 12 h light/6 h dark (L₁₂D₆), 8 h light/4 h dark (L₈D₄), and 4 h light/2 h dark (L₄D₂), all under LED lamps with white combined red chips at the same light intensity of 250 μmol m⁻² s⁻¹. Photosynthetic performance and growth index were measured during the slow and rapid growth stages, corresponding to days 9 and 21 after transplanting, respectively. For Frillice, L₁₂D₆ achieved the highest shoot dry weight and light and electricity energy use efficiencies on days 9 and 21 after transplanting, primarily due to the largest leaf area, leaf number, and net photosynthetic rate. For Crunchy, L₁₂D₆ and L₈D₄ increased shoot fresh and dry weights due to larger leaf area and leaf number on day 9 after transplanting compared with L₁₆D₈. Subsequently, the lettuces in L₁₆D₈ exhibited a rapid increase in leaf area and leaf number, along with a high net photosynthetic rate during the rapid growth stage, resulting in fast shoot biomass accumulation. There were no significant differences in the shoot dry weight and energy use efficiency between L₁₆D₈ and L₁₂D₆ on day 21 after transplanting. Two lettuce cultivars in L₁₆D₈ both exhibited the highest water use efficiency on day 21 after transplanting. In conclusion, the light/dark cycle lighting can alter lettuce biomass accumulation by modifying plant morphology and leaf net photosynthetic rate. Additionally, the physiological response to the light/dark cycle was cultivar-dependent. Our findings provide valuable insights for optimizing hydroponic lettuce production to achieve high yield in LED plant factories. Full article

(This article belongs to the Special Issue Physiological, Biochemical, and Molecular Response in Plants under Light-Emitting Diode (LED) Treatment (Volume II))

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11 pages, 1204 KiB

Open AccessArticle

Ecological Correlates of Ecological Specialization of Avian Communities in University Campuses of China

by Ling-Ying Shuai, Di Meng, Wan-Lan Ma, Jing-Wen Bai, Yue Luo, Yu-Xin Luo, Zhu-Cheng Gao, Hao Zhu and Zhu-Qin Long

Biology 2025, 14(5), 570; https://doi.org/10.3390/biology14050570 - 19 May 2025

Abstract

With the rapid process of urbanization at a global scale, university campuses have been viewed as important urban green spaces for biodiversity conservation. However, little is known about the role of university campuses in protecting ecological specialists, the species usually vulnerable to anthropogenic [...] Read more.

With the rapid process of urbanization at a global scale, university campuses have been viewed as important urban green spaces for biodiversity conservation. However, little is known about the role of university campuses in protecting ecological specialists, the species usually vulnerable to anthropogenic disturbance. We assessed the associations between several ecological variates and ecological specialization of bird communities across 198 Chinese university campuses. A total of 398 bird species were recorded, including 109 diet specialist species and 104 foraging stratum specialist species. We found that the elevation of campuses was positively related to diet specialist species richness, and the campus area was positively related to foraging stratum specialist species richness. NDVI was positively associated with the community-wide foraging stratum specialization index, but negatively associated with the community-wide diet specialization index. Our results suggest that campuses with larger areas or located at high elevations play an important role in maintaining ecological specialization of bird communities. Full article

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

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18 pages, 4426 KiB

Open AccessArticle

TWIK Complex Expression in Prostate Cancer: Insights into the Biological and Therapeutic Significances of Potassium Ion Channels in Clinical Cancer

by Abdulaziz Alfahed

Biology 2025, 14(5), 569; https://doi.org/10.3390/biology14050569 - 19 May 2025

Abstract

Ion channels play ubiquitous roles in the maintenance of tumour cell homeostasis and hence are attractive targets in the molecular pathogenesis and progression of prostate cancer (PCa). This study aimed to investigate the roles of the potassium ion channel complex TWIK, a member [...] Read more.

Ion channels play ubiquitous roles in the maintenance of tumour cell homeostasis and hence are attractive targets in the molecular pathogenesis and progression of prostate cancer (PCa). This study aimed to investigate the roles of the potassium ion channel complex TWIK, a member of the two-pore-domain potassium channel subfamily, in clinical PCa. The clinicopathological, gene expression, and copy number data of three clinical PCa cohorts from cancer genomics databases were analysed to determine the clinicopathological, biological, and therapeutic significances of the TWIK expression signature using statistical correlations and gene enrichment techniques. The results show that the PCa subset with high TWIK expression exhibited associations with worse pathological tumours, nodes, and overall tumour stages, as well as with high Gleason scores, high prognostic grade groups, and poorer responses to androgen deprivation therapy. Furthermore, a combination of gene set and gene ontology enrichment analyses showed that the PCa subset with high TWIK complex expression was differentially enriched for known oncogenic signalling pathways, aberrant ubiquitination and glucuronidation activities, and for gene sets of ion channel blockers and chemotherapeutic agents. The implications of these findings with respect to cancer progression, therapeutic response, and opportunities for therapeutic targeting of the TWIK complex are discussed, along with the potential of the TWIK complex as a predictive biomarker for integrated, multitargeted therapy. Full article

(This article belongs to the Special Issue Ion Channels in Cancer Progression)

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14 pages, 2789 KiB

Open AccessArticle

High-Pressure Microfluidic Homogenization Improves the Stability and Antioxidant Properties of Coenzyme Q10 Nanoliposomes

by Xinyu Li, Xingyu Zhao, Jing Wang, Baoshun Xu, Jin Feng and Wuyang Huang

Biology 2025, 14(5), 568; https://doi.org/10.3390/biology14050568 - 19 May 2025

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Abstract

Coenzyme Q10 is a natural antioxidant with anti-tumor and mitochondrial protective effects. However, its unstable physicochemical properties and large molecular weight result in low bioavailability. This study aimed to develop an effective technique for constructing nanoliposomes to improve the physicochemical properties of CoQ10 [...] Read more.

Coenzyme Q10 is a natural antioxidant with anti-tumor and mitochondrial protective effects. However, its unstable physicochemical properties and large molecular weight result in low bioavailability. This study aimed to develop an effective technique for constructing nanoliposomes to improve the physicochemical properties of CoQ10 by using high-pressure microfluidic homogenization. Liposomes were prepared using the ethanol injection method and homogenized by high-pressure microfluidics to optimize their physicochemical properties. Liposome morphology and microstructure were observed via transmission electron microscopy (TEM). The particle size distribution, polydispersity index (PDI), and encapsulation efficiency were assessed, while effects on cell viability and antioxidant properties were investigated in HepG2 cells. The results indicate that the prepared liposomes exhibit favorable characteristics, including high encapsulation efficiency (>96%) and low PDI (<0.3), indicating uniform particle size distribution and good stability. The storage stability of liposomes at room temperature was significantly enhanced compared to liposomes not subjected to high pressure homogenization. In vitro cell experiments confirmed the liposomes’ non-cytotoxicity and substantial antioxidant activity, ensuring their safety for biomedical applications. This study introduced a liposome preparation method combining ethanol injection and high-pressure microfluidic homogenization, offering a novel approach for liposome modification with potential for development and application in innovative drug delivery systems and antioxidant therapy. Full article

(This article belongs to the Section Biotechnology)

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20 pages, 44320 KiB

Open AccessArticle

Multi-Omics Pan-Cancer Profiling of HSD17B10 Unveils Its Prognostic Potential, Metabolic Regulation, and Immune Microenvironment Interactions

by Tao Qi, Xiao Chang and Yiming Wang

Biology 2025, 14(5), 567; https://doi.org/10.3390/biology14050567 - 19 May 2025

Viewed by 38

Abstract

This study systematically analyzed the expression and clinical significance of Hydroxysteroid 17-beta dehydrogenase type 10 (HSD17B10) in 33 cancers by integrating TCGA, GTEx, and other multi-omics databases. HSD17B10 was highly expressed in 14 cancers, like GBM and LGG, but low in [...] Read more.

This study systematically analyzed the expression and clinical significance of Hydroxysteroid 17-beta dehydrogenase type 10 (HSD17B10) in 33 cancers by integrating TCGA, GTEx, and other multi-omics databases. HSD17B10 was highly expressed in 14 cancers, like GBM and LGG, but low in 5, such as KIRC. Its expression correlated closely with overall survival (OS) and disease-free survival (DFS). In GBM-LGG, LGG, and other cancers, high HSD17B10 expression was linked to lower survival rates, indicating that it could be an independent prognostic marker. HSD17B10 also had a two-way relationship with the tumor’s immune microenvironment. In cancers such as GBM-LGG, high expression correlated positively with immune/stromal scores. However, in most cancers like LUAD, it was negatively associated with B- and T-cell infiltration. Epigenetic analysis showed that low methylation in the HSD17B10 promoter region might drive its high expression in tumors such as SARC, and specific methylation sites (e.g., CG26323797) were significantly related to patient survival. Functional enrichment analysis revealed that HSD17B10 participated in tumor progression by regulating oxidative phosphorylation, mitochondrial metabolism, and RNA methylation. Single-cell and spatial transcriptome data further demonstrated that HSD17B10 had a cell-type-specific expression pattern in colorectal cancer. This study provides a theoretical basis for HSD17B10 as a pan-cancer prognostic marker and therapeutic target. Full article

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

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33 pages, 16266 KiB

Open AccessArticle

Integrated Bioinformatics Analysis and Cellular Experimental Validation Identify Lipoprotein Lipase Gene as a Novel Biomarker for Tumorigenesis and Prognosis in Lung Adenocarcinoma

by Wanwan He, Meilian Wei, Yan Huang, Junsen Qin, Meng Liu, Na Liu, Yanli He, Chuanbing Chen, Yali Huang, Heng Yin and Ren Zhang

Biology 2025, 14(5), 566; https://doi.org/10.3390/biology14050566 - 19 May 2025

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Abstract

Lung adenocarcinoma (LUAD) is one of the leading causes of death worldwide, and thus, more biomarker and therapeutic targets need to be explored. Herein, we aimed to explore new biomarkers of LUAD by integrating bioinformatics analysis with cell experiments. We firstly identified 266 [...] Read more.

Lung adenocarcinoma (LUAD) is one of the leading causes of death worldwide, and thus, more biomarker and therapeutic targets need to be explored. Herein, we aimed to explore new biomarkers of LUAD by integrating bioinformatics analysis with cell experiments. We firstly identified 266 druggable genes that were significantly differentially expressed between LUAD tissues and adjacent normal lung tissues. Among these genes, SMR analysis with p-value correction suggested that declining lipoprotein lipase (LPL) levels may be causally associated with an elevated risk of LUAD, which was corroborated by co-localization analysis. Analyses of clinical data showed that LPL in lung cancer tissues has considerable diagnostic value for LUAD, and elevated LPL levels were positively associated with improved patient survival outcomes. Cell experiments with an LPL activator proved these findings; the activator inhibited the proliferation and migration of lung cancer cells. Next, we found that LPL promoted the infiltration of immune cells such as DCs, IDCs, and macrophages in LUAD by mononuclear sequencing analysis and TIMER2.0. Meanwhile, patients with low levels of LPL expression demonstrated superior immunotherapeutic responses to anti-PD-1 therapy. We conclude that LPL acts as a diagnostic and prognostic marker for LUAD. Full article

(This article belongs to the Special Issue Disease Biomarker Discovery and Validation)

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23 pages, 4971 KiB

Open AccessArticle

Functional Characterization of MIP_07528 of Mycobacterium indicus pranii for Tyrosine Phosphatase Activity Displays Sensitivity to Oxidative Inactivation and Plays a Role in Immunomodulation

by Raunak Raunak, Roopshali Rakshit, Aayush Bahl, Soumya Sinha, Saurabh Pandey, Sashi Kant and Deeksha Tripathi

Biology 2025, 14(5), 565; https://doi.org/10.3390/biology14050565 - 18 May 2025

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Abstract

Mycobacterium indicus pranii (MIP), an atypical mycobacterium originally developed as an anti-leprosy vaccine, has emerged as a potent immunomodulator with diverse therapeutic applications. Despite its clinical significance, molecular mechanisms underlying MIP’s immunomodulatory properties remain largely unexplored. Bacterial phosphatases are recognized as crucial virulence [...] Read more.

Mycobacterium indicus pranii (MIP), an atypical mycobacterium originally developed as an anti-leprosy vaccine, has emerged as a potent immunomodulator with diverse therapeutic applications. Despite its clinical significance, molecular mechanisms underlying MIP’s immunomodulatory properties remain largely unexplored. Bacterial phosphatases are recognized as crucial virulence factors that enable pathogens to evade host defenses by modulating host immune signaling pathways, including phosphoinositide metabolism. MIP_07528 was identified as a putative protein tyrosine phosphatase B (PtpB) ortholog through in silico analysis, with significant sequence conservation observed within catalytic domains of pathogenic mycobacterial PtpB proteins. Phosphatase activity was detected in both cell lysate and culture filtrate fractions, revealing differential expression patterns between MIP and M. tuberculosis. Upregulation of MIP_07528 was demonstrated under oxidative stress, suggesting involvement in stress adaptation. The recombinant protein exhibited distinctive kinetic properties, characterized by higher substrate affinity yet increased susceptibility to oxidative inactivation compared to its M. tuberculosis counterpart. In macrophages, MIP_07528 suppressed pro-inflammatory cytokines while enhancing anti-inflammatory IL-10 production. These findings establish MIP_07528 as a functional phosphatase that may contribute to MIP’s immunomodulatory properties. This work advances understanding of phosphatase function in non-pathogenic mycobacteria while providing insights into virulence factor evolution and establishing a foundation for novel antimicrobial strategies. Full article

(This article belongs to the Special Issue Host–Pathogen Interactions and Pathogenesis)

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18 pages, 1801 KiB

Open AccessArticle

MaxEnt Modeling of the Impacts of Human Activities and Climate Change on the Potential Distribution of Plantago in China

by Da Liao, Bing Zhou, Haiyan Xiao, Yuxin Zhang, Shujian Zhang, Qitao Su and Xiaohong Yan

Biology 2025, 14(5), 564; https://doi.org/10.3390/biology14050564 - 17 May 2025

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Abstract

Human activities exert both beneficial and detrimental impacts on the ecosystem. In recent years, greenhouse gas emissions have significantly increased due to global climate change, causing profound alterations in ecosystem distribution and productivity. The synergistic interplay between climatic shifts and anthropogenic activities is [...] Read more.

Human activities exert both beneficial and detrimental impacts on the ecosystem. In recent years, greenhouse gas emissions have significantly increased due to global climate change, causing profound alterations in ecosystem distribution and productivity. The synergistic interplay between climatic shifts and anthropogenic activities is intensifying ecological transformations and disturbances, and accelerating biodiversity depletion. The Plantago genus (Plantaginaceae family) includes 14 herbaceous species among China’s flora. This study was conducted to elucidate the spatial distribution of Plantago species patterns across China and evaluate their differential responses to impending climate change and human interventions. In this study, we projected the potential distributions of Plantago species under three climate scenarios (SSP126, SSP245, and SSP585) across current and future temporal intervals (2021–2040, 2041–2060, 2061–2080, and 2081–2100) using the MaxEnt model integrated with ArcGIS V10.8 spatial analysis. A spatial trend analyses was also conducted to assess habitat suitability dynamics by incorporating anthropogenic influence parameters. The model validation yielded AUC values exceeding 0.9, demonstrating excellent model performance and predictive reliability. Precipitation variability and anthropogenic pressure emerged as the most predominant determinants shaping Plantago distributions. Centroid migration analyses further indicated the progressive northward displacement of optimal habitats under the projected climate scenarios. These findings significantly advance our understanding of Plantago species’ adaptive responses to environmental changes. This study also offers an invaluable scientific foundation for sustainable resource management and ecological conservation strategies. Full article

(This article belongs to the Section Ecology)

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14 pages, 1946 KiB

Open AccessArticle

Enhancing H11 Protein-Induced Immune Protection Against Haemonchus contortus in Goats: A Nano-Adjuvant Formulation Strategy

by Lisha Ye, Simin Wu, Fuqiang Liu, Juan Zhang, Jie Wan, Chunqun Wang, Hui Liu and Min Hu

Biology 2025, 14(5), 563; https://doi.org/10.3390/biology14050563 - 17 May 2025

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Abstract

The only vaccine against Haemonchus contortus is limited by short-lived antibody persistence and the need for frequent booster immunizations. This study leveraged the advantages of nano-adjuvants in enhancing antigen presentation and immune regulation to evaluate the efficacy of novel adjuvants (IMX, AddaS03) and [...] Read more.

The only vaccine against Haemonchus contortus is limited by short-lived antibody persistence and the need for frequent booster immunizations. This study leveraged the advantages of nano-adjuvants in enhancing antigen presentation and immune regulation to evaluate the efficacy of novel adjuvants (IMX, AddaS03) and the conventional QuilA combined with H11 protein. Goats were divided into four groups (IMX + H11, AddaS03 + H11, QuilA + H11, and infected control). They were immunized three times and challenged with 6000 infective third-stage larvae (iL3s) of H. contortus on the day of the third immunization, with the experiment lasting for 98 days. The results showed that vaccination with IMX + H11 conferred the strongest protection, demonstrating 88.3% efficacy in fecal egg count (FEC) reduction and 75.8% efficacy against worm burden, followed by QuilA + H11 (85.2% FEC reduction and 68% worm burden reduction) and AddaS03 + H11 (79.4% FEC reduction and 61.3% worm burden reduction). Serum IgG analysis revealed high antibody levels in all immunized groups. Cytokine detection found that IMX + H11 significantly upregulated IL-2 and IFN-γ expression in PBMCs and TNF-α expression in splenocytes, activating Th1-type responses and immune memory. QuilA + H11 showed weaker Th1 activation, and AddaS03 + H11 faced limitations due to insufficient antibody persistence for long-term protection. These findings suggest that IMX can induce highly efficient humoral and cellular immunity, providing a new direction for the optimization of H. contortus vaccines and suggesting the importance of nano-adjuvants for precise regulation of immune patterns. Full article

(This article belongs to the Special Issue Immune Response Regulation in Animals)

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18 pages, 4943 KiB

Open AccessArticle

The Coexistence of Bicellular and Tricellular Pollen Might Be the Third Type of Pollen Cell Number: Evidence from Annonaceae

by Yangying Gan, Qi Zhang, Chunfen Xiao and Jingyao Ping

Biology 2025, 14(5), 562; https://doi.org/10.3390/biology14050562 - 17 May 2025

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Abstract

Anther is thought to release either bicellular or tricellular pollen when mature. Though a few species had been found to shed both bicellular and tricellular pollen, due to their low frequency, they had been overlooked as special cases of bicellular or tricellular pollen [...] Read more.

Anther is thought to release either bicellular or tricellular pollen when mature. Though a few species had been found to shed both bicellular and tricellular pollen, due to their low frequency, they had been overlooked as special cases of bicellular or tricellular pollen in previous phylogenetic studies. In the present work, the pollen cytologies of 89 species from 26 genera of Annonaceae were observed using the overall transparency method and paraffin sectioning method. The results show that 73 species from 25 genera distribute bicellular pollen, while 16 species from 10 genera shed both bicellular and tricellular pollen. This is the first time that so many species with both types of pollen has been observed in the same family. Combined with reports from other families, the plants that were known to shed both types of pollen included 15 families, 40 genera, and 52 species. Our results indicate that the coexistence of bicellular and tricellular pollen might be the third type of pollen cell number. And the systematic relationship among them is needed to be reanalyzed. Full article

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19 pages, 3187 KiB

Open AccessArticle

IL-1 Superfamily Across 400+ Species: Therapeutic Targets and Disease Implications

by Weibin Wang, Dawei Li, Kaiyong Luo, Baozheng Chen, Tingting Hao, Xuzhen Li, Dazhong Guo, Yang Dong and Ya Ning

Biology 2025, 14(5), 561; https://doi.org/10.3390/biology14050561 - 17 May 2025

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Abstract

An important area of interest for therapeutic development is the IL-1 superfamily, a critical group of immune regulators with profound implications in a variety of disorders. This study clarifies the evolutionary patterns of IL-1 family members by thoroughly analyzing more than 400 animal [...] Read more.

An important area of interest for therapeutic development is the IL-1 superfamily, a critical group of immune regulators with profound implications in a variety of disorders. This study clarifies the evolutionary patterns of IL-1 family members by thoroughly analyzing more than 400 animal species, demonstrating their ancient roots that extend back to the earliest vertebrates. Important results show that, although IL-1 ligands expanded significantly over the evolution of mammals, their corresponding receptors remained remarkably structurally conserved. Identifying both lineage-specific adaptations and evolutionarily conserved residues provides vital information for treatment design. These findings point to the possibility of two different therapeutic strategies: addressing species-specific variants may allow for more targeted interventions, whereas focusing on conserved motifs may result in broad-acting treatments. The study also identified less well-known species as useful models for comprehending early immune systems. In addition to advancing our knowledge of the function of the IL-1 family in autoimmune, inflammatory, and carcinogenic illnesses, this research lays the groundwork for the development of more potent targeted therapeutics by creating an evolutionary framework for the IL-1 family. Full article

(This article belongs to the Section Evolutionary Biology)

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19 pages, 5960 KiB

Open AccessArticle

Coixol Protects Against Acute Kidney Injury by Reducing Cell Senescence

by Kang Li, Xiaoxue Wang, Huidi Tang, Feifan Wang, Zetong Qu, Xiaojie Wang, Xiang Li and Xiaoqing Cao

Biology 2025, 14(5), 560; https://doi.org/10.3390/biology14050560 - 17 May 2025

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Abstract

Acute kidney injury (AKI) is associated with increased in-hospital mortality, yet effective therapeutic agents remain limited. Coixol, a polyphenolic compound derived from Coix, possesses anti-inflammatory properties, but its role in AKI remains unclear. In this study, we demonstrate that Coixol exerts protective effects [...] Read more.

Acute kidney injury (AKI) is associated with increased in-hospital mortality, yet effective therapeutic agents remain limited. Coixol, a polyphenolic compound derived from Coix, possesses anti-inflammatory properties, but its role in AKI remains unclear. In this study, we demonstrate that Coixol exerts protective effects against ischemia/reperfusion (I/R)-induced AKI by alleviating cellular senescence. Coixol treatment significantly reduced serum creatinine (SCr) and blood urea nitrogen (BUN) levels and decreased the expression of KIM1 and NGAL. RNA sequencing and validation experiments revealed that Coixol suppressed cellular senescence in AKI. Through a weighted gene co-expression network analysis and machine learning, we identified Plaur as a key target of Coixol, which was further validated using RNA-seq data. Notably, Plaur overexpression in AKI mice diminished the protective effects of Coixol, confirming its crucial role. Additionally, molecular docking and molecular dynamics simulations demonstrated strong binding affinity between Coixol and Plaur. These findings highlight Coixol as a promising renal protective agent targeting Plaur and cellular senescence in AKI. Full article

(This article belongs to the Section Medical Biology)

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22 pages, 6610 KiB

Open AccessArticle

Tricky with Heat and Salt: Soil Factors, Thermotaxis, and Potential for Heat–Saline Agar Trapping of Strongyloides Larvae

by Nuttapon Ekobol, Sirintip Boonjaraspinyo, Chatanun Eamudomkarn and Thidarut Boonmars

Biology 2025, 14(5), 559; https://doi.org/10.3390/biology14050559 - 16 May 2025

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Abstract

The viability and host-seeking behavior of Strongyloides larvae are significantly influenced by soil conditions, emphasizing the critical role of environmental control in disease management. This is particularly relevant given the growing concerns about drug resistance resulting from mass chemotherapy or the use of [...] Read more.

The viability and host-seeking behavior of Strongyloides larvae are significantly influenced by soil conditions, emphasizing the critical role of environmental control in disease management. This is particularly relevant given the growing concerns about drug resistance resulting from mass chemotherapy or the use of chemical nematicides. Strongyloides stercoralis was effectively inactivated by exposure to 50 °C for both 12 and 24 h (long-term exposure). Strongyloides ratti was inactivated by 50 °C for 20 min (short-term exposure), 9% saline for 50 min, and a combination of 4% saline and 40 °C for 50 min. The combined treatment successfully inactivated S. ratti in four soil mediums using 5% saline at a central temperature of 40 °C. Thermotaxis responses to noxious heat revealed attraction at 40 °C, increased localized searching at 45 °C, and complete inactivation at 50 °C. Larvae migrating within agar at 45 °C were more readily inactivated. Long-range heat attraction at 5 cm resulted in the inactivation of up to 50% of incoming larvae; however, heat-high concentration saline traps at 3 cm distance proved ineffective. Thermal–saline agar trapping demonstrated promise for larval removal in sand, loam, and laterite soils. This method offers a promising approach to larval removal while minimizing hazards to non-target organisms. Full article

(This article belongs to the Section Infection Biology)

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26 pages, 3958 KiB

Open AccessReview

The Role of Somatostatin in the Gastrointestinal Tract

by Konstantinos Papantoniou, Ioanna Aggeletopoulou, Ploutarchos Pastras and Christos Triantos

Biology 2025, 14(5), 558; https://doi.org/10.3390/biology14050558 - 16 May 2025

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Abstract

The gastrointestinal (GI) tract is responsible for food digestion and host protection from harmful stimuli; however, its function as an endocrine organ is also well documented. Somatostatin (SST) was first discovered in the hypothalamus, but the GI tract is its main producer and [...] Read more.

The gastrointestinal (GI) tract is responsible for food digestion and host protection from harmful stimuli; however, its function as an endocrine organ is also well documented. Somatostatin (SST) was first discovered in the hypothalamus, but the GI tract is its main producer and target organ. SST is a potent inhibitor of many GI functions, including peristalsis, hormone secretion, and gastric acid production, while its anti-inflammatory effects contribute to the integrity of the intestinal barrier. These data make SST and its analogs useful agents in clinical practice. As our understanding of SST metabolism and function evolves, their use in a wide variety of medical conditions can improve patient care. Full article

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24 pages, 2772 KiB

Open AccessArticle

Differential Proneness to Obesity in Two Rat Strains with Diverse Immune Responses

by Dina Tucović, Aleksandra Popov Aleksandrov, Dušanka Popović, Anastasija Malešević, Vesna Subota, Emilija Brdarić, Svetlana Soković Bajić, Milica Živković, Milena Kataranovski, Ivana Mirkov, Stanislava Stanojević and Jelena Kulaš

Biology 2025, 14(5), 557; https://doi.org/10.3390/biology14050557 - 16 May 2025

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Abstract

Although obesity and metabolic syndrome (comprising at least three of the following traits—abdominal obesity, elevated blood pressure, triglycerides and glucose/insulin resistance, and reduced high-density lipoprotein cholesterol in serum) are known to impact immune system activity, these conditions are often not considered when immune [...] Read more.

Although obesity and metabolic syndrome (comprising at least three of the following traits—abdominal obesity, elevated blood pressure, triglycerides and glucose/insulin resistance, and reduced high-density lipoprotein cholesterol in serum) are known to impact immune system activity, these conditions are often not considered when immune response characteristics are investigated in various rodent strains. In this work, metabolic syndrome indices are compared in 3 month-old (young) and 6 month-old (adult) rats of Dark Agouti (DA) and Albino Oxford (AO) strains, while parameters of coagulation, inflammation and oxidative stress were determined in young animals. Study reveals that both young and adult AO rats are obese, intolerant to glucose with higher levels of triglycerides and lower levels of high-density lipoprotein cholesterol when compared to age-matched DA rats. Parameters of coagulation, inflammation and oxidative stress that may contribute to the worsening of metabolic syndrome during aging are also higher in young AO rats. Metabolic syndrome observed in young and intensified in adult AO rats should be taken into consideration when analyzing alterations in immune reactivity during aging in this rat strain. Full article

(This article belongs to the Section Physiology)

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40 pages, 11073 KiB

Open AccessArticle

Bioinformatic Analysis of Complex In Vitro Fertilization Data and Predictive Model Design Based on Machine Learning: The Age Paradox in Reproductive Health

by Myrto A. Lantzi, Eleni Papakonstantinou and Dimitrios Vlachakis

Biology 2025, 14(5), 556; https://doi.org/10.3390/biology14050556 - 16 May 2025

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Abstract

Since its inception in 1987, in vitro fertilization (IVF) has constituted a significant medical achievement in the field of fertility treatment, offering a viable solution to the challenge of infertility. The continuous evolution of assisted reproductive technology (ART) has brought its relationship with [...] Read more.

Since its inception in 1987, in vitro fertilization (IVF) has constituted a significant medical achievement in the field of fertility treatment, offering a viable solution to the challenge of infertility. The continuous evolution of assisted reproductive technology (ART) has brought its relationship with the rapidly developing field of artificial intelligence (AI), in particular with techniques such as machine learning (ML), a rapidly evolving area of specialization. In fact, it is responsible for significant developments in the field of precision medicine, as well as in preventive and predictive medicine. The analysis focuses on a large volume of clinical data and patient characteristics of those who underwent assisted reproduction treatments. Concurrently, the utilization of machine learning algorithms has facilitated the development and implementation of predictive models. The objective is to predict the success of treatments for external fertilization based on processed clinical data. This study encompasses statistical analysis techniques and artificial intelligence algorithms for the correlation of variables, such as patient characteristics, the history of pregnancies, and the clinical and embryological parameters. The analysis and creation of prognostic models were compared with the objective of identifying factors that influence the outcome of IVF treatments. The potential for implementing a predictive model in routine clinical practice was also investigated. The findings revealed trends and factors that warrant attention. Such findings may prompt questions regarding the impact of the patient’s age on treatment efficacy. Moreover, the value of developing a predictive model based entirely on patient data prior to the commencement of treatment was also investigated. This approach to the processing and utilization of clinical data demonstrates the potential for optimization and documentation of therapeutic procedures. The objective is to reduce costs and the emotional burden while increasing the success rate of IVF treatments. Full article

(This article belongs to the Section Bioinformatics)

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14 pages, 4753 KiB

Open AccessArticle

Effect of Acrylonitrile Butadiene Styrene (ABS) Secondary Microplastics on the Demography of Moina macrocopa (Cladocera)

by Diana Laura Manríquez-Guzmán, Diego de Jesús Chaparro-Herrera, Pedro Ramírez-García and Cesar Alejandro Zamora-Barrios

Biology 2025, 14(5), 555; https://doi.org/10.3390/biology14050555 - 16 May 2025

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Abstract

Microplastics (MPs) are emerging pollutants that are ubiquitous in aquatic ecosystems and can affect the stability of aquatic food webs. They are intentionally produced in a size of less than 5 mm for specific purposes or are the result of the fragmentation of [...] Read more.

Microplastics (MPs) are emerging pollutants that are ubiquitous in aquatic ecosystems and can affect the stability of aquatic food webs. They are intentionally produced in a size of less than 5 mm for specific purposes or are the result of the fragmentation of larger plastic debris. Zooplankton can be affected directly by the ingestion of MPs or indirectly by interference caused by suspended plastic particles. Various environmental agencies recommend the genus Moina for assessing risk from water pollutants. However, this genus has received less attention in research compared to non-indigenous cladocerans commonly used as test organisms. We evaluated the effects of artificially fragmented acrylonitrile butadiene styrene microplastics (ABS-MPs) on key demographic parameters such as survival, mortality, life expectancy, fecundity, and feeding rates of Moina macrocopa americana. We exposed M. macrocopa neonates to a diet consisting of the green microalgae Chlorella vulgaris and ABS-MP particles. Four treatments were set with different concentrations of ABS-MP particles (5, 10, and 20 mg L⁻¹). Survivorship, mortality, and reproduction were recorded daily until the last individual from the original cohort died. ABS-MPs significantly reduced M. macrocopa consumption rates of C. vulgaris, with an 85% decrease compared to the control. Although no statistically significant differences were found in life expectancy, net reproduction, or generation time among the toxic treatments, these parameters were drastically reduced compared to the control, even at the lowest concentration (5 mg L⁻¹); this resulted in a 34% reduction in average lifespan. The ABS-MPs interfere with the long-term population dynamics of M. macrocopa and change their consumption rates, potentially decreasing their fitness. Full article

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

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19 pages, 4023 KiB

Open AccessArticle

Integrating Proteomics and GWAS to Identify Key Tissues and Genes Underlying Human Complex Diseases

by Chao Xue and Miao Zhou

Biology 2025, 14(5), 554; https://doi.org/10.3390/biology14050554 - 16 May 2025

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Abstract

Background: The tissues of origin and molecular mechanisms underlying human complex diseases remain incompletely understood. Previous studies have leveraged transcriptomic data to interpret genome-wide association studies (GWASs) for identifying disease-relevant tissues and fine-mapping causal genes. However, according to the central dogma, proteins more [...] Read more.

Background: The tissues of origin and molecular mechanisms underlying human complex diseases remain incompletely understood. Previous studies have leveraged transcriptomic data to interpret genome-wide association studies (GWASs) for identifying disease-relevant tissues and fine-mapping causal genes. However, according to the central dogma, proteins more directly reflect cellular molecular activities than RNA. Therefore, in this study, we integrated proteomic data with GWAS to identify disease-associated tissues and genes. Methods: We compiled proteomic and paired transcriptomic data for 12,229 genes across 32 human tissues from the GTEx project. Using three tissue inference approaches—S-LDSC, MAGMA, and DESE—we analyzed GWAS data for six representative complex diseases (bipolar disorder, schizophrenia, coronary artery disease, Crohn’s disease, rheumatoid arthritis, and type 2 diabetes), with an average sample size of 260 K. We systematically compared disease-associated tissues and genes identified using proteomic versus transcriptomic data. Results: Tissue-specific protein abundance showed a moderate correlation with RNA expression (mean correlation coefficient = 0.46, 95% CI: 0.42–0.49). Proteomic data accurately identified disease-relevant tissues, such as the association between brain regions and schizophrenia and between coronary arteries and coronary artery disease. Compared to GWAS-based gene association estimates alone, incorporating proteomic data significantly improved gene association detection (AUC difference test, p = 0.0028). Furthermore, proteomic data revealed unique disease-associated genes that were not identified using transcriptomic data, such as the association between bipolar disorder and CREB1. Conclusions: Integrating proteomic data enables accurate identification of disease-associated tissues and provides irreplaceable advantages in fine-mapping genes for complex diseases. Full article

(This article belongs to the Special Issue Multi-omics Data Integration in Complex Diseases)

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23 pages, 6975 KiB

Open AccessArticle

Secreted Expression of Thymosin β4 from Pinctada fucata in Pichia pastoris and Its Biological Activity

by Peng Liu, Xiaojian Mo, Jianbing Liu, Wenyue Li, Jiaxing Tang, Qiting Li and Jiang Lin

Biology 2025, 14(5), 553; https://doi.org/10.3390/biology14050553 - 15 May 2025

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Abstract

The aim of this study was to achieve the high secretion and expression of thymosin β4 derived from Pinctada fucata in Pichia pastoris, as well as to investigate its antibacterial properties and biological effects in promoting wound healing. The recombinant thymosin β4 [...] Read more.

The aim of this study was to achieve the high secretion and expression of thymosin β4 derived from Pinctada fucata in Pichia pastoris, as well as to investigate its antibacterial properties and biological effects in promoting wound healing. The recombinant thymosin β4 protein (rTβ4) exhibited no hemolytic activity on rabbit red blood cells and demonstrated significant antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), with a minimum inhibitory concentration (MIC) of 25 μg/mL. It effectively inhibited bacterial growth and disrupted the cell wall and membrane structure of the bacteria. In the Sprague Dawley (SD) rat wound healing model, the wound healing rate in the rTβ4 treatment groups (at concentrations of 12.5 and 25 μg/mL) was significantly higher than that in the control group (p < 0.05), and the healing effect was comparable to that of the positive control group (Kangfu Xin solution, KFX). The histopathological study demonstrated that rTβ4 could reduce the infiltration of inflammatory cells and promote the proliferation and re-epithelialization of granulation tissue. In conclusion, this study successfully achieved the high expression of thymosin β4 derived from Pinctada fucata in Pichia pastoris and validated its antibacterial and wound healing potential through both In vitro and In vivo experiments. Full article

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

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17 pages, 8723 KiB

Open AccessArticle

Research on the Economic Loss Model of Invasive Alien Species Based on Multidimensional Data Spatialization—A Case Study of Economic Losses Caused by Hyphantria cunea in Jiangsu Province

by Cheng Li, Yongbin Zhou, Cong Wang, Xubin Pan, Ying Wang, Xiaofeng Qi and Fanghao Wan

Biology 2025, 14(5), 552; https://doi.org/10.3390/biology14050552 - 15 May 2025

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Abstract

IAS imposes significant impacts on native ecosystems and economies. Current assessment methods for economic losses predominantly rely on habitat suitability estimation and database extrapolation, often lacking integration of causal inference and dynamic spatial drivers. H. cunea, a pervasive invasive pest in Jiangsu [...] Read more.

IAS imposes significant impacts on native ecosystems and economies. Current assessment methods for economic losses predominantly rely on habitat suitability estimation and database extrapolation, often lacking integration of causal inference and dynamic spatial drivers. H. cunea, a pervasive invasive pest in Jiangsu Province, China, exemplifies this challenge through its rapid spread and multi-sector economic impacts. To address these limitations, we innovatively integrated three models: (1) Difference-in-Differences (DID) quantified causal economic impacts through spatiotemporal comparison of infested/non-infested areas; (2) GeoDetector identified key spatial drivers via stratified heterogeneity analysis; (3) MaxEnt projected ecological suitability under climate scenarios. The synergy enabled dynamic loss attribution: GeoDetector optimized DID’s variable selection, while MaxEnt constrained loss extrapolation to ecologically plausible zones, achieving multi-scale causal–spatial–climate integration absent in conventional approaches. In Jiangsu Province, H. cunea caused CNY 89.2 million in primary sector losses in 2022, with forestry disproportionately impacted, accounting for 58.3% of the total losses. The DID model revealed nonlinear temporal impacts indicating a loss of 0.163 forestry per 30 m² grid, while MaxEnt projected 22% habitat contraction under the SSP5–8.5 scenario by 2060, which corresponds to climate-adjusted losses of CNY 147 million. Spatial prioritization identified northern Jiangsu (e.g., Xuzhou, Lianyungang) as high-risk zones requiring immediate intervention. The framework enables spatially explicit prioritization of containment efforts—grids identified as high-risk necessitate a tripling of funding in comparison to low-risk areas. And SSP-specific loss projections support dynamic budget planning under climate uncertainty. By integrating causal attribution, ecological realism, and climate resilience, this model transforms IAS management from reactive firefighting to proactive, data-driven governance. It provides a replicable toolkit for balancing ecological preservation and economic stability in the Anthropocene. Full article

(This article belongs to the Special Issue Risk Assessment for Biological Invasions)

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