Biology

25 pages, 2831 KB

Open AccessArticle

Cockle Population Dynamics in a Complex Ecological Aquatic System

by Simão Correia, Marta Lobão Lopes, Ana Picado, João M. Dias, Nuno Vaz, Rosa Freitas and Luísa Magalhães

Biology 2025, 14(10), 1427; https://doi.org/10.3390/biology14101427 (registering DOI) - 17 Oct 2025

Abstract

Cerastoderma edule, the European edible cockle, is a key species in the coastal ecosystems of Portugal, particularly in Ria de Aveiro, a biodiversity hotspot and a critical area for cockle harvesting. This study aimed to assess the population dynamics of C. edule [...] Read more.

Cerastoderma edule, the European edible cockle, is a key species in the coastal ecosystems of Portugal, particularly in Ria de Aveiro, a biodiversity hotspot and a critical area for cockle harvesting. This study aimed to assess the population dynamics of C. edule in Ria de Aveiro, focusing on spatial and seasonal patterns in density, growth, cohort composition, and recruitment areas, to provide baseline data for sustainable management. Our results revealed marked spatial and seasonal variability in cockle density, ranging from complete absence at some upstream sites to peaks of over 5900 ind. m⁻², with recruitment concentrated in summer and early autumn. Environmental gradients, particularly decreasing salinity inland, seasonal temperature shifts, and current velocity, strongly shaped the distribution of recruits and adults, while cohort lifespan and growth performance varied with sediment conditions and lagoon position. Concerningly, the maximum mean shell length observed is close to the legal minimum catch size, raising questions about population sustainability under current harvesting pressures. This interplay of environmental drivers and harvesting pressures poses risks to population viability. Effective management strategies, including adjusted catch sizes, seasonal harvesting bans, and habitat conservation, are essential to ensure the sustainable exploitation of cockles in Ria de Aveiro. Enhanced research and monitoring efforts are recommended to support informed management decisions and protect this valuable resource. Full article

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25 pages, 5147 KB

Open AccessArticle

Potential Distribution and Response to Climate Change in Puccinellia tenuiflora in China Projected Using Optimized MaxEnt Model

by Hao Yang, Xiaoting Wei, Manyin Zhang and Jinxin Zhang

Biology 2025, 14(10), 1426; https://doi.org/10.3390/biology14101426 - 16 Oct 2025

Abstract

Global climate change is accelerating and human pressures are intensifying, exerting profound impacts on biodiversity and ecosystem service functions. The accurate prediction of species distributions has thus become a critical research direction in ecological conservation and restoration. This study selected Puccinellia tenuiflora, [...] Read more.

Global climate change is accelerating and human pressures are intensifying, exerting profound impacts on biodiversity and ecosystem service functions. The accurate prediction of species distributions has thus become a critical research direction in ecological conservation and restoration. This study selected Puccinellia tenuiflora, a species distributed across China, as its research subject. Utilizing 169 occurrence records and 10 environmental variables, we applied a parameter-optimized MaxEnt model to simulate the species’ current and future (2050s–2090s) potential suitable habitats under the SSP126, SSP370, and SSP585 scenarios. The results identified the human footprint index (HFI, 43.3%) and temperature seasonality (Bio4, 26.9%) as the dominant factors influencing its distribution. The current suitable area is primarily concentrated in northern China, covering approximately 258.26 × 10⁴ km². Under all future scenarios, a contraction of suitable habitat is projected, with the most significant reduction observed under SSP585 by the 2090s (a decrease of 56.2%). The distribution centroid is projected to shift northeastward by up to 145.36 km. This study elucidates the response mechanism of P. tenuiflora distribution to climate change and human activities. The projected habitat contraction and spatial displacement highlight the potential vulnerability of this species to future climate change. These findings, derived from a rigorously optimized and spatially validated model, provide a scientific basis for the conservation, reintroduction, and adaptive management of P. tenuiflora under climate change. Full article

(This article belongs to the Section Ecology)

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25 pages, 2474 KB

Open AccessArticle

Data Augmentation-Enhanced Myocardial Infarction Classification and Localization Using a ResNet-Transformer Cascaded Network

by Yunfan Chen, Qi Gao, Jinxing Ye, Yuting Li and Xiangkui Wan

Biology 2025, 14(10), 1425; https://doi.org/10.3390/biology14101425 - 16 Oct 2025

Abstract

Accurate diagnosis of myocardial infarction (MI) holds significant clinical importance for public health systems. Deep learning-based ECG, classification and localization methods can automatically extract features, thereby overcoming the dependence on manual feature extraction in traditional methods. However, these methods still face challenges such [...] Read more.

Accurate diagnosis of myocardial infarction (MI) holds significant clinical importance for public health systems. Deep learning-based ECG, classification and localization methods can automatically extract features, thereby overcoming the dependence on manual feature extraction in traditional methods. However, these methods still face challenges such as insufficient utilization of dynamic information in cardiac cycles, inadequate ability to capture both global and local features, and data imbalance. To address these issues, this paper proposes a ResNet-Transformer cascaded network (RTCN) to process time frequency features of ECG signals generated by the S-transform. First, the S-transform is applied to adaptively extract global time frequency features from the time frequency domain of ECG signals. Its scalable Gaussian window and high phase resolution can effectively capture the dynamic changes in cardiac cycles that traditional methods often fail to extract. Then, we develop an architecture that combines the Transformer attention mechanism with ResNet to extract multi-scale local features and global temporal dependencies collaboratively. This compensates for the existing deep learning models’ insufficient ability to capture both global and local features simultaneously. To address the data imbalance problem, the Denoising Diffusion Probabilistic Model (DDPM) is applied to synthesize high-quality ECG samples for minority classes, increasing the inter-patient accuracy from 61.66% to 68.39%. Gradient-weighted Class Activation Mapping (Grad-CAM) visualization confirms that the model’s attention areas are highly consistent with pathological features, verifying its clinical interpretability. Full article

(This article belongs to the Special Issue Advancing Translational Science Using Bioinformatics and Big Data-Driven Approaches)

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20 pages, 3523 KB

Open AccessArticle

Microsatellite Markers Developed Based on Transcriptomic Data Reveal the Genetic Diversity and Population Genetic Structure of Angulyagra polyzonata in Guangxi, China

by Shengjie Zhang, Dapeng Wang, Kangqi Zhou, Yong Lin, Zhong Chen, Junqi Qin, Xuesong Du, Liuping Long, Caiqun Zhang, Xianhui Pan and Wenhong Li

Biology 2025, 14(10), 1424; https://doi.org/10.3390/biology14101424 - 16 Oct 2025

Abstract

Angulyagra polyzonata is a significant freshwater snail species in southern China. However, its wild resources have sharply declined due to overfishing. To assess the current status of germplasm resources in the Guangxi region, during this study, we first successfully developed nine pairs of [...] Read more.

Angulyagra polyzonata is a significant freshwater snail species in southern China. However, its wild resources have sharply declined due to overfishing. To assess the current status of germplasm resources in the Guangxi region, during this study, we first successfully developed nine pairs of primers that enable the amplification of highly polymorphic microsatellite markers (SSRs) with trinucleotide and tetranucleotide repeat sequences (PIC values ranging from 0.662 to 0.861) using transcriptomic data. Then, these designed primers were tested and applied for the genetic investigation of selected wild populations of the species. Finally, a genetic diversity analysis was conducted based on 12 wild populations (360 individuals) in Guangxi. After 798,244 SSR loci were screened out via high-throughput sequencing, the results showed that dinucleotide repeats accounted for the highest proportion (47.64%), mainly consisting of (AC/GT)n repeat units. Among the SSR loci in A. polyzonata, microsatellite loci with 5 to 20+ repeats are the most abundant. All nine selected and tested SSR loci significantly deviated from Hardy–Weinberg equilibrium (p < 0.001) and had heterozygote deficiency (average inbreeding coefficient of F = 0.390), indicating widespread inbreeding. The fixation index among populations was high (average Fst = 0.175), with 73% of the genetic variation occurring within populations and 27% between populations. Gene flow (Nm) was generally restricted (most population pairs had Nm < 1), with the (Tiandeng) TD and (Long’an) LA populations showing the smallest differentiation (Fst = 0.017), and the (Qinnan) QN and (Yinhai) YH populations showing the greatest differentiation (Fst = 0.409). UPGMA clustering and structure analysis (K = 2) divided the 12 populations into two subgroups. Overall, our research suggests that the genetic diversity of the wild population of A. polyzonata in the Guangxi region has declined. Thus, prioritizing the protection of highly genetically diverse populations, such as the LA population, is urgently needed. This study provides a scientific basis for the protection and sustainable utilization of A. polyzonata resources in Guangxi. Full article

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

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13 pages, 3482 KB

Open AccessArticle

Phylogenetic Position and Morphological Characteristics of the Plagiorchioid Trematode, Skrjabinoplagiorchis polonicus (Soltys, 1957), a Parasite of Rodents

by Alexander A. Kirillov, Nadezhda Y. Kirillova and Sergei V. Shchenkov

Biology 2025, 14(10), 1423; https://doi.org/10.3390/biology14101423 - 16 Oct 2025

Abstract

The genus Skrjabinoplagiorchis is monotypic, with Skrjabinoplagiorchis polonicus parasitizing rodents in the Western Palaearctic. This genus is classified within the family Plagiorchiidae; however, its taxonomic position remains unclear. In the present study, two species of digeneans, S. polonicus and Rubenstrema exasperatum, found [...] Read more.

The genus Skrjabinoplagiorchis is monotypic, with Skrjabinoplagiorchis polonicus parasitizing rodents in the Western Palaearctic. This genus is classified within the family Plagiorchiidae; however, its taxonomic position remains unclear. In the present study, two species of digeneans, S. polonicus and Rubenstrema exasperatum, found in small mammals in the Middle Volga region (European Russia), were examined. We provide morphological descriptions of the studied trematodes complemented with a molecular phylogenetic analysis of partial sequences of the 28S rDNA gene, obtained for these helminths of mammals in Russia for the first time. Based on morphological data and the results of molecular phylogenetic analysis, we reassign the genus Skrjabinoplagiorchis from the subfamily Plagiorchiinae to the subfamily Omphalometrinae. Previously, digeneans of the subfamily Omphalometrinae were known only as parasites of insectivores of the order Eulipotyphla. Full article

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15 pages, 660 KB

Open AccessReview

Aldose Reductase Involvement in EMT: Emerging Insights and Current Proposed Molecular Mechanisms

by Gemma Sardelli, Francesca Felice, Rossella Mosca, Martina Avanatti and Roberta Moschini

Biology 2025, 14(10), 1422; https://doi.org/10.3390/biology14101422 - 16 Oct 2025

Abstract

Aldose reductase (AKR1B1) is a member of the aldo-keto reductase (AKR) family and plays a variety of roles in many metabolic and physiological processes. Although its function in the polyol pathway and defense against reactive carbonyl species is well-documented, many of aldose reductase’s [...] Read more.

Aldose reductase (AKR1B1) is a member of the aldo-keto reductase (AKR) family and plays a variety of roles in many metabolic and physiological processes. Although its function in the polyol pathway and defense against reactive carbonyl species is well-documented, many of aldose reductase’s roles remain poorly understood. Recently, accumulating evidence has suggested a strong correlation between aldose reductase expression and/or activity and the epithelial-to-mesenchymal transition (EMT), a process fundamental to both physiological conditions (e.g., embryonic development and wound healing) and pathological states (such as fibrosis and metastasis). Specifically, aldose reductase appears to be a potent promoter of EMT in both tumor and non-tumor contexts, although the molecular mechanisms through which it drives EMT remain unclear. This review aims to summarize the growing body of studies highlighting the association between AKR1B1 and EMT, as well as to analyze the molecular mechanisms proposed by various authors. Finally, the main findings on EMT responses following AKR1B1 inhibition will be discussed, providing a comprehensive overview of current knowledge and identifying the critical gaps that must be addressed to fully elucidate the role of aldose reductase in this process. Full article

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

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13 pages, 239 KB

Open AccessReview

Insights into the Anti-Inflammatory Effects of Soft Tissue Manipulation

by Jonathan W. Lowery, Basil Mustaklem, Connor Wakefield, Hailey Brown, Madeline M. Sasse, Samuel Baule, Sierra Street, Liza Pradhan, Simran Sandhu, Carmela L. Marciano, David C. Eland, Mary Terry Loghmani and Tien-Min Gabriel Chu

Biology 2025, 14(10), 1421; https://doi.org/10.3390/biology14101421 - 15 Oct 2025

Abstract

Soft tissue manipulation (STM) is widely used by physical therapists, massage therapists, athletic trainers, and osteopathic physicians to manage musculoskeletal pain, yet its biological mechanisms remain poorly understood. Preclinical studies indicate that STM can alter immune cell behavior in animal models, increasing anti-inflammatory [...] Read more.

Soft tissue manipulation (STM) is widely used by physical therapists, massage therapists, athletic trainers, and osteopathic physicians to manage musculoskeletal pain, yet its biological mechanisms remain poorly understood. Preclinical studies indicate that STM can alter immune cell behavior in animal models, increasing anti-inflammatory cytokines (IL-4, IL-10) and reducing chemokines such as RANTES/CCL5. Single-cell transcriptomic analyses suggest mechanical treatment may reprogram stromal cells and shift immune cell recruitment in aged or inflamed tissues. However, many of these mechanistic findings have yet to be confirmed in human studies. Early clinical trials show massage therapy can modify circulating leukocytes and reduce cytokine responses, but direct tissue-level evidence in human subjects remains limited. This narrative review summarizes existing insights and emphasizes the need for future clinical investigations targeting populations with chronic inflammation, repetitive-use injuries, post-surgical fibrosis, or age-related muscle decline. We advocate for studies incorporating tissue or fluid sampling, cytokine profiling, and molecular assays such as flow cytometry or transcriptomics to characterize STM’s immunological effects in people. Rather than simply easing symptoms, STM may act as a precision mechanical stimulus that recalibrates immune tone and promotes tissue repair. Bridging basic science with clinical research will be essential to establish STM as a biologically informed, mechanobiology-based therapeutic strategy. Full article

3 pages, 178 KB

Open AccessEditorial

Pollination Biology: From Pollinators and Floral Traits to Landscape Management

by Yu Gao

Biology 2025, 14(10), 1420; https://doi.org/10.3390/biology14101420 - 15 Oct 2025

Abstract

Pollination biology examines the mechanisms, agents, and ecological significance of pollination [...] Full article

(This article belongs to the Special Issue Pollination Biology)

27 pages, 4889 KB

Open AccessArticle

Macroalgal–Coral Interactions in New Caledonia South West Lagoon: Diversity, Abundance, and Spatial Patterns

by Christophe Vieira, Christophe Peignon, Olivier De Clerck and Claude Payri

Biology 2025, 14(10), 1419; https://doi.org/10.3390/biology14101419 - 15 Oct 2025

Abstract

Macroalgal–coral interactions (MCI) are an integral yet understudied component of coral reef ecology, particularly in healthy systems where they may represent stable coexistence rather than competition. This study provides the first comprehensive assessment of MCI diversity, abundance, and spatial patterns in the South [...] Read more.

Macroalgal–coral interactions (MCI) are an integral yet understudied component of coral reef ecology, particularly in healthy systems where they may represent stable coexistence rather than competition. This study provides the first comprehensive assessment of MCI diversity, abundance, and spatial patterns in the South West Lagoon of New Caledonia (SWLNC). Across 26 coral-dominated habitats, MCI accounted for an average of 16.4% of the benthic cover, with local values reaching 70% in high-interaction areas. A total of 43 unique macroalgal–coral genus pairings were documented, involving 16 macroalgal and 10 coral genera. Lobophora (47%), Halimeda (20%), and Hypnea (9%) were the dominant macroalgae, while Acropora (61%), Montipora (19%), Seriatopora (13%), and Porites (5%) were the most frequent coral interactants. The most abundant specific interactions were Lobophora–Acropora (29%), Hypnea–Acropora (15%), Halimeda–Montipora (10%), Lobophora–Seriatopora (10%), and Halimeda–Acropora (10%). MCI abundance varied markedly among habitat levels, differing across reef types, zonation, and benthic cover. Six recurrent typologies of physical association were identified, and the Coralgal Biotic Interaction Compass (CBIC) is introduced as a conceptual framework to distinguish the nature of macroalgal-coral associations. Overall, the study demonstrates that MCI in the SWLNC are diverse, structured, and non-random, shaped by both interactant identity and habitat filtering rather than ubiquity, providing a robust ecological baseline for future analyses of macroalgal-coral dynamics in Indo-Pacific reef systems. Full article

(This article belongs to the Section Ecology)

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22 pages, 1139 KB

Open AccessArticle

Fruits and Seeds as Indicators of the Genetic Diversity of Hymenaea martiana (Fabaceae) in Northeast Brazil

by Joyce Naiara da Silva, Guilherme Vinícius Gonçalves de Pádua, Caroline Marques Rodrigues, João Henrique Constantino Sales Silva, Cosma Layssa Santos Gomes, Marília Hortência Batista Silva Rodrigues, Maria Karoline Ferreira Bernardo, Eduardo Luã Fernandes da Silva, Luís Gustavo Alves de Almeida, Lenyneves Duarte Alvino de Araújo, Aline das Graças Souza, Naysa Flávia Ferreira do Nascimento and Edna Ursulino Alves

Biology 2025, 14(10), 1418; https://doi.org/10.3390/biology14101418 - 15 Oct 2025

Abstract

Hymenaea martiana is a species native to Brazil. It has ecological value, contributes to forest restoration, and is economically important because of the use of its wood and fruits. However, it is frequently exploited. Therefore, understanding genetic diversity becomes essential for guiding conservation [...] Read more.

Hymenaea martiana is a species native to Brazil. It has ecological value, contributes to forest restoration, and is economically important because of the use of its wood and fruits. However, it is frequently exploited. Therefore, understanding genetic diversity becomes essential for guiding conservation strategies as well as ecological restoration actions in the face of climate change and anthropogenic pressures. Thus, this study aimed to evaluate the intraspecific diversity of 160 H. martiana mother plants on the basis of morphological descriptors of fruits and seeds and physiological indicators of seed quality, identifying the most discriminating characters. Eighteen traits were analyzed and subjected to analysis of variance and the Scott–Knott test (p < 0.05), with estimates of heritability and the ratio between genetic and environmental coefficients of variation. Phenotypic divergence was obtained via the Mahalanobis distance (D²) and grouped via UPGMA, whereas the relative contribution of the traits was estimated via the Singh method. The results revealed that seed length and weight, emergence speed index, and shoot dry mass were the most effective descriptors for discriminating parent plants. Multivariate analysis revealed the formation of eleven phenotypically distinct groups, demonstrating high variability. These findings support the selection of superior genotypes and representative seed collection, as well as practical initiatives such as the formation of germplasm banks, the selection of breeding stock for forest nurseries, and reintroduction programs. Thus, the data obtained offer technical and scientific support for biodiversity conservation and ecosystem recovery in the semiarid region of Brazil. Full article

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

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21 pages, 4695 KB

Open AccessArticle

Comparative Proteomics Analysis Reveals Differential Immune Responses of Paralichthys olivaceus to Edwardsiella tarda Infection Under High and Low Temperature

by Xiaojuan Chen, Lejia Luo, Beibei Zhang, Xiaowei Zhou, Kaipeng Zhang, Panpan Zhang and Bin Sun

Biology 2025, 14(10), 1417; https://doi.org/10.3390/biology14101417 - 15 Oct 2025

Abstract

Fluctuating water temperatures and bacterial pathogens such as Edwardsiella tarda pose a serious threat to mariculture, resulting in significant economic losses within the flounder industry. A previous study revealed that elevated temperature enhanced E. tarda dissemination in flounder tissues. However, the underlying mechanism [...] Read more.

Fluctuating water temperatures and bacterial pathogens such as Edwardsiella tarda pose a serious threat to mariculture, resulting in significant economic losses within the flounder industry. A previous study revealed that elevated temperature enhanced E. tarda dissemination in flounder tissues. However, the underlying mechanism has not been fully explained, especially the changes in protein level. In this study, label-free proteomics was utilized to investigate the impact of high temperature (23 °C) and low temperature (15 °C) on flounder immune response to E. tarda infection. Our results identified 317 differentially abundant proteins (DAPs) in the low-temperature group (LI-LC) and 302 DAPs in the high-temperature group (HI-HC). GO and KEGG analyses of DAPs revealed numerous immune-related proteins and pathways. Twenty-six key DAPs in the LI-LC group and twenty-seven key DAPs in the HI-HC group were further identified and formed extensive interaction networks, respectively. Through the analysis of key immune-related DAPs that were specifically identified in both groups via Venn diagram analysis, we demonstrated that the endocytosis capacity and complement activity were enhanced in the HI-HC group, while histone abundance and RNA transport function were, respectively, increased and severely interfered with in the LI-LC group. These findings highlight a clear divergence in the immune response of flounder to E. tarda infection between 15 °C and 23 °C, providing valuable insights into how temperature variation influences antibacterial immunity in fish. Full article

(This article belongs to the Topic Immunology and Disease Prevention and Control in Aquatic Animals)

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17 pages, 9344 KB

Open AccessArticle

Methodological Pitfalls of Monitoring: Water Conditions Affect the Efficiency of Bottle Traps and Capture Success

by Teodor J. Purger, Boldizsár Szűcs, József Dezső, László Wágner, Dragica Purger and Jenő J. Purger

Biology 2025, 14(10), 1416; https://doi.org/10.3390/biology14101416 - 15 Oct 2025

Abstract

Wetland diversity and associated wildlife is declining globally. The Szaporca Old-Drava oxbow, one of Hungary’s first wetlands designated under the Ramsar Convention, has been threatened by desiccation, prompting the implementation of water replenishment interventions. This study aimed to determine which aquatic vertebrate species [...] Read more.

Wetland diversity and associated wildlife is declining globally. The Szaporca Old-Drava oxbow, one of Hungary’s first wetlands designated under the Ramsar Convention, has been threatened by desiccation, prompting the implementation of water replenishment interventions. This study aimed to determine which aquatic vertebrate species can be detected using bottle traps in the oxbow and whether the traps’ efficiency and capture success change following hydrological restoration. Our results showed that the relative frequency of smooth newts caught with bottle traps was 10%, while that of other amphibians (Danube crested newt, common spadefoot toad, edible frog) and fish (European weather loach, European mudminnow, Danube whitefin gudgeon) species did not even reach 1%. Based solely on the relative frequency data of the smooth newt, we found that both the capture efficiency (10.4% vs. 3%) and capture success (17% vs. 7.4%) of bottle traps significantly declined following an increase in water volume in the oxbow. Sex ratio patterns also shifted markedly: in the year of water scarcity, the male-to-female ratio of smooth newt was 2.7:1, whereas during water-abundant conditions it increased to 7:1. Water replenishment raised the water level by nearly one meter, resulting in the partial inundation of terrestrial vegetation and consequent habitat alterations. While water supplementation clearly supports the persistence of rare, protected, strictly protected and endemic aquatic species, our findings highlight the importance of considering hydrological conditions when interpreting the results of long-term monitoring in wetland ecosystems. Full article

(This article belongs to the Section Ecology)

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27 pages, 2448 KB

Open AccessReview

Preclinical Models of Donation-After-Circulatory-Death and Brain-Death: Advances in Kidney Preservation and Transplantation

by Tamara S. Ortas, Omer Choudhary, George J. Dugbartey and Alp Sener

Biology 2025, 14(10), 1415; https://doi.org/10.3390/biology14101415 - 14 Oct 2025

Abstract

Chronic kidney disease (CKD) affects over 10% of the global population, with end-stage renal disease (ESRD) necessitating renal replacement therapy. Kidney transplantation remains the optimal treatment for ESRD. However, the global donor kidney shortage crisis has led to increased reliance on deceased donor [...] Read more.

Chronic kidney disease (CKD) affects over 10% of the global population, with end-stage renal disease (ESRD) necessitating renal replacement therapy. Kidney transplantation remains the optimal treatment for ESRD. However, the global donor kidney shortage crisis has led to increased reliance on deceased donor kidneys. Donors are classified as either donation after brain death (DBD) or donation after circulatory death (DCD), each associated with distinct ischemic injuries that impact graft function. Ischemia–reperfusion injury (IRI) plays a pivotal role in transplant outcomes, triggering oxidative stress, inflammation, and endothelial dysfunction. While static cold storage (SCS) remains the gold standard for organ preservation, alternative strategies such as hypothermic or normothermic machine perfusion (HMP and NMP), use of oxygen carriers during storage, and supplemental compounds to storage solutions have emerged, offering potential benefits in preserving graft viability. This review explores the cellular and molecular mechanisms of ischemic injury in deceased donor kidneys, preservation strategies tested in preclinical models, and emerging therapeutic interventions aimed at improving adverse post-transplant outcomes. Full article

(This article belongs to the Special Issue The Role of Innate Immunity in Organ Transplantation)

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16 pages, 3674 KB

Open AccessArticle

The Ubiquitination of Mycobacterium tuberculosis Rv3717 Promotes Proteasomal Degradation of Interleukin Enhancer-Binding Factor

by Xu-Wen Gui, Teng-Fei Zhang, An-Qi Zheng, Ming-Xin Guo, Qian-Wei Dong and Tao Jiang

Biology 2025, 14(10), 1414; https://doi.org/10.3390/biology14101414 - 14 Oct 2025

Abstract

Mycobacterium tuberculosis (M. tuberculosis) has developed some strategies to evade host immune responses through ubiquitination, thereby facilitating persistent mycobacterial infection. The Rv3717 protein has been identified as a peptidoglycan (PG) amidase that contributes to mycobacterial survival, but its exact mechanism is [...] Read more.

Mycobacterium tuberculosis (M. tuberculosis) has developed some strategies to evade host immune responses through ubiquitination, thereby facilitating persistent mycobacterial infection. The Rv3717 protein has been identified as a peptidoglycan (PG) amidase that contributes to mycobacterial survival, but its exact mechanism is still unclear. The findings of this study indicate that Rv3717 inhibits mycobacterial clearance within pulmonary epithelial cells. To elucidate the molecular mechanisms by which Rv3717 facilitates persistent infection, we identified intracellular candidates interacting with Rv3717 using co-immunoprecipitation (Co-IP) combined with liquid chromatography–mass spectrometry (LC-MS/MS). The unique proteins are categorized into three functional networks: mRNA splicing, the immune system process, and the translation process through Protein–Protein Interaction (PPI) analysis. The candidate interacting proteins of Rv3717 are involved in interleukin-2 enhancer-binding factor 2 (ILF2) and TAF15, as well as the polyubiquitin chain (UBC) and E3 ubiquitin ligase TRIM21. Our results suggest that intracellular Rv3717 is likely to influence biological processes through the potential interacting proteins. Our findings confirmed that Rv3717 interacted with interleukin enhancer-binding factor 2 (ILF2) through Co-IP and immunofluorescence assays. Furthermore, Rv3717 was verified to bind with ubiquitin and be degraded through the proteasome system. More importantly, the ubiquitination of Rv3717 accelerated the proteasomal degradation of ILF2 and downregulated the expression of IL-2. This study is the first to propose that the ubiquitination of the mycobacterial membrane vesicle-associated protein Rv3717 facilitates the proteasomal degradation of ILF2, resulting in the downregulation of IL-2 expression. Overall, the role of intracellular Rv3717 in promoting mycobacterial survival is associated with its ubiquitination and the proteasomal degradation of ILF2. Full article

(This article belongs to the Section Infection Biology)

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18 pages, 7114 KB

Open AccessArticle

Elucidating the Molecular Basis of Thermal Stress Response in Juvenile Turbot (Scophthalmus maximus) via an Integrative Transcriptome–Metabolome Approach

by Xiatian Chen, Tao Gao, Ziwen Wang, Shuaiyu Chen, Nan Zhang, Xiaoming Zhang and Yudong Jia

Biology 2025, 14(10), 1413; https://doi.org/10.3390/biology14101413 - 14 Oct 2025

Abstract

Temperature has always been an important environmental factor, and changes in water temperature are closely related to the entire life process of fish. Investigating the impact of thermal stress on fish physiology is critical for optimizing aquaculture. This study employed transcriptomic and metabolomic [...] Read more.

Temperature has always been an important environmental factor, and changes in water temperature are closely related to the entire life process of fish. Investigating the impact of thermal stress on fish physiology is critical for optimizing aquaculture. This study employed transcriptomic and metabolomic approaches to investigate temperature-induced variations in the gene expression and metabolic profiles of turbot. The results showed that thermal stress could induce abnormal genes transcription, and functional annotation demonstrated predominant associations of these genes with key pathways including PI3K-Akt signaling, PPAR regulation, steroid biosynthesis, fatty acid metabolism, and FoxO signaling cascade. Metabolomic analysis revealed that amino acid metabolism was dysregulated, such as valine, leucine, and isoleucine. Joint analysis revealed significant positive associations between CDH1, Col9a1, and ECT2 genes and leucine/isoleucine metabolism. The expression levels of Plch2 and Col9a1 genes exhibited significant regulatory effects on valine metabolism. Moreover, the gene cluster comprising DNAJB6, Gcnt1 and trim71 was significantly involved in the metabolic regulation of galactonic acid. Collectively, these findings demonstrate that thermal stress induces significant alterations in gene expression, metabolic profiles, and signaling pathways in turbot, offering new perspectives for thermal stress mitigation strategies. Full article

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

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14 pages, 4850 KB

Open AccessArticle

Ectoplana limuli, a Parasite of the Horseshoe Crab (Tachypleus tridentatus): A New Record in China

by Zimeng Luo, Lingtong Ye, Ziwei Ying, Chenxiang Deng, Xiaoyong Xie, Xiaohai Chen and Ting Li

Biology 2025, 14(10), 1412; https://doi.org/10.3390/biology14101412 - 14 Oct 2025

Abstract

The mortality rate of first- to second-instar horseshoe crabs during molting is extremely high under culture conditions (pH of 7.6 ± 0.1, salinity of 27 ± 2, temperature of 26–32 °C), and we preliminarily speculate that it is related to disease. Our team [...] Read more.

The mortality rate of first- to second-instar horseshoe crabs during molting is extremely high under culture conditions (pH of 7.6 ± 0.1, salinity of 27 ± 2, temperature of 26–32 °C), and we preliminarily speculate that it is related to disease. Our team found that Ectoplana limuli was attached to the ventral limbs of adult horseshoe crabs during culture. Parasite samples were collected from the external appendages and mouthparts of adult Tachypleus tridentatus for classification and identification. The primary objective of this experiment was to identify the species of this parasite and determine its taxonomic status. To this end, the experiment employed a combination of morphological methods and 18S rDNA gene molecular markers. The obtained sequences showed over 99% homology with Ectoplana limuli. Sequence alignment and phylogenetic tree results indicated that Ectoplana limuli showed a closer genetic relationship with Nerpa fistulata, but more distant relationships with Paucumara and Baikalobia. This is the first time that this parasite has been found in China, providing additional information for the study of horseshoe crab diseases. Full article

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15 pages, 14943 KB

Open AccessArticle

Molecular Docking of Detoxification Enzymes from Oides leucomelaena with Volatiles of Star Anise

by Yingxue Yang, Zhixiao Zhang, Huifen Ma, Lianrong Hu, Kai Li, Ning Zhao, Ling Liu and Jielong Zhou

Biology 2025, 14(10), 1411; https://doi.org/10.3390/biology14101411 - 14 Oct 2025

Abstract

Star anise, an economically and medicinally important crop, is highly susceptible to infestation by Oides leucomelaena Weise, leading to significant yield losses. This study employed transcriptome sequencing and bioinformatic analysis to systematically identify detoxification genes (CYP, GST, and CarE) in O. leucomelaena and [...] Read more.

Star anise, an economically and medicinally important crop, is highly susceptible to infestation by Oides leucomelaena Weise, leading to significant yield losses. This study employed transcriptome sequencing and bioinformatic analysis to systematically identify detoxification genes (CYP, GST, and CarE) in O. leucomelaena and evaluated their binding potential with star anise volatiles via molecular docking. A total of 64 CYP, 21 GST, and 44 CarE genes were identified, with several genes showing high expression across multiple tissues. Molecular docking revealed strong binding affinity between seven CYP proteins and star anise volatiles, notably the antennae-specific CYP, which exhibited robust binding with multiple volatiles. Detoxification genes in O. leucomelaena may mediate host adaptation by metabolizing star anise volatiles, providing potential targets for eco-friendly pest control. Full article

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13 pages, 1352 KB

Open AccessArticle

Long-Term Potentiation and Neurotransmitter Expression Change in Dysautonomia Linked to Binge Eating Disorder: Protective Role of Exercise

by Fernanda Veladiz-Gracia, Diana Elinos, Constanza González-Sierra, Angel Rubio-Galicia, Fredy Cifuentes and Miguel Angel Morales

Biology 2025, 14(10), 1410; https://doi.org/10.3390/biology14101410 - 14 Oct 2025

Abstract

The autonomic nervous system (ANS) regulates internal organ function to maintain homeostasis. Dysautonomias are ANS disorders involving reduced or excessive sympathetic or parasympathetic activity and can be associated with metabolic syndrome and eating disorders such as binge eating disorder (BED). The ANS exhibits [...] Read more.

The autonomic nervous system (ANS) regulates internal organ function to maintain homeostasis. Dysautonomias are ANS disorders involving reduced or excessive sympathetic or parasympathetic activity and can be associated with metabolic syndrome and eating disorders such as binge eating disorder (BED). The ANS exhibits synaptic plasticity phenomena, including long-term potentiation (LTP) and neurotransmitter expression changes, which may influence autonomic function. BED is defined as recurrent, compulsive intake of large amounts of high-calorie food in a short time. Here, we examined dysautonomia in a rat BED model induced by cycles of food restriction and access to highly caloric food, and assessed whether exercise prevents these alterations. After confirming BED induction, we characterized LTP in the superior cervical ganglion (SCG) and analyzed acetylcholine (ACh) and GABA expression and their co-localization/segregation. BED rats exhibited impaired LTP and increased GABA expression. Voluntary aerobic exercise prevented BED onset and the associated changes in LTP and GABA. We propose that BED-associated dysautonomia proceeds at least in the ganglionic sympathetic cholinergic transmission, with reduced sympathetic activity. These results may contribute to a better understanding of the autonomic disorder associated with BED and support exercise as a protective intervention. Full article

(This article belongs to the Special Issue The Plasticity of Autonomic Ganglia)

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21 pages, 4509 KB

Open AccessArticle

Multi-Omics Analysis and Comparison of the Developmental Characteristics of Muscle Fiber Types Between Huainan and Large White Pigs in Early Postnatal Period

by Jing Wang, Mingyang Jia, Hanbing Zhang, Yaping Guo, Qi Zhang, Xiangzhou Yan, Qingxia Lu, Sihuan Zhang and Baosong Xing

Biology 2025, 14(10), 1409; https://doi.org/10.3390/biology14101409 - 14 Oct 2025

Abstract

To investigate the molecular mechanisms underlying muscle fiber development in different pig breeds and their impact on meat quality, this study collected the longissimus dorsi muscle of the indigenous Huainan pig and the commercial Large White pig at four developmental stages (0, 7, [...] Read more.

To investigate the molecular mechanisms underlying muscle fiber development in different pig breeds and their impact on meat quality, this study collected the longissimus dorsi muscle of the indigenous Huainan pig and the commercial Large White pig at four developmental stages (0, 7, 14, and 21 days postnatal). Muscle fiber types were identified using myosin ATPase staining, while transcriptomics and non-targeted metabolomics were employed to analyze differences in gene expression and metabolite composition. The results showed that the Huainan pig had a higher proportion of oxidative muscle fibers, indicating superior aerobic metabolic capacity and meat quality. Transcriptome data identified 18 differentially expressed genes common to both pig breeds, including KLF4, NOS1, SH3KBP1, and TRARG1, which were upregulated in Huainan pigs to regulate muscle fiber type composition and meat quality by influencing mitochondrial function, nitric oxide synthesis, and glucose/lipid metabolism. Metabolomics analysis revealed significantly elevated levels of carnosine, citrulline, serine, and glycerol-3-phosphate in Huainan pigs, which are associated with metabolic pathways promoting muscle fiber transformation via enhancing energy supply, antioxidant capacity, and fatty acid oxidation. Notably, integrated transcriptome–metabolome analysis showed that oxidative metabolism genes (e.g., KLF4) and metabolites (e.g., citrulline) formed an AMPK-mediated ‘gene–metabolite’ loop in Huainan pigs, which synergistically promotes mitochondrial function and fiber differentiation. In summary, this study provides new insights into the molecular mechanisms underlying meat quality differences between pig breeds and offers a theoretical basis for the breeding and development of high-quality pork. Full article

(This article belongs to the Section Genetics and Genomics)

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