Biology

38 pages, 1860 KiB

Open AccessReview

Modified Lipid Particle Recognition: A Link Between Atherosclerosis and Cancer?

by Amy E. Hall, Dhananjay Jade, Faheem Shaik, Shervanthi Homer-Vanniasinkam, Stephen P. Muench, Michael A. Harrison and Sreenivasan Ponnambalam

Biology 2025, 14(6), 675; https://doi.org/10.3390/biology14060675 - 11 Jun 2025

Abstract

Cardiovascular disease and cancer are major global causes of mortality. Dysfunctional lipid metabolism causes atherosclerosis, a driving force in arterial disease leading to heart attacks and strokes. In this review, we focus on emerging evidence for links between atherosclerosis and cancer. In atherosclerosis, [...] Read more.

Cardiovascular disease and cancer are major global causes of mortality. Dysfunctional lipid metabolism causes atherosclerosis, a driving force in arterial disease leading to heart attacks and strokes. In this review, we focus on emerging evidence for links between atherosclerosis and cancer. In atherosclerosis, modified and oxidized lipid particles promote plaque initiation and progression, with wider effects on cell and tissue responses. Oxidized and modified lipid particles bind to scavenger receptors (SRs) and promote intracellular signaling and pro-inflammatory responses. Increasing evidence points to SR-mediated activation and signaling promoting cancer cell growth and spread. In particular, the lectin-like oxidized low-density lipoprotein (LOX-1) scavenger receptor activates NF-κB-regulated signal transduction pathways which modulate different cellular responses. LOX-1-regulated signaling events are implicated in both atherosclerosis and cancer, depending on the cell type. LOX-1 signaling modulates cell proliferation, epithelial–mesenchymal transition, neutrophil recruitment and apoptosis. Elevated LOX-1 levels are linked to poor prognosis in arterial disease and prostate, colorectal and lung cancers. Inhibition of LOX-1 function could thus provide new therapeutic strategies for targeting both atherosclerosis and cancer. Full article

(This article belongs to the Section Cancer Biology)

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19 pages, 3430 KiB

Open AccessArticle

2,4-Epibrassinolide Mitigates Cd Stress by Enhancing Chloroplast Structural Remodeling and Chlorophyll Metabolism in Vigna angularis Leaves

by Suyu Chen, Zihan Tang, Jialin Hou, Jie Gao, Xin Li, Yuxian Zhang and Qiang Zhao

Biology 2025, 14(6), 674; https://doi.org/10.3390/biology14060674 - 10 Jun 2025

Abstract

Cadmium (Cd) is a highly hazardous heavy metal that has an extensive impact throughout the world. 2,4-Epibrassinolide (BR) is an endogenous hormone that can enhance plant tolerance to various abiotic stresses. Herein, Vigna angularis cultivar “Zhen Zhuhong” was grown hydroponically and treated with [...] Read more.

Cadmium (Cd) is a highly hazardous heavy metal that has an extensive impact throughout the world. 2,4-Epibrassinolide (BR) is an endogenous hormone that can enhance plant tolerance to various abiotic stresses. Herein, Vigna angularis cultivar “Zhen Zhuhong” was grown hydroponically and treated with 0, 1, and 2 mg·L⁻¹ cadmium chloride (CdCl₂) at the V1 stage, and foliar sprayed with or without 1 μM BR solution to analyze the effects of BR treatment on the physiology of Vigna angularis seedling leaves under Cd stress. BR treatment significantly alleviated the growth inhibition induced by Cd stress, which was associated with an increase in the plant height (11.15–17.83%), leaf area (35.59–56.72%), leaf dry weight (45.57–50.65%), and above-ground dry weight (50.86–55.17%). In addition, BR treatment induced significant reductions in Cd accumulation across different tissues of V. angularis, with decreases of 20.38–35.93% in leaves, 21.24–32.74% in stems, and 15.38–16.00% in petioles. Compared with the Cd treatment, BR treatment significantly enhanced the activities of peroxidase (5.02–13.22%), ascorbate peroxidase (27.13–70.28%), catalase (20.46–32.30%), and superoxide dismutase (16.54–21.81%), and increased the ascorbic acid content (27.55–45.52%), which contributed to a reduction in the accumulation of reactive oxygen species, cellular membrane damage, and cytoplasmic exosmosis. RNA-seq and real-time quantitative reverse transcription PCR analyses revealed that the BR treatment under Cd stress significantly upregulated the expression of genes involved in chlorophyll biosynthesis, transformation, and degradation, thereby enhancing the chlorophyll cycle. Furthermore, the BR treatment significantly increased the number of grana lamellae in the mesophyll cells, which enhanced the biosynthesis of chloroplasts. The increase in the chlorophyll content improved the capture of light energy, electron transport in photosynthesis, and the biosynthesis and metabolism of carbohydrates in the leaves of V. angularis under Cd stress. Full article

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17 pages, 8099 KiB

Open AccessArticle

Linking Ecological Stoichiometry to Biomass Allocation in Plants Under Cadmium and Petroleum Stress in the Yellow River Delta

by Shuo Li, Haidong Xu, Hui Ye, Cheng Chang, Jinxiang Zhao and Jiangbao Xia

Biology 2025, 14(6), 673; https://doi.org/10.3390/biology14060673 - 10 Jun 2025

Abstract

Cadmium and petroleum are the main pollutants in coastal wetland ecosystems that affect plant nutrient balance and growth. Scholars have discovered how saline plants adapt to single stresses. How plant ecology and physiology correspond to complex cadmium and petroleum pollution, especially regarding the [...] Read more.

Cadmium and petroleum are the main pollutants in coastal wetland ecosystems that affect plant nutrient balance and growth. Scholars have discovered how saline plants adapt to single stresses. How plant ecology and physiology correspond to complex cadmium and petroleum pollution, especially regarding the pollution impacts on carbon (C), nitrogen (N), and phosphorus (P) stoichiometry and biomass allocation in coastal wetland plants, remains unclear, limiting their application in regard to pollution remediation. This study focuses on Suaeda salsa, a popular species used in vegetation restoration in the Yellow River Delta’s coastal wetlands. Through the use of pot experiments, the dynamic changes in plant–soil ecological stoichiometry and biomass allocation were systematically investigated in response to individual and combined cadmium (0, 5, and 10 mg kg⁻¹) and petroleum (0, 6, and 12 g kg⁻¹) treatments. Compared with the control (CK), petroleum stress significantly increased the total nitrogen (TN) and plant total phosphorus (TP) contents, but did not substantially impact the total carbon (TC) content, resulting in 19.7% and 26.6% decreases in the plant C/N and C/P ratios, respectively. The soil organic carbon (SOC) content increased significantly under petroleum stress, whereas the TN and TP contents did not notably change, considerably increasing the soil C/N and C/P ratios, which were 1.5 times and 1.3 times greater than those of the CK, respectively. Cadmium stress alone or with petroleum stress did not significantly affect the C, N, or P stoichiometry or biomass allocation in S. salsa. The soil C/N/P stoichiometry redundancy analysis revealed that the contribution rates (especially the soil C/P and C/N ratios) to the total biomass and its allocation in S. salsa (64.5%) were greater than those of the control group plants (35.5%). The correlation analysis revealed that the total growth biomass of S. salsa was negatively correlated with the soil carbon content, C/N ratio, and C/P ratio, but positively correlated with the plant C/N and C/P ratios. The aboveground biomass proportion in S. salsa was significantly negatively correlated with the soil N/P ratio. The belowground biomass proportion exhibited the opposite trend. Petroleum pollution was the main factor driving S. salsa stoichiometry and growth changes, increasing the soil C/N and C/P ratios, reducing the nitrogen and phosphorus nutrient absorption capacities in plant roots, limiting plant nitrogen and phosphorus nutrients, and inhibiting biomass accumulation. Appropriate N and P supplementation alleviated plant growth inhibition due to petroleum pollution stress, which was conducive to improving vegetation ecological restoration in the Yellow River Delta. Full article

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

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23 pages, 3018 KiB

Open AccessArticle

Research on Plant RNA-Binding Protein Prediction Method Based on Improved Ensemble Learning

by Hongwei Zhang, Yan Shi, Yapeng Wang, Xu Yang, Kefeng Li, Sio-Kei Im and Yu Han

Biology 2025, 14(6), 672; https://doi.org/10.3390/biology14060672 - 10 Jun 2025

Abstract

(1) RNA-binding proteins (RBPs) play a crucial role in regulating gene expression in plants, affecting growth, development, and stress responses. Accurate prediction of plant-specific RBPs is vital for understanding gene regulation and enhancing genetic improvement. (2) Methods: We propose an ensemble learning method [...] Read more.

(1) RNA-binding proteins (RBPs) play a crucial role in regulating gene expression in plants, affecting growth, development, and stress responses. Accurate prediction of plant-specific RBPs is vital for understanding gene regulation and enhancing genetic improvement. (2) Methods: We propose an ensemble learning method that integrates shallow and deep learning. It integrates prediction results from SVM, LR, LDA, and LightGBM into an enhanced TextCNN, using K-Peptide Composition (KPC) encoding (k = 1, 2) to form a 420-dimensional feature vector, extended to 424 dimensions by including those four prediction outputs. Redundancy is minimized using a Pearson correlation threshold of 0.80. (3) Results: On the benchmark dataset of 4992 sequences, our method achieved an ACC of 97.20% and 97.06% under 5-fold and 10-fold cross-validation, respectively. On an independent dataset of 1086 sequences, our method attained an ACC of 99.72%, an

{F 1}_{s c o r e}

of 99.72%, an MCC of 99.45%, an SN of 99.63%, and an SP of 99.82%, outperforming RBPLight by 12.98 percentage points in ACC and the original TextCNN by 25.23 percentage points. (4) Conclusions: These results highlight our method’s superior accuracy and efficiency over PSSM-based approaches, enabling large-scale plant RBP prediction. Full article

(This article belongs to the Special Issue Machine Learning Applications in Biology—2nd Edition)

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21 pages, 19072 KiB

Open AccessArticle

Spatiotemporal Assessment and Driving Factors of Ecosystem Health: A Case Study of Two Provinces in Southern China

by Yujun Cai, Yu Zhang, Yefeng Jiang and Xi Guo

Biology 2025, 14(6), 671; https://doi.org/10.3390/biology14060671 - 9 Jun 2025

Abstract

The concept of ecosystem health (EH), proposed in the 1980s [...] Full article

(This article belongs to the Special Issue Young Researchers in Ecology)

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17 pages, 8766 KiB

Open AccessArticle

Analysis of Software Read Cross-Contamination in DNBSEQ Data

by Dmitry N. Konanov, Vera Y. Tereshchuk, Ignat V. Sonets, Elena V. Korneenko, Aleksandra V. Lukina-Gronskaya, Anna S. Speranskaya and Elena N. Ilina

Biology 2025, 14(6), 670; https://doi.org/10.3390/biology14060670 - 9 Jun 2025

Abstract

DNA nanoball sequencing (DNBSEQ) is one of the most rapidly developing sequencing technologies and is widely applied in genomic and transcriptomic investigations. Recently, a new PE300 sequencing option primarily recommended for amplicon analysis was released for DNBSEQ-G99 and G400 devices. Given their unprecedentedly [...] Read more.

DNA nanoball sequencing (DNBSEQ) is one of the most rapidly developing sequencing technologies and is widely applied in genomic and transcriptomic investigations. Recently, a new PE300 sequencing option primarily recommended for amplicon analysis was released for DNBSEQ-G99 and G400 devices. Given their unprecedentedly high data yield per flow cell, the new PE300 kits could be a great choice for various sequencing tasks, but we found that combining different types of DNA libraries in a single run could lead to undesired artifacts in the data. In this study, we investigate the occasional read cross-contamination that we first observed in our DNBSEQ PE300 run. The phenomenon, which we refer to as “software contamination”, is not actual contamination but primarily manifests as improper forward/reverse read pairing, improper demultiplexing, or as “digital chimeric” reads. Although rare, these artifacts were found in all runs we have analyzed, including several MGI demo datasets (both PE100 and PE150). In this study, we demonstrate that these artifacts arise primarily from the incorrect resolution of sequencing signals produced by neighboring DNA nanoballs, leading to mixing out forward and reverse reads or improper demultiplexing. The artifacts occur most frequently with read pairs where the length of insert sequence is shorter than the read length. Based on a few external NA12878 human exome sequencing data, we conclude that the total improper pairing rate in DNBSEQ data is comparable to Illumina ones. Overall, the problem only affects the analysis results when simultaneously sequenced libraries have markedly different insert size distribution or flow cell loading. Additionally, we demonstrate here that raw DNBSEQ data might contain ~2% optical duplicates, resulting from the same effect of close neighboring of DNB-sites in the flow cell. Full article

(This article belongs to the Section Biotechnology)

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19 pages, 484 KiB

Open AccessReview

A Biochemical View on Intermittent Fasting’s Effects on Human Physiology—Not Always a Beneficial Strategy

by Willian F. Zambuzzi, Marcel Rodrigues Ferreira, Zifan Wang and Maikel P. Peppelenbosch

Biology 2025, 14(6), 669; https://doi.org/10.3390/biology14060669 - 9 Jun 2025

Abstract

Intermittent fasting (IF) has emerged as a widely practiced dietary regimen, increasingly utilized in both clinical and non-clinical settings for its potential health benefits. Evidence suggests that IF can improve metabolic health by enhancing insulin sensitivity, reducing inflammation, and aiding weight management. Recent [...] Read more.

Intermittent fasting (IF) has emerged as a widely practiced dietary regimen, increasingly utilized in both clinical and non-clinical settings for its potential health benefits. Evidence suggests that IF can improve metabolic health by enhancing insulin sensitivity, reducing inflammation, and aiding weight management. Recent studies have also explored its role in mitigating obesity-related diseases, such as type 2 diabetes and non-alcoholic fatty liver disease, and its ability to support cardiovascular health and mental function. The effects of IF, however, vary depending on individual health conditions. Some patients show no clinical improvement, while others experience worsened outcomes. Mechanistically, IF induces metabolic switching and activates adenosine monophosphate-activated protein kinase (AMPK), both of which contribute to its therapeutic potential. These responses are influenced by factors such as underlying pathology, baseline metabolic state, and dietary composition. While preclinical data indicate potential therapeutic effects in diseases like cancer, rheumatoid arthritis, and neurodegenerative conditions, these findings are not yet sufficiently supported by human studies. This review argues that IF holds promise as a disease-modifying intervention. However, its implementation should be personalized according to patient-specific characteristics, and future clinical trials must prioritize identifying optimal fasting protocols to maximize therapeutic outcomes. Full article

(This article belongs to the Section Physiology)

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19 pages, 6496 KiB

Open AccessArticle

Potential Distribution and Cultivation Areas of Argentina anserina (Rosaceae) in the Upper Reaches of the Dadu River and Minjiang River Basin Under Climate Change: Applications of Ensemble and Productivity Dynamic Models

by Yi Huang, Jian Yang, Guanghua Zhao and Yang Yang

Biology 2025, 14(6), 668; https://doi.org/10.3390/biology14060668 - 9 Jun 2025

Abstract

Argentina anserina (Rosaceae), a perennial herb, forms enlarged tuberous roots (commonly referred to as “ginseng fruit”) exclusively in the Qinghai–Tibet Plateau, making it a unique medicinal and edible plant resource in this region. The upper reaches of the Dadu River and Minjiang River [...] Read more.

Argentina anserina (Rosaceae), a perennial herb, forms enlarged tuberous roots (commonly referred to as “ginseng fruit”) exclusively in the Qinghai–Tibet Plateau, making it a unique medicinal and edible plant resource in this region. The upper reaches of the Dadu River and Minjiang River are one of its primary production areas in China. This study employs an ensemble model to simulate the potential distribution of A. anserina in this region, predicting the impacts of future climate change on its distribution, ecological niche, and centroid migration patterns. Additionally, a cultivation productivity evaluation model integrating ecological suitability and nutritional components was developed to delineate potential cultivation areas. Results indicate that high-suitability habitats span 0.37 × 10⁴ km² (7.39% of the total suitable area), exhibiting a patchy and fragmented distribution in Aba County, Rangtang County, Jiuzhi County, and Banma County. Core cultivation areas cover 3.78 × 10⁴ km², distributed across Aba County, Rangtang County, Jiuzhi County, Seda County, Banma County, Hongyuan County, and Markam City. Under future climate scenarios, the suitable distribution area of A. anserina will gradually decline with rising temperatures, migrating to higher-latitude northern regions, accompanied by increased niche migration. By the 2090s under the SSP5-8.5 scenario, the centroid demonstrates the largest migration amplitude, with high-suitability habitats showing a “collapsing” polarization pattern and near-complete niche separation from the previous period, indicating significant changes. Collectively, these results provide a theoretical basis for the sustainable utilization of A. anserina in the upper Dadu River and Minjiang River basin. Full article

(This article belongs to the Section Ecology)

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31 pages, 1713 KiB

Open AccessReview

Aquatic Organisms in Response to Salinity Stress: Ecological Impacts, Adaptive Mechanisms, and Resilience Strategies

by Tariq Dildar, Wenxiao Cui, Mhd Ikhwanuddin and Hongyu Ma

Biology 2025, 14(6), 667; https://doi.org/10.3390/biology14060667 - 9 Jun 2025

Abstract

Salinity stress presents a major ecological challenge for aquatic organisms, particularly in environments where salinity levels fluctuate. These fluctuations are becoming more pronounced due to climate change, further destabilizing aquatic ecosystems. Understanding how organisms adapt to such variability is essential for biodiversity conservation [...] Read more.

Salinity stress presents a major ecological challenge for aquatic organisms, particularly in environments where salinity levels fluctuate. These fluctuations are becoming more pronounced due to climate change, further destabilizing aquatic ecosystems. Understanding how organisms adapt to such variability is essential for biodiversity conservation and the sustainable management of aquatic resources. This review examines the physiological, molecular, and behavioral adaptations that enable aquatic organisms to survive and thrive under salinity stress. Specifically, it explores mechanisms of osmotic regulation, ion transport, and oxidative stress responses, highlighting key signaling pathways—such as AMP-activated protein kinase (AMPK), Phosphatidylinositol 3-kinase–protein kinase (PI3K-AKT), Mitogen-activated protein kinase (MAPK), and the Hippo pathway—that facilitate these adaptive processes. The review also emphasizes the genetic and epigenetic modifications that contribute to resilience, underscoring the importance of genetic diversity for species survival in fluctuating salinity conditions. Furthermore, the interactions between host organisms and their microbiomes are discussed as critical factors influencing resilience. The review addresses the impact of salinity fluctuations on species distribution and biodiversity, with a focus on the implications of climate change for aquatic ecosystems. Finally, strategies for mitigating salinity stress, such as nutritional interventions and the development of salinity-resistant varieties, are explored, particularly in aquaculture. Overall, this review consolidates current knowledge on organismal adaptations, molecular mechanisms, and environmental challenges, offering valuable insights for ecological research and aquaculture practices in the face of climate change. Full article

(This article belongs to the Topic The Importance of Fish Phenotype in Aquaculture, Fisheries and Conservation)

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14 pages, 1692 KiB

Open AccessArticle

AgileMultiIdeogram: Rapid Identification and Visualization of Autozygous Regions Using Illumina Short-Read Sequencing Data

by Christopher M. Watson, Carolina Lascelles, Morag Raynor, Marilena Elpidorou, Ummey Hany, Laura Crinnion, Colin A. Johnson, Eamonn Sheridan, Alexander F. Markham, James A. Poulter, David T. Bonthron and Ian M. Carr

Biology 2025, 14(6), 666; https://doi.org/10.3390/biology14060666 - 9 Jun 2025

Abstract

Rare autosomal recessive diseases are a major cause of mortality and morbidity. They occur more frequently in individuals with consanguineous parents, in which case the pathogenic variants are often located within regions of genetic identity by descent. A well-established and effective way of [...] Read more.

Rare autosomal recessive diseases are a major cause of mortality and morbidity. They occur more frequently in individuals with consanguineous parents, in which case the pathogenic variants are often located within regions of genetic identity by descent. A well-established and effective way of identifying these “autozygous” genomic regions has been to search for runs of homozygous genotypes in microarray SNP data. However, with the widespread use of whole-genome and exome sequencing in both diagnostic and research settings, it has become desirable to be able to both map autozygous regions and identify the deleterious variants using a single dataset. We have developed AgileMultiIdeogram, an application that can identify and visualize autozygous regions in inbred individuals using exome data as well as microarray SNP genotype data. This application has been successfully used in both research and diagnostic settings to map pathogenic mutations. Full article

(This article belongs to the Section Bioinformatics)

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11 pages, 1391 KiB

Open AccessBrief Report

A Deep Learning Approach to Measure Visual Function in Zebrafish

by Manjiri Patil, Annabel Birchall, Hammad Syed, Vanessa Rodwell, Ha-Jun Yoon, William H. J. Norton and Mervyn G. Thomas

Biology 2025, 14(6), 663; https://doi.org/10.3390/biology14060663 - 9 Jun 2025

Abstract

Visual behaviour in zebrafish, often measured by the optokinetic reflex (OKR), serves as a valuable model for studying aspects of human neurological and ocular diseases and for conducting therapeutic or toxicology assays. Traditional methods for OKR analysis often rely on binarization techniques (threshold-based [...] Read more.

Visual behaviour in zebrafish, often measured by the optokinetic reflex (OKR), serves as a valuable model for studying aspects of human neurological and ocular diseases and for conducting therapeutic or toxicology assays. Traditional methods for OKR analysis often rely on binarization techniques (threshold-based conversion of images to black and white) or costly software, which limits their utility in low-contrast settings or hypopigmented disease models. Here, we present a novel deep learning pipeline for OKR analysis, using ResNet-50 within the DeepLabCut framework in a Python Version 3.10 environment. Our approach employs object tracking to enable robust eye movement quantification, regardless of variations in contrast or pigmentation. OKR responses were elicited in both wild-type and slc45a2 (albino) mutant zebrafish larvae at 5 days post-fertilisation, using a mini-LED arena with a rotating visual stimulus. Eye movements were recorded and analysed using both conventional software and our deep learning approach. We demonstrate that the deep learning model achieves comparable accuracy to traditional methods, with the added benefits of applicability in diverse lighting conditions and in hypopigmented larvae. Statistical analyses, including Bland–Altman tests, confirmed the reliability of the deep learning model. While this study focuses on 5-day-old zebrafish larvae under controlled conditions, the pipeline is adaptable across developmental stages, pigmentation types, and behavioural assays. With appropriate adjustments to experimental parameters, it could be applied to broader behavioural studies, including social interactions and predator–prey dynamics in ocular and neurological disease models. Full article

(This article belongs to the Special Issue AI Deep Learning Approach to Study Biological Questions (2nd Edition))

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16 pages, 3694 KiB

Open AccessArticle

Feeding Behavior and Ecological Significance of Craspedacusta sowerbii in a Freshwater Reservoir: Insights from Prey Composition and Trophic Interactions

by Hailong Yan, Yu Wang, Mengyao Wu, Yuying Li, Wanping Wang, Dongliang Zhang, Jingjing Guo, Nicola Fohrer and Bailian Larry Li

Biology 2025, 14(6), 665; https://doi.org/10.3390/biology14060665 - 7 Jun 2025

Viewed by 235

Abstract

This study investigates the feeding behavior and ecological role of Craspedacusta sowerbii in the Danjiangkou Reservoir, a crucial freshwater source in central China. Through in situ cultivation, microscopic examination, and amplicon sequencing analysis, we identified the primary food sources of C. sowerbii within [...] Read more.

This study investigates the feeding behavior and ecological role of Craspedacusta sowerbii in the Danjiangkou Reservoir, a crucial freshwater source in central China. Through in situ cultivation, microscopic examination, and amplicon sequencing analysis, we identified the primary food sources of C. sowerbii within the reservoir’s aquatic food web. Our results indicate that C. sowerbii predominantly consumes zooplankton, specifically rotifers, copepods, and cladocerans, while phytoplankton is ingested less frequently and often remains undigested. Amplicon sequencing data further confirms that the prey composition of C. sowerbii is enriched in zooplanktonic communities compared to phytoplanktonic communities. Our findings suggest that C. sowerbii plays a significant role in regulating plankton populations and shaping the planktonic community structure in the Danjiangkou Reservoir, thereby contributing to the ecosystem’s functions and trophic dynamics. This study enhances our understanding of the feeding ecology of C. sowerbii and highlights its potential as a bioindicator species for assessing freshwater ecosystem health and monitoring water quality. Full article

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18 pages, 415 KiB

Open AccessSystematic Review

Aspergillus Infections in Cetaceans: A Systematic Review of Clinical, Ecological, and Conservation Perspectives

by Victor Garcia-Bustos, Inmaculada Rosario Medina, Marta Dafne Cabanero-Navalon, Rosie S. Williams, Shaheed Karl Macgregor, Shinto Kunjamma John, Francisco Javier Aznar, Patricia Gozalbes and Begoña Acosta-Hernández

Biology 2025, 14(6), 664; https://doi.org/10.3390/biology14060664 - 7 Jun 2025

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Abstract

Aspergillus spp., particularly A. fumigatus, are increasingly reported as emerging pathogens in cetaceans, yet their clinical and ecological relevance remains poorly characterized. This systematic review synthesizes evidence from 34 studies involving 106 animals, identifying respiratory, neurological, and otic infections as the most [...] Read more.

Aspergillus spp., particularly A. fumigatus, are increasingly reported as emerging pathogens in cetaceans, yet their clinical and ecological relevance remains poorly characterized. This systematic review synthesizes evidence from 34 studies involving 106 animals, identifying respiratory, neurological, and otic infections as the most frequent presentations with potential interspecies tropism. Invasive disease, frequently fatal, was linked to co-infections—especially with morbillivirus—and environmental stressors such as pollution- and climate-related immune suppression. Despite cetaceans’ role as sentinel species, antifungal susceptibility testing and species-level identification were inconsistently performed. Additionally, azole-resistant A. fumigatus strains were isolated from wild porpoises, indicating environmental antifungal exposure and potential public health implications. Aspergillosis remains underdiagnosed in free-ranging populations, particularly in remote or pelagic species. Conservation implications were scarcely addressed, despite evidence suggesting that fungal disease may contribute to morbidity, stranding, and population impact. This review underscores the need for enhanced surveillance, integrative diagnostics, and recognition of fungal pathogens in a One Health framework. The growing intersection of climate change, emerging mycoses, and wildlife conservation positions Aspergillus infections in cetaceans as both a marine mammal health concern and an ecological indicator of broader environmental changes. Full article

(This article belongs to the Special Issue Exploring the Biodiversity, Taxonomy, Ecology and Genomics of Fungi)

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23 pages, 411 KiB

Open AccessReview

Neurobiology of Chronic Pain, Posttraumatic Stress Disorder, and Mild Traumatic Brain Injury

by Gerald Young, Hella Thielen, Kristin Samuelson and Joel Jin

Biology 2025, 14(6), 662; https://doi.org/10.3390/biology14060662 - 7 Jun 2025

Viewed by 97

Abstract

Objectives: This article describes the neurobiology of psychological injuries—chronic pain, concussion/mild traumatic brain injury (MTBI), and fear/posttraumatic stress disorder (PTSD)—toward elucidating common mechanisms in central and peripheral sensitization that contribute to their onset, exacerbation, and maintenance. Central sensitization refers to central nervous system [...] Read more.

Objectives: This article describes the neurobiology of psychological injuries—chronic pain, concussion/mild traumatic brain injury (MTBI), and fear/posttraumatic stress disorder (PTSD)—toward elucidating common mechanisms in central and peripheral sensitization that contribute to their onset, exacerbation, and maintenance. Central sensitization refers to central nervous system (CNS) and related processes, while peripheral sensitization is typically referred to as receptor field expansion. The three psychological injury diagnoses/conditions are accompanied by impairments in function after negligent events (such as motor vehicle accidents (MVAs)) that lead to tort court action. Methods: The conducted literature review involved an extensive scoping review of recent neurobiological literature on chronic pain, PTSD, and MTBI. The literature review sought biological markers that distinguish them. Results: For chronic pain, concussion/MTBI, and fear/PTSD, this article reviewed definitions and critical neurobiological research. The literature review did not find evidence of biological markers, but the role of sensitization emerged as important. Conclusions: Common therapeutic processes, such as focusing on sensitization, might be helpful for these conditions. As for causal mechanisms related to sensitization in the causality of psychological injuries, the major ones hypothesized relate to the biopsychosocial model, psychological control, and activation–inhibition coordination. Full article

(This article belongs to the Special Issue Neurobiology of Traumatic Brain Injury)

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13 pages, 2466 KiB

Open AccessArticle

Trichophyton rubrum Phenotypic Virulence Factors in Mexican Strains

by Esther Conde-Cuevas, Rigoberto Hernández-Castro, Claudia Erika Fuentes-Venado, Roberto Arenas, María Guadalupe Frías-De-León, Gabriela Moreno-Coutiño, María Esther Ocharan-Hernández, Eunice D. Farfan-Garcia, Rodolfo Pinto-Almazán and Erick Martínez-Herrera

Biology 2025, 14(6), 661; https://doi.org/10.3390/biology14060661 - 7 Jun 2025

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Abstract

(1) Background: T. rubrum is the most important agent in tinea pedis, tinea manuum, tinea cruris, tinea corporis, and even in subcutaneous dermatophytosis. T. rubrum must overcome several obstacles to adhere, grow, and invade the host, for which their [...] Read more.

(1) Background: T. rubrum is the most important agent in tinea pedis, tinea manuum, tinea cruris, tinea corporis, and even in subcutaneous dermatophytosis. T. rubrum must overcome several obstacles to adhere, grow, and invade the host, for which their virulence factors are important. Previous studies have demonstrated the capability of T. rubrum strains to produce proteases, phospholipases, hemolysins, and elastases. The aim of this work was the genotypic identification of clinical isolates of T. rubrum to subsequently determine production of the main phenotypic virulence factors associated with this pathogen responsible for different types of dermatophytosis in Mexican patients. (2) Methods: Twenty samples of T. rubrum were obtained from different body parts of patients treated in the Mycology section. The colonies were transferred to specific agars to analyze the production of phenotypical virulence factors (lipase, phospholipase, hemolysin, and elastase). (3) Results: Almost all the strains of T. rubrum showed growth in the test culture medium. A significantly smaller size of the halo diameter of elastase (26.51 ± 11.95 mm) in comparison to lipase (59.51 ± 16.00 mm) and phospholipase (55.97 ± 19.60 mm) was measured. Additionally, a significantly reduced size of the halo diameter of hemolysin (42.01 ± 5.49 mm) was observed compared to lipase. When comparing the virulence factors, greater expression of lipase was observed, followed by phospholipase, hemolysins, and elastase. T. rubrum strains were classified as being between high and ultra-lipase producers; most of the strains were also considered low producers of phospholipase and hemolysins; and most of the strains (n = 13) were classified as non-producers of elastase. (4) Conclusions: Almost all the T. rubrum strains of the study were found to be ultra-producers of lipase, and low producers of hemolysins and phospholipases. Elastase was the least expressed virulence factor in these strains. Full article

(This article belongs to the Section Medical Biology)

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18 pages, 1105 KiB

Open AccessReview

Heavy Metal Poisoning and Its Impacts on the Conservation of Amazonian Parrots: An Interdisciplinary Review

by Marina Sette Camara Benarrós, Ketelen Ayumi Corrêa Sakata, Brenda Juliane Silva dos Santos and Felipe Masiero Salvarani

Biology 2025, 14(6), 660; https://doi.org/10.3390/biology14060660 - 6 Jun 2025

Viewed by 208

Abstract

Amazonian parrots (Psittacidae) are essential to ecosystem balance. Already vulnerable to habitat fragmentation and weak environmental regulations, they are now increasingly threatened by heavy metal contamination. This review synthesizes evidence on the sources, transgenerational bioaccumulation, and physiological impacts of metals such as mercury [...] Read more.

Amazonian parrots (Psittacidae) are essential to ecosystem balance. Already vulnerable to habitat fragmentation and weak environmental regulations, they are now increasingly threatened by heavy metal contamination. This review synthesizes evidence on the sources, transgenerational bioaccumulation, and physiological impacts of metals such as mercury (Hg), lead (Pb), cadmium (Cd), zinc (Zn), and arsenic (As) in these birds. Anthropogenic activities, including illegal gold mining, agricultural intensification, and urban expansion, release metals that biomagnify along food webs. Parrots, as long-lived, high-trophic consumers, accumulate metals in vital tissues, leading to severe neurotoxic effects, immunosuppression, reproductive failure, and reduced survival. Furthermore, maternal transfer of contaminants to eggs exacerbates genetic erosion and threatens population viability. While biomonitoring tools and habitat restoration have been proposed, current strategies are insufficient against the synergistic pressures of pollution and climate change. Addressing heavy metal exposure is critical to conserving Amazonian biodiversity and safe-guarding ecosystem services. Future efforts should prioritize multidisciplinary predictive models, bioremediation actions, and the strengthening of international environmental governance to ensure the survival of these sentinel species. Full article

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

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14 pages, 6680 KiB

Open AccessArticle

Early Vascular Developmental Toxicity and Underlying Mechanisms of 1-Bromo-3,6-dichlorocarbazole (1-B-36-CCZ) in Zebrafish Larvae

by Jie Gu, Ziyu Gong, Yue Fan, Jun Hu, Liguo Guo, Wenming Pei and Daqiang Yin

Biology 2025, 14(6), 659; https://doi.org/10.3390/biology14060659 - 6 Jun 2025

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Abstract

Polyhalogenated carbazoles (PHCZs) are emerging persistent organic pollutants that have attracted widespread attention due to their environmental occurrence and potential ecological risks. 1-Bromo-3,6-dichlorocarbazole (1-B-36-CCZ), which is a typical homolog of PHCZs produced as a byproduct in the dye industry, has been widely detected [...] Read more.

Polyhalogenated carbazoles (PHCZs) are emerging persistent organic pollutants that have attracted widespread attention due to their environmental occurrence and potential ecological risks. 1-Bromo-3,6-dichlorocarbazole (1-B-36-CCZ), which is a typical homolog of PHCZs produced as a byproduct in the dye industry, has been widely detected in various environmental media. In this study, we employed an integrated approach using an in vivo zebrafish model and network toxicology methods to systematically evaluate the vascular developmental toxicity of 1-B-36-CCZ and elucidate its underlying mechanisms. The experimental results revealed that the 96 h-LC₅₀ of 1-B-36-CCZ in zebrafish larvae was 4.52 mg/L. Sublethal exposures (0.045–45 μg/L) significantly induced an increase in heart rate (p < 0.05) and an enlargement of the pericardial edema area (p < 0.01). Using Tg(flk:eGFP) transgenic zebrafish embryos to assess vascular toxicity at concentrations of 0, 0.045, 0.45, 4.5, and 45 μg/L, we observed that 1-B-36-CCZ exposure significantly reduced the length and anastomosis rate of intersegmental vessels (ISVs) at 30 hpf, and inhibited the development of the common cardinal vein (CCV) at 48 and 72 hpf as well as the subintestinal vessel (SIV) at 72 hpf. Quantitative PCR (qPCR) analysis further revealed that the expression of key angiogenic genes (flk, kdr, and vegfa) was significantly downregulated, thus corroborating the phenotypic observations. Moreover, a “compound–target–pathway” network model predicted that SRC kinase is a key molecular target for 1-B-36-CCZ action. Enrichment analysis of target protein-coding genes and verapamil replication experiments indicated that 1-B-36-CCZ may cause damage to early vascular development in zebrafish larvae by altering intracellular calcium ion content through the activation of the SRC-mediated calcium ion signaling pathway. This study provides new experimental evidence for elucidating the toxic mechanisms of PHCZ-type pollutants and offers a theoretical basis for environmental health risk assessments. Full article

(This article belongs to the Special Issue Advances in Aquatic Ecological Disasters and Toxicology)

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14 pages, 1680 KiB

Open AccessArticle

Comparison of Superovulated Embryo Quality in Simmental Cattle Inseminated with 0 °C-Refrigerated and Liquid Nitrogen-Frozen Semen

by Jie-Ru Wang, Fei Huang, Peng Niu, Hong Cheng, Hui-Min Qu, Xiao-Peng Li, Xue-Yan Wang, Jie Wang, Jia-Jia Suo, Di Fang and Qing-Hua Gao

Biology 2025, 14(6), 658; https://doi.org/10.3390/biology14060658 - 6 Jun 2025

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Abstract

Semen quality plays a crucial role in bovine in vivo embryo production. This study aimed to compare the effects of 0 °C-refrigerated semen and liquid nitrogen-frozen semen on embryo quality in Simmental cattle. Semen collected from five bulls was equally divided into two [...] Read more.

Semen quality plays a crucial role in bovine in vivo embryo production. This study aimed to compare the effects of 0 °C-refrigerated semen and liquid nitrogen-frozen semen on embryo quality in Simmental cattle. Semen collected from five bulls was equally divided into two groups: one diluted with a 0 °C refrigeration solution and stored at 0 °C, and the other diluted with a cryopreservation solution and stored in liquid nitrogen for 24 h. We evaluated sperm motility, progressive motility (assessed via a computer-assisted sperm analyzer), acrosome integrity, and plasma membrane integrity in both groups. Fifty superovulated Simmental cows were artificially inseminated with semen from both groups. Embryos were non-surgically flushed on day seven, followed by BrdU proliferation staining and TUNEL apoptosis staining. Proliferation and apoptosis levels were quantified using marker genes. Results showed that 0 °C-refrigerated semen exhibited significantly higher sperm motility, progressive motility, acrosome integrity, and plasma membrane integrity compared to liquid nitrogen-frozen semen (p < 0.05). While total embryo numbers showed no significant difference between groups (p ≥ 0.05), embryos from 0 °C-refrigerated semen contained significantly more proliferative cells (p < 0.05) and fewer apoptotic cells (p < 0.05) than those from frozen semen. These findings demonstrate that 0 °C-refrigerated semen outperforms liquid nitrogen-frozen semen in both sperm quality parameters and resultant embryo quality. Full article

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

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23 pages, 3020 KiB

Open AccessArticle

Effects of Monoterpene-Based Biostimulants on Chickpea (Cicer arietinum L.) Plants: Functional and Molecular Insights

by Lamyae Et-Tazy, Riccardo Fedeli, Oussama Khibech, Abdeslam Lamiri, Allal Challioui and Stefano Loppi

Biology 2025, 14(6), 657; https://doi.org/10.3390/biology14060657 - 5 Jun 2025

Viewed by 384

Abstract

This study evaluated the physiological and biochemical responses of chickpea (Cicer arietinum L.) to foliar application of cineole, carvacrol, and thymol at concentrations of 500 and 1000 ppm. Carvacrol at 1000 ppm significantly enhanced fresh biomass (+15.4%) and aerial biomass (+46.2%), whereas [...] Read more.

This study evaluated the physiological and biochemical responses of chickpea (Cicer arietinum L.) to foliar application of cineole, carvacrol, and thymol at concentrations of 500 and 1000 ppm. Carvacrol at 1000 ppm significantly enhanced fresh biomass (+15.4%) and aerial biomass (+46.2%), whereas thymol significantly reduced plant height (−20.2%) and overall biomass, yet notably increased chlorophyll content (+23.3%) and vitamin C levels (+41.4%) at the same concentration. Cineole significantly improved antioxidant capacity by increasing total phenolic content (+15.5% at 1000 ppm) and total flavonoid content (+19.1% at 500 ppm), but simultaneously decreased soluble protein synthesis and chlorophyll content (−39% at 500 ppm). Mineral analysis showed notable increases in calcium content following treatment with cineole (+30.5% at 1000 ppm) and carvacrol (+32% at 500 ppm), while thymol at 1000 ppm significantly reduced phosphorus, potassium, manganese, iron, copper, and zinc accumulation. Molecular docking and dynamic simulations revealed strong interactions of thymol and carvacrol with essential enzymes, specifically ascorbate peroxidase and phenylalanine ammonia-lyase, which are involved in antioxidant and phenolic metabolism pathways. These molecular interactions suggest potential contributions of thymol and carvacrol to plant stress resilience mechanisms, although further experimental validation is needed to confirm their roles in vivo. These findings emphasize the importance of optimizing monoterpene concentrations, indicating that carefully calibrated treatments could effectively enhance chickpea growth, nutritional quality, and stress tolerance within sustainable agricultural practices. Full article

(This article belongs to the Section Plant Science)

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17 pages, 3655 KiB

Open AccessArticle

Comprehensive Ubiquitome Analysis of Nicotiana benthamiana Leaves Infected with Tomato Brown Rugose Fruit Virus

by Jiali Yang, Donghai Wang, Boshen Zhang, Mangle Chen, Jianping Chen, Fei Yan and Shaofei Rao

Biology 2025, 14(6), 656; https://doi.org/10.3390/biology14060656 - 5 Jun 2025

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Abstract

Tomato brown rugose fruit virus (ToBRFV) is an important emerging virus that poses a serious threat to the global agricultural economy. Ubiquitination is one of the key post-translational protein modification types in plant responses to biotic stress, but the extent to which ToBRFV [...] Read more.

Tomato brown rugose fruit virus (ToBRFV) is an important emerging virus that poses a serious threat to the global agricultural economy. Ubiquitination is one of the key post-translational protein modification types in plant responses to biotic stress, but the extent to which ToBRFV infection alters the overall ubiquitination status has not been reported. This study conducted integrated ubiquitome and proteome analyses of Nicotiana benthamiana leaves infected with ToBRFV and identified differentially ubiquitinated proteins. A total of 346 lysine sites on 302 identified proteins were found to be affected, with 260 sites exhibiting upregulated ubiquitination levels in 224 proteins and 86 sites showing downregulated ubiquitination levels in 80 proteins. The differentially ubiquitinated proteins were primarily localized in the cytoplasm (29%), nucleus (18%), plasma membrane (8.9%), mitochondria (5.1%), and chloroplasts (4.6%). Fourteen conserved ubiquitination motifs, including ENNNK, ENNK, SK, and KNG, were identified. Furthermore, enrichment analysis indicated that ToBRFV infection induces an increase in the ubiquitination levels of proteins associated with ion transport, MAPK signaling pathways, and plant hormone signal transduction, while the ubiquitination levels of proteins related to carbon metabolism and secondary metabolite synthesis decreased. Functional analysis of the three differentially ubiquitinated proteins revealed that a RING/U-box superfamily protein negatively regulates ToBRFV infection. Our work provides the first systematic analysis of the ubiquitination profile in N. benthamiana leaves following ToBRFV infection, providing important resources for further studies on the regulatory mechanisms of ubiquitination in plant responses to ToBRFV. Full article

(This article belongs to the Section Plant Science)

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18 pages, 1787 KiB

Open AccessArticle

Enhanced Lethal Effects of Combined P-tert-Butylcatechol and L-Lysine on Microcystis aeruginosa

by Heyun Jiao, Gangwei Jiao, Ruitong Jiang, Yifei Shen, Peimin He and Liu Shao

Biology 2025, 14(6), 655; https://doi.org/10.3390/biology14060655 - 5 Jun 2025

Viewed by 190

Abstract

Allelochemicals are recognized as promising algaecides due to their environmental safety. Para-tert-butylcatechol (TBC) and L-lysine exhibit significant potential in suppressing harmful algal blooms (HABs); however, their combined effects and algae inhibition mechanisms remain unelucidated. Therefore, this study systematically investigated the growth inhibition of [...] Read more.

Allelochemicals are recognized as promising algaecides due to their environmental safety. Para-tert-butylcatechol (TBC) and L-lysine exhibit significant potential in suppressing harmful algal blooms (HABs); however, their combined effects and algae inhibition mechanisms remain unelucidated. Therefore, this study systematically investigated the growth inhibition of Microcystis aeruginosa by TBC and L-lysine individually and in combination, while simultaneously examining their combined effects on algal growth, cell membrane integrity, photosynthetic activity, antioxidant responses, and microcystin production. The results revealed a significant interactive effect between TBC (0.04 mg/L) and L-lysine (1 mg/L), achieving over 90% growth inhibition within 96 h. The combined treatment significantly inhibited M. aeruginosa growth through impaired photosynthetic efficiency and elevated oxidative stress. Compared to the control group, the treatment group exhibited a continuous decline in chlorophyll-a content, phycobiliprotein levels, F_v/F_m, YII, α, and rETR_max, while phosphoenolpyruvate carboxylase (PEPC) activity decreased by 96.48% by day 8. And antioxidant enzymes, including superoxide dismutase (SOD) and reduced glutathione (GSH), showed a progressive increase in activity. In addition, the structure and integrity of the cell membrane of M. aeruginosa were damaged after treatment, and the conductivity of the treatment groups increased continuously from 2.32 to 4.63 μs/cm. In addition, under combined treatment, intra- and extracellular microcystin levels initially increased (peaking at day 2) but sharply declined thereafter, becoming significantly lower than controls by day 8. These findings highlight the potential of combining TBC and L-lysine as an eco-friendly and cost-effective strategy for mitigating M. aeruginosa-dominated harmful algal blooms. Full article

(This article belongs to the Special Issue Advances in Aquatic Ecological Disasters and Toxicology)

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20 pages, 1115 KiB

Open AccessReview

Genomic and Molecular Mechanisms of Goat Environmental Adaptation

by Ying Lu, Ruoshan Ma, Dongfang Li, Yuyang Gao, Zhengmei Sheng, Jinpeng Shi, Yilong Peng, Zhengdong Gao, Weidong Deng and Xiaoming He

Biology 2025, 14(6), 654; https://doi.org/10.3390/biology14060654 - 5 Jun 2025

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Abstract

Goats (Capra hircus) are a widely distributed livestock known for their exceptional environmental adaptability. This review presents an integrated overview of recent advances in understanding the genetic and molecular mechanisms underlying goat adaptation to heat, cold, and high-altitude hypoxia. We first [...] Read more.

Goats (Capra hircus) are a widely distributed livestock known for their exceptional environmental adaptability. This review presents an integrated overview of recent advances in understanding the genetic and molecular mechanisms underlying goat adaptation to heat, cold, and high-altitude hypoxia. We first discuss the development of high-quality reference genomes, including recent telomere-to-telomere assemblies. We then examine major adaptive genes such as HSP70, ACTHR, EPAS1, SLC2A1, FGF12, and UCP1, and their roles in thermoregulation, oxygen metabolism, and stress resistance. Additionally, the review explores the synergistic role of immune signaling pathways in environmental adaptation, as well as the regulatory effects of epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNAs. Future efforts should focus on integrating multi-omics data to uncover the complex molecular networks involved in goat adaptation. This comprehensive synthesis offers valuable insights for precision breeding and long-term sustainability in the context of environmental challenges and climate change. Full article

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14 pages, 1967 KiB

Open AccessArticle

Genomic Evolution of White Spot Syndrome Virus in Shrimp: Insights from Transposon Dynamics

by Zhouquan Li, Guanghua Huang, Jingyi Zhang, Mingyou Li, Zhizhi Liu, Sihua Peng, Rui Wang and Dong Liu

Biology 2025, 14(6), 653; https://doi.org/10.3390/biology14060653 - 4 Jun 2025

Viewed by 238

Abstract

White spot syndrome virus (WSSV) has emerged as a significant threat to global shrimp aquaculture, causing economic losses because of its rapid spread and high mortality rates. This study aims to elucidate the genetic and evolutionary dynamics of WSSV through a comprehensive genome [...] Read more.

White spot syndrome virus (WSSV) has emerged as a significant threat to global shrimp aquaculture, causing economic losses because of its rapid spread and high mortality rates. This study aims to elucidate the genetic and evolutionary dynamics of WSSV through a comprehensive genome analysis. Utilizing 27 complete genome sequences sourced from public databases, this study investigates the genetic variability, potential recombination events, and evolutionary patterns of WSSV. Our results identified multiple genomic deletions, 14 novel single-nucleotide polymorphism sites, and variable number tandem repeats across different strains, underscoring the virus’s genetic diversity. A recombination event between freshwater and marine strains highlights a complex transmission pathway, potentially facilitated by aquaculture practices. A phylogenetic tree constructed using ancestral genes suggests that WSSV originated in Southeast Asia and subsequently globally spread, influenced by both natural and anthropogenic factors. Genomic shrinkage of the virus occurred in time series, while the host’s viral infection induced transposon transposition and insertion into the earlier virus genome to provide a basis for genomic shrinkage. Our research emphasizes the importance of advanced molecular characterization and evolutionary models of the virus in understanding the spread of viral pathogens in aquaculture environments. Full article

(This article belongs to the Special Issue Internal Defense System and Evolution of Aquatic Animals)

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17 pages, 2067 KiB

Open AccessArticle

Pro-Arrhythmic Effect of Chronic Stress-Associated Humoral Factors in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

by Shi Su, Jinglei Sun, Suhua Qiu, Wenting Wu, Jiali Zhang, Yi Wang, Chenxia Shi and Yanfang Xu

Biology 2025, 14(6), 652; https://doi.org/10.3390/biology14060652 - 4 Jun 2025

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Abstract

Under chronic stress, the pro-arrhythmic effect and mechanism of circulating humoral factors in human cardiomyocytes remain unknown. In the present study, we observed the effect of serum from chronic-stress mice on the electrical activity of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Male C57/BL6J [...] Read more.

Under chronic stress, the pro-arrhythmic effect and mechanism of circulating humoral factors in human cardiomyocytes remain unknown. In the present study, we observed the effect of serum from chronic-stress mice on the electrical activity of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Male C57/BL6J mice were subjected to 35 days of chronic unpredictable mild stress (CUMS). The serum from CUMS mice induced arrhythmia-like events (cell arrhythmias) in hiPSC-CMs in a time- and concentration-dependent manner. Patch clamp recordings in the heterologous expression system demonstrated that the serum derived from CUMS mice exerted an inhibitory effect on the cloned human potassium currents (I_to, I_Kr, I_Ks) that mediate action potential repolarization. In addition, serum from CUMS reduced the expression of relevant channel proteins. Moreover, both heat-inactivated serum and deproteinized serum evoked similar severity of cell arrhythmias in hiPSC-CMs as the untreated serum, indicating that circulating substances with small molecules were mainly involved in the occurrence of arrhythmias. Furthermore, metabolomics analysis showed that 90 small-molecule metabolites increased and 390 decreased in CUMS serum. We concluded that circulating humoral substances under chronic stress conditions have direct arrhythmogenic effects by inducing ion channel dysfunction in myocardial cells. Full article

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28 pages, 2194 KiB

Open AccessReview

AI-Driven Transcriptome Prediction in Human Pathology: From Molecular Insights to Clinical Applications

by Xiaoya Chen, Huinan Xu, Shengjie Yu, Wan Hu, Zhongjin Zhang, Xue Wang, Yue Yuan, Mingyue Wang, Liang Chen, Xiumei Lin, Yinlei Hu and Pengfei Cai

Biology 2025, 14(6), 651; https://doi.org/10.3390/biology14060651 - 4 Jun 2025

Viewed by 441

Abstract

Gene expression regulation underpins cellular function and disease progression, yet its complexity and the limitations of conventional detection methods hinder clinical translation. In this review, we define “predict” as the AI-driven inference of gene expression levels and regulatory mechanisms from non-invasive multimodal data [...] Read more.

Gene expression regulation underpins cellular function and disease progression, yet its complexity and the limitations of conventional detection methods hinder clinical translation. In this review, we define “predict” as the AI-driven inference of gene expression levels and regulatory mechanisms from non-invasive multimodal data (e.g., histopathology images, genomic sequences, and electronic health records) instead of direct molecular assays. We systematically examine and analyze the current approaches for predicting gene expression and diagnosing diseases, highlighting their respective advantages and limitations. Machine learning algorithms and deep learning models excel in extracting meaningful features from diverse biomedical modalities, enabling tools like PathChat and Prov-GigaPath to improve cancer subtyping, therapy response prediction, and biomarker discovery. Despite significant progress, persistent challenges—such as data heterogeneity, noise, and ethical issues including privacy and algorithmic bias—still limit broad clinical adoption. Emerging solutions like cross-modal pretraining frameworks, federated learning, and fairness-aware model design aim to overcome these barriers. Case studies in precision oncology illustrate AI’s ability to decode tumor ecosystems and predict treatment outcomes. By harmonizing multimodal data and advancing ethical AI practices, this field holds immense potential to propel personalized medicine forward, although further innovation is needed to address the issues of scalability, interpretability, and equitable deployment. Full article

(This article belongs to the Section Genetics and Genomics)

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19 pages, 1701 KiB

Open AccessArticle

A Preclinical Investigation of Estrogenic Bone Protection in a Hypertensive Rat Model Under Gender-Affirming Hormone Therapy

by Lucas Streckwall, Germán A. Colareda, Daiana Escudero, Romina G. Diaz and Juan M. Fernández

Biology 2025, 14(6), 650; https://doi.org/10.3390/biology14060650 - 3 Jun 2025

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Abstract

The goal of gender-affirming hormone therapy (GAHT) is to align an individual’s physical characteristics with their gender identity by suppressing endogenous sex hormones and replacing them with those consistent with their gender. Transgender women undergoing GAHT are at higher risk of cardiovascular complications, [...] Read more.

The goal of gender-affirming hormone therapy (GAHT) is to align an individual’s physical characteristics with their gender identity by suppressing endogenous sex hormones and replacing them with those consistent with their gender. Transgender women undergoing GAHT are at higher risk of cardiovascular complications, and since clinical evidence suggests that hypertension is associated with increased bone loss, we investigated the effects of estrogen treatment on bone health in a hypertensive transgender animal model. Male spontaneously hypertensive rats were orchiectomized (Orch), and half of them received estrogen treatment (Orch + Es), while a third group remained intact as controls. Bone marrow progenitor cells (BMPCs) were isolated to assess osteogenic potential, and femurs were collected for histological and mechanical analysis. BMPCs from Orch + Es rats exhibited enhanced osteogenic potential compared to those from Orch rats. Histological analysis revealed a higher number of osteocytes and fewer adipocytes in the Orch + Es group. Mechanical testing showed reduced bone strength in Orch rats, which was partially preserved in Orch + Es animals. In conclusion, estrogen administration mitigated the deleterious effects of testosterone depletion on BMPCs and provided protective effects on bone structure and strength in this preclinical model of GAHT in hypertensive rats. Full article

(This article belongs to the Special Issue Osteoblast Differentiation in Health and Disease)

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23 pages, 2579 KiB

Open AccessReview

Role of C-Jun N-Terminal Kinases on a Stressed Epithelium: Time for Testing Isoform Specificity

by Nitesh Shashikanth, Osama Alaidi, Lohitha Basa, Shreya Taank, RadhaKrishna Rao and Jayaraman Seetharaman

Biology 2025, 14(6), 649; https://doi.org/10.3390/biology14060649 - 3 Jun 2025

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Abstract

Biological, physiological, and psychological stressors cause a “stress response” in our bodies. Stressors that are sensorily perceived (either acute or chronic) trigger hormonal responses from the sympathetic nervous system—the SAM and HPA axis—that effect intended organs to alert the individual. Other stressors have [...] Read more.

Biological, physiological, and psychological stressors cause a “stress response” in our bodies. Stressors that are sensorily perceived (either acute or chronic) trigger hormonal responses from the sympathetic nervous system—the SAM and HPA axis—that effect intended organs to alert the individual. Other stressors have a direct effect on the target organ(s) of the body—e.g., physical injury and wounds, toxins, ionizing, and UV radiation. Both kinds of stressors change cell equilibrium, often leading to reactive oxygen species (ROS) accumulation and cellular damage. Among the signaling pathways involved in fighting these stressors, the c-Jun-N-terminal kinases (JNK) respond to diverse kinds of stressors. This review focuses on JNK1 and JNK2, both of which are ubiquitously present in all cell types, and attention is paid to gastrointestinal tract epithelial cells and their response—including tight junction disruption and cytoskeletal changes. We discuss the seemingly opposite roles of JNK1 and JNK2 in helping cells choose pro-survival and pro-apoptotic pathways. We examine the common features of the JNK protein structure and the possibilities of discovering JNK-isoform-specific inhibitors since, although JNK1 and JNK2 are involved in multiple diseases, including cancer, obesity, diabetes, musculoskeletal and liver disease, no cell-specific or isoform-specific inhibitors are available. Full article

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

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19 pages, 1905 KiB

Open AccessArticle

Comprehensive Assessment and Trading Mechanism of Carbon Sink in China’s Marine Aquaculture

by Xuan Yu, Haonan Guo and Qi Chen

Biology 2025, 14(6), 648; https://doi.org/10.3390/biology14060648 - 3 Jun 2025

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Abstract

This study develops species-specific assessment models for carbon sink in marine aquaculture (CSMA) using provincial data from China’s coastal regions (2004–2023). Key findings are as follows: (1) Cumulative CSMA reached 46.3618 million tonnes, exhibiting three growth phases—initial fluctuations (2004–2008), rapid growth (2008–2015), and [...] Read more.

This study develops species-specific assessment models for carbon sink in marine aquaculture (CSMA) using provincial data from China’s coastal regions (2004–2023). Key findings are as follows: (1) Cumulative CSMA reached 46.3618 million tonnes, exhibiting three growth phases—initial fluctuations (2004–2008), rapid growth (2008–2015), and optimization and maturation (2015–2023). (2) Species contributions were heterogeneous: shellfish dominated at 45%, followed by shrimp (24%), fish (15%), crab (11%), and algae (5%). (3) Spatially, Guangdong, Fujian, and Shandong consistently lead in CSMA; Guangxi, Liaoning, and Zhejiang form a second tier, whereas Hebei, Hainan, and Jiangsu remain at the lower end. (4) Province-specific dominance patterns were observed: shellfish-dominant pattern in Shandong, Fujian, and Liaoning; shrimp-dominant pattern in Hebei and Hainan; shellfish-and-shrimp dual-cores in Guangdong and Guangxi; and a multifaceted profile in Jiangsu and Zhejiang. To facilitate the realization of CSMA’s value, we propose a dedicated trading mechanism. Based on the derivations from the effect analysis model and the illustrative case studies, we explore the potential economic and ecological benefits of CSMA trading. Full article

(This article belongs to the Section Marine Biology)

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15 pages, 4171 KiB

Open AccessArticle

Comparative Analysis of Microalgae’s Physiological Responses to Fibrous and Layered Clay Minerals

by Zhongquan Jiang, Tianyi Wei, Sijia Wu, Zhongyang Wang, Zhonghua Zhao, Lu Zhang, Ying Ge and Zhen Li

Biology 2025, 14(6), 647; https://doi.org/10.3390/biology14060647 - 3 Jun 2025

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Abstract

Microalgae interact with mineral particles in an aqueous environment, yet how clay minerals affect physiological processes in algal cells remains unexplored. In this study, we compared the effects of palygorskite (Pal) and montmorillonite (Mt), which respectively represent fibrous and layered clay minerals, on [...] Read more.

Microalgae interact with mineral particles in an aqueous environment, yet how clay minerals affect physiological processes in algal cells remains unexplored. In this study, we compared the effects of palygorskite (Pal) and montmorillonite (Mt), which respectively represent fibrous and layered clay minerals, on the physiological processes of Chlamydomonas reinhardtii. It was observed that C. reinhardtii responded differently to the treatments of Pal and Mt. The Pal particles bound tightly to and even inserted themselves into cells, resulting in a significant decrease in cell numbers from 27.35 to 21.02 × 10⁷ mL⁻¹. However, Mt was only loosely attached to the cell surface. The photosynthesis in the algal cells was greatly inhibited by Pal, with the rETR_max significantly reduced from 103.80 to 56.67 μmol electrons m⁻²s⁻¹ and the downregulation of IF2CP, psbH and OHP1, which are key genes involved in photosynthesis. In addition, Pal reduced the quantities of proteins and polysaccharides in extracellular polymeric substances (EPSs) and the P uptake by C. reinhardtii when the P level in the culture was 3.15 mg/L. However, no significant changes were found regarding the above EPS components or the amount of P in algal cells upon the addition of Mt. Together, the impacts of fibrous Pal on C. reinhardtii was more profound than those of layered Mt. Full article

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

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19 pages, 4294 KiB

Open AccessArticle

Fermentation Products Originated from Bacillus subtilis Promote Hepatic–Intestinal Health in Largemouth Bass, Micropterus salmoides

by Kaifang Liu, Shubin Liu, Dexiang Feng, Pengwei Xun, Hanjun Jiang, Yanwei Zhang, Gaoliang Yuan and Xusheng Guo

Biology 2025, 14(6), 646; https://doi.org/10.3390/biology14060646 - 2 Jun 2025

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Abstract

The fermentation product FP-WeiGuangSu is regarded as a novel, green and efficient antibiotic substitute. Such products constitute one of the principal strategies for addressing bacterial diseases in aquaculture in the future. This study investigates the effects of FPs derived from Bacillus subtilis on [...] Read more.

The fermentation product FP-WeiGuangSu is regarded as a novel, green and efficient antibiotic substitute. Such products constitute one of the principal strategies for addressing bacterial diseases in aquaculture in the future. This study investigates the effects of FPs derived from Bacillus subtilis on the antioxidant capacity and gut microbiota of Largemouth Bass (Micropterus salmoides). Experimental diets containing 0, 1%, 3% and 5% FPs (Control, H1, H2 and H3) were fed to M. salmoides. Although short-term administration of FPs exerted no significant influence on the growth performance of Largemouth Bass, serological findings demonstrated that supplementation with FPs decreased the contents of the liver injury markers ALT, AST and AKP, along with liver MDA content, and enhanced antioxidant capacity (SOD, CAT and GSH-px). Notably, the addition of 1% FPs significantly improved the systemic antioxidant performance (SOD, CAT, GSH-px and T-AOC). Moreover, the FP supplementation increased the expression levels of il-10 and IgM, and lipolysis-related genes. The results of gut microbiota analysis revealed that FPs significantly altered the diversity and structure of gut microbiota. The LEfSe results indicated that the microbial marker of the control group was Cetobacterium, those of the H1 group were Bacillus and Mycoplasma, those of the H2 group were Acinetobacter, Paenibacillus and g_unclassified_Rhizobiaceae, and that of the H3 group was Enterococcus. The most significant microbial marker upon the addition of FPs was Paenibacillus, and the pathways for biosynthesis of secondary metabolites, biosynthesis of antibiotics, and biosynthesis of amino acids were significantly activated. The Bugbase analysis results suggested that, compared with the control group, the abundance of anaerobic bacteria in the FP group decreased, while the abundance of microorganisms with mobile-element-containing and oxidative-stress-tolerant phenotypes increased. Hence, this study demonstrated that 1–3% FP dietary supplementation can be used to enhance antioxidant ability, and liver and intestine health of M. salmoides in the aquaculture industry and can be regarded as a promising feed additive in aquaculture. Full article

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