Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (18,388)

Search Parameters:
Keywords = RNA sequencing

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
25 pages, 1970 KiB  
Article
DRFormer: A Benchmark Model for RNA Sequence Downstream Tasks
by Jianqi Fu, Haohao Li, Yanlei Kang, Hancan Zhu, Tiren Huang and Zhong Li
Genes 2025, 16(3), 284; https://doi.org/10.3390/genes16030284 (registering DOI) - 26 Feb 2025
Abstract
Background/Objectives: RNA research is critical for understanding gene regulation, disease mechanisms, and therapeutic development. Constructing effective RNA benchmark models for accurate downstream analysis has become a significant research challenge. The objective of this study is to propose a robust benchmark model, DRFormer, for [...] Read more.
Background/Objectives: RNA research is critical for understanding gene regulation, disease mechanisms, and therapeutic development. Constructing effective RNA benchmark models for accurate downstream analysis has become a significant research challenge. The objective of this study is to propose a robust benchmark model, DRFormer, for RNA sequence downstream tasks. Methods: The DRFormer model utilizes RNA sequences to construct novel vision features based on secondary structure and sequence distance. These features are pre-trained using the SWIN model to develop a SWIN-RNA submodel. This submodel is then integrated with an RNA sequence model to construct a multimodal model for downstream analysis. Results: We conducted experiments on various RNA downstream tasks. In the sequence classification task, the MCC reached 94.4%, surpassing the state-of-the-art RNAErnie model by 1.2%. In the protein–RNA interaction prediction, DRFormer achieved an MCC of 0.492, outperforming advanced models like BERT-RBP and PrismNet. In RNA secondary structure prediction, the F1 score was 0.690, exceeding the widely used SPOT-RNA model by 1%. Additionally, generalization experiments on DNA tasks yielded satisfactory results. Conclusions: DRFormer is the first RNA sequence downstream analysis model that leverages structural features to construct a vision model and integrates sequence and vision models in a multimodal manner. This approach yields excellent prediction and analysis results, making it a valuable contribution to RNA research. Full article
(This article belongs to the Section RNA)
14 pages, 2690 KiB  
Article
First Description of Intergenic Sequences in Corydoradinae and Introducing the Complete Mitogenome of Hoplisoma concolor (Siluriformes: Callichthyidae)
by Seong Duk Do and Jae-Sung Rhee
Genes 2025, 16(3), 282; https://doi.org/10.3390/genes16030282 - 26 Feb 2025
Viewed by 19
Abstract
: Background/Objectives: In this study, we report the complete mitochondrial genome sequence of Hoplisoma concolor Weitzman, 1961 (Siluriformes: Callichthyidae), a callichthyid catfish. Methods: DNA sequencing was performed to obtain its complete mitogenome using the HiSeq platform. To assess the phylogenetic relationships, maximum-likelihood and [...] Read more.
: Background/Objectives: In this study, we report the complete mitochondrial genome sequence of Hoplisoma concolor Weitzman, 1961 (Siluriformes: Callichthyidae), a callichthyid catfish. Methods: DNA sequencing was performed to obtain its complete mitogenome using the HiSeq platform. To assess the phylogenetic relationships, maximum-likelihood and Bayesian inference phylogenetic trees were constructed using two ribosomal RNA (rRNA) genes and all protein-coding sequences (PCGs) concatenated from the H. concolor mitogenome, along with 31 other Siluriformes mitogenomes. Results: The complete mitogenome of H. concolor is 16,579 base pairs in length, with a nucleotide composition of 32.2% A, 26.0% T, 15.3% G, and 26.5% C. It contains 13 PCGs, 22 transfer RNA genes, and 2 rRNA genes. Phylogenetic analysis based on all PCGs and two rRNAs of the complete mitogenome confirms H. concolor as a sister species of H. panda within the subfamily Corydoradinae. In addition, intergenic sequences between atp6 and cox3 of 21 species of Corydoradinae provide further support for their phylogenetic relationship. Conclusions: Given the lack of detailed descriptions regarding the length and nucleotide composition of these intergenic sequences, our study contributes valuable insights into the genetic diversity and evolutionary complexity of Callichthyidae. Full article
(This article belongs to the Special Issue Mitochondrial DNA Replication and Transcription)
16 pages, 1339 KiB  
Article
The Gut Microbiota of the Greater Horseshoe Bat Confers Rapidly Corresponding Immune Cells in Mice
by Shan Luo, Xinlei Huang, Siyu Chen, Junyi Li, Hui Wu, Yuhua He, Lei Zhou, Boyu Liu and Jiang Feng
Animals 2025, 15(5), 685; https://doi.org/10.3390/ani15050685 - 26 Feb 2025
Viewed by 9
Abstract
Background: Emerging infectious diseases threaten human and animal health, with most pathogens originating from wildlife. Bats are natural hosts for many infectious agents. Previous studies have demonstrated that changes in some specific genes in bats may contribute to resistance to viral infections, but [...] Read more.
Background: Emerging infectious diseases threaten human and animal health, with most pathogens originating from wildlife. Bats are natural hosts for many infectious agents. Previous studies have demonstrated that changes in some specific genes in bats may contribute to resistance to viral infections, but they have mostly overlooked the immune function of the bat gut microbiota. Aims: In this study, we used fecal transplants to transfer the gut microbiota from the Greater Horseshoe Bat (Rhinolophus ferrumequinum) into mice treated with antibiotics. The gut microbiota changes in mice were detected using 16S rRNA high-throughput sequencing technology. Flow cytometry was used to detect changes in associated immune cells in the spleen and mesenteric lymph nodes of the mice. Results: The results showed that the gut microbiota of mice showed characteristics of some bat gut microbiota. The Greater Horseshoe Bat’s gut microbiota changed some immune cells’ composition in the spleen and mesenteric lymph nodes of mice and also conferred a faster and higher proportion of natural killer cell activation. Conclusion: This result provides new evidence for the regulatory immune function of bat gut microbiota and contributes to a deeper insight into the unique immune system of bats. Full article
(This article belongs to the Section Wildlife)
10 pages, 2324 KiB  
Article
Conservation and Variability in Mitochondrial Genomes of Perlodidae: Insights from Comparative Mitogenomics
by Xiao Yang, Qing-Bo Huo, Abdur Rehman, Ya-Fei Zhu and Yu-Zhou Du
Insects 2025, 16(3), 245; https://doi.org/10.3390/insects16030245 - 26 Feb 2025
Abstract
The mitochondrial genomes of three stoneflies, e.g., Tibetisoperla wangluyui Huo and Du, 2021, Perlodinella kozlovi Klapálek, 1912 and Perlodinella epiproctalis (Zwick, 1997), were sequenced in this study, with lengths 16,043 bp, 16,024 bp, and 16,071 bp, respectively. Each mitogenome contained 37 genes including [...] Read more.
The mitochondrial genomes of three stoneflies, e.g., Tibetisoperla wangluyui Huo and Du, 2021, Perlodinella kozlovi Klapálek, 1912 and Perlodinella epiproctalis (Zwick, 1997), were sequenced in this study, with lengths 16,043 bp, 16,024 bp, and 16,071 bp, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Meanwhile, in this paper, three newly published mitochondrial genomes and 11 existing mitochondrial genomes of the Perlodidae from NCBI were analyzed. Among the 13 PCGs in the mitochondrial genome of Perlodidae, the lengths of atp6, atp8, cox2, cox3, cytb, nad1, nad2, nad3, and nad4 are exactly the same, and the length of cox1 is 1536–1569 bp. The length of nad4L is 297, but the length of Arcynopteryx dichroa is 300. The length of nad5 ranges from 1732 bp to 1752 bp, while that of nad6 ranges from 525 bp to 534 bp. The length of rrnL is between 1292 and 391 bp, and the length of rrnS is between 793 and 869 bp. In addition, we found that atp8 in Isoperlinae started with GTG as a start codon but in Perlodinae, it started with ATG. Despite these advances, mitochondrial genome data from the Perlodidae are still needed. Full article
(This article belongs to the Special Issue Aquatic Insects Biodiversity and eDNA Monitoring)
21 pages, 2936 KiB  
Article
Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks
by Amirhossein Manzourolajdad and Mohammad Mohebbi
Non-Coding RNA 2025, 11(2), 18; https://doi.org/10.3390/ncrna11020018 - 26 Feb 2025
Viewed by 3
Abstract
RNA inverse design is an essential part of many RNA therapeutic strategies. To date, there have been great advances in computationally driven RNA design. The current machine learning approaches can predict the sequence of an RNA given its 3D structure with acceptable accuracy [...] Read more.
RNA inverse design is an essential part of many RNA therapeutic strategies. To date, there have been great advances in computationally driven RNA design. The current machine learning approaches can predict the sequence of an RNA given its 3D structure with acceptable accuracy and at tremendous speed. The design and engineering of RNA regulators such as riboswitches, however, is often more difficult, partly due to their inherent conformational switching abilities. Although recent state-of-the-art models do incorporate information about the multiple structures that a sequence can fold into, there is great room for improvement in modeling structural switching. In this work, a relational geometric graph neural network is proposed that explicitly incorporates alternative structures to predict an RNA sequence. Converting the RNA structure into a geometric graph, the proposed model uses edge types to distinguish between the primary structure, secondary structure, and spatial positioning of the nucleotides in representing structures. The results show higher native sequence recovery rates over those of gRNAde across different test sets (eg. 72% vs. 66%) and a benchmark from the literature (60% vs. 57%). Secondary-structure edge types had a more significant impact on the sequence recovery than the spatial edge types as defined in this work. Overall, these results suggest the need for more complex and case-specific characterization of RNA for successful inverse design. Full article
16 pages, 5759 KiB  
Article
Comprehensive SHAP Values and Single-Cell Sequencing Technology Reveal Key Cell Clusters in Bovine Skeletal Muscle
by Yaqiang Guo, Fengying Ma, Peipei Li, Lili Guo, Zaixia Liu, Chenxi Huo, Caixia Shi, Lin Zhu, Mingjuan Gu, Risu Na and Wenguang Zhang
Int. J. Mol. Sci. 2025, 26(5), 2054; https://doi.org/10.3390/ijms26052054 - 26 Feb 2025
Abstract
The skeletal muscle of cattle is the main component of their muscular system, responsible for supporting and movement functions. However, there are still many unknown areas regarding the ranking of the importance of different types of cell populations within it. This study conducted [...] Read more.
The skeletal muscle of cattle is the main component of their muscular system, responsible for supporting and movement functions. However, there are still many unknown areas regarding the ranking of the importance of different types of cell populations within it. This study conducted in-depth research and made a series of significant findings. First, we trained 15 bovine skeletal muscle models and selected the best-performing model as the initial model. Based on the SHAP (Shapley Additive exPlanations) analysis of this initial model, we obtained the SHAP values of 476 important genes. Using the contributions of these 476 genes, we reconstructed a 476-gene SHAP value matrix, and relying solely on the interactions among these 476 genes, successfully mapped the single-cell atlas of bovine skeletal muscle. After retraining the model and further interpretation, we found that Myofiber cells are the most representative cell type in bovine skeletal muscle, followed by neutrophils. By determining the key genes of each cell type through SHAP values, we conducted analyses on the correlations among key genes and between cells for Myofiber cells, revealing the critical role these genes play in muscle growth and development. Further, by using protein language models, we performed cross-species comparisons between cattle and pigs, deepening our understanding of Myofiber cells as key cells in skeletal muscle, and exploring the common regulatory mechanisms of muscle development across species. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
19 pages, 5768 KiB  
Article
Weizmannia coagulans BC99: A Novel Adjunct to Protein Supplementation for Enhancing Exercise Endurance and Reducing Fatigue
by Minghan Guo, Lina Zhao, Li Cao, Xuan Li, Jie Zhang, Yao Dong, Ying Wu and Shaobin Gu
Foods 2025, 14(5), 801; https://doi.org/10.3390/foods14050801 (registering DOI) - 26 Feb 2025
Viewed by 82
Abstract
Adequate protein consumption is essential for optimal physical fitness and enhancing athletic performance. This study explored the impact of Weizmannia coagulans BC99 on protein-supplemented male fatigued mice, examining aspects such as protein digestion, exercise endurance, fatigue-related biochemistry, oxidative stress, and gut microbiota alterations. [...] Read more.
Adequate protein consumption is essential for optimal physical fitness and enhancing athletic performance. This study explored the impact of Weizmannia coagulans BC99 on protein-supplemented male fatigued mice, examining aspects such as protein digestion, exercise endurance, fatigue-related biochemistry, oxidative stress, and gut microbiota alterations. Results indicate that the synergistic effect of probiotics and protein significantly boosts the activity of protein-digesting enzymes, enhances protein absorption, and reduces serum levels of urea nitrogen, lactate, lactate dehydrogenase, creatine kinase, malondialdehyde, and the inflammatory cytokines interleukin-1β and interleukin-6 in skeletal muscle. Additionally, serum catalase, glutathione, superoxide dismutase levels, interleukin-4 in skeletal muscle, and glycogen stores in muscle and liver were notably increased. The study also found elevated mRNA expression levels of Nrf2 and HO-1 in skeletal muscle. Furthermore, an increase in short-chain fatty acids was observed in the probiotic treatment group, and 16S rDNA sequencing revealed that Weizmannia coagulans BC99 enhanced gut microbiota diversity and augmented beneficial bacterial populations including Roseburia, Mucispirillum, Rikenella, and Kineothrix. Collectively, these findings suggest that combining BC99 with protein supplementation can effectively improve gut flora, thereby enhancing exercise capacity and exerting potent anti-fatigue effects. Our research provides a new possibility for alleviating exercise-induced fatigue. Full article
Show Figures

Figure 1

20 pages, 1857 KiB  
Article
Human Milk Microbiota Across Lactation Stages and Free Glutamate Concentrations in Healthy Ecuadorian Women
by Manuel E. Baldeon, Paul Cardenas, Valentina Arevalo, Belen Prado-Vivar, Mario Uchimiya, Lizbeth Peña, Andrea Denisse Benitez, Andrés Suárez-Jaramillo, Arthur S. Edison, Alonso Herrera, Linda Arturo and Marco Fornasini
Nutrients 2025, 17(5), 805; https://doi.org/10.3390/nu17050805 - 26 Feb 2025
Viewed by 118
Abstract
Background/Objectives: There is limited information on human milk (HM) microbiome composition and function in Latin America. Also, interactions between HM constituents and its microbiome have received partial attention. Objective: To characterize the HM microbiota composition considering lactation stages (colostrum, transition, and mature HM) [...] Read more.
Background/Objectives: There is limited information on human milk (HM) microbiome composition and function in Latin America. Also, interactions between HM constituents and its microbiome have received partial attention. Objective: To characterize the HM microbiota composition considering lactation stages (colostrum, transition, and mature HM) and free glutamate concentrations in Ecuadorian mothers. Methods: We recruited 20 mothers that gave birth to normal full-term babies and donated colostrum, transition, and mature milk. Samples were assessed by 16S rRNA gene sequencing by Oxford Nanopore Technologies (ONT). Free glutamate concentrations were measured by proton nuclear magnetic resonance (NMR) spectroscopy. Results: For each lactation stage and in order of frequency, the majority of ASVs were assigned to Staphylococcus, Streptococcus, (Firmicutes); Escherichia, Acinetobacter, (Proteobacteria); Corynebacterium, Lactobacillus, Cutibacterium, (Actinobacteriota); Chryseobacterium, and Flavobacterium (Bacteroidota). Alfa diversity was similar in HM samples and tended to be higher in milk intended for male infants. We observed significant differences in qualitative β-diversity metrics between samples with low and high glutamate concentrations. Functional predictions of HM microbiota demonstrated the presence of polyamine biosynthesis II super pathway in samples with high glutamate concentrations. Conclusions: The core bacterial components of the HM microbiota in Ecuadorian women were similar to those reported from different parts of the world, with variations at the genus level. Free glutamate dynamics in HM need to be studied considering maternal production and bacterial metabolism to better understand HM composition for optimal infant nutrition. Full article
(This article belongs to the Section Proteins and Amino Acids)
Show Figures

Figure 1

21 pages, 5838 KiB  
Article
In Silico Characterization of GmbHLH18 and Its Role in Improving Soybean Cyst Nematode Resistance via Genetic Manipulation
by Shuo Qu, Shihao Hu, Miaoli Zhang, Gengchen Song, Fang Liu, Weili Teng, Yuhang Zhan, Yongguang Li, Haiyan Li, Xue Zhao and Yingpeng Han
Agronomy 2025, 15(3), 574; https://doi.org/10.3390/agronomy15030574 - 26 Feb 2025
Viewed by 37
Abstract
Soybean is crucial to food processing and agricultural output. However, pests and diseases can easily impact soybeans, reducing their production. Soybean cyst nematode (SCN) is a soilborne pathogen that has a large geographic range, a long lifespan, and the potential to inflict substantial [...] Read more.
Soybean is crucial to food processing and agricultural output. However, pests and diseases can easily impact soybeans, reducing their production. Soybean cyst nematode (SCN) is a soilborne pathogen that has a large geographic range, a long lifespan, and the potential to inflict substantial harm to the soybean industry. Persistent use of major resistance genes leads to a progressive loss of resistance; therefore, continuous identification of new soybean strains and genes is essential for continued sustainable soybean production. In this research, the SCN-resistant and SCN-sensitive germplasm DN-L10 and Heinong 37 were inoculated with SCN 3. After stress treatment, the stressed roots were collected for RNA-Seq analysis. The sequencing results screened out the differentially expressed gene GmbHLH18. The GmbHLH18 gene was cloned, and the overexpression vector pCAMBIA3300-GmbHLH18 was constructed. Agrobacterium infected soybean hairy roots and genetically modified the roots of DN50 soybeans, and transgenic root seedlings were obtained. The transgenically identified root seedlings were transplanted in soil infested with SCN 3, and resistance to root nematodes was determined by magenta staining. The secondary and tertiary structures of the protein, phosphorylation sites, as well as the hydrophilicity related to the GmbHLH18 gene were analyzed. Subsequently, the recombinant subcellular localization vector pCAMBIA1302-GmbHLH18 was employed. Agrobacterium was injected into tobacco leaves, and organelle-specific expression was observed. Finally, stress resistance-related indexes of the roots of overexpressing plants and WT plants under SCN 3 stress were measured. The results showed that overexpression and subcellular localization vectors were successfully constructed and transformed into Agrobacterium K599 and GV3101, respectively. The encoded protein had 1149 amino acids, a molecular weight of 95.76 kDa, an isoelectric point of 5.04, 60 phosphorylation sites, a tertiary structure of a-helix (36.39%), random coil (53.40%), extended chain (8.64%), and corner (1.57%), and was hydrophilic. The protein that the gene encoded was a nuclear-localized protein, according to the results of subcellular localization analysis. Moreover, the Agrobacterium-induced hairy root test revealed that the number of overexpressed pCAMBIA3300-GmbHLH18 transgenic roots in the unit area of DN50 was substantially lower than in the control group, which at first suggested that the gene had partial resistance to SCN 3. Stress resistance-related indexes suggest that the contents of POD, SOD, and proline in the overexpressing root significantly increase after SCN 3 stress, demonstrating that this gene can enhance the plant’s resistance to the SCN 3 pathogen. Future research could focus on further elucidating the molecular mechanism underlying the gene’s resistance to SCN 3 and exploring its potential application in breeding soybean varieties with enhanced resistance. Full article
Show Figures

Figure 1

20 pages, 12981 KiB  
Article
MicroRNA Profiling Identifies Age-Associated MicroRNAs and Potential Biomarkers for Early Diagnosis of Autism
by Salam Salloum-Asfar, Samia M. Ltaief, Rowaida Z. Taha, Wared Nour-Eldine, Sara A. Abdulla and Abeer R. Al-Shammari
Int. J. Mol. Sci. 2025, 26(5), 2044; https://doi.org/10.3390/ijms26052044 - 26 Feb 2025
Viewed by 55
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder in which early diagnosis is critical for effective intervention and improved outcomes. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and have emerged as promising biomarkers for neurological disorders, including ASD. In our [...] Read more.
Autism spectrum disorder (ASD) is a neurodevelopmental disorder in which early diagnosis is critical for effective intervention and improved outcomes. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and have emerged as promising biomarkers for neurological disorders, including ASD. In our previous discovery study, we identified dysregulated expression of several miRNAs in the plasma samples of children with ASD aged 5–12 years. In this study, we aimed to validate these findings in a younger cohort with ASD (aged 2–4 years) and assess their potential use as biomarkers for the early diagnosis of ASD. A total of 108 young children aged 2–4 years were recruited, including 66 children with ASD and 42 age- and sex-matched controls. Using next-generation sequencing and advanced bioinformatics, we validated the differential expression of 17 miRNAs in ASD, which showed consistent dysregulation across both the current and previous cohorts. We also observed significant correlations between several miRNAs and participants’ age, suggesting that age is a key factor influencing dynamic miRNA changes, particularly in the ASD group. Pathway analysis linked these miRNAs to critical regulatory networks involved in neurodevelopment and immune responses. Finally, we found that a combination of four miRNAs (miR-4433b-5p, miR-15a-5p, miR-335-5p, and miR-1180-3p) exhibited high diagnostic accuracy, with an area under the curve (ROC-AUC) of 0.936 (95% CI = 0.892, 0.980; p < 0.001). These findings support the use of this four-miRNA panel as a robust biomarker for early ASD diagnosis and lay the groundwork for future research into miRNA-based diagnostic tools and therapeutic strategies for ASD. Full article
Show Figures

Figure 1

22 pages, 1695 KiB  
Article
Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-Reared Bombyx mori Hybrids
by Ma. Ysabella Elaine D. Conde, Jose Planta and Ma. Anita M. Bautista
Insects 2025, 16(3), 243; https://doi.org/10.3390/insects16030243 - 26 Feb 2025
Viewed by 38
Abstract
In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This [...] Read more.
In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This study, therefore, aims to investigate the basis of hybrid vigor and generate molecular resources through whole-silkworm larvae transcriptome sequencing, assembly, and analysis. Differential gene expression was also conducted among the parental strains and hybrids. Assembly of the pre-processed reads was also performed using de novo and reference-based protocols. As expected, the reference-based assembly was better than de novo, based on E90N50, N50, and BUSCO assembly completeness metrics. The Analysis of the differentially expressed genes (DEGs) revealed 202 upregulated and 182 downregulated genes in the hybrids (with the parents as the reference) and 66 upregulated and 753 downregulated genes in NC144 (with CN144 as the reference). Among these were genes encoding heat shock proteins and antimicrobial peptides, which may serve as markers for marker-assisted breeding. The genes were further validated using quantitative real-time PCR. Moreover, the inducible nature of these genes under stressors like extreme temperature and bacterial exposure suggests their potential as diagnostic tools for stress assessment. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
Show Figures

Figure 1

23 pages, 4082 KiB  
Article
Biocontrol Potential of Bacillus Strains from Grapevine Rhizosphere Against Allorhizobium vitis, Causal Agent of Crown Gall Disease in Moroccan Vineyards
by Hiba Yahyaoui, Nadia El Allaoui, Amine Batbat, Aziz Aziz, Faical Aoujil, Majida Hafidi and Khaoula Habbadi
Int. J. Plant Biol. 2025, 16(1), 27; https://doi.org/10.3390/ijpb16010027 - 26 Feb 2025
Viewed by 36
Abstract
Beneficial bacteria are recognised for their antimicrobial compounds, making them valuable for disease control in agriculture. Bacillus species stand out for their stability, versatility, and selectivity as biocontrol agents. This study aimed to identify potential antagonists within the rhizosphere microorganisms by isolating bacterial [...] Read more.
Beneficial bacteria are recognised for their antimicrobial compounds, making them valuable for disease control in agriculture. Bacillus species stand out for their stability, versatility, and selectivity as biocontrol agents. This study aimed to identify potential antagonists within the rhizosphere microorganisms by isolating bacterial strains from grapevine roots and rhizosphere soil in Moroccan vineyards. The antimicrobial activities of these isolates against Allorhizobium vitis, the causative agent of grapevine crown gall, were evaluated in vitro using a disc diffusion assay, followed by in planta assessments under preventive and simulated inoculation conditions. Screening led to the isolation of 123 strains, with six showing strong antagonistic properties, achieving inhibition percentages up to 39.6%. 16S rRNA sequencing led to identifying five Bacillus species: B. amyloliquefaciens, B. velezensis, B. halotolerans, B. subtilis, and B. anthracis. These strains were further characterised by their biochemical traits and plant growth-promoting abilities. Compatibility assays identified optimal combinations for microbial consortia, demonstrating pathogen inhibition up to 37.4%. In planta bioassays confirmed the effectiveness of the isolates and consortia, reducing tumour size. These findings highlight the potential of these Bacillus strains as biocontrol agents and underscore the value of microbial consortia as a sustainable approach to managing grapevine crown gall. Full article
(This article belongs to the Section Plant–Microorganisms Interactions)
Show Figures

Figure 1

15 pages, 3693 KiB  
Article
Two Complete Mitochondrial Genomes of Potamanthidae (Ephemeroptera): Genome Features and Phylogenetic Implications
by Ran Li, Chao Xue, Zhenxing Ma and Changfa Zhou
Diversity 2025, 17(3), 164; https://doi.org/10.3390/d17030164 - 26 Feb 2025
Viewed by 146
Abstract
The family Potamanthidae is widely distributed across the Holarctic and Oriental regions, with nymphs often utilized as bioindicators for water pollution and human-induced environmental disturbances. However, limited mitochondrial genomes (mitogenomes) have been reported for this family. This study presents the first complete mitochondrial [...] Read more.
The family Potamanthidae is widely distributed across the Holarctic and Oriental regions, with nymphs often utilized as bioindicators for water pollution and human-induced environmental disturbances. However, limited mitochondrial genomes (mitogenomes) have been reported for this family. This study presents the first complete mitochondrial genome sequences of two Potamanthidae species, Potamanthus longitibius and Rhoenanthus youi. The mitogenome sizes were 15,430 bp and 15,232 bp, with A + T contents of 68.79% and 66.75%, respectively. The most abundant amino acids were phenylalanine (Phe), isoleucine (Ile), glycine (Gly), and alanine (Ala), with leucine (Leu2) showing the highest relative synonymous codon usage (RSCU) value. The analysis of tRNA secondary structures revealed high conservation among the tRNAs encoded on the H-strand. Phylogenetic reconstruction, incorporating 40 species from 13 families of Ephemeroptera, confirmed the monophyly of all the families and supported a sister group relationship between Potamanthidae and Ephemeridae. Additionally, the sequence previously identified as Rhoenanthus sp. JZ-2021 was reassigned to the genus Potamanthus. This study provides valuable insights into the evolutionary relationships within Potamanthidae and lays a foundation for future phylogenetic and taxonomic research. Full article
(This article belongs to the Special Issue Freshwater Zoobenthos Biodiversity, Evolution and Ecology)
Show Figures

Figure 1

14 pages, 2000 KiB  
Article
Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity
by Amruta Nair, Swapnil Prakash Doijad, Mangesh Vasant Suryavanshi, Anwesha Dey, Satya Veer Singh Malik, Bas E. Dutilh and Sukhadeo Baliram Barbuddhe
Microbiol. Res. 2025, 16(3), 54; https://doi.org/10.3390/microbiolres16030054 - 26 Feb 2025
Viewed by 52
Abstract
The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a [...] Read more.
The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-value indigenous Indian chicken breed, using sequencing of the V3–V4 region 16S rRNA gene. To assess microbiome composition and bacterial abundance shifts, three chickens per growth phase (3, 28, and 35 days) were sampled, with microbiota analyzed from three gut regions (crop, small intestine, and ceca) per bird. The results revealed Firmicutes as the most abundant phylum and Lactobacillus as the dominant genus across all stages. Lactobacillus was particularly abundant in the crop at early stages (3 and 28 days), while the ceca exhibited a transition towards the dominance of genus Phocaeicola by day 35. Microbial richness and evenness increased with age, reflecting microbiome maturation, and the analyses of the microbial community composition revealed distinct spatiotemporal differences, with the ceca on day 35 showing the highest differentiation. Pathogen analysis highlighted a peak in poultry-associated taxa Campylobacter, Staphylococcus, and Clostridium paraputrificum in 3-day-old Kadaknath, particularly in the small intestine, underscoring the vulnerability of early growth stages. These findings provide critical insights into age-specific microbiome development and early life-stage susceptibility to pathogens, emphasizing the need for targeted interventions to optimize poultry health management and growth performance. Full article
Show Figures

Figure 1

17 pages, 8059 KiB  
Article
Cancer-Associated Fibroblasts Genes and Transforming Growth Factor Beta Pathway in Gastric Cancer for Novel Therapeutic Strategy
by Hiroyuki Minoura, Riku Okamoto, Naoki Hiki and Keishi Yamashita
Cancers 2025, 17(5), 795; https://doi.org/10.3390/cancers17050795 - 26 Feb 2025
Viewed by 37
Abstract
Background-Objective: Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment of gastric cancer (GC). Understanding the molecular characteristics of CAFs-associated genes (CAFGs) is essential for elucidating their role in tumor progression and prognosis. This review aims to summarize the current knowledge [...] Read more.
Background-Objective: Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment of gastric cancer (GC). Understanding the molecular characteristics of CAFs-associated genes (CAFGs) is essential for elucidating their role in tumor progression and prognosis. This review aims to summarize the current knowledge on CAFGs, highlighting their expression patterns, prognostic significance, and potential functional mechanisms. Methods: A comprehensive review of existing literature was conducted, focusing on molecular features of CAFGs in GC. Single-cell RNA sequencing (scRNA-seq) analyses were examined to assess the expression patterns of CAFGs in broad-sense CAFs, which include both CAFs and pericytes. Additionally, clinicopathological studies validating the prognostic significance of CAFGs were reviewed. Results: ScRNA-seq analyses revealed that CAFGs are not necessarily restricted to CAFs alone but may also reflect the activation status of surrounding cells. Several CAFGs, including SPARC, THBS2, COL1A1, COL3A1, INHBA, PDGFC, and SDC2, have been validated for their prognostic relevance in GC. However, compared with other cancers, the functional mechanisms of these genes in GC remain poorly understood. While CAFGs exhibit synchronized expression with TGFB1 in colorectal cancer (CRC), such patterns have yet to be confirmed in GC due to the limitations of available microdissected data. Conclusions: A comprehensive understanding of CAFGs and their interaction with the TGFB pathway, including LTBP family genes, may be critical for developing novel therapeutic strategies for GC. Further research is needed to elucidate their functional mechanisms and therapeutic potential. Full article
(This article belongs to the Special Issue Gastric Cancer Metastases)
Show Figures

Figure 1

Back to TopTop