Biology

15 pages, 9108 KiB

Open AccessStudy Protocol

Habitat Suitability Shifts of Eucommia ulmoides in Southwest China Under Climate Change Projections

by Qi Liu, Longjiang Liu, Juan Xue, Peiyao Shi and Shanshan Liang

Biology 2025, 14(4), 451; https://doi.org/10.3390/biology14040451 - 21 Apr 2025

As a Chinese endemic species with dual medicinal–industrial importance, Eucommia ulmoides faces habitat challenges under climate change. Using 21 bioclimatic variables and 704 occurrence records, we modeled current and future (2021–2100) distributions via MaxEnt 3.4.4 and ArcGIS 10.8. The results indicate the following: [...] Read more.

As a Chinese endemic species with dual medicinal–industrial importance, Eucommia ulmoides faces habitat challenges under climate change. Using 21 bioclimatic variables and 704 occurrence records, we modeled current and future (2021–2100) distributions via MaxEnt 3.4.4 and ArcGIS 10.8. The results indicate the following: (1) current optimal habitats cluster in the mid-elevation valleys of Daba–Wuling Mountains (Guizhou–Chongqing core); (2) SSP5-8.5 projections suggest a 19.2% reduction in high-suitability areas by 2081–2100 versus SSP1-2.6; and (3) distribution centroids migrate southward under both scenarios. Our multi-temporal analysis provides actionable intelligence for ex situ conservation and agroforestry planning. Full article

► Show Figures

Graphical abstract

12 pages, 1070 KiB

Open AccessArticle

Seminal F₂-IsoP and RvD1 Levels in Idiopathic Infertile Men

by Elena Moretti, Giulia Collodel, Caterina Marcucci, Laura Liguori, Laura Gambera and Cinzia Signorini

Biology 2025, 14(4), 450; https://doi.org/10.3390/biology14040450 - 21 Apr 2025

Abstract

30 percent of infertile men are diagnosed with idiopathic infertility. This study aimed to assess oxidative stress in the semen of 77 patients with idiopathic infertility by measuring F₂-isoprostane (F₂-IsoP), resolvin D1 (RvD1) levels, and semen parameters. The presence [...] Read more.

30 percent of infertile men are diagnosed with idiopathic infertility. This study aimed to assess oxidative stress in the semen of 77 patients with idiopathic infertility by measuring F₂-isoprostane (F₂-IsoP), resolvin D1 (RvD1) levels, and semen parameters. The presence and localization of 8-IsoProstaglandin F_2α were determined using immunofluorescence. No significant correlations were observed for F₂-IsoP and RvD1 levels with the semen variables. Based on F₂-IsoP levels, individuals were classified into two groups: Group 1 (F₂-IsoPs ≤ 29.96 ng/mL, 51%) and Group 2 (F₂-IsoPs > 29.96 ng/mL, 49%). In comparison to Group 1, Group 2 showed significantly higher F₂-IsoP levels (13.33 ng/mL vs. 44.80 ng/mL; p < 0.05), a lower progressive motility percentage (30% vs. 25%; p < 0.05), and increased RvD1 levels (36.09% vs. 44.94%). Immunofluorescence analysis revealed a different localization of 8-IsoProstaglandin F_2α in the ejaculated sperm of Group 1 compared to that observed in Group 2. A weak signal was detected in the sperm tail (Group 1, 79.1% vs. Group 2, 36.9; p < 0.01). In spermatozoa of Group 2 patients, a strong signal in the acrosome, midpiece, and tail was highlighted. These findings suggest the need to test oxidative stress during routine semen analysis in patients with idiopathic infertility to improve diagnosis and treatment. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

► Show Figures

Figure 1

12 pages, 2110 KiB

Open AccessArticle

Genetic Diversity and Structure of Korean Pacific Oyster (Crassostrea gigas) for Determining Selective Breeding Groups

by Kang-Rae Kim, Dain Lee, Kyung-Hee Kim, Hyun Chul Kim, So Hee Kim, Su Jin Park and Deok-Chan Lee

Biology 2025, 14(4), 449; https://doi.org/10.3390/biology14040449 - 21 Apr 2025

Abstract

This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas [...] Read more.

This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas was relatively low. Analysis using AMOVA, genetic differentiation, and DAPC revealed a genetic structure that was consistent with one group. This study identified reference populations to be used for selective breeding to increase the genetic diversity of Korean C. gigas and provided essential data on genetic diversity and structure for future selective breeding efforts in C. gigas. Full article

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

► Show Figures

Figure 1

21 pages, 3935 KiB

Open AccessArticle

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Hippophae salicifolia

by Zhefei Zeng, Chunmin Mao, Zhuo Shang, Ngawang Norbu, Ngawang Bonjor, Xiaoyan Jia, Wei Li, Wenju Zhang, Junwei Wang and La Qiong

Biology 2025, 14(4), 448; https://doi.org/10.3390/biology14040448 - 20 Apr 2025

Abstract

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 [...] Read more.

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 tRNA, three rRNA, and three pseudogenes). We identified extensive repetitive elements, including 188 SSRs, 20 tandem repeats, and 455 dispersed repeats, and explored their potential roles in genome evolution. Codon usage analysis showed a bias for codons ending in A or U, while RNA editing analysis revealed 415 sites that mostly convert hydrophilic to hydrophobic amino acids. Phylogenetic and collinearity analyses clarified evolutionary relationships within Hippophae and uncovered genome rearrangements. In addition, extensive gene transfer was detected between the mitochondrial and chloroplast genomes. Ka/Ks and nucleotide diversity analyses indicate that most genes are under purifying selection, with some possibly undergoing positive selection. Overall, these findings enhance our understanding of the structural and evolutionary features of the H. salicifolia mitochondrial genome and provide valuable insights for the genetic improvement and conservation of Hippophae species. Full article

► Show Figures

Figure 1

15 pages, 906 KiB

Open AccessArticle

Effects of Varying Dietary Concentrations of Menadione Nicotinamide Bisulphite (VK₃) on Growth Performance, Muscle Composition, Liver and Muscle Menaquinone-4 Concentration, and Antioxidant Capacities of Coho Salmon (Oncorhynchus kisutch) Alevins

by Han Zhang, Leyong Yu, Abdur Rahman, Sattanathan Govindharajan, Lingyao Li, Hairui Yu and Muhammad Waqas

Biology 2025, 14(4), 447; https://doi.org/10.3390/biology14040447 - 20 Apr 2025

Abstract

Vitamin K₃ (VK₃) is an essential micronutrient for fish growth and metabolism. To determine the optimal required dietary concentration of VK, a 12-week-long trial was planned to investigate the impact of VK₃ on growth performance, muscle composition, liver menaquinone-4 [...] Read more.

Vitamin K₃ (VK₃) is an essential micronutrient for fish growth and metabolism. To determine the optimal required dietary concentration of VK, a 12-week-long trial was planned to investigate the impact of VK₃ on growth performance, muscle composition, liver menaquinone-4 (MK-4), whole-body MK-4 concentration, and antioxidant capacity (T-AOC) in coho salmon alevins. A total of 2100 coho salmon alevins were divided into twenty-one tanks, with 100 alevins in each tank, and three tanks represented one group. Each of the seven groups were randomly assigned to one of the experimental diets formulated with varying levels of menadione nicotinamide bisulphite (VK₃), i.e., 0.16 (control), 5.25, 10.22, 14.93, 20.51, 40.09, and 59.87 mg/kg, respectively. The results revealed that the inclusion of VK₃ from 5.25 to 40.09 mg/kg improved (p < 0.05) the survival rate (SR), weight gain (WG), specific growth rate (SGR), and feed conversion ratio (FCR), while no effect (p > 0.05) was observed on the hepatosomatic index (HSI), viscerosomatic index (VSI), Fulton’s condition factor (K), and muscle composition. The whole-body MK-4, liver MK-4, liver T-AOC, total superoxide dismutase (T-SOD), and catalase (CAT) enzymes were also increased (p < 0.05). Malondialdehyde (MDA) contents were reduced (p < 0.05) in all supplemented groups with a decreasing trend. The predicted optimal required dietary concentrations of VK₃ were found to be 34.0, 43.5, 38.54, and 31.97 mg/kg based on WG, SGR, liver MK-4 concentration, and T-AOC, respectively, by quadratic regression analysis. It is concluded that the dietary VK₃ has improved the growth performance and antioxidant status in alevins during early development in the range of 31.97 to 43.5 mg/kg diet. Full article

(This article belongs to the Special Issue Nutrition, Environment, and Fish Physiology)

► Show Figures

Figure 1

20 pages, 7607 KiB

Open AccessArticle

Identification of the Dof Gene Family in Quinoa and Its Potential Role in Regulating Flavonoid Synthesis Under Different Stress Conditions

by Guangtao Qian, Jinrong Yang, Mingyu Wang and Lixin Li

Biology 2025, 14(4), 446; https://doi.org/10.3390/biology14040446 - 20 Apr 2025

Abstract

Quinoa (Chenopodium quinoa Willd.), often referred to as the “golden grain”, is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, [...] Read more.

Quinoa (Chenopodium quinoa Willd.), often referred to as the “golden grain”, is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, antiviral, anticancer, and antidepressant properties. The DNA binding with one finger (Dof) transcription factor is crucial for regulating growth, development, and stress responses. However, the identification of the Dof family using the latest quinoa genomic data and its function in abiotic stress response have not been fully elucidated. Here, 36 CqDof genes were identified from the quinoa genome and classified into ten subfamilies through phylogenetic analysis. Physicochemical property analysis predicted that CqDofs predominantly encode basic, hydrophilic, and unstable nuclear proteins. CqDofs were distributed across 15 chromosomes, with segmental duplication being the primary driver of their expansion. Subsequently, basic information on CqDofs was systematically analyzed, including conserved motifs, gene structure, cis-acting elements, and expression patterns. Notably, the promoter regions of all CqDof genes were enriched with cis-acting elements related to light responsiveness. Further analysis revealed that red and blue light significantly affected CqDof expression and flavonoid accumulation (epigallocatechin, rutin, naringenin, morin, pinocembrin, quercetin-7-O-rutinoside, quercetin-3-O-glucoside, and naringenin), in which 5 CqDofs exhibited a pronounced response to both light conditions and showed a significant correlation with flavonoid levels. Finally, RT-PCR analysis indicated that the expression levels of CqDofs (except CqDof21) were significantly upregulated under drought, salt, and saline-alkali stresses. These findings lay the groundwork for future studies on how CqDofs regulate flavonoid biosynthesis under different light qualities and function in abiotic stress. Full article

► Show Figures

Figure 1

19 pages, 3360 KiB

Open AccessArticle

CRISPR/Cas9-Mediated Development of Potato Varieties with Long-Term Cold Storage and Bruising Resistance

by Gabriela Alejandra Massa, Cecilia Andrea Décima Oneto, Matías Nicolás González, Anabela Poulsen Hornum, Ailín Arizmendi, Sofía Sucar, Silvina Beatriz Divito and Sergio Enrique Feingold

Biology 2025, 14(4), 445; https://doi.org/10.3390/biology14040445 - 20 Apr 2025

Abstract

Enzymatic browning and cold-induced sweetening (CIS) affect the post-harvest quality of potato tubers. Browning is caused by polyphenol oxidase 2 (PPO2), which is activated by mechanical damage during harvest and storage. CIS occurs when vacuolar invertase converts sucrose into reducing sugars, which react [...] Read more.

Enzymatic browning and cold-induced sweetening (CIS) affect the post-harvest quality of potato tubers. Browning is caused by polyphenol oxidase 2 (PPO2), which is activated by mechanical damage during harvest and storage. CIS occurs when vacuolar invertase converts sucrose into reducing sugars, which react with amino acids during frying, forming brown pigments and acrylamide. While cold storage prevents sprouting and disease, it also increases vacuolar invertase expression, leading to quality loss. Using CRISPR/Cas9, we developed gene-edited potato lines with improved resistance to browning and CIS. Line 6A (cv. Atlantic) and E03-3 (cv. Spunta) exhibited complete vacuolar invertase (InvVac) knockout, maintaining chip quality for at least 60 days at 4 °C. Line 6A, renamed PIRU INTA, was tested in field trials and preserved frying quality for up to 90 days under cold storage. PIRU INTA is currently undergoing registration as a new variety. Additionally, lines E04-5B and E03-3 (cv. Spunta) showed partial PPO2 gene edits, reducing enzymatic browning by 80% and 40%, respectively. This study demonstrates the potential of CRISPR/Cas9 to develop non-transgenic, gene-edited potatoes with enhanced storage quality, benefiting both growers and the food industry. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

► Show Figures

Graphical abstract

18 pages, 7788 KiB

Open AccessArticle

C3H10T1/2 Mesenchymal Stem Cell Line as a New In Vitro Tool for Studying Adipocyte Dedifferentiation

by Yuriko Yuuki, Takeshi Katafuchi, Tomohiko Kazama, Taro Matsumoto and Makoto Makishima

Biology 2025, 14(4), 444; https://doi.org/10.3390/biology14040444 - 20 Apr 2025

Viewed by 25

Abstract

Dedifferentiated fat (DFAT) cells are adipocyte-derived cells that are able to differentiate into multiple cell lineages such as adipocytes, osteoblasts and chondrocytes, similar to mesenchymal stem cells (MSCs). Despite their great potential for developing novel clinical interventions by using their multipotency, the detailed [...] Read more.

Dedifferentiated fat (DFAT) cells are adipocyte-derived cells that are able to differentiate into multiple cell lineages such as adipocytes, osteoblasts and chondrocytes, similar to mesenchymal stem cells (MSCs). Despite their great potential for developing novel clinical interventions by using their multipotency, the detailed mechanisms of how adipocytes undergo dedifferentiation into DFAT cells are not completely understood, because useful in vitro tools for studying adipocyte dedifferentiation are missing. In this study, we show that mature adipocytes derived from the MSC cell line C3H10T1/2 underwent dedifferentiation into cells with DFAT cell-like characteristics, when they were cultured in an inverted flask. During the dedifferentiation, expression levels of genes and protein specific to adipocytes were continuously decreased, whereas those for MSC, proliferation and WNT/β-catenin signaling were gradually increased. These DFAT-like cells also underwent differentiation into adipocytes, osteoblasts and chondrocytes with their specific cell morphology and gene expression. We also observed that an individually cultured single adipocyte also underwent dedifferentiation into DFAT-like cells that were able to differentiate into the multiple cell lineages. Our results indicate that C3H10T1/2 cells could be a great tool for determining molecular biological and biochemical mechanisms underlying adipocyte dedifferentiation. Full article

► Show Figures

Figure 1

18 pages, 1049 KiB

Open AccessArticle

Phosphate-Solubilizing Bacteria Cereibacter sphaeroides ST16 and ST26 Enhanced Soil Phosphorus Solubility, Rice Growth, and Grain Yield in Acidic-Contaminated Saline Soil

by Le Tien Dat, Le Thi Chinh, Ly Ngoc Thanh Xuan, Le Thanh Quang, Pham Thi Phuong Thao, Do Thi Xuan, Le Thi My Thu, Nguyen Duc Trong, Tran Trong Khoi Nguyen and Nguyen Quoc Khuong

Biology 2025, 14(4), 443; https://doi.org/10.3390/biology14040443 - 19 Apr 2025

Viewed by 51

Abstract

Soil phosphorus is heavily restricted by soil acidification and salinization. There is a need to determine a biological solution for this issue to replace the overuse of chemical phosphorus fertilizer that aggravates adverse conditions, such as salinity, acidity, and metallic toxicity. Therefore, this [...] Read more.

Soil phosphorus is heavily restricted by soil acidification and salinization. There is a need to determine a biological solution for this issue to replace the overuse of chemical phosphorus fertilizer that aggravates adverse conditions, such as salinity, acidity, and metallic toxicity. Therefore, this study aimed at determining the phosphorus dynamics in terms of the soil, growth, and yield of rice under the supplementation of phosphate (P)-solubilizing purple nonsulfur bacteria (PNSB), Cereibacter sphaeroides ST16 and ST26, in salinized soil collected from An Bien district, Kien Giang province, Vietnam, under greenhouse conditions. The experiment followed a completely randomized block design with two factors and four replications. In particular, the reduced percentages of P fertilizer (A) were 0%, 25%, 50%, 75%, and 100% P. The supplementations of C. sphaeroides strains (B) were the negative control, ST16, ST26, and a mixture of both ST16 and ST26. The results showed that supplying the C. sphaeroides ST16 and ST26 reduced the insoluble P content by 10.1–10.6% Fe-P, 10.3–12.2% Ca-P, and 12.7–43.1% Al-P and increased available P by 8.33–27.8%, leading to total P uptake in plants increasing by 29.4–56.1%. The C. sphaeroides strains also reduced soil Na⁺. Therefore, supplying the C. sphaeroides strains increased the rice growth and yield components of rice, leading to a greater yield of 26.5–51.0%. Supplying each strain of ST16 and ST26 reduced 50–100% P fertilizer as recommended. Ultimately, inoculation of the bacterial mixture allowed a reduction by 100% P fertilizer percentage as recommended but the yield remained the still. Full article

► Show Figures

Figure 1

28 pages, 1358 KiB

Open AccessReview

Biomolecules Interacting with Long Noncoding RNAs

by Hidenori Tani

Biology 2025, 14(4), 442; https://doi.org/10.3390/biology14040442 - 19 Apr 2025

Viewed by 30

Abstract

This review explores the complex interactions between long noncoding RNAs (lncRNAs) and other biomolecules, highlighting their pivotal roles in gene regulation and cellular function. LncRNAs, defined as RNA transcripts exceeding 200 nucleotides without encoding proteins, are involved in diverse biological processes, from embryogenesis [...] Read more.

This review explores the complex interactions between long noncoding RNAs (lncRNAs) and other biomolecules, highlighting their pivotal roles in gene regulation and cellular function. LncRNAs, defined as RNA transcripts exceeding 200 nucleotides without encoding proteins, are involved in diverse biological processes, from embryogenesis to pathogenesis. They interact with DNA through mechanisms like triplex structure formation, influencing chromatin organization and gene expression. LncRNAs also modulate RNA-mediated processes, including mRNA stability, translational control, and splicing regulation. Their versatility stems from their forming of complex structures that enable interactions with various biomolecules. This review synthesizes current knowledge on lncRNA functions, discusses emerging roles in development and disease, and evaluates potential applications in diagnostics and therapeutics. By examining lncRNA interactions, it provides insights into the intricate regulatory networks governing cellular processes, underscoring the importance of lncRNAs in molecular biology. Unlike the majority of previous reviews that primarily focused on individual aspects of lncRNA biology, this comprehensive review uniquely integrates structural, functional, and mechanistic perspectives on lncRNA interactions across diverse biomolecules. Additionally, this review critically evaluates cutting-edge methodologies for studying lncRNA interactions, bridges fundamental molecular mechanisms with potential clinical applications, and highlights their potential. Full article

(This article belongs to the Special Issue RNA Biology and mRNA in Diseases)

► Show Figures

Figure 1

12 pages, 3930 KiB

Open AccessArticle

Microplastic Contamination of the Turkish Worm Lizard (Blanus strauchi Bedriaga, 1884) in Muğla Province (Türkiye)

by Cantekin Dursun, Nagihan Demirci, Kamil Candan, Elif Yıldırım Caynak, Yusuf Kumlutaş, Çetin Ilgaz and Serkan Gül

Biology 2025, 14(4), 441; https://doi.org/10.3390/biology14040441 - 19 Apr 2025

Viewed by 69

Abstract

Because of their diversity, microplastics (MPs), which are synthetic particles smaller than 5 mm, are highly bioavailable and widely distributed. The prevalence of microplastics in aquatic habitats has been extensively studied but less is known about their presence in terrestrial environments and biota. [...] Read more.

Because of their diversity, microplastics (MPs), which are synthetic particles smaller than 5 mm, are highly bioavailable and widely distributed. The prevalence of microplastics in aquatic habitats has been extensively studied but less is known about their presence in terrestrial environments and biota. This study examined MP intake in terrestrial environments utilizing gastrointestinal tracts (GITs), with a particular focus on the Turkish worm lizard (Blanus strauchi). Suspected particles discovered in the GITs were removed, measured, and characterized based on size, shape, color, and polymer type in order to evaluate MP ingestion. Out of 118 samples analyzed, 29 specimens (or 24.57%) had microplastic particlesMP length did not significantly correlate with snout–vent length (SVL) and weight. These correlations were tested to determine whether the size or weight of Blanus strauchi influenced the amount or size of MPs found within the GITs. Also, MP consumption by the worm lizard did not correlate with the year of sampling. All particles identified as fibers through FT-IR spectroscopy analysis. The most common type of microplastic was polyethylene terephthalate (PET). The most often detected color was blue, with mean MP lengths ranging from 133 µm to 2929 µm. It has been demonstrated that worm lizards inhabiting soil or sheltering under stones in bushy areas with sparse vegetation consume MPs. Predation is regarded to be the most likely way through which MPs infiltrate terrestrial food webs. Full article

(This article belongs to the Section Ecology)

► Show Figures

Figure 1

16 pages, 3570 KiB

Open AccessArticle

Insights into the Regulatory Role of MicroRNAs in Penaeus monodon Under Moderately Low Salinity Stress

by Jianzhi Shi, Song Jiang, Yangyang Ding, Hongshan Diao, Wenzhe Li, Yundong Li, Jianhua Huang, Lishi Yang, Qibin Yang and Falin Zhou

Biology 2025, 14(4), 440; https://doi.org/10.3390/biology14040440 - 18 Apr 2025

Viewed by 153

Abstract

MicroRNAs (miRNAs) play crucial roles in regulating various biological processes in crustaceans, including stress responses. Under acute low salinity stress conditions, miRNAs exhibit dynamic expression patterns that significantly influence the physiological and molecular responses of the shrimp. However, research on miRNAs in P. [...] Read more.

MicroRNAs (miRNAs) play crucial roles in regulating various biological processes in crustaceans, including stress responses. Under acute low salinity stress conditions, miRNAs exhibit dynamic expression patterns that significantly influence the physiological and molecular responses of the shrimp. However, research on miRNAs in P. monodon is very limited, and their functions under low salinity stress remain unclear. In this study, by using high-throughput sequencing technology, we identified miRNAs and investigated their regulatory mechanism in P. monodon under low salinity stress. A total of 118 miRNAs were differentially expressed after low salinity exposure. These miRNAs were found to target genes involved in metabolism, pathogen infection, immune response and stress signaling pathways. By modulating the expression of these target genes, miRNAs were able to fine-tune the stress response of P. monodon, thereby enhancing its tolerance to low salinity. This study provides new insights into the regulatory roles of miRNAs in the stress response of aquatic organisms and suggests potential targets for genetic improvement to enhance stress tolerance in P. monodon aquaculture. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)

► Show Figures

Figure 1

23 pages, 20076 KiB

Open AccessArticle

Transcriptomic Analysis Identifies Molecular Response of the Tolerant Alfalfa (Medicago sativa) Cultivar Nongjing 1 to Saline-Alkali Stress

by Dongmei Zhang, Jinxia Li, Yiming Zhang, Yuanhao Zhang, Wenhui Wang, Zhaohui Li, Peng Zhu, Yongshun Huang, Long Han, Mingyu Wang, Zijian Zhang, Zhongbao Shen, Weibo Han, Linlin Mou, Xu Zhuang, Qiuying Pang, Jianli Wang and Lixin Li

Biology 2025, 14(4), 439; https://doi.org/10.3390/biology14040439 - 18 Apr 2025

Viewed by 92

Abstract

Alfalfa (Medicago sativa) is a perennial forage crop with significant economic and ecological significance. If alfalfa can be planted in saline-alkali land, it will not only improve the utilization rate of marginal land and alleviate the competition between forage and cereal [...] Read more.

Alfalfa (Medicago sativa) is a perennial forage crop with significant economic and ecological significance. If alfalfa can be planted in saline-alkali land, it will not only improve the utilization rate of marginal land and alleviate the competition between forage and cereal crops for arable land but will also increase the yield of high-quality domestic forage. In this study, we conducted transcriptomic analysis on the saline-alkali-tolerant alfalfa cultivar NQ-1 and compared its metabolite accumulation levels with saline-alkali-sensitive cultivars. The results showed that under saline-alkali stress, the photosynthesis and some secondary metabolic pathways in NQ-1 were activated, such as α-Linolenic acid metabolism, Phenylpropanoid and Flavonoid biosynthesis, and Photosynthesis-related pathways, providing substances and energy for enhancing NQ-1 stress tolerance. Furthermore, some specific flavonoids were detected that may contribute to the saline-alkali tolerance of NQ-1. In addition, transcription factors that may regulate flavonoid biosynthesis in NQ-1 under saline-alkali stress were also identified. This study deepens the understanding of the resistance mechanism of saline-alkali-tolerant cultivars of alfalfa and provides valuable information for molecular design breeding strategies for stress-resistant alfalfa. Full article

► Show Figures

Figure 1

15 pages, 727 KiB

Open AccessReview

Battle of the Biomarkers of Systemic Inflammation

by Emilia Stec-Martyna, Karolina Wojtczak, Dariusz Nowak and Robert Stawski

Biology 2025, 14(4), 438; https://doi.org/10.3390/biology14040438 - 18 Apr 2025

Viewed by 59

Abstract

Systemic inflammation is monitored with various biomarkers; of these, C-reactive protein (CRP) is widely used due to its cost effectiveness and widespread implementation. However, its lack of specificity and delayed kinetics have directed interest in cell-free DNA (cfDNA), which offers rapid responses to [...] Read more.

Systemic inflammation is monitored with various biomarkers; of these, C-reactive protein (CRP) is widely used due to its cost effectiveness and widespread implementation. However, its lack of specificity and delayed kinetics have directed interest in cell-free DNA (cfDNA), which offers rapid responses to cellular damage. Our review compares the use of CRP and cfDNA in myocardial infarction, sepsis, and physical exercise, focusing on their origins, kinetics, and clinical utility. cfDNA release from apoptotic or damaged cells increases within minutes to hours, providing an early marker of cellular stress. In myocardial infarction, cfDNA peaks early, indicating acute injury, while CRP rises later, reflecting prolonged inflammation. In sepsis, cfDNA correlates strongly with disease severity and prognosis, outperforming CRP in early diagnosis. During physical exercise, cfDNA offers an immediate picture of cellular stress, whereas CRP’s delayed response limits its utility in this context. The interaction between CRP and cfDNA suggests their combined application could improve diagnostic accuracy and prognostic assessments. As cfDNA testing becomes more widely available, researchers will need to develop standardized protocols and determine how it can best complement CRP measurements in clinical practice. This approach offers promise for improving the management of systemic inflammation across diverse medical conditions. Full article

(This article belongs to the Section Physiology)

► Show Figures

Figure 1

16 pages, 2997 KiB

Open AccessArticle

Evaluating the Effect of an Essential Oil Blend on the Growth and Fitness of Gram-Positive and Gram-Negative Bacteria

by Kelechi A. Ike, Paul C. Omaliko, Mizpha C. Fernander, Brittany M. Sanders, James M. Enikuomehin, Joel O. Alabi, Oludotun O. Adelusi, Ahmed E. Kholif, Misty D. Thomas and Uchenna Y. Anele

Biology 2025, 14(4), 437; https://doi.org/10.3390/biology14040437 - 18 Apr 2025

Viewed by 160

Abstract

The increasing prevalence of antibiotic-resistant bacteria has necessitated the exploration of alternative antimicrobial agents, particularly natural products like essential oils. This study investigated the antibacterial potential of a unique blend of four essential oils (EOB) across a gradient of concentrations (0.1 to 50%) [...] Read more.

The increasing prevalence of antibiotic-resistant bacteria has necessitated the exploration of alternative antimicrobial agents, particularly natural products like essential oils. This study investigated the antibacterial potential of a unique blend of four essential oils (EOB) across a gradient of concentrations (0.1 to 50%) against Gram-positive and Gram-negative bacteria using an adapted broth microdilution method, minimum inhibitory concentrations (MICs), and 24-h growth assays. The Gram-positive bacteria were Staphylococcus epidermidis and Bacillus subtilis, while the Gram-negative bacteria were Escherichia coli and Klebsiella aerogenes. The results demonstrated that the EOB exerted a concentration-dependent inhibitory effect on bacterial growth, with MICs determined at 25% for all the species tested. Growth curve analysis revealed that lower concentrations of the EOB (0.1 to 0.78%) allowed for normal bacterial proliferation, while at intermediate concentrations (1.56 to 3.13%), inconsistent trends in growth were exhibited. At higher concentrations (25 and 50%), the EOB effectively halted bacterial growth, as indicated by flat growth curves. The increase in the lag phase and the decrease in the growth rate at a sub-MIC concentration (12.5%) suggest a significant effect on bacterial adaptation and survival. Relative fitness analyses further highlighted the inhibitory effects of higher essential oil concentrations. S. epidermidis and E. coli had a significant (p < 0.05) reduction in fitness starting from the 6.25% concentration, while the other two species experienced a significant (p < 0.001) reduction in relative fitness from a concentration of 12.5%. These findings underscore the potential of this EOB as an effective antimicrobial agent, particularly in the context of rising antibiotic resistance. Furthermore, the study suggests that the EOB used in the present study could be integrated into therapeutic strategies as a natural alternative or adjunct to traditional antibiotics, offering a promising avenue for combating resistant bacterial strains. Full article

(This article belongs to the Special Issue Nutraceutical and Bioactive Compounds in Foods)

► Show Figures

Figure 1

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

Viewed by 176

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

► Show Figures

Figure 1

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

Viewed by 209

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)

► Show Figures

Figure 1

15 pages, 3049 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

Viewed by 169

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

► Show Figures

Figure 1

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

Viewed by 246

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)

► Show Figures

Figure 1

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

Viewed by 149

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)

► Show Figures

Figure 1

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

Viewed by 185

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)

► Show Figures

Figure 1

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

Viewed by 222

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)

► Show Figures

Figure 1

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

Viewed by 217

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))

► Show Figures

Figure 1

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

Viewed by 119

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

► Show Figures

Figure 1

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

Viewed by 404

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)

► Show Figures

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

Viewed by 215

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)

► Show Figures

Figure 1

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

Viewed by 145

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

► Show Figures

Figure 1

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

Viewed by 191

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)

► Show Figures

Figure 1

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

Viewed by 255

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)

► Show Figures

Graphical abstract

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

Viewed by 232

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)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Biology, Volume 14, Issue 4 (April 2025) – 134 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI