Biology

18 pages, 5497 KiB

Open AccessSystematic Review

Effect of Aflatoxin B1 on the Nervous System: A Systematic Review and Network Analysis Highlighting Alzheimer’s Disease

by Samira Ranjbar, Pantea Mohammadi, Somayeh Pashaei, Masoud Sadeghi, Masomeh Mehrabi, Sasan Shabani, Ali Ebrahimi, Annette B. Brühl, Reza Khodarahmi and Serge Brand

Biology 2025, 14(4), 436; https://doi.org/10.3390/biology14040436 - 17 Apr 2025

Abstract

Exposure to aflatoxin (AF) triggers the production of inflammatory molecules and free radicals, leading to chronic inflammation, cancer, and neurodegenerative diseases. This systematic review evaluated the effects of AFB1 on the nervous system, particularly focusing on Alzheimer’s disease (AD). A comprehensive search was [...] Read more.

Exposure to aflatoxin (AF) triggers the production of inflammatory molecules and free radicals, leading to chronic inflammation, cancer, and neurodegenerative diseases. This systematic review evaluated the effects of AFB1 on the nervous system, particularly focusing on Alzheimer’s disease (AD). A comprehensive search was conducted in Scopus, Cochrane Library, PubMed, and Web of Science databases up to 1 June 2024, without restrictions. From 993 records retrieved, 16 articles were included in the systematic review. AFB1 participates in various biochemical processes and pathological conditions. The study highlights that AFB1 contributes to AD by inducing DNA damage, oxidative stress, and endoplasmic reticulum (ER) stress, impairing DNA repair mechanisms. This results in neuronal damage, cognitive decline, and neurodegeneration. AFB1 also affects key signaling pathways, reduces sodium–potassium pump activity, and disrupts cell cycle regulation involving p53, leading to neurotoxicity, inflammation, and the formation of amyloid-beta (Aβ) plaques and neurofibrillary tangles. Additionally, network analysis revealed 309 genes associated with AD, inflammation, angiopathy, and aflatoxin B1 (AFB1). Among these, ESR1 exhibited the highest number of direct connections to other nodes within the network. The gene TP53 played a pivotal role in mediating communication among genes, while the EP300 gene significantly influenced the overall network structure. Additionally, KEGG enrichment analysis demonstrated that these 309 genes are substantially involved in pathways related to cancer, the FoxO signaling pathway, apoptosis, and AD. In summary, the study highlights that AFB1 causes DNA damage and stress, leading to cognitive decline and neurodegeneration. It disrupts signaling pathways, damages neurons, and affects DNA repair, contributing to neurotoxicity and inflammation. PROSPERO registration number: CRD420250651007. Full article

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27 pages, 1441 KiB

Open AccessReview

Microbiota-Driven Mechanisms in Multiple Sclerosis: Pathogenesis, Therapeutic Strategies, and Biomarker Potential

by Mohammad Hosein Nemati, Esmaeil Yazdanpanah, Roya Kazemi, Niloufar Orooji, Sepehr Dadfar, Valentyn Oksenych and Dariush Haghmorad

Biology 2025, 14(4), 435; https://doi.org/10.3390/biology14040435 - 17 Apr 2025

Abstract

Multiple sclerosis (MS) is a well-known, chronic autoimmune disorder of the central nervous system (CNS) involving demyelination and neurodegeneration. Research previously conducted in the area of the gut microbiome has highlighted it as a critical contributor to MS pathogenesis. Changes in the commensal [...] Read more.

Multiple sclerosis (MS) is a well-known, chronic autoimmune disorder of the central nervous system (CNS) involving demyelination and neurodegeneration. Research previously conducted in the area of the gut microbiome has highlighted it as a critical contributor to MS pathogenesis. Changes in the commensal microbiota, or dysbiosis, have been shown to affect immune homeostasis, leading to elevated levels of pro-inflammatory cytokines and disruption of the gut–brain axis. In this review, we provide a comprehensive overview of interactions between the gut microbiota and MS, especially focusing on the immunomodulatory actions of microbiota, such as influencing T-cell balance and control of metabolites, e.g., short-chain fatty acids. Various microbial taxa (e.g., Prevotella and Faecalibacterium) were suggested to lay protective roles, whereas Akkermansia muciniphila was associated with disease aggravation. Interventions focusing on microbiota, including probiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary therapies to normalize gut microbial homeostasis, suppress inflammation and are proven to improve clinical benefits in MS patients. Alterations in gut microbiota represent opportunities for identifying biomarkers for early diagnosis, disease progression and treatment response monitoring. Further studies need to be conducted to potentially address the interplay between genetic predispositions, environmental cues, and microbiota composition to get the precise mechanisms of the gut–brain axis in MS. In conclusion, the gut microbiota plays a central role in MS pathogenesis and offers potential for novel therapeutic approaches, providing a promising avenue for improving clinical outcomes in MS management. Full article

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

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15 pages, 7766 KiB

Open AccessArticle

Transcriptome Profiling Revealed Light-Mediated Gene Expression Patterns of Plants in Forest Vertical Structures

by Qiming Mei, Yi Zheng, Jiayi Feng, Zhengfeng Wang, Honglin Cao and Juyu Lian

Biology 2025, 14(4), 434; https://doi.org/10.3390/biology14040434 - 17 Apr 2025

Abstract

Light is a critical environmental factor that shapes forest communities. The canopy trees intercept the light, thus understory plants become shaded. Shade leads to the attenuation of light intensity and a shift in the spectrum through the forest vertical structure. The capacity of [...] Read more.

Light is a critical environmental factor that shapes forest communities. The canopy trees intercept the light, thus understory plants become shaded. Shade leads to the attenuation of light intensity and a shift in the spectrum through the forest vertical structure. The capacity of forest trees to survive and grow under conditions of light heterogeneity is closely related to the intrinsic property of these species. Therefore, identifying how plants interact with light-regime variability is an important research objective of community ecology. In this study, we investigated the light-mediated gene expression patterns in forest vertical structures utilizing transcriptome profiling. The expression levels of 20 annotated genes closely related to photosynthesis, light receptors, and photoprotection were used as traits to estimate how variable light environments influence the plants in forest vertical structures. In summary, the shade-tolerant species were characterized by higher levels of photoreceptor (Phot1/2 and PhyA/B), photorespiration (pglp1/2), and photoprotection genes (Lhca5, Lhca7, and PsbS and photolyases), but with a lower abundance of photosynthetic light-harvesting genes (Lhca1/2 and Lhcb1/2). Also, the expression of light-harvesting and photoprotection genes were generally up-regulated by intense light, while the expression of photoreceptor genes was up-regulated by shade. This research highlights how differential plant responses to light shape the vertical structure of plant communities in a subtropical forest. Full article

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29 pages, 3497 KiB

Open AccessReview

Biogeochemical Cycles in Plant–Soil Systems: Significance for Agriculture, Interconnections, and Anthropogenic Disruptions

by Wajid Zaman, Asma Ayaz and Daniel Puppe

Biology 2025, 14(4), 433; https://doi.org/10.3390/biology14040433 - 17 Apr 2025

Abstract

Biogeochemical cycles are fundamental to the functioning of plant–soil systems, driving the availability and transfer of essential nutrients (like carbon (C), nitrogen (N), phosphorus (P), and sulfur (S)) as well as beneficial elements (like silicon (Si)). These interconnected cycles regulate ecosystem productivity, biodiversity, [...] Read more.

Biogeochemical cycles are fundamental to the functioning of plant–soil systems, driving the availability and transfer of essential nutrients (like carbon (C), nitrogen (N), phosphorus (P), and sulfur (S)) as well as beneficial elements (like silicon (Si)). These interconnected cycles regulate ecosystem productivity, biodiversity, and resilience, forming the basis of critical ecosystem services. This review explores the mechanisms and dynamics of biogeochemical C, N, P, S, and Si cycles, emphasizing their roles in nutrient/element cycling, plant growth, and soil health, especially in agricultural plant–soil systems. The coupling between these cycles, facilitated mainly by microbial communities, highlights the complexity of nutrient/element interactions and corresponding implications for ecosystem functioning and stability. Human activities including industrial agriculture, deforestation, and pollution disrupt the underlying natural processes leading to nutrient/element imbalances, soil degradation, and susceptibility to climate impacts. Technological advancements such as artificial intelligence, remote sensing, and real-time soil monitoring offer innovative solutions for studying and managing biogeochemical cycles. These tools enable precise nutrient/element management, identification of ecosystem vulnerabilities, and the development of sustainable practices. Despite significant progress, research gaps remain, particularly in understanding the interlinkages between biogeochemical cycles and their responses to global change. This review underscores the need for integrated approaches that combine interdisciplinary research, technological innovation, and sustainable land-use strategies to mitigate human-induced disruptions and enhance ecosystem resilience. By addressing these challenges, biogeochemical processes and corresponding critical ecosystem services can be safeguarded, ensuring the sustainability of plant–soil systems in the face of environmental change. Full article

(This article belongs to the Special Issue Biogeochemical Element Cycling in Plant–Soil Systems: Implications for Ecosystem Dynamics and Services)

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15 pages, 4531 KiB

Open AccessArticle

RNA Binding to CCRRM of PABPN1 Induces Conformation Change

by Shengping Zhang, Ting Chen, Yunlong Zhang and Changrui Lu

Biology 2025, 14(4), 432; https://doi.org/10.3390/biology14040432 - 17 Apr 2025

Abstract

Poly(A) Binding Protein Nuclear 1 (PABPN1) is a nuclear poly(A)-binding protein that is highly conserved in eukaryotes. It plays multifaceted roles in RNA processing and metabolism, with its dysregulation closely linked to various diseases. PABPN1 contains an alanine-rich N-terminus, a central coiled-coil domain [...] Read more.

Poly(A) Binding Protein Nuclear 1 (PABPN1) is a nuclear poly(A)-binding protein that is highly conserved in eukaryotes. It plays multifaceted roles in RNA processing and metabolism, with its dysregulation closely linked to various diseases. PABPN1 contains an alanine-rich N-terminus, a central coiled-coil domain (CC), a conserved RNA recognition motif (RRM) and a C-terminal extension. PABPN1 influences mRNA splicing and stability through its RNA-binding capabilities, thereby modulating gene expression. While PABPN1 is known to interact with RNA, the molecular mechanism underlying this interaction with RNA awaits further investigation. Here, we designed and purified a PABPN1 fragment encompassing the RNA-binding domain (CCRRM fragment, amino acids 114–254). Using a combination of 3D modeling, small-angle X-ray scattering (SAXS) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) assay, our result indicated that CCRRM exhibits a high affinity for poly(A) RNA, a moderate affinity for GU-rich and CU-rich sequences, and negligible binding to AU-rich and CA-rich sequences. RNA binding induces conformation change in the CC. These results suggest that PABPN1 could potentially be involved in cytoplasmic polyadenylation and may influence the regulation of mRNA translation and degradation, although further investigation is required to confirm this role. Full article

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

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23 pages, 10812 KiB

Open AccessArticle

Discovery of Genomic Targets and Therapeutic Candidates for Liver Cancer Using Single-Cell RNA Sequencing and Molecular Docking

by Biplab Biswas, Masahiro Sugimoto and Md. Aminul Hoque

Biology 2025, 14(4), 431; https://doi.org/10.3390/biology14040431 - 17 Apr 2025

Abstract

Liver cancer is one of the most common malignancies and the second leading cause of cancer-related deaths worldwide, particularly in developing countries, where it poses a significant financial burden. Early detection and timely treatment remain challenging due to the complex mechanisms underlying the [...] Read more.

Liver cancer is one of the most common malignancies and the second leading cause of cancer-related deaths worldwide, particularly in developing countries, where it poses a significant financial burden. Early detection and timely treatment remain challenging due to the complex mechanisms underlying the initiation and progression of liver cancer. This study aims to uncover key genomic features, analyze their functional roles, and propose potential therapeutic drugs identified through molecular docking, utilizing single-cell RNA sequencing (scRNA-seq) data from liver cancer studies. We applied two advanced hybrid methods known for their robust identification of differentially expressed genes (DEGs) regardless of sample size, along with four top-performing individual methods. These approaches were used to analyze four scRNA-seq datasets, leading to the identification of essential DEGs. Through a protein−protein-interaction (PPI) network, we identified 25 hub-of-hub genes (hHubGs) and 20 additional hHubGs from two naturally occurring gene clusters, ultimately validating a total of 36 hHubGs. Functional, pathway, and survival analyses revealed that these hHubGs are strongly linked to liver cancer. Based on molecular docking and binding-affinity scores with 36 receptor proteins, we proposed 10 potential therapeutic drugs, which we selected from a pool of 300 cancer meta-drugs. The choice of these drugs was further validated using 14 top-ranked published receptor proteins from a set of 42. The proposed candidates include Adozelesin, Tivozanib, NVP-BHG712, Nilotinib, Entrectinib, Irinotecan, Ponatinib, and YM201636. This study provides critical insights into the genomic landscape of liver cancer and identifies promising therapeutic candidates, serving as a valuable resource for advancing liver cancer research and treatment strategies. Full article

(This article belongs to the Section Cancer Biology)

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20 pages, 4211 KiB

Open AccessArticle

The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis

by Hélène Laguerre, Cyril Noël, Camille Jégou, Yannick Fleury and Patrick Le Chevalier

Biology 2025, 14(4), 430; https://doi.org/10.3390/biology14040430 - 16 Apr 2025

Abstract

In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the [...] Read more.

In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential “specific” microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio. Full article

(This article belongs to the Special Issue Current Advances in Echinoderm Research)

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31 pages, 9950 KiB

Open AccessArticle

Effects of Low and High Doses of Deoxynivalenol on Growth Performance, Blood Biochemistry, Histology, Metabolites, and Microbial Community in Adult Rats

by Jinyoung Jeong, Junsik Kim, Boram Lee, Cheolju Park and Minseok Kim

Biology 2025, 14(4), 429; https://doi.org/10.3390/biology14040429 - 16 Apr 2025

Abstract

Deoxynivalenol (DON) is a widespread mycotoxin which contaminates several crops, including maize, wheat, and barley. In this study, we investigated the effects of orally administered DON on growth performance, blood biochemistry, histology, the gut microbiome, and metabolism in rats. Six-week-old rats, acclimatized for [...] Read more.

Deoxynivalenol (DON) is a widespread mycotoxin which contaminates several crops, including maize, wheat, and barley. In this study, we investigated the effects of orally administered DON on growth performance, blood biochemistry, histology, the gut microbiome, and metabolism in rats. Six-week-old rats, acclimatized for one week, were subjected to different dietary treatments for 42 days, as follows: CON (control): 0.9% saline; T1: 0.5 ppm DON; T2: 50 ppm DON; and T3: 100 ppm DON. The T3 group had the lowest final body weight (298.5 ± 3.69 g) and average daily gain compared with the control group (338.9 ± 6.43 g, p < 0.05). The feed conversion ratio was highest in the T3 group (4.28 ± 0.28) compared with that in the control group (3.12 ± 0.13, p < 0.05). DON treatment significantly reduced serum levels of creatinine, amylase, urea nitrogen, and alkaline phosphatase, but not alanine aminotransferase. Fibrosis and apoptosis were exacerbated in various tissues with increasing DON concentration. The metabolite profiles of several tissues were significantly different in the DON-treated and control groups. In the cecum, DON treatment increased the abundance of Desulfobacteria, while decreasing that of Firmicutes. Our results indicate that DON levels above the maximum residue limit have serious health consequences for animals. Full article

(This article belongs to the Special Issue Gut Microbiome in Health and Disease (2nd Edition))

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29 pages, 4075 KiB

Open AccessReview

Osteopontin in Chronic Inflammatory Diseases: Mechanisms, Biomarker Potential, and Therapeutic Strategies

by Fuyuan Lang, Yuanheng Li, Ruizhe Yao and Meixiu Jiang

Biology 2025, 14(4), 428; https://doi.org/10.3390/biology14040428 - 16 Apr 2025

Abstract

Chronic inflammatory diseases, such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis (MS), atherosclerosis, and inflammatory bowel disease (IBD), pose major global health concerns. These disorders are marked by persistent inflammation, immune system dysfunction, tissue injury, and fibrosis, ultimately leading to [...] Read more.

Chronic inflammatory diseases, such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis (MS), atherosclerosis, and inflammatory bowel disease (IBD), pose major global health concerns. These disorders are marked by persistent inflammation, immune system dysfunction, tissue injury, and fibrosis, ultimately leading to severe organ dysfunction and diminished quality of life. Osteopontin (OPN), a multifunctional extracellular matrix protein, plays a crucial role in immune regulation, inflammation, and tissue remodeling. It promotes immune cell recruitment, stimulates pro-inflammatory cytokine production, and contributes to fibrosis through interactions with integrins and CD44 receptors. Additionally, OPN activates key inflammatory pathways, including NF-κB, MAPK, and PI3K/Akt, further aggravating tissue damage in chronic inflammatory conditions. Our review highlights the role of OPN in chronic inflammation, its potential as a biomarker, and its therapeutic implications. We explore promising preclinical approaches, such as monoclonal antibodies, small molecule inhibitors, and natural compounds like curcumin, which have demonstrated potential in mitigating OPN-driven inflammation. However, challenges persist in selectively targeting OPN while maintaining its essential physiological roles, including bone remodeling and wound healing. Our review offers insights into therapeutic strategies and future research directions. Full article

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14 pages, 1441 KiB

Open AccessCase Report

Ticking Down Sodium Levels—An Atypical Link Between Chronic Hyponatremia and Borreliosis

by Raluca Maria Vlad, Carmen Vasile and Alexandra Mirică

Biology 2025, 14(4), 427; https://doi.org/10.3390/biology14040427 - 16 Apr 2025

Abstract

Lyme disease (LD), caused by the spirochete Borrelia burgdorferi, is the most prevalent tick-borne disease in Europe, including Romania, where endemic areas are well documented. It has a wide range of clinical manifestations and severity, including rare neurological complications. Persistent hyponatremia is [...] Read more.

Lyme disease (LD), caused by the spirochete Borrelia burgdorferi, is the most prevalent tick-borne disease in Europe, including Romania, where endemic areas are well documented. It has a wide range of clinical manifestations and severity, including rare neurological complications. Persistent hyponatremia is an atypical presentation of Lyme neuroborreliosis and can be associated with the syndrome of inappropriate antidiuretic hormone secretion (SIADH). SIADH is characterized by unregulated antidiuretic hormone release, leading to impaired water excretion, dilutional hyponatremia, and low serum osmolality. We report the case of a 16-year-old female with clinically well-tolerated, but severe, refractory hyponatremia, who was poorly responsive to intravenous sodium supplementation and fluid management. Complex investigations ruled out multiple causes of hyponatremia; neuroborreliosis was confirmed via positive Borrelia serologies, despite the absence of a suggestive history of exposure. SIADH likely symptomatology resulted from central nervous system inflammation induced by Borrelia, a mechanism rarely documented in the medical literature. Treatment with antibiotics and fluid restriction led to a gradual improvement in fluid balance and sodium homeostasis. This case emphasizes the importance of considering rare infectious causes, such as LD, in patients with unexplained SIADH, especially in endemic areas. It highlights the importance of a multidisciplinary approach in intricate, complex cases. Full article

(This article belongs to the Special Issue Zoonotic Diseases)

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Graphical abstract

11 pages, 892 KiB

Open AccessArticle

Visualization of Runs of Homozygosity and Classification Using Convolutional Neural Networks

by Siroj Bakoev, Maria Kolosova, Timofey Romanets, Faridun Bakoev, Anatoly Kolosov, Elena Romanets, Anna Korobeinikova, Ilona Bakoeva, Vagif Akhmedli and Lyubov Getmantseva

Biology 2025, 14(4), 426; https://doi.org/10.3390/biology14040426 - 16 Apr 2025

Abstract

Runs of homozygosity (ROH) are key elements of the genetic structure of populations, reflecting inbreeding levels, selection history, and potential associations with phenotypic traits. This study proposes a novel approach to ROH analysis through visualization and classification using convolutional neural networks (CNNs). Genetic [...] Read more.

Runs of homozygosity (ROH) are key elements of the genetic structure of populations, reflecting inbreeding levels, selection history, and potential associations with phenotypic traits. This study proposes a novel approach to ROH analysis through visualization and classification using convolutional neural networks (CNNs). Genetic data from Large White (n = 568) and Duroc (n = 600) pigs were used to construct ROH maps, where each homozygous segment was classified by length and visualized as a color-coded image. The analysis was conducted in two stages: (1) classification of animals by breed based on ROH maps and (2) identification of the presence or absence of a phenotypic trait (limb defects). Genotyping was performed using the GeneSeek^® GGP SNP80x1_XT chip (Illumina Inc., San Diego, CA, USA), and ROH segments were identified using the software tool PLINK v1.9. To visualize individual maps, we utilized a modified function from the HandyCNV package. The results showed that the CNN model achieved 100% accuracy, sensitivity, and specificity in classifying pig breeds based on ROH maps. When analyzing the binary trait (presence or absence of limb defects), the model demonstrated an accuracy of 78.57%. Despite the moderate accuracy in predicting the phenotypic trait, the high negative predictive value (84.62%) indicates the model’s reliability in identifying healthy animals. This method can be applied not only in animal breeding research but also in medicine to study the association between ROH and hereditary diseases. Future plans include expanding the method to other types of genetic data and developing mechanisms to improve the interpretability of deep learning models. Full article

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

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19 pages, 6343 KiB

Open AccessArticle

Design, Screening, and Impact of sgRNAs Targeting Bovine Prolactin Gene Receptor on Embryonic Development Using Stably Transfected Cell Lines

by Daqing Wang, Guifang Cao, Xin Li, Xin Cheng, Zhihui Guo, Lu Li, Hong Su, Kai Zhang, Yuanyuan Zhang, Min Zhang, Feifei Zhao, Yifan Zhao, Junxi Liang, Yiyi Liu and Yong Zhang

Biology 2025, 14(4), 425; https://doi.org/10.3390/biology14040425 - 15 Apr 2025

Abstract

This study designed three sgRNAs (sgRNA139, sgRNA128, and sgRNA109) targeting the prolactin gene receptor (PRLR) in fetal cattle, utilized Cas9 to cleave endogenous DNA, and screened stable cell lines for somatic cell nuclear transfer experiments to investigate the impact of different editing sites [...] Read more.

This study designed three sgRNAs (sgRNA139, sgRNA128, and sgRNA109) targeting the prolactin gene receptor (PRLR) in fetal cattle, utilized Cas9 to cleave endogenous DNA, and screened stable cell lines for somatic cell nuclear transfer experiments to investigate the impact of different editing sites on embryonic development. The results showed that sgRNA139 had the highest cleavage efficiency (Fcut = 0.65, Indels = 42.19%), while sgRNA109 had the lowest (Fcut = 0.45, Indels = 35.31%). No significant differences were observed in cell growth status after electroporation (p > 0.05), and the transfection efficiency exceeded 90% after five days of culture. In the evaluation of key embryonic development indicators, sgRNA109 significantly reduced the cleavage rate and blastocyst rate (p < 0.01), whereas sgRNA139 showed no significant effect on the cleavage rate (p > 0.05), but its blastocyst rate was slightly lower than that of the control group (p > 0.05). This study demonstrates that highly specific sgRNAs and stable edited cell lines used as donor cells can significantly regulate the later stages of embryonic development. This study not only provides new experimental evidence for the functional study of the PRLR but also lays an important theoretical foundation for the innovation of molecular breeding technologies in dairy cattle. Full article

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16 pages, 3296 KiB

Open AccessArticle

miR-4428 and miR-185-5p as Key Modulators of Insulin Sensitivity and Glucose Homeostasis: Insights into Pathways and Therapeutic Potential in Type 2 Diabetes Mellitus

by Yanisa Rattanapan, Thitinat Duangchan, Thaveesak Sai-ong and Takol Chareonsirisuthigul

Biology 2025, 14(4), 424; https://doi.org/10.3390/biology14040424 - 15 Apr 2025

Abstract

Type 2 Diabetes Mellitus (T2DM) is a chronic metabolic disorder characterized by insulin resistance and dysregulation of glucose metabolism. MicroRNAs (miRNAs) such as miR-4428 and miR-185-5p play critical roles in post-transcriptional regulation of genes involved in these processes, but their specific contributions to [...] Read more.

Type 2 Diabetes Mellitus (T2DM) is a chronic metabolic disorder characterized by insulin resistance and dysregulation of glucose metabolism. MicroRNAs (miRNAs) such as miR-4428 and miR-185-5p play critical roles in post-transcriptional regulation of genes involved in these processes, but their specific contributions to T2DM pathogenesis remain unclear. Plasma samples from T2DM patients and non-diabetic controls were analyzed for miR-4428 and miR-185-5p expression using microarray and bioinformatics tools. Target genes were predicted, and pathway enrichment analysis was performed to explore biological roles. Differential expression analysis revealed a 2.3-fold upregulation of miR-4428 and a 14.4-fold downregulation of miR-185-5p in T2DM patients compared to controls. Predicted targets such as ADAR, KLF9, and SOGA1 were linked to glucose metabolism and insulin signaling pathways. Enrichment analysis highlighted associations with neuronal signaling, chromatin remodeling, and metabolic regulation pathways. miR-4428 and miR-185-5p regulate critical insulin sensitivity and glucose metabolism pathways, making them promising biomarkers and therapeutic targets for managing T2DM. Future studies should validate these findings experimentally to advance miRNA-based interventions for T2DM and its complications. Full article

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

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21 pages, 3640 KiB

Open AccessArticle

Postfire Scenarios Shape Dung Beetle Communities in the Orinoquía Riparian Forest–Savannah Transition

by Carlos Julián Moreno-Fonseca, Walter Garcia-Suabita and Dolors Armenteras-Pascual

Biology 2025, 14(4), 423; https://doi.org/10.3390/biology14040423 - 15 Apr 2025

Abstract

The Orinoquía region of Colombia includes diverse ecosystems such as riparian forests and seasonal savannas, which play vital roles as biodiversity reservoirs. However, increased fire activity, driven by both natural and anthropogenic pressures, poses mounting threats to these ecosystems. Despite their importance, the [...] Read more.

The Orinoquía region of Colombia includes diverse ecosystems such as riparian forests and seasonal savannas, which play vital roles as biodiversity reservoirs. However, increased fire activity, driven by both natural and anthropogenic pressures, poses mounting threats to these ecosystems. Despite their importance, the effects of fire on faunal communities, especially in transitional habitats, are not well understood. Understanding biodiversity responses to fire across different recovery stages is essential for conservation planning. This study aimed to assess the effects of fire occurrence and recovery time on dung beetle communities as an indicator of ecosystem resilience. We analyzed taxonomic responses—including species richness, abundance, and Hill diversity indices (D₀, D₁, D₂)—as well as functional traits such as guild richness, biomass, and food relocation behavior, across riparian forest–savanna ecotones under varying fire histories. Our results indicate that recent fires (≤1 year) and high fire frequencies (4–5 events) negatively affect species diversity and abundance. Dominance by a few disturbance-tolerant species, such as Digitonthophagus gazella, was observed in burned savannas, while forest habitats supported both rare and dominant taxa. Despite taxonomic declines, functional redundancy was maintained, largely due to the prevalence of small-bodied species. However, we observed a general resilience effect in which core species contributed to postfire community reassembly. Functional redundancy was maintained, with small dung beetles dominating the biomass and guild composition. The conservation status of transitional habitats, particularly the forest–savanna ecotone, played a critical role in postfire dung beetle community restructuring. The presence of resilient assemblages highlights the importance of dung beetles in sustaining key ecosystem functions following fire events. These findings underscore the potential of dung beetles as bioindicators for postfire monitoring and emphasize the need for improved fire management strategies in sensitive ecosystems. Full article

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

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19 pages, 2437 KiB

Open AccessArticle

Space and Time Dynamics of Honeybee (Apis mellifera L.)-Melliferous Resource Interactions Within a Foraging Area: A Case Study in the Banja Luka Region (Bosnia & Herzegovina)

by Samuel Laboisse, Michel Vaillant, Clovis Cazenave, Biljana Kelečević, Iris Chevalier and Ludovic Andres

Biology 2025, 14(4), 422; https://doi.org/10.3390/biology14040422 - 15 Apr 2025

Abstract

Interactions between honeybees and the environment are often difficult to achieve, particularly when the purpose is to optimize beekeeping production. The present study proposed to monitor the space-time variations of melliferous resources potentially exploited by colonies within a foraging area in Bosnia & [...] Read more.

Interactions between honeybees and the environment are often difficult to achieve, particularly when the purpose is to optimize beekeeping production. The present study proposed to monitor the space-time variations of melliferous resources potentially exploited by colonies within a foraging area in Bosnia & Herzegovina, characterized by contrasting landscapes. The combination of methods involving Geographical Information Systems, floristic monitoring, and modelling enabled honey production potential to be calculated for the entire foraging area. In particular, the location of taxa, their abundance, diversity, and phenology enabled us to determine the spatial distribution and temporal variation of production potential. Robinia pseudoacacia and Rubus sp. made a major contribution. This potential was highly contrasted, with distant areas from the apiary more attractive than closer ones, depending on the moment. Specific periods, such as June were particularly conducive to establishing a high potential. Forest and grassland played a major role in the temporal succession, mainly because of the area covered, but moments with lower potential were supported by specific land uses (orchards). Land uses with a small surface area, such as orchards, wasteland, and riparian zones had a high potential per unit area, and improving the production potential within a foraging area could involve increasing these specific surfaces. Full article

(This article belongs to the Special Issue Pollination Biology)

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35 pages, 3639 KiB

Open AccessArticle

Virgulinella fragilis in the North Adriatic Coastal Sediments: A New Non-Indigenous Benthic Foraminiferal Taxon?

by Roberta D’Onofrio, Maria Letizia Vitelletti, Francesco Riminucci, Veronica Rossi and Lucilla Capotondi

Biology 2025, 14(4), 421; https://doi.org/10.3390/biology14040421 - 14 Apr 2025

Abstract

The Mediterranean Sea is considered a hotspot for bioinvaders. Nonetheless, information on non-indigenous benthic foraminifera is still fragmented. This study documents for the first time the presence along the northwestern Adriatic coast of the non-indigenous benthic foraminifera species Virgulinella fragilis, Grindell and [...] Read more.

The Mediterranean Sea is considered a hotspot for bioinvaders. Nonetheless, information on non-indigenous benthic foraminifera is still fragmented. This study documents for the first time the presence along the northwestern Adriatic coast of the non-indigenous benthic foraminifera species Virgulinella fragilis, Grindell and Collen (1976). Due to the low abundance recorded in the study area, the presence of this species may represent an early colonization phase. We discuss the temporal and spatial patterns of V. fragilis arrival in the Mediterranean and Adriatic Seas, and we hypothesize stowaway transport (via ship fouling or ballast water) as the main introduction pathway. Morphological test analyses suggest that V. fragilis prefers a low oxygen content, consistent with the ecological requirements reported for this taxon in the literature. The application of Maximum Entropy (MaxEnt) modeling indicates that the key factor influencing the presence of V. fragilis in the Mediterranean basin is the bacterial concentration expressed as NO₃. Projections under future climate scenarios (RCP 4.5) point to a decline of habitat suitability conditions, making widespread invasion unlikely in the Mediterranean. We emphasize the importance of continuous biomonitoring for early detection of alien species, improving our understanding of invasion dynamics and enabling prompt conservation actions, especially in regions impacted by anthropogenic activities. Full article

(This article belongs to the Special Issue Alien Marine Species in the Mediterranean Sea)

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6 pages, 385 KiB

Open AccessCommentary

A Novel Approach to Relocate Misplaced Proteins in Cells

by Grace Hohman, Ava Watson and Mohamed A. Eldeeb

Biology 2025, 14(4), 420; https://doi.org/10.3390/biology14040420 - 14 Apr 2025

Abstract

Proper cellular function hinges on appropriate subcellular protein localization. When cellular proteins become mislocalized, they can accumulate, cause cellular damage, and disrupt many biochemical and cellular processes. Notably, mislocalized protein accumulation and the resulting cytotoxic effects are salient features of neurodegenerative diseases including [...] Read more.

Proper cellular function hinges on appropriate subcellular protein localization. When cellular proteins become mislocalized, they can accumulate, cause cellular damage, and disrupt many biochemical and cellular processes. Notably, mislocalized protein accumulation and the resulting cytotoxic effects are salient features of neurodegenerative diseases including Alzheimer’s, Parkinson’s disease, and ALS. The detrimental cellular consequences of mislocalized proteins accumulation make it crucial to develop techniques and approaches that counteract this malfunction. Remarkably, a recent study by Ng et al. introduced targeted relocalization-activating molecules (TRAMs) as a novel molecular tool for relocalizing endogenous target proteins to counteract disease-associated mislocalized proteins. The authors developed a quantitative single-cell analysis to evaluate the strength and relocalization capability of TRAMs by coupling a target protein and a shuttle protein. Herein, we briefly highlight and discuss the potential molecular implications for targeted protein relocalization as an effective approach for correcting mislocalized proteins. Full article

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

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16 pages, 1590 KiB

Open AccessArticle

Environmental Effects on the Ecological Carrying Capacity of Marine Ranching in the Northern South China Sea

by Ziwen Wang, Lijun Yao, Jing Yu, Yuxiang Chen, Xue Feng and Pimao Chen

Biology 2025, 14(4), 419; https://doi.org/10.3390/biology14040419 - 14 Apr 2025

Abstract

The marine ecological carrying capacity (MECC) of marine ranching serves as a crucial indicator for assessing the conservation effect of fishery resources and forms a significant basis for scientific management of coastal fisheries. The environmental impacts on the MECC of marine ranching in [...] Read more.

The marine ecological carrying capacity (MECC) of marine ranching serves as a crucial indicator for assessing the conservation effect of fishery resources and forms a significant basis for scientific management of coastal fisheries. The environmental impacts on the MECC of marine ranching in the northern South China Sea were analyzed quantitatively by employing Generalized Additive Models (GAMs), which have been successfully applied to the study of the relationship between fishery resources and environmental factors, and factor analysis, using satellite and survey observations. Results showed that 95.40% of the total variation in MECC was explained by these factors. Based on the GAMs, the most important factor was Year (calendar years), with a contribution of 66.20%, followed by Chlorophyll a concentration (Chl-a), Sea Surface Temperature (SST), Dissolved Inorganic Nitrogen (DIN) and Water Current, with contributions of 20.60%, 4.40%, 3.60%, and 0.60%, respectively. The findings of this study inspire us to establish a long-term marine ranching resource and environment monitoring platform, and an early warning and forecasting expert decision-making system, providing scientific references for planning and management of coastal marine ranching. Full article

(This article belongs to the Section Ecology)

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20 pages, 37059 KiB

Open AccessArticle

Influence of Variation in Hind Leg Structure of Auchenorrhyncha on Their Jumping Performance

by Yifei Xu, Christopher H. Dietrich and Wu Dai

Biology 2025, 14(4), 418; https://doi.org/10.3390/biology14040418 - 13 Apr 2025

Abstract

Four species representing four different families of the hemipteran insect suborder Auchenorrhyncha, Lepyronia coleoptrata (Aphrophoridae), Euricania ocellus (Ricaniidae), Kolla sp. (Cicadellidae) and Tricentrus sp. (Membracidae) were investigated using high-speed photography and scanning electron microscopy to identify hind leg structures that may influence jumping [...] Read more.

Four species representing four different families of the hemipteran insect suborder Auchenorrhyncha, Lepyronia coleoptrata (Aphrophoridae), Euricania ocellus (Ricaniidae), Kolla sp. (Cicadellidae) and Tricentrus sp. (Membracidae) were investigated using high-speed photography and scanning electron microscopy to identify hind leg structures that may influence jumping performance. The coxa–trochanteral joint, femur and tibia were found to have distinct structural adaptations that vary among these jumping insects. Froghoppers and planthoppers possess a coxal protrusion which is absent in leafhoppers and treehoppers, the latter featuring a more recessed coxal fossa. The medial coxae of these insects exhibit fields of microtrichia that vary in density and fine structure. Medial gears on the trochanters of Tricentrus sp. are implicated in the storage of energy prior to their jumps. These structural differences manifest in the insects’ jumping performance. The study demonstrated a correlation between the robustness of the microtrichia field interaction and the insect’s jumping capability. Specifically, leafhoppers, equipped with a pair of rivet-like structures connecting the hind coxae, were observed to achieve quicker and more stable take-offs. The study reveals that structural variations in the hind legs of Auchenorrhyncha species significantly influence their jumping performance, with implications for both efficiency and stability. Full article

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