Biology

18 pages, 3551 KiB

Open AccessArticle

Exploring the Bacterial Microbiome of High-Moisture Plant-Based Meat Substituted Soybean Flour with Mung Bean Protein and Duckweed Powder

by Jutamat Klinsoda, Theera Thurakit, Kullanart Tongkhao, Khemmapas Treesuwan, Kanokwan Yodin and Hataichanok Kantrong

Biology 2025, 14(6), 735; https://doi.org/10.3390/biology14060735 - 19 Jun 2025

Viewed by 560

Abstract

(1) Background: This study aimed to investigate the bacterial microbiomes in the ingredients and final PBM products during a storage period of 28 days at 2–4 °C for food safety and quality. (2) Methods: DNA from raw ingredients (i.e., defatted soy flour, potato [...] Read more.

(1) Background: This study aimed to investigate the bacterial microbiomes in the ingredients and final PBM products during a storage period of 28 days at 2–4 °C for food safety and quality. (2) Methods: DNA from raw ingredients (i.e., defatted soy flour, potato starch, wheat gluten, mung bean protein, and duckweed) and three PBM formulations were extracted and sequenced using 16S rRNA gene sequencing. (3) Results: Alpha diversity (Simpson and Shannon) was high in the raw ingredients (p ≤ 0.05). Beta diversity showed dissimilarities between the samples. Firmicutes and Proteobacteria were the core microflora in these ingredients. The heat-stable microbes in PBM (e.g., Nostocaceae in SF and Cyanobacteriale in MB and DW) survived after extrusion. After the ingredients were stored at room temperature, the bacterial communities shifted, with Paucibacter being the majority population in raw ingredients and PBM in the 2nd batch. The predictions of Potential_Pathogens related to the abundance of Aeromonadaceae and Enterobacteriaceae need to be monitored during storage. (4) Conclusions: Our results showed that the bacterial community in PBM containing 30% MB and 3% DW did not drastically change during 28 days of storage at cold temperatures. Uncovering bacterial microbiomes in the ingredients should be emphasized for quality and safety, as ingredients influence the microbiome in the final products. Full article

(This article belongs to the Section Microbiology)

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15 pages, 952 KiB

Open AccessArticle

Potential Role of Probiotic Strain Lactiplantibacillus plantarum in Control of Histamine Metabolism

by Gina Cavaliere, Egidia Costanzi, Beniamino Cenci-Goga, Marco Misuraca and Giovanna Traina

Biology 2025, 14(6), 734; https://doi.org/10.3390/biology14060734 - 19 Jun 2025

Viewed by 359

Abstract

Histamine intolerance is a condition that occurs when there is an imbalance between the accumulation and degradation of histamine within the body. Excess histamine is metabolized and then degraded by two enzymes, of which the most abundant is the vesicular diamine oxidase (DAO). [...] Read more.

Histamine intolerance is a condition that occurs when there is an imbalance between the accumulation and degradation of histamine within the body. Excess histamine is metabolized and then degraded by two enzymes, of which the most abundant is the vesicular diamine oxidase (DAO). An imbalance or a state of dysbiosis of the intestinal microbiota has been observed in patients with histamine intolerance compared to healthy individuals. Studies indicate that the administration of bifidobacteria or lactobacilli alone or in mixtures can alter colonic microbiota populations and metabolic activities. The present study has evaluated the ability of a probiotic bacterial strain to stimulate the release of cellular DAO from an in vitro model of the human intestinal epithelial barrier. The results indicate that, under the experimental conditions used, probiotic strain Lactiplantibacillus plantarum LP115 has a significant stimulatory effect on DAO secretion in adenocarcinoma cell line HT-29. Full article

(This article belongs to the Special Issue Editorial Board Members' Collection Series: Cell Signaling in Health and Disease)

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20 pages, 2283 KiB

Open AccessArticle

Functional and Genomic Evidence of L-Arginine-Dependent Bacterial Nitric Oxide Synthase Activity in Paenibacillus nitricinens sp. nov.

by Diego Saavedra-Tralma, Alexis Gaete, Carolina Merino-Guzmán, Maribel Parada-Ibáñez, Francisco Nájera-de Ferrari and Ignacio Jofré-Fernández

Biology 2025, 14(6), 733; https://doi.org/10.3390/biology14060733 - 19 Jun 2025

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Abstract

Although nitric oxide (NO) production in bacteria has traditionally been associated with denitrification or stress responses in model or symbiotic organisms, functionally validated L-arginine-dependent nitric oxide synthase (bNOS) activity has not been documented in free-living, non-denitrifying soil bacteria. This paper reports Paenibacillus nitricinens [...] Read more.

Although nitric oxide (NO) production in bacteria has traditionally been associated with denitrification or stress responses in model or symbiotic organisms, functionally validated L-arginine-dependent nitric oxide synthase (bNOS) activity has not been documented in free-living, non-denitrifying soil bacteria. This paper reports Paenibacillus nitricinens sp. nov., a bacterium isolated from rainforest soil capable of synthesizing NO via a bNOS under aerobic conditions. A bnos-specific PCR confirmed gene presence, while whole-genome sequencing (6.7 Mb, 43.79% GC) revealed two nitrogen metabolism pathways, including a bnos-like gene. dDDH (<70%) and ANI (<95%) values with related Paenibacillus strains support the delineation of this isolate as a distinct species. Extracellular and intracellular NO measurements under aerobic conditions showed a dose-dependent response, with detectable production at 0.1 µM L-arginine and saturation at 100 µM. The addition of L-NAME reduced NO formation, confirming enzymatic mediation. The genomic identification of a bnos-like gene strongly supports the presence of a functional pathway. The absence of canonical nitric oxide reductase (Nor) genes or other typical denitrification-related enzymes reinforces that NO production arises from an alternative, intracellular enzymatic mechanism rather than classical denitrification. Consequently, P. nitricinens expands the known repertoire of microbial NO synthesis and suggests a previously overlooked source of NO flux in well-aerated soils. Full article

(This article belongs to the Section Microbiology)

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23 pages, 4572 KiB

Open AccessArticle

Mechanisms of Zooplankton Community Assembly and Their Associations with Environmental Drivers in Arid-Region Reservoirs of Northwest China

by Xuelian Qiu, Fangze Zi, Long Yun, Qiang Huo, Liting Yang, Yong Song and Shengao Chen

Biology 2025, 14(6), 732; https://doi.org/10.3390/biology14060732 - 19 Jun 2025

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Abstract

This study investigates the mechanisms of zooplankton community assembly and their relationship to environmental factors in high-latitude arid regions. We conducted seasonal sampling at four reservoirs in the upper Tarim River Basin from 2023 to 2024: Shangyou Reservoir (SY), Shengli Reservoir (SL), Duolang [...] Read more.

This study investigates the mechanisms of zooplankton community assembly and their relationship to environmental factors in high-latitude arid regions. We conducted seasonal sampling at four reservoirs in the upper Tarim River Basin from 2023 to 2024: Shangyou Reservoir (SY), Shengli Reservoir (SL), Duolang Reservoir (DL) and Xinjingzi Reservoir (XJZ). The zooplankton community was categorized into five functional groups based on the predominant species, with small crustacean filter feeders (SCF) in all reservoirs except XJZ, where a seasonal shift between rotifer collectors (RC) in the wet season and SCF in the dry season was observed. Pearson correlation and canonical correspondence analysis (CCA) revealed that interspecific competition, pH, conductivity (COND), and salinity (SALIN) were the main determinants of zooplankton community composition. Significant correlations (p < 0.05) were detected among functional groups RC (rotifers carnivora), RF (rotifers filter feeders), SCF (small copepods and claocera filter feeders), and MCC (middle copepods and claocera carnivora). Environmental factors showed significant spatial heterogeneity, while zooplankton biomass was positively correlated with pH and COND. Cluster similarity analyses indicated complex interactions between 29 zooplankton species, with RF identified as an important positive predictor for larger groups. The network of co-occurrences showed predominantly positive relationships, emphasizing the mutual facilitation between the species. Our results suggest that interspecific interactions have stronger effects on community structuring than environmental factors, with mutual facilitation emerging as an important survival strategy. This study provides important insights into the dynamics of zooplankton communities in dry reservoirs and establishes a framework for understanding ecological patterns and assembly mechanisms under drought conditions. Full article

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

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23 pages, 3615 KiB

Open AccessArticle

Mechanisms of Aletris spicata (Thunb.) Franch. Extract in Asthma Therapy: Oxidative Stress, Inflammation, and Gut Microbiota

by Jing Yang, Zhiyong Chen, Yue Zhu, Teng Chen, Ying Zhou and Zuhua Wang

Biology 2025, 14(6), 731; https://doi.org/10.3390/biology14060731 - 19 Jun 2025

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Abstract

Aletris spicata (Thunb.) Franch. (AS), a traditional edible and medicinal plant for treating asthma, was investigated for its therapeutic mechanisms. Liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS) analysis identified 33 compounds in AS. In ovalbumin (OVA)-induced asthmatic mice, AS significantly reduced inflammatory cells (neutrophils, [...] Read more.

Aletris spicata (Thunb.) Franch. (AS), a traditional edible and medicinal plant for treating asthma, was investigated for its therapeutic mechanisms. Liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS) analysis identified 33 compounds in AS. In ovalbumin (OVA)-induced asthmatic mice, AS significantly reduced inflammatory cells (neutrophils, lymphocytes, eosinophils) in bronchoalveolar lavage fluid (BALF) and decreased IL-4, IL-5, IL-13, TNF-α, and serum IgE while increasing IFN-γ. AS alleviated lung and intestinal inflammation, reduced ROS and MDA levels, and enhanced SOD activity. Immunohistochemistry and Western blot revealed AS upregulated Nrf2/HO-1 expression and inhibited NF-κB p65 nuclear translocation. Gut microbiota studies demonstrated AS restored intestinal flora homeostasis by modulating the richness, diversity, and composition. Spearman correlation analysis identified significant relationships between oxidative stress markers, inflammatory cytokines, and specific gut bacteria. These findings indicate that AS mitigates asthma through antioxidant effects (Nrf2/HO-1 pathway), anti-inflammatory actions (NF-κB pathway), and gut microbiota modulation. The study provides a scientific basis for developing AS as a natural anti-asthma treatment or functional food. The multi-target mechanism involving oxidative stress, inflammation, and gut flora highlights AS’s comprehensive therapeutic potential for asthma management. Full article

(This article belongs to the Special Issue Pathophysiology of Chronic Inflammatory Diseases)

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59 pages, 11519 KiB

Open AccessArticle

DNA Specimen Preservation Using DESS and DNA Extraction in Museum Collections

by Eri Ogiso-Tanaka, Daisuke Shimada, Akito Ogawa, Genki Ishiyama, Ken-ichi Okumura, Kentaro Hosaka, Chikako Ishii, Kyung-Ok Nam, Masakazu Hoshino, Shuhei Nomura, Showtaro Kakizoe, Yasuhide Nakamura, Isao Nishiumi, Minako Abe Ito, Taiju Kitayama, Norio Tanaka, Tsuyoshi Hosoya and Utsugi Jinbo

Biology 2025, 14(6), 730; https://doi.org/10.3390/biology14060730 - 19 Jun 2025

Viewed by 275

Abstract

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at −80 °C. DNA analysis has become an essential tool for taxonomic research [...] Read more.

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at −80 °C. DNA analysis has become an essential tool for taxonomic research and biodiversity assessment; however, freezer storage for all samples is impractical due to space limitations and operational costs. This creates a pressing need to develop more widely applicable DNA preservation methods. We investigated the comparative effects of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation on both morphology and DNA integrity using museum specimens from various taxonomic groups. Our results demonstrated that DESS preservation maintained high-quality DNA fragments exceeding >15 kb at room temperature across all examined species, with nematode samples maintaining DNA integrity even after 10 years of storage. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing. Full article

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

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19 pages, 1223 KiB

Open AccessReview

Effect of Exercise on Regulating miRNA Expression in Brain Health and Diseases

by Jian Zhang, Fengmei Gu and Anand Thirupathi

Biology 2025, 14(6), 729; https://doi.org/10.3390/biology14060729 - 19 Jun 2025

Viewed by 297

Abstract

Physical exercise induces epigenetic modifications that significantly influence the expression of a set of small non-coding RNAs known as miRNAs. These changes can enhance exercise performance and impact the neurological system, suggesting that understanding miRNA-mediated mechanisms during exercise may offer valuable insights into [...] Read more.

Physical exercise induces epigenetic modifications that significantly influence the expression of a set of small non-coding RNAs known as miRNAs. These changes can enhance exercise performance and impact the neurological system, suggesting that understanding miRNA-mediated mechanisms during exercise may offer valuable insights into using exercise as a therapeutic approach for neurodegenerative diseases. The existing literature on exercise-induced molecular pathways often presents inherent biases, complicating the establishment of exercise-induced miRNAs as reliable biomarkers for various chronic conditions due to their variable expression at tissue, organ, and systemic levels. Specifically, miRNA expression can downregulate critical signaling pathways such as TGF-β, FOXO, and NOTCH, which are implicated in the progression of neurodegenerative diseases. Exercise can override this scenario by targeting the expression of these miRNAs. However, the link between exercise modality-induced benefits (types, intensity, and duration) and the miRNA expression in brain cells is poorly understood. Therefore, this review aims to discuss how exercise-mediated miRNA expression affects brain pathophysiology, particularly in the context of neurodegenerative diseases. Full article

(This article belongs to the Special Issue Redox Signaling and Oxidative Stress in Health and Disease)

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13 pages, 2865 KiB

Open AccessArticle

Effect of Maternal Hyperglycemia on Fetal Pancreatic Islet Development

by Carina Pereira Dias, Michel Raony Teixeira Paiva de Moraes, Fernanda Angela Correia Barrence, Camila Stephanie Balbino da Silva, Basilio Smuckzec, Fernanda Ortis and Telma Maria Tenório Zorn

Biology 2025, 14(6), 728; https://doi.org/10.3390/biology14060728 - 19 Jun 2025

Viewed by 325

Abstract

Hyperglycemia during fetal development disturbs extracellular matrix (ECM) synthesis and deposition patterns, which disrupts organogenesis and adult organ function. Although the ECM cooperates in pancreas development, little is known about the effects of hyperglycemia on the pancreatic ECM during development. This study investigates [...] Read more.

Hyperglycemia during fetal development disturbs extracellular matrix (ECM) synthesis and deposition patterns, which disrupts organogenesis and adult organ function. Although the ECM cooperates in pancreas development, little is known about the effects of hyperglycemia on the pancreatic ECM during development. This study investigates the effect of severe maternal hyperglycemia on ECM composition and endocrine pancreas development in E19.0 mouse fetuses. Deposition patterns of pan-laminin, laminin (alpha 1 and gamma 1 chains) and integrin alpha 3 were evaluated by immunostaining. The proliferative index of islet cells and alpha and beta cell distribution were evaluated by PCNA, glucagon and insulin immunostaining, respectively. Pdx1 and Pax4 expressions were analyzed by RT-qPCR. While for pan-laminin and laminin (alpha1 and gamma1 chains) deposition was weaker in the endocrine pancreas of hyperglycemic mothers’ fetuses, integrin alpha 3 deposition in the basement membrane was increased. The proliferative index of endocrine cells was lower in the hyperglycemic group, while the beta-cell area was increased. In addition, there was a tendency towards lower Pdx1 and increased Pdx4 expression. These data suggest that maternal hyperglycemia alters fetal endocrine pancreas morphogenesis by modifying peri-islet basement membrane molecule patterns, promoting a decrease in endocrine cell proliferation associated with changes in the expression of important growth factors for the beta cells differentiated and the proliferative state. Full article

(This article belongs to the Section Cell Biology)

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15 pages, 4104 KiB

Open AccessArticle

Metabolic and Biochemical Responses of Juvenile Babylonia areolata to Hypoxia Stress

by Baojun Tang, Xiaoyao Ren, Zhiguo Dong, Hanfeng Zheng, Yujia Liu and Tao Wei

Biology 2025, 14(6), 727; https://doi.org/10.3390/biology14060727 - 19 Jun 2025

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Abstract

As an important aquaculture species, the marine snail Babylonia areolata is frequently subjected to fluctuation in dissolved oxygen concentration during farming and transportation processes. In the present study, we investigated the metabolic rates, transcription, and enzyme level responses of juvenile B. areolata exposed [...] Read more.

As an important aquaculture species, the marine snail Babylonia areolata is frequently subjected to fluctuation in dissolved oxygen concentration during farming and transportation processes. In the present study, we investigated the metabolic rates, transcription, and enzyme level responses of juvenile B. areolata exposed to long-term stress (144 h). The results showed that the mortality rate of juvenile B. areolata was higher in the 0.5 mg O₂/L group compared to the 2 mg O₂/L group. During the hypoxic stress period, both oxygen consumption and ammonia excretion rates were observed to be lower in juvenile B. areolata than those in the control group. As hypoxic stress duration prolonged, juvenile B. areolata demonstrated significantly elevated activities of pyruvate kinase (PK) and alkaline phosphatase (AKP), alongside reduced activities of lactic dehydrogenase (LDH), acid phosphatase (ACP), and superoxide dismutase (SOD). Significant changes in the expression levels of PK and LDH genes were observed during the hypoxic stress. The expression levels of ACP and SOD genes were significantly downregulated, while juvenile B. areolata exhibited elevated AKP gene expression levels under 0.5 mg O₂/L. Our findings suggest that under long-term exposure to hypoxia, B. areolata failed to maintain energy homeostasis and suffered biochemical disruptions, leading to a reduction in survival. The mortality rate of B. areolata can be substantially decreased by ensuring that transportation time does not exceed 48 h. Full article

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

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18 pages, 3320 KiB

Open AccessArticle

Isolation and Bioactive Characterization of Berberis kaschgarica Rupr-Derived Exosome-Like Nanovesicles: Exploring Therapeutic Potential in Atherosclerosis Pathogenesis

by Dilihuma Dilimulati, Nuerbiye Nueraihemaiti, Alhar Baishan, Sendaer Hailati, Alifeiye Aikebaier, Yipaerguli Paerhati and Wenting Zhou

Biology 2025, 14(6), 726; https://doi.org/10.3390/biology14060726 - 19 Jun 2025

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Abstract

Berberis kaschgarica Rupr.-derived exosome-like nanovesicles (BELNs), a type of plant-derived extracellular vesicle, consist of proteins, lipids, and nucleic acids. In this research, we employed differential centrifugation and ultracentrifugation techniques to isolate and purify BELNs. Subsequently, we conducted a comprehensive multi-omics analysis to systematically [...] Read more.

Berberis kaschgarica Rupr.-derived exosome-like nanovesicles (BELNs), a type of plant-derived extracellular vesicle, consist of proteins, lipids, and nucleic acids. In this research, we employed differential centrifugation and ultracentrifugation techniques to isolate and purify BELNs. Subsequently, we conducted a comprehensive multi-omics analysis to systematically determine their physicochemical properties. Experiments were conducted in vitro with Human Umbilical Vein Endothelial Cells (HUVECs) to verify the therapeutic impact of BELNSs on atherosclerosis. The isolated BELNs exhibited a distinctive teacup-shaped exosome morphology. The extraction yield was approximately 2.1 × 10¹³ particles per milliliter, and the average particle size was measured to be 179.1 nm. These nanovesicles were lipid-rich. The protein content predominantly comprised cytoplasmic proteins. In-depth analysis revealed the presence of five highly conserved plant microRNAs: miR166, miR156, miR399, miR171, and miR395. These miRNAs are involved in regulating plant growth and responses to both biotic and abiotic stresses. Functional assays demonstrated that Berberis kaschgarica Rupr.-derived exosome-like nanovesicles substantially decreased the lipid deposition in HUVECs that was triggered by Palmitic Acid (PA). This research establishes the inaugural utilization of multi-omics platforms to systematically elucidate the bioactivity profile of BELNs from Berberis kaschgarica Rupr., thereby laying the groundwork for advancing its therapeutic potential. Full article

(This article belongs to the Special Issue Plant Natural Products: Mechanisms of Action for Promoting Health)

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17 pages, 7493 KiB

Open AccessArticle

Profiling Genetic Variation: Divergence Patterns and Population Structure of Thailand’s Endangered Celastrus paniculatus Willd

by Kornchanok Kaenkham, Warayutt Pilap, Weerachai Saijuntha and Sudarat Thanonkeo

Biology 2025, 14(6), 725; https://doi.org/10.3390/biology14060725 - 19 Jun 2025

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Abstract

This study examined genetic diversity in the endangered medicinal plant Celastrus paniculatus using 62 individual samples from seven natural populations in northern and northeastern Thailand to inform conservation strategies. The analysis of the nuclear internal transcribed spacer (ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [...] Read more.

This study examined genetic diversity in the endangered medicinal plant Celastrus paniculatus using 62 individual samples from seven natural populations in northern and northeastern Thailand to inform conservation strategies. The analysis of the nuclear internal transcribed spacer (ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) markers revealed 17 haplotypes (CpI1–CpI17) across these populations, with 15 being population-specific. The genetic diversity varied significantly among populations: CMI showed the highest diversity (Hd = 0.944 ± 0.070), while LEI and LPN displayed complete homogeneity. The haplotype network identified a central shared haplotype (CpI4), suggesting a common ancestry, with the PLK population showing a distinct genetic divergence through unique haplotypes separated by multiple mutation steps. Genetic distance calculations revealed close relationships between LEI and NPM populations (distance = 0.0004), with greater differentiation between PLK and other populations (distances > 0.005). Phylogenetic analyses confirmed the species integrity while highlighting population clusters, especially PLK in ITS analyses and LPN in rbcL analyses. This genetic structure information provides a foundation for targeted conservation planning. Results suggest that conservation efforts should prioritize both genetically diverse populations (like CMI and MKM) and genetically distinct ones (like PLK) to preserve the maximum evolutionary potential. This study delivers crucial molecular data for developing evidence-based conservation strategies to protect this valuable medicinal species from further decline. Full article

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

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19 pages, 3955 KiB

Open AccessArticle

Study on the Degradation of Aflatoxin B1 by Myroides odoratimimus 3J2MO

by Xue Wang, Yao-Yao Gao, Dun Wang, Qi Zhang, Hao-Ran Wang, Ting-Ting Zhang, Meng-Jie Zhu, Jing Dong, Dong Ling, Peng Feng, Xue-Hui Tang and Pei-Wu Li

Biology 2025, 14(6), 724; https://doi.org/10.3390/biology14060724 - 19 Jun 2025

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Abstract

To address the issue of aflatoxin contamination, which poses a significant threat to food safety and human health, we have conducted extensive research. We have isolated a strain of Myroides odoratimimus (3J2MO) from the soil that exhibited remarkable efficiency in degrading various aflatoxin [...] Read more.

To address the issue of aflatoxin contamination, which poses a significant threat to food safety and human health, we have conducted extensive research. We have isolated a strain of Myroides odoratimimus (3J2MO) from the soil that exhibited remarkable efficiency in degrading various aflatoxin types, including AFB1, AFB2, AFG1, AFG2, and AFM1. SDS-PAGE analysis confirmed the purity of the enzymes to be over 95%. Through fluorescence assays, we quantified the enzymatic activity, with an AFB1 degradation rate of 95% achieved at 37 °C and a pH of 8.0. Further analysis using HPLC-MS/MS identified the degradation intermediates, revealing the mechanisms of lactone ring cleavage and epoxy group hydrolysis. GO/COG/KEGG annotations provided insights into the functions of these enzymes, with peroxidase linked to reactive oxygen species (ROS) generation and helicase associated with ATP-dependent conformational changes. Helicase, on the other hand, hydrolyzes ATP, driving conformational changes in AFB1 and facilitating its breakdown into non-toxic metabolites. The potential industrial-scale application of this discovery could significantly mitigate aflatoxin-related economic losses while minimizing chemical residues in the food chain. Full article

(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))

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23 pages, 4049 KiB

Open AccessArticle

Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study

by Alaa Talal Qumsani

Biology 2025, 14(6), 723; https://doi.org/10.3390/biology14060723 - 19 Jun 2025

Viewed by 402

Abstract

The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This [...] Read more.

The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10⁹ CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy. Full article

(This article belongs to the Section Microbiology)

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16 pages, 1873 KiB

Open AccessArticle

Optimizing Cellular Metabolism Through Mass Balance Analysis to Improve Skin Wound Healing

by Luis Ramirez Agudelo, Gabriel Yarmush, Suneel Kumar and Francois Berthiaume

Biology 2025, 14(6), 722; https://doi.org/10.3390/biology14060722 - 18 Jun 2025

Viewed by 465

Abstract

Accelerating healing is a clinical goal in both acute and chronic non-healing skin wounds. We leveraged the public Recon database, which seeks to aggregate all of the metabolic pathways in the human body, to uncover whether increasing the supply of specific metabolites can [...] Read more.

Accelerating healing is a clinical goal in both acute and chronic non-healing skin wounds. We leveraged the public Recon database, which seeks to aggregate all of the metabolic pathways in the human body, to uncover whether increasing the supply of specific metabolites can bolster cellular metabolism and, in turn, enhance wound healing. The database was reduced to a set of 357 reactions and 339 metabolites that were better suited for human cells in culture. Monte Carlo simulations were performed to identify the impact of 25 different inputs on the metabolic fluxes within the cellular biochemical network. Biomass and ATP production were used as surrogate markers for cell proliferation and cell migration (an energy-intensive process), respectively, both of which are critical to wound healing. The subset of simulations yielding the highest ATP production or biomass production were those where glycine and/or glutamine uptake was increased. Maximizing ATP and biomass also generally increased oxygen uptake. Due to its low availability in chronic wounds, another set of simulations was carried out in which oxygen uptake was held constant to mimic the effect of a limited oxygen supply. However, even with this constraint, glycine and glutamine remained the most promising interventions. The predictions were tested in vitro using immortalized human keratinocytes. Amino acid uptake was tentatively increased by supplementing the base culture media with additional glycine and/or glutamine, with valine supplementation with a similar nitrogen load as a control. Glycine supplementation significantly increased cellular proliferation above the base media and accelerated wound closure rate in wound scratch assay. However, glutamine and valine supplementation did not improve these parameters above base media, and glutamine even suppressed the benefit of glycine in cultures supplemented with both amino acids. In conclusion, glycine supplementation enhances cellular processes that are associated with wound healing. Full article

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16 pages, 1678 KiB

Open AccessArticle

The Diversity and Composition of Insect Communities in Urban Forest Fragments near Panama City

by Jeancarlos Abrego and Enrique Medianero

Biology 2025, 14(6), 721; https://doi.org/10.3390/biology14060721 - 18 Jun 2025

Viewed by 246

Abstract

Fragments of urban forests can host a remarkable diversity of insects, even in environments that have been greatly transformed. This study evaluates the diversity, abundance, and composition of insects that belong to seven families in four urban forest fragments near Panama City, i.e., [...] Read more.

Fragments of urban forests can host a remarkable diversity of insects, even in environments that have been greatly transformed. This study evaluates the diversity, abundance, and composition of insects that belong to seven families in four urban forest fragments near Panama City, i.e., Ciudad del Saber (CDS), Parque Natural Metropolitano (PNM), Corozal (COR), and Albrook (ALB). A total of 2038 individuals were collected via Malaise traps and categorized into 403 morphospecies, 75 genera, and 43 subfamilies. The highest richness of morphospecies was observed in CDS (223), whereas PNM exhibited the highest abundance of individuals (862). The alpha diversity indices (Shannon-Wiener > 4.3; Margalef > 21; Pielou ≈ 1.0; and Simpson’s inverse > 0.95) reflected communities that were characterized by high levels of diversity and equity. The level of similarity observed among the fragments was moderate (Diserud–Odegaard index = 0.543), thus indicating differences among the sites evaluated as part of this research in terms of their taxonomic composition. These results provide evidence concerning the variability of entomological communities in tropical urban landscapes and the role of forest fragments as possible reservoirs of biodiversity. Full article

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

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16 pages, 2498 KiB

Open AccessArticle

Liver Transcriptome Analysis Reveals a Potential Mechanism of Heat Stress Increasing Susceptibility to Salmonella Typhimurium in Chickens

by Qi Zhang, Yvqing Zhu, Zixuan Wang, Qinghe Li, Guiping Zhao and Qiao Wang

Biology 2025, 14(6), 720; https://doi.org/10.3390/biology14060720 - 18 Jun 2025

Viewed by 239

Abstract

Salmonella infection poses a serious threat to the poultry industry, causing significant economic losses. Under global warming conditions, the underlying molecular mechanisms by which heat stress affects bacterial infections in poultry remain unclear. This study conducted a Salmonella Typhimurium infection under heat stress [...] Read more.

Salmonella infection poses a serious threat to the poultry industry, causing significant economic losses. Under global warming conditions, the underlying molecular mechanisms by which heat stress affects bacterial infections in poultry remain unclear. This study conducted a Salmonella Typhimurium infection under heat stress in Guang Ming broilers. A total of 100 chickens were randomly divided into three groups: control group (CTL), Salmonella Typhimurium (ST) infection group, and heat stress and Salmonella Typhimurium (HS + ST) co-stimulation group. By integrating inflammatory phenotypes, liver transcriptome profiles, and weighted gene co-expression network analysis (WGCNA), we systematically investigated the key regulatory factors through which heat stress affects host susceptibility to Salmonella. The results demonstrated that heat stress reduced body weight gain, exacerbated Salmonella Typhimurium-induced inflammatory responses, and increased mortality. Transcriptome results revealed that heat stress led to excessive inflammatory responses and antioxidant defense imbalances. Combined differential expression analysis and WGCNA identified three hub regulatory genes: PTGDS and WISP2 showed significant correlations with the heterophil/lymphocyte ratio, while SLC6A9 was significantly correlated with serum IL-8 levels. Validation in HD11 cell infection models confirmed the differential expression of these genes under heat stress and Salmonella Typhimurium co-stimulation, indicating their critical roles in host immune regulation. This study elucidates the intrinsic regulatory relationships through which heat stress promotes Salmonella pathogenicity and inflammatory responses, providing important insights for disease-resistant poultry breeding and prevention strategies. Full article

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29 pages, 9846 KiB

Open AccessArticle

A Deep Learning and Explainable AI-Based Approach for the Classification of Discomycetes Species

by Aras Fahrettin Korkmaz, Fatih Ekinci, Şehmus Altaş, Eda Kumru, Mehmet Serdar Güzel and Ilgaz Akata

Biology 2025, 14(6), 719; https://doi.org/10.3390/biology14060719 - 18 Jun 2025

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Abstract

This study presents a novel approach for classifying Discomycetes species using deep learning and explainable artificial intelligence (XAI) techniques. The EfficientNet-B0 model achieved the highest performance, reaching 97% accuracy, a 97% F1-score, and a 99% AUC, making it the most effective model. MobileNetV3-L [...] Read more.

This study presents a novel approach for classifying Discomycetes species using deep learning and explainable artificial intelligence (XAI) techniques. The EfficientNet-B0 model achieved the highest performance, reaching 97% accuracy, a 97% F1-score, and a 99% AUC, making it the most effective model. MobileNetV3-L followed closely, with 96% accuracy, a 96% F1-score, and a 99% AUC, while ShuffleNet also showed strong results, reaching 95% accuracy and a 95% F1-score. In contrast, the EfficientNet-B4 model exhibited lower performance, achieving 89% accuracy, an 89% F1-score, and a 93% AUC. These results highlight the superior feature extraction and classification capabilities of EfficientNet-B0 and MobileNetV3-L for biological data. Explainable AI (XAI) techniques, including Grad-CAM and Score-CAM, enhanced the interpretability and transparency of model decisions. These methods offered insights into the internal decision-making processes of deep learning models, ensuring reliable classification results. This approach improves traditional taxonomy by advancing data processing and supporting accurate species differentiation. In the future, using larger datasets and more advanced AI models is recommended for biodiversity monitoring, ecosystem modeling, medical imaging, and bioinformatics. Beyond high classification performance, this study offers an ecologically meaningful approach by supporting biodiversity conservation and the accurate identification of fungal species. These findings contribute to developing more precise and reliable biological classification systems, setting new standards for AI-driven research in biological sciences. Full article

(This article belongs to the Section Bioinformatics)

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21 pages, 5095 KiB

Open AccessArticle

Molecular Adaptations and Quality Enhancements in a Hybrid (Erythroculter ilishaeformis ♀ × Ancherythroculter nigrocauda ♂) Cultured in Saline–Alkali Water

by Lang Zhang, Qiuying Qin, Qing Li, Yali Yu, Ziwei Song, Li He, Yanhong Sun, Liting Ye, Guiying Wang and Jing Xu

Biology 2025, 14(6), 718; https://doi.org/10.3390/biology14060718 - 18 Jun 2025

Viewed by 365

Abstract

Declining freshwater resources have spurred interest in saline–alkali (SA) water aquaculture, with species like tilapia and rainbow trout demonstrating ecological plasticity in such environments. However, the molecular mechanisms underlying fish adaptation and quality impacts remain unclear. This study investigated the hybrid fish “Xianfeng [...] Read more.

Declining freshwater resources have spurred interest in saline–alkali (SA) water aquaculture, with species like tilapia and rainbow trout demonstrating ecological plasticity in such environments. However, the molecular mechanisms underlying fish adaptation and quality impacts remain unclear. This study investigated the hybrid fish “Xianfeng No. 1” (Erythroculter ilishaeformis × Ancherythroculter nigrocauda), a key aquaculture species in China, under 60-day SA exposure. The results showed increased levels of oxidative stress markers (MDA) and antioxidant enzymes (SOD, CAT, GSH-Px), alongside improved quality traits. Transcriptomics revealed differentially expressed genes (DEGs) in muscle tissue associated with oxidative stress (UQCRFS1, UQCR10, CYC1), ion transport (COX5A, COX7C, COX7B), and the immune response (ATG9A, ATG2B, ATG2A, ULK1, ULK2, CFI, CFH). Metabolomics identified increased non-volatile flavors (e.g., glycine, proline) and collagen-related compounds. Integrated analysis highlighted the upregulation of GSR and GGT, and the downregulation of CHDH and GBSA, potentially driving glycine accumulation. These findings suggest that SA stress enhances antioxidant capacity, activates immune pathways, and modulates ion transport, enabling adaptation while improving meat quality. This study elucidates molecular mechanisms of fish acclimation to SA environments, providing insights for sustainable aquaculture development and breeding of stress-tolerant species in SA regions. Full article

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

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17 pages, 2046 KiB

Open AccessArticle

Spatial Transcriptomics Reveals Regional and Temporal Dynamics of Gene Expression in the Mouse Brain Across Development and Aging

by Benjamin Conacher, Amanda Moore, Liduo Yin, Yu Lin, Xiguang Xu, Qinwen Mao and Hehuang Xie

Biology 2025, 14(6), 717; https://doi.org/10.3390/biology14060717 - 18 Jun 2025

Viewed by 434

Abstract

Investigating transcriptomic changes during healthy development and aging provides insights into the molecular mechanisms that regulate the maturation of brain functions and drive age-related decline. Although it has been speculated that aging may represent a reversal of late-stage brain development, direct molecular comparisons [...] Read more.

Investigating transcriptomic changes during healthy development and aging provides insights into the molecular mechanisms that regulate the maturation of brain functions and drive age-related decline. Although it has been speculated that aging may represent a reversal of late-stage brain development, direct molecular comparisons between these two processes have remained limited. This study employs spatial transcriptomics to analyze the mouse brain at three key timepoints: postnatal day 21 (P21), 3 months (adult), and 28 months (aged), to identify region-specific differential gene expression dynamics. We identify widespread transcriptional changes across both brain development and aging, with all brain regions exhibiting distinct, region-specific gene expression dynamics that reflect divergent regulatory trajectories across the lifespan. During development, gene expression patterns were strongly enriched for neurogenesis, synaptic plasticity, and myelination, reflecting active circuit formation and white matter maturation. In contrast, aging was characterized by a decline in myelination-related gene expression and a pronounced increase in inflammatory and glial activation pathways, particularly within the hippocampus. While both development and aging involved changes in myelination-associated genes, the underlying mechanisms appear distinct: developmental upregulation supports circuit establishment and refinement, whereas aging-related downregulation may reflect secondary consequences of neuroinflammation and reactive gliosis. These findings underscore that, despite some overlap in affected pathways, neural maturation and age-related decline are driven by fundamentally different regulatory programs. These findings establish a novel spatial transcriptomic reference for brain development and aging, offering a valuable data resource for investigating neurodevelopmental and neurodegenerative mechanisms. Full article

(This article belongs to the Section Genetics and Genomics)

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14 pages, 2102 KiB

Open AccessArticle

Effect of Far-Red Light and Nutrient Solution Formulas on Calendula Production in a Plant Factory

by Maitree Munyanont, Na Lu, Thanit Ruangsangaram and Michiko Takagaki

Biology 2025, 14(6), 716; https://doi.org/10.3390/biology14060716 - 18 Jun 2025

Viewed by 266

Abstract

Calendula (Calendula officinalis L.), an edible and medicinal flower, faces challenges in yield uniformity and quality stability under open-field cultivation. Plant factories with artificial lighting (PFALs) are highly controlled systems that enable year-round production, efficient resource use, and consistent crop quality, making [...] Read more.

Calendula (Calendula officinalis L.), an edible and medicinal flower, faces challenges in yield uniformity and quality stability under open-field cultivation. Plant factories with artificial lighting (PFALs) are highly controlled systems that enable year-round production, efficient resource use, and consistent crop quality, making them promising for the cultivation for calendula. To optimize calendula cultivation in PFALs, this study investigates the effects of far-red (FR) light and nutrient solution modification on calendula growth, flowering, and nutrient use efficiency (NUE). The experiment was conducted using a dwarf calendula cultivar, ‘Orange Gem’. After transplanting, seedlings were subjected to a 2 × 3 factorial design comprising white (W) and end-of-day far-red (EOD-FR) lighting, in combination with three ammonium (NH₄⁺) levels (1/3×, 1×, and 3× of the Enshi formula). The EOD-FR lighting and the increase in the NH₄⁺ level resulted in taller plants and earlier first flower appearance. The shoot fresh and dry weight, the number of flowers, and the flower yield also increased under the higher NH₄⁺ concentration, regardless of the light treatment. The 3× NH₄⁺ treatment tended to enhance the nutrient absorption, leading to the highest nutrient use efficiency (NUE) based on the flower yield. These findings suggest that the application of EOD-FR lighting and high NH₄⁺ in nutrient solution can improve calendula productivity and resource-use efficiency in PFALs. Full article

(This article belongs to the Section Plant Science)

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13 pages, 10386 KiB

Open AccessArticle

Vitamin D Modified DSS-Induced Colitis in Mice via STING Signaling Pathway

by Zhihao Wu, Baohua Ma, Min Xiao, Qian Ren, Yanhua Shen and Zhengyu Zhou

Biology 2025, 14(6), 715; https://doi.org/10.3390/biology14060715 - 18 Jun 2025

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Abstract

Although the underlying mechanisms are not yet fully understood, vitamin D has been proven to be associated with the pathogenesis of inflammatory bowel disease, participating in immune response and regulating gut microbiota composition. In this study, we established a dextran sodium sulfate-induced colitis [...] Read more.

Although the underlying mechanisms are not yet fully understood, vitamin D has been proven to be associated with the pathogenesis of inflammatory bowel disease, participating in immune response and regulating gut microbiota composition. In this study, we established a dextran sodium sulfate-induced colitis model and intervened with vitamin D. Subsequently, colonic histopathology, serum biochemistry, transcription of inflammatory cytokines, gut microbiota, and key signaling pathways were examined. Our research demonstrated that intervention with vitamin D reduced the disease activity index of DSS-induced colitis and improved histopathological changes, protecting tight junction protein ZO-1 and intestinal glands from damage induced by DSS. Analysis of gut microbiota revealed alterations in both α diversity and β diversity in DSS-induced colitis, whereas interventions with active vitamin D corrected the changes in certain bacterial abundance and improved the composition of gut microbiota. The transcription levels of inflammatory cytokines, including IL-23, IL-1β, IFN-γ, IL-6, IL-17, and STING, were elevated in the DSS-induced colitis model. However, intervention with active vitamin D effectively suppressed the transcription of these factors. Finally, immunohistochemistry and Western blotting revealed that the intervention with vitamin D suppressed the expression of proteins associated with the STING pathway, including GATA1, STING, IRF3, and IKBα, leading to inhibition of downstream IFN-β production. Vitamin D administration can ameliorate the severity of DSS-induced colitis by preserving intestinal barrier integrity, modulating gut microbiota composition through suppression of the STING pathway. Full article

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

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17 pages, 2159 KiB

Open AccessArticle

Feasibility of Multiplex Cytokine Profiling in Preterm Labor: Towards Biomarker Discovery

by Ruth Llano, Inés Ardao, José Manuel Brea, Luz Romero, María P. Pata, Antón L. Martínez, Manuel Macía and María Isabel Loza

Biology 2025, 14(6), 714; https://doi.org/10.3390/biology14060714 - 17 Jun 2025

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Abstract

Preterm delivery affects approximately 10% of pregnancies worldwide and remains a major clinical challenge due to the lack of reliable early predictive tools. Existing strategies are often invasive, relying on blood or amniotic fluid samples and requiring complex processing. In this study, we [...] Read more.

Preterm delivery affects approximately 10% of pregnancies worldwide and remains a major clinical challenge due to the lack of reliable early predictive tools. Existing strategies are often invasive, relying on blood or amniotic fluid samples and requiring complex processing. In this study, we describe a novel non-invasive approach based on the multiplex detection of inflammatory cytokines in small urine volumes from pregnant women. To account for clinical and temporal variability, we applied Generalized Additive Models for Location, Scale, and Shape (GAMLSS) to adjust for gestational age at sampling and obstetric factors. Correlation network analyses revealed cytokine interactions that distinguished preterm from term deliveries, with macrophage-derived cytokines—MIP-1α, MIP-1β, IL-15, and IL-22—emerging as central nodes. These findings highlight the involvement of the IL-1 pathway in the pathophysiology of preterm labor. Furthermore, urinary IL-5 and IL-31 levels correlated positively with pregnancy duration, whereas IL-1β and IL-1Ra in urine and TNFα in amniotic fluid showed inverse associations. Altogether, this non-invasive methodology provides insight into immune dynamics during pregnancy and offers a foundation for future studies focused on biomarker discovery and mechanistic understanding of preterm birth. Full article

(This article belongs to the Special Issue Pregnancy Health and Complications: Molecular Processes and Mechanisms)

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15 pages, 2585 KiB

Open AccessArticle

Time-of-Day-Dependent Effects of Aerobic Exercise on Carotid Hemodynamics in Sedentary Adults

by Bingyi Shen, Haibin Liu, Shuying Zhang, Lihong Chen and Guangrui Yang

Biology 2025, 14(6), 713; https://doi.org/10.3390/biology14060713 - 17 Jun 2025

Viewed by 230

Abstract

Aerobic exercise (AE) modulates vascular function through hemodynamic responses, thereby influencing cardiovascular health and risk, with the circadian rhythm system playing a crucial role. This chronobiological study investigated diurnal variations in exercise-induced hemodynamic changes in the common carotid artery. In a randomized crossover [...] Read more.

Aerobic exercise (AE) modulates vascular function through hemodynamic responses, thereby influencing cardiovascular health and risk, with the circadian rhythm system playing a crucial role. This chronobiological study investigated diurnal variations in exercise-induced hemodynamic changes in the common carotid artery. In a randomized crossover trial, twenty-two sedentary adults completed eight AE interventions (one per laboratory visit day), with each session performed at one of eight evenly distributed time points (from 06:00 to 20:00). Vascular ultrasound imaging and hemodynamic parameter calculations were performed both pre- and post-exercise. Compared to other time points, AE at 06:00 and 18:00 induced a greater and more sustained increase in mean flow rate and wall shear stress (WSS). Moreover, AE at 06:00 was associated with a smaller increase in oscillatory shear index and a larger decrease in peripheral resistance compared to other time points. Exercise-induced hemodynamic responses exhibited significant temporal variations. These findings emphasize the importance of exercise timing in optimizing vascular benefits for sedentary individuals. Full article

(This article belongs to the Special Issue Biological Rhythms and Molecular Clockworks in Physiology and Pathology)

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15 pages, 4081 KiB

Open AccessArticle

3-Hydroxyacyl CoA Dehydratase 2 Is Essential for Embryonic Development and Hepatic Metabolic Function Under a Low-Fat, High-Carbohydrate Diet

by Lengyun Wei, Fengli Wang, Luoxue Hua, Qun Wang, Benfei Hu, Ziye Yang, Letao Li, Chenfeng Liu and Kezhen Wang

Biology 2025, 14(6), 712; https://doi.org/10.3390/biology14060712 - 17 Jun 2025

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Abstract

The conversion of carbohydrates into fatty acids is central for energy storage and the development and functioning of organs. Our previous study revealed that Hacd2 deficiency alleviates the fatty liver and diabetes induced by HFD. This study aimed to explore the roles of [...] Read more.

The conversion of carbohydrates into fatty acids is central for energy storage and the development and functioning of organs. Our previous study revealed that Hacd2 deficiency alleviates the fatty liver and diabetes induced by HFD. This study aimed to explore the roles of Hacd2 in organ development and metabolic homeostasis under an LFHCD, which still need to be more deeply explored. We found that the germline deletion of Hacd2 impairs long-chain fatty acid synthesis, which caused embryonic abnormalities after 7.5 days and led to embryonic lethality, as confirmed via photograph and hematoxylin-eosin staining. We next constructed Hacd2LKO mice and found that Hacd2LKO mice were largely normal when fed a chow diet, except for reduced inguinal white adipose tissue formation and glucose metabolism. Meanwhile, under an LFHCD, Hacd2 deletion markedly controlled body weight and white adipose tissue formation, leading to lower cholesterol and triglycerides in serum; however, it unexpectedly resulted in enlarged liver volume, hepatocyte swelling and nuclear abnormalities, and infiltration of inflammatory cells, including macrophages, neutrophils and dendritic cells. Furthermore, inhibition of Hacd2 also reduced triglyceride levels and the expression of related lipogenic genes during adipocyte differentiation, as confirmed via RNA interference analysis. These findings highlight the critical roles of Hacd2 in embryonic development and metabolic diseases, revealing its protective function in maintaining liver homeostasis under an LFHCD. Therefore, targeted interventions involving Hacd2 for metabolic diseases must take into account dietary changes and the functioning of the liver. Full article

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

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15 pages, 1061 KiB

Open AccessSystematic Review

The Physiological Effects of Whole-Body Vibration Combined with Other Exercise Modalities in Overweight and Obese Individuals: A Systematic Review

by Daniel Batouli-Santos, Ana Carolina Coelho-Oliveira, Vanessa Amaral Mendonça, Alexei Wong, Adérito Seixas, Ana Cristina Rodrigues Lacerda, Anelise Sonza, Ayman Alhammad, Mario Bernardo-Filho, Danúbia da Cunha de Sá-Caputo and Redha Taiar

Biology 2025, 14(6), 711; https://doi.org/10.3390/biology14060711 - 17 Jun 2025

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Abstract

Introduction: Emerging evidence indicates that whole-body vibration (WBV) may be a relevant adjunct in interventions targeting overweight and obese individuals. Moreover, WBV has been applied in combination with other exercise modalities and therapeutic strategies, with various physiological responses observed in this population. Objective: [...] Read more.

Introduction: Emerging evidence indicates that whole-body vibration (WBV) may be a relevant adjunct in interventions targeting overweight and obese individuals. Moreover, WBV has been applied in combination with other exercise modalities and therapeutic strategies, with various physiological responses observed in this population. Objective: The current systematic review aimed to assess the physiological effects of WBV with other modalities of exercises in overweight and obese individuals. Methods: Searches in PubMed, Embase, Web of Science, Scopus, and Cochrane databases were conducted to assess physiological responses to the combination of WBV with other modalities of exercises in overweight and obese individuals. Publications were identified and the screening was performed by two reviewers, independently. Irrelevant studies were excluded based on the eligibility criteria. Results: Seven studies, analyzing different outcomes, were included, with a mean methodological quality score of 7. Four studies analyzed the acute effect and three studied the cumulative effect, with different intervention protocols. Increases in growth hormone (GH) concentrations and bioelectrical phase angles, and reductions in fat mass, blood triglycerides, and cholesterol concentrations, as well as blood pressure, heart rate, and arterial stiffness, were reported. Conclusions: WBV combined with other exercise modalities seems to promote important physiological responses in overweight and obese individuals. However, more large-scale, long-term randomized controlled trials with WBV and other modalities of exercises in overweight and obese cohorts are needed to corroborate and expand the findings of the current systematic review. Full article

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42 pages, 6908 KiB

Open AccessArticle

Vegetation Analysis of Wetland Ecosystems in Southern Turkey Using the Fuzzy Means Method

by Deniz Boz

Biology 2025, 14(6), 710; https://doi.org/10.3390/biology14060710 - 17 Jun 2025

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Abstract

In this study, the vegetation of the natural area of the Göksu Delta Special Environmental Protection Agency (SEPA), one of Turkey’s most important wetlands, is researched. The importance of this study in terms of contributing to environmental protection and land use planning studies [...] Read more.

In this study, the vegetation of the natural area of the Göksu Delta Special Environmental Protection Agency (SEPA), one of Turkey’s most important wetlands, is researched. The importance of this study in terms of contributing to environmental protection and land use planning studies reveals that this natural area, where rare ecosystems are found, has started to degrade and disappear under human influence. This study was conducted because the area is not only a designated RAMSAR wetland (a wetland site designated of international importance especially for the Waterfowl Habitat under the Ramsar Convention) but also includes nearby residential developments. With this study, the vegetation of the area was studied to determine the syntaxonomic units across different habitats. The natural area of Göksu Delta is divided into three main habitat groups: aquatic, sand dune, and halophytic. In the research, the Braun-Blanquet method was used. During the research in the Göksu Delta, 279 sample areas were surveyed. The data were analysed according to the fuzzy means cluster method. During the investigation, 29 associations were identified, and 16 of them are considered a new finding for science. These 29 associations can be classified as follows: aquatic vegetation is represented with four associations (three of them belong to Phragmito-Magnocaricetea and one of them belongs to Potametea classes), sand dune vegetation is represented with 12 associations (belonging to Ammophiletea Br.-Bl. & Tüxen ex Westhoff, Dijk, & Passchier 1946 class), and halophytic vegetation is represented with 13 associations (six of them belong to Salicornietea fruticosae Br.-Bl. & Tüxen ex A. & O. Bolòs 1950, six of them belong to Juncetea maritimi Br.-Bl. in Br.-Bl., Roussine & Nègre 1952, and one of them belong to Molinio-Juncetea Br.-Bl. (1931) 1947 classes). Three (Onopordum boissieri, Ambrosia maritima, and Chlamydophora tridentata) of the endemics and rare plants that were explored during the study were recorded as new alliance characteristics. Full article

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

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15 pages, 1363 KiB

Open AccessReview

Unveiling the Defenses: A Current and Comprehensive Review of Coleoptera Carabidae Strategies

by Teresa Bonacci

Biology 2025, 14(6), 709; https://doi.org/10.3390/biology14060709 - 17 Jun 2025

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Abstract

The Carabidae family, or ground beetles, is a wide and ecologically significant group within the Coleoptera order, known for its role as natural predators of agricultural pests and as bioindicators of ecosystem health. These beetles employ a variety of behavioral, morphological, and chemical [...] Read more.

The Carabidae family, or ground beetles, is a wide and ecologically significant group within the Coleoptera order, known for its role as natural predators of agricultural pests and as bioindicators of ecosystem health. These beetles employ a variety of behavioral, morphological, and chemical defense strategies to protect themselves from predators. These mechanisms include gregariousness, stridulation, regurgitation, and chemical defenses, such as the secretion of irritating compounds from specialized glands. The defensive strategies of carabids are classified into passive and active systems, each with varying energetic costs. Chemical substances (e.g., Formic acid, Methacrylic acid, Tiglic acid, Ethacrilic acid, Isovaleric acid, Salicylaldehyde, 1,4-Benzoquinone, Toluquinone, 13-2Kt tridecan-2-one, Undecane, Tridecane, Pentadecane, M-cresol) are particularly important, as they serve to deter predators and combat pathogens like bacteria and fungi. Ground beetles utilize both polar and non-polar compounds in their defense, all contributing to their ecological success. This review explores the array of defensive mechanisms in the Carabidae family, highlighting experimental studies, field observations, and reviews published over the last five decades. The aim is to provide a comprehensive understanding of how these strategies enhance the survival and fitness of carabid beetles in their natural environments. Full article

(This article belongs to the Section Behavioural Biology)

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15 pages, 17305 KiB

Open AccessArticle

Response of cbbL Carbon-Sequestering Microorganisms to Simulated Warming in the River Source Wetland of the Wayan Mountains

by Shijia Zhou, Kelong Chen, Ni Zhang, Siyu Wang, Zhiyun Zhou and Jianqing Sun

Biology 2025, 14(6), 708; https://doi.org/10.3390/biology14060708 - 16 Jun 2025

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Abstract

As a globally critical carbon reservoir, the response mechanism of wetland ecosystems to climate change on the Qinghai–Tibet Plateau (QTP) has attracted significant scientific scrutiny. This study investigated the temperature sensitivity of cbbL-harboring carbon-sequestering microbial communities and their coupling with carbon–nitrogen cycle dynamics [...] Read more.

As a globally critical carbon reservoir, the response mechanism of wetland ecosystems to climate change on the Qinghai–Tibet Plateau (QTP) has attracted significant scientific scrutiny. This study investigated the temperature sensitivity of cbbL-harboring carbon-sequestering microbial communities and their coupling with carbon–nitrogen cycle dynamics through a simulated field warming experiment conducted in the Wayan Mountains’ river source wetland in the northeastern QTP. Key findings revealed that warming markedly elevated Alpha diversity (ACE and Chao1 indices), whereas Shannon and Simpson indices remained stable, indicating that temperature increases primarily altered community composition by enhancing species richness rather than evenness. Taxonomic analysis demonstrated significant increases in the relative abundances of Cyanobacteria and Actinobacteria, while Proteobacteria retained dominance but exhibited reduced relative abundance. At the genus level, Thioflexothrix, Ferrithrix, and Rhodospirillum dominated the community, with Thioflexothrix and Ferrithrix showing warming-induced abundance increments. Functional predictions indicated that warming preferentially stimulated heterotrophic and photoheterotrophic functional guilds. Soil physicochemical analyses further revealed warming-driven increases in nitrate nitrogen (NN), total carbon (TC), and total nitrogen (TN), concurrent with decreased soil moisture. Redundancy analysis identified TC as the predominant determinant of microbial community structure (followed by TN > NN), while pH and ammonium nitrogen (AN) exerted comparatively limited influence. Strong positive correlations between microbial communities and carbon/nitrogen indicators suggested that enhanced carbon–nitrogen resource availability served as the central driver of community succession. These findings elucidate the temperature-responsive mechanisms of cbbL-type carbon-sequestering microorganisms in alpine wetlands, offering critical insights for the adaptive management of carbon cycling in high-altitude ecosystems and advancing strategies toward achieving carbon neutrality goals. Full article

(This article belongs to the Section Microbiology)

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17 pages, 3825 KiB

Open AccessArticle

Population Structure, Growth Characteristics, Resource Dynamics, and Management Strategies of Schizopygopsis younghusbandi in Four Tributaries of the Yarlung Zangbo River, Tibet

by Haoxiang Han, Lin Wang, Chi Zhang, Hongchi Li and Bo Ma

Biology 2025, 14(6), 707; https://doi.org/10.3390/biology14060707 - 16 Jun 2025

Viewed by 247

Abstract

Aquatic biodiversity of the Yarlung Zangbo River is both unique and fragile, with its ecological environment currently under significant pressure. However, comprehensive studies on the biological characteristics and resource status of fish in its tributaries remain insufficient. In this study, we analyzed the [...] Read more.

Aquatic biodiversity of the Yarlung Zangbo River is both unique and fragile, with its ecological environment currently under significant pressure. However, comprehensive studies on the biological characteristics and resource status of fish in its tributaries remain insufficient. In this study, we analyzed the population structure, growth characteristics, and resource dynamics of 2058 specimens of Schizopygopsis younghusbandi that were collected from four major tributaries in the middle reaches of the Yarlung Zangbo River (Duoxiong Zangbo, Lhasa River, Niyang River, and Nianchu River) between 2023 and 2024. Population parameters were estimated using the Von Bertalanffy growth equation, revealing asymptotic body lengths (L∞) between 387.877 and 414.535 mm and growth coefficients (k) ranging from 0.154 to 0.174. Notably, the k values exhibited a gradual decline in growth rate with increasing altitude. Based on calculations from FiSAT II software, the exploitation rate (E) revealed that the Duoxiong Zangbo population remained within a safe range (E < 0.5), whereas the Nianchu, Lhasa, and Niyang River populations were overexploited (E > 0.5), with their population structures showing signs of under-ageing and miniaturization. To ensure stable population continuity, the minimum catchable body lengths were estimated as 248 mm, 240 mm, 233 mm, and 236 mm for the Duoxiong Zangbo, Nianchu, Lhasa, and Niyang Rivers, respectively, with slight variations among tributaries. These findings suggest that S. younghusbandi populations in the Yarlung Zangbo River tributaries are adversely affected by external pressures and face a decline, necessitating effective conservation and restoration strategies. Full article

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

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18 pages, 2243 KiB

Open AccessArticle

Optimizing LED Light Intensity and Photoperiod to Promote Growth and Rooting of Medicinal Cannabis in Photoautotrophic Micropropagation

by Juwen Liang, Fang Ji, Qing Zhou and Dongxian He

Biology 2025, 14(6), 706; https://doi.org/10.3390/biology14060706 - 16 Jun 2025

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Abstract

Conventional micropropagation of cannabis struggles with excessive callus hyperhydration, slow growth, low rooting efficiency, and high contamination risk, all of which greatly restrict its feasibility for large-scale propagation. In contrast, photoautotrophic micropropagation (PAM) has emerged as an efficient and cost-effective propagation strategy that [...] Read more.

Conventional micropropagation of cannabis struggles with excessive callus hyperhydration, slow growth, low rooting efficiency, and high contamination risk, all of which greatly restrict its feasibility for large-scale propagation. In contrast, photoautotrophic micropropagation (PAM) has emerged as an efficient and cost-effective propagation strategy that can significantly enhance plantlet growth and improve seedling quality by optimizing the LED lighting environment. This study investigated the effects of four light intensities (50, 100, 150, and 200 µmol m⁻² s⁻¹) and three photoperiods (16, 20, and 24 h d⁻¹) on the growth and rooting of two medicinal cannabis cultivars (the short-day cultivar ‘Charlotte’ and the day-neutral cultivar ‘Auto Charlotte’). Cluster analysis revealed that plantlets grown under the photoperiod of 20 h d⁻¹ and light intensity of 100–150 µmol m⁻² s⁻¹ exhibited optimal growth performance in terms of plant height, root length, leaf number, leaf area, biomass, and root activity. Moreover, increasing the light intensity from 50 to 100–150 µmol m⁻² s⁻¹ significantly enhanced net CO₂ exchange rates by 41.5% and 204.9% for Charlotte and Auto Charlotte, respectively, along with corresponding increases in dry matter accumulation of 44.3% and 27.9%. However, the plantlets exhibited photooxidative damage under continuous lighting and light intensity of 200 µmol m⁻² s⁻¹, as evidenced by reduced photosynthetic pigment content and suppressed antioxidant enzyme activity. Therefore, PAM of medicinal cannabis is recommended under the LED lighting environment with light intensity of 100–150 µmol m⁻² s⁻¹ and photoperiod of 20 h d⁻¹ to achieve optimal growth and rooting. These findings provide essential technical support for the large-scale propagation of vigorous, disease-free female plantlets with well-developed root systems and high genetic uniformity, thereby meeting the stringent quality standards for planting materials in the commercial cultivation of cannabis for medical and pharmaceutical use. Full article

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

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