Processing math: 100%
 
 
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

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

Search Results (10,396)

Search Parameters:
Keywords = gene Q

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
20 pages, 7597 KiB  
Article
Auxin Dynamics and Transcriptome–Metabolome Integration Determine Graft Compatibility in Litchi (Litchi chinensis Sonn.)
by Zhe Chen, Tingting Yan, Mingchao Yang, Xianghe Wang, Biao Lai, Guolu He, Farhat Abbas and Fuchu Hu
Int. J. Mol. Sci. 2025, 26(9), 4231; https://doi.org/10.3390/ijms26094231 - 29 Apr 2025
Viewed by 85
Abstract
Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). [...] Read more.
Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). The anatomical and growth investigations demonstrated significant disparities between compatible (FZX as scion and ZNX as rootstock) and incompatible (ZNX as scion and FZX as rootstock) grafts, with the latter showing reduced levels of indole acetic acid (IAA). Exogenous 1-naphthalene acetic acid (NAA) application markedly improved the graft survival, shoot development, and hormonal synergy, whereas the auxin inhibitor tri-iodobenzoic acid (TIBA) diminished these parameters. The incompatible grafts showed downregulation of auxin transporter genes, including ATP-binding cassette (ABC) transporter, AUXIN1/LIKE AUX1 (AUX/LAX), and PIN-FORMED (PIN) genes, suggesting impaired vascular tissue growth. Metabolomic profiling revealed dynamic interactions between auxin, salicylic acid, and jasmonic acid, with NAA-treated grafts exhibiting enhanced levels of stress-responsive metabolites. Transcriptome sequencing identified differentially expressed genes (DEGs) linked to auxin signaling (ARF, GH3), seven additional phytohormones, secondary metabolism (terpenoids, anthocyanins, and phenylpropanoids), and ABC transporters. Gene ontology and KEGG analyses highlighted the significance of hormone interactions and the biosynthesis of secondary metabolites in successful grafting. qRT-PCR validation substantiated the veracity of the transcriptome data, emphasizing the significance of auxin transport and signaling in effective graft development. This study provides an in-depth review of the molecular and physiological factors influencing litchi grafting. These findings provide critical insights for enhancing graft success rates in agricultural operations via targeted hormonal and genetic approaches. Full article
(This article belongs to the Special Issue The Role of Cytokinins and Other Phytohormones in Plant Life)
Show Figures

Figure 1

19 pages, 10572 KiB  
Article
Development and Application of a TaqMan-Based qPCR Assay for Detecting ENTV-2 in Goats
by Pengfei Li, Haike Yin, Xiaoan Cao, Xi Lan, Jinyan Wu, Jijun He, Ligang Yuan and Youjun Shang
Genes 2025, 16(5), 529; https://doi.org/10.3390/genes16050529 - 29 Apr 2025
Viewed by 53
Abstract
Background: In recent years, enzootic nasal tumor virus 2 (ENTV-2) has become prevalent in China, resulting in substantial economic losses for the goat industry. In order to enrich the availability of detection methods for ENTV-2, this study developed an expedited and accurate reverse-transcription [...] Read more.
Background: In recent years, enzootic nasal tumor virus 2 (ENTV-2) has become prevalent in China, resulting in substantial economic losses for the goat industry. In order to enrich the availability of detection methods for ENTV-2, this study developed an expedited and accurate reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) assay to facilitate the detection and quantification of ENTV-2. Methods: Specifically, a pair of primers and a TaqMan probe targeting conserved regions of the pro gene were designed to allow the specific amplification and detection of viral RNA in clinical samples. Moreover, modifying the method for use in a quantitative real-time PCR (qPCR) assay enables the detection of proviral DNA in tumor specimens. Results: Both methods exhibited a detection limit for the ENTV-2 standard plasmid at 100 copies/µL. The detection methods we established exhibited high specificity and sensitivity to ENTV-2, without cross-reactivity with other pathogens causing respiratory diseases or endogenous retroviruses (EBRVs). We performed an ENTV-2 analysis of clinical samples in goats via RT-qPCR using nasal swab samples (n = 558) collected from three geographically distinct flocks in Lingyou County, Baoji City, Shaanxi Province, China, and 58 positive samples were detected for a positivity rate of 10.4%. After euthanasia, the autopsy report showed nasal cavity masses. Histopathological analysis demonstrated an epithelial neoplasm, in compliance with the features of enzootic nasal adenocarcinoma (ENA). Three full-length genomes were sequenced to assess genomic sequence conservation and variation. Multiple-sequence alignment demonstrated the existence of sequence variations among strains. Phylogenetic analysis of the nucleotide sequences revealed that the ENTV-2 SX1~3 isolates were phylogenetically related to the Chinese ENTV-2 isolates, especially the JY strain. Furthermore, recombination analysis suggested that both ENTV-2 SX1 and ENTV-2 SX2 might be recombinant variants. Conclusions: In conclusion, both methods are highly specific for the pro gene of ENTV-2, and the development of this assay has been deemed crucial to the early identification and subsequent control of this viral infection. Our results provide valuable information for further research on the genetic variation and evolution of ENTV-2 in China. Full article
(This article belongs to the Section Animal Genetics and Genomics)
Show Figures

Figure 1

16 pages, 8001 KiB  
Article
Epitranscriptomic Analysis of the Ventral Hippocampus in a Mouse Model of Post-Traumatic Stress Disorder Following Deep Brain Stimulation Treatment of the Basolateral Amygdala
by Mingxi Ma, Hao Fan, Hui Zhang, Yao Yin, Yizheng Wang and Yan Gao
Brain Sci. 2025, 15(5), 473; https://doi.org/10.3390/brainsci15050473 - 29 Apr 2025
Viewed by 131
Abstract
Background: Basolateral amygdala (BLA) deep brain stimulation (DBS) has been shown to alleviate the symptoms of post-traumatic stress disorder (PTSD), but the specific mechanisms remain incompletely understood. The hippocampus, a brain region closely connected to the amygdala, plays a key role in the [...] Read more.
Background: Basolateral amygdala (BLA) deep brain stimulation (DBS) has been shown to alleviate the symptoms of post-traumatic stress disorder (PTSD), but the specific mechanisms remain incompletely understood. The hippocampus, a brain region closely connected to the amygdala, plays a key role in the pathological processes of PTSD. The N6-methyladenosine (m6A) methylation of RNAs in the hippocampus is known to play a significant role in regulating the brain’s response to stress and emotional disorders. Methods: This study aimed to comprehensively analyze the roles of transcriptome-wide m6A modifications of the hippocampus in the BLA DBS treatment of a PTSD mouse model using m6A sequencing. Results: Significant alterations in functional connectivity between the ventral hippocampus (vHPC) and BLA were observed in foot shock (FS) mice through functional magnetic resonance imaging (fMRI) analysis. Furthermore, we observed that the expression of the key m6A methyltransferase enzyme, METTL3, in the FS and BLA DBS groups was higher than that in the control group. At the same time, both FS and BLA DBS induced the widespread m6A methylation of RNAs in the vHPC. Gene ontology (GO) enrichment analysis revealed that FS altered methylation in metabolic, developmental, and cytoskeletal pathways, while BLA DBS targeted metabolic, cell cycle, and neuroplasticity-related genes. Additionally, BLA DBS reversed the aberrant methylation of genes associated with multiple functional pathways induced by FS, including those related to cholinergic transmission, sodium and calcium ion homeostasis, and stress hormone responsiveness. We identified a set of RNAs with methylation changes that were reversed by BLA DBS in the FS vs. Ctrl (control) comparison, including those associated with cholinergic transmission, sodium and calcium ion balance, and stress hormone response. Additionally, we detected several specific BLA DBS-related genes through MeRIP-qPCR, indicating that DBS influences crucial genes linked to calcium signaling and synaptic plasticity. Conclusions: We draw two conclusions from these findings: BLA DBS may alleviate PTSD-like symptoms by reversing FS-induced methylation changes and by altering the methylation levels of crucial genes. These findings indicate that epigenetic m6A modifications in the vHPC may play an important role in the amelioration of PTSD using BLA DBS. Full article
(This article belongs to the Section Molecular and Cellular Neuroscience)
Show Figures

Figure 1

28 pages, 7091 KiB  
Article
Role of Long Non-Coding RNA X-Inactive-Specific Transcript (XIST) in Neuroinflammation and Myelination: Insights from Cerebral Organoids and Implications for Multiple Sclerosis
by Nihan Aktas Pepe, Busra Acar, Gozde Erturk Zararsiz, Serife Ayaz Guner and Alaattin Sen
Non-Coding RNA 2025, 11(3), 31; https://doi.org/10.3390/ncrna11030031 - 29 Apr 2025
Viewed by 170
Abstract
Background/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods [...] Read more.
Background/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods: Human cerebral organoids with oligodendrocytes were produced from XIST-silenced H9 cells, and the mature organoids were subsequently treated with either FTY720 or DMF. Gene expression related to inflammation and myelination was subsequently analyzed via qRT-PCR. Immunofluorescence staining was used to assess the expression of proteins related to inflammation, myelination, and neuronal differentiation. Alpha-synuclein protein levels were also checked via ELISA. Finally, transcriptome analysis was conducted on the organoid samples. Results: XIST-silenced organoids presented a 2-fold increase in the expression of neuronal stem cells, excitatory neurons, microglia, and mature oligodendrocyte markers. In addition, XIST silencing increased IL-10 mRNA expression by 2-fold and MBP and PLP1 expression by 2.3- and 0.6-fold, respectively. Although XIST silencing tripled IBA1 protein expression, it did not affect organoid MBP expression. FTY720, but not DMF, distinguished MBP and IBA1 expression in XIST-silenced organoids. Furthermore, XIST silencing reduced the concentration of alpha-synuclein from 300 to 100 pg/mL, confirming its anti-inflammatory role. Transcriptomic and gene enrichment analyses revealed that the differentially expressed genes are involved in neural development and immune processes, suggesting the role of XIST in neuroinflammation. The silencing of XIST modified the expression of genes associated with inflammation, myelination, and neuronal growth in cerebral organoids, indicating a potential involvement in the pathogenesis of MS. Conclusions: XIST may contribute to the MS pathogenesis as well as neuroinflammatory diseases such as and Alzheimer’s and Parkinson’s diseases and may be a promising therapeutic target. Full article
(This article belongs to the Section Long Non-Coding RNA)
Show Figures

Figure 1

9 pages, 1023 KiB  
Review
A Novel Frameshift Variant and a Partial EHMT1 Microdeletion in Kleefstra Syndrome 1 Patients Resulting in Variable Phenotypic Severity and Literature Review
by Maria Tzetis, Anastasios Mitrakos, Ioanna Papathanasiou, Vasiliki Koute, Konstantina Kosma, Roser Pons, Aspasia Michoula, Ioanna Grivea and Aspasia Tsezou
Genes 2025, 16(5), 521; https://doi.org/10.3390/genes16050521 - 29 Apr 2025
Viewed by 127
Abstract
Background: Kleefstra syndrome 1(KLEFS1, OMIM#610253) is a rare neurodevelopmental disorder (NDD) instigated by heterozygous variants or microdeletions occurring in the 9q34.4 genomic region of the euchromatic histone methyltransferase-1 (EHMT1) gene and is inherited in an autosomal dominant (AD) manner. The clinical [...] Read more.
Background: Kleefstra syndrome 1(KLEFS1, OMIM#610253) is a rare neurodevelopmental disorder (NDD) instigated by heterozygous variants or microdeletions occurring in the 9q34.4 genomic region of the euchromatic histone methyltransferase-1 (EHMT1) gene and is inherited in an autosomal dominant (AD) manner. The clinical phenotype of KLEFS1 includes moderate to severe intellectual disability (ID), hypotonia, and distinctive facial features and additionally involves other organ systems (heart, renal, genitourinary, sensory) albeit with phenotypic heterogeneity between patients. The purpose of this study is to expand the genotypic spectrum of KLEFS1 and compare phenotypic features of the syndrome of already published cases. Methods: Exome sequencing (ES), chromosomal microarray analysis (CMA), as well as sanger sequencing, for confirmation of the de novo status of the frameshift variant, were used. Results: Here we describe two more cases, both males with a similar age and carriers of novel variants; one with a frameshift variant involving exon 13: p.Val692Glyfs*64 and the other with the smallest so far described, 11 Kb (exons 19-25), 9q34.4 microdeletion: 9q34.3 (140703393-140714454). Both presented with an NDD disorder with one showing more severe ID with significant social disabilities, while the other with the microdeletion had mild ID and following a normal education curriculum. Neither of them were obese nor had any other significant organ system disorder. Conclusions: The observed phenotypic variability due to genotypic differences in the two children contributes to the expanding spectrum of KLEFS1 disease phenotypes. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
Show Figures

Figure 1

24 pages, 4048 KiB  
Article
Transcriptome-Wide Analysis and Experimental Validation from FFPE Tissue Identifies Stage-Specific Gene Expression Profiles Differentiating Adenoma, Carcinoma In-Situ and Adenocarcinoma in Colorectal Cancer Progression
by Faisal Alhosani, Reem Sami Alhamidi, Burcu Yener Ilce, Alaa Muayad Altaie, Nival Ali, Alaa Mohamed Hamad, Axel Künstner, Cyrus Khandanpour, Hauke Busch, Basel Al-Ramadi, Rania Harati, Kadria Sayed, Ali AlFazari, Riyad Bendardaf and Rifat Hamoudi
Int. J. Mol. Sci. 2025, 26(9), 4194; https://doi.org/10.3390/ijms26094194 - 28 Apr 2025
Viewed by 231
Abstract
Colorectal cancer (CRC) progression occurs through three stages: adenoma (pre-cancerous lesion), carcinoma in situ (CIS) and adenocarcinoma, with tumor stage playing a pivotal role in the prognosis and treatment outcomes. Despite therapeutic advancements, the lack of stage-specific biomarkers hinders the development of accurate [...] Read more.
Colorectal cancer (CRC) progression occurs through three stages: adenoma (pre-cancerous lesion), carcinoma in situ (CIS) and adenocarcinoma, with tumor stage playing a pivotal role in the prognosis and treatment outcomes. Despite therapeutic advancements, the lack of stage-specific biomarkers hinders the development of accurate diagnostic tools and effective therapeutic strategies. This study aims to identify stage-specific gene expression profiles and key molecular mechanisms in CRC providing insights into molecular alterations across disease progression. Our methodological approach integrates the use of absolute gene set enrichment analysis (absGSEA) on formalin-fixed paraffin-embedded (FFPE)-derived transcriptomic data, combined with large-scale clinical validation and experimental confirmation. A comparative whole transcriptomic analysis (RNA-seq) was performed on FFPE samples including adenoma (n = 10), carcinoma in situ (CIS) (n = 8) and adenocarcinoma (n = 11) samples. Using absGSEA, we identified significant cellular pathways and putative molecular biomarkers associated with each stage of CRC progression. Key findings were then validated in a large independent CRC patient cohort (n = 1926), with survival analysis conducted from 1336 patients to assess the prognostic relevance of the candidate biomarkers. The key differentially expressed genes were experimentally validated using real-time PCR (RT-qPCR). Pathway analysis revealed that in CIS, apoptotic processes and Wnt signaling pathways were more prominent than in adenoma samples, while in adenocarcinoma, transcriptional co-regulatory mechanisms and protein kinase activity, which are critical for tumor growth and metastasis, were significantly enriched compared to adenoma. Additionally, extracellular matrix organization pathways were significantly enriched in adenocarcinoma compared to CIS. Distinct gene signatures were identified across CRC stages that differentiate between adenoma, CIS and adenocarcinoma. In adenoma, ARRB1, CTBP1 and CTBP2 were overexpressed, suggesting their involvement in early tumorigenesis, whereas in CIS, RPS3A and COL4A5 were overexpressed, suggesting their involvement in the transition from benign to malignant stage. In adenocarcinoma, COL1A2, CEBPZ, MED10 and PAWR were overexpressed, suggesting their involvement in advanced disease progression. Functional analysis confirmed that ARRB1 and CTBP1/2 were associated with early tumor development, while COL1A2 and CEBPZ were involved in extracellular matrix remodeling and transcriptional regulation, respectively. Experimental validation with RT-qPCR confirmed the differential expression of the candidate biomarkers (ARRB1, RPS3A, COL4A5, COL1A2 and MED10) across the three CRC stages reinforcing their potential as stage-specific biomarkers in CRC progression. These findings provide a foundation to distinguish between the CRC stages and for the development of accurate stage-specific diagnostic and prognostic biomarkers, which helps in the development of more effective therapeutic strategies for CRC. Full article
Show Figures

Figure 1

12 pages, 763 KiB  
Article
Circulation and Spillover of pdmH1N1 Influenza A Virus at an Educational Swine Farm in Chile, 2019–2023
by Soledad Ruiz, Constanza Díaz-Gavidia, María Antonieta González, Pablo Galdames, Cristóbal Oyarzún, Cecilia Baumberger, Camila Rojas, Christopher Hamilton-West, Bridgett Sharp, Shaoyuan Tan, Stacey Schultz-Cherry and Pedro Jimenez-Bluhm
Viruses 2025, 17(5), 635; https://doi.org/10.3390/v17050635 (registering DOI) - 28 Apr 2025
Viewed by 156
Abstract
Educational farms provide students with hands-on experience in agricultural and animal practices. However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission, yet research on infectious diseases in such settings remains limited. This study investigates the [...] Read more.
Educational farms provide students with hands-on experience in agricultural and animal practices. However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission, yet research on infectious diseases in such settings remains limited. This study investigates the ongoing spillovers of human-origin influenza A virus (IAV) into swine at an educational farm in central Chile, describing IAV prevalence, outbreak dynamics, and the genomic characterization of detected strains. The Menesianos educational farm, located in Melipilla, central Chile, houses approximately 40 swine alongside other domestic animals, such as horses and cows. As part of an active IAV surveillance project, monthly nasal swab samples were collected from pigs between June 2019 and September 2023 for IAV detection via RT-qPCR targeting the M gene, with positive samples subsequently sequenced. During the study period, monthly IAV prevalence ranged from 0% to 52.5%, with a notable outbreak detected between May and June 2023. The outbreak lasted 5 weeks, peaking at 52.5% prevalence during week 3. Nine IAV strains were isolated over the study period, eight of which were obtained during weeks 2 and 3 of the outbreak. Phylogenetic analysis revealed that all strains were closely related to the pandemic H1N1 2009 influenza virus, with the closest related strains being those circulating in humans in Chile during the same years. These findings highlight the importance of conducting regular IAV surveillance on educational farms, where close interactions between animals and individuals—particularly children and young people—can facilitate viral spillovers and potential reverse zoonosis events. Full article
(This article belongs to the Section Animal Viruses)
Show Figures

Figure 1

23 pages, 9594 KiB  
Article
Cold-Tolerance Candidate Gene Identification in Maize Germination Using BSA, Transcriptome and Metabolome Profiling
by Cheng Wang, Nan Hao, Yueming Li, Nan Sun, Liwei Wang and Yusheng Ye
Agronomy 2025, 15(5), 1067; https://doi.org/10.3390/agronomy15051067 - 27 Apr 2025
Viewed by 108
Abstract
Exploring the characteristics of maize’s tolerance to low-temperature stress is of great significance for enhancing maize’s adaptability to such stress and for developing valuable germplasm resources. In this study, a combined analysis of genomics, transcriptomics, and metabolomics was conducted on maize 245 F7 [...] Read more.
Exploring the characteristics of maize’s tolerance to low-temperature stress is of great significance for enhancing maize’s adaptability to such stress and for developing valuable germplasm resources. In this study, a combined analysis of genomics, transcriptomics, and metabolomics was conducted on maize 245 F7 recombinant inbred lines (RILs) to screen for candidate genes and differential metabolites controlling the cold tolerance of maize during the germination stage. Bulked segregant analysis-sequencing (BSA-seq) located four candidate regions on chromosome 1 (qSGRL1-2, qSGRL1-3, and qSGRL1-4) and chromosome 10 (qSGRL10), which altogether contained 109 candidate genes. Combined with the transcriptome sequencing results, among the genes screened by quantitative trait locus sequencing (QTL-seq), seven genes (Zm00001eb043000, Zm00001eb043620, Zm00001eb043650, Zm00001eb043680, Zm00001eb043720, Zm00001eb043400, and Zm00001eb043490) were identified as common candidate genes related to the cold tolerance of maize during the germination stage. Combined with the metabolomic analysis results, low-temperature stress induced the differential expression of relevant genes, leading to the differential accumulation of metabolites such as L-glutamic acid, 4-aminobutyric acid, and Lysophosphatidylcholine (LPC). These results enrich the information for molecular marker-assisted selection of maize tolerance to low-temperature stress and provide genetic resources for the maize varieties breeding. Full article
(This article belongs to the Section Crop Breeding and Genetics)
Show Figures

Figure 1

15 pages, 7732 KiB  
Article
Construction of Diagnostic Model for Regulatory T Cell-Related Genes in Sepsis Based on Machine Learning
by Xuesong Wang, Zhe Guo, Xinrui Wang and Zhong Wang
Biomedicines 2025, 13(5), 1060; https://doi.org/10.3390/biomedicines13051060 - 27 Apr 2025
Viewed by 97
Abstract
Background: Sepsis is a complex syndrome caused by a severe infection that occurs with a severe inflammatory response. Regulatory T cells (Tregs) have immunosuppressive effects and play a crucial role in modulating the immune response. There-fore, the number of Tregs is significantly increased [...] Read more.
Background: Sepsis is a complex syndrome caused by a severe infection that occurs with a severe inflammatory response. Regulatory T cells (Tregs) have immunosuppressive effects and play a crucial role in modulating the immune response. There-fore, the number of Tregs is significantly increased in sepsis patients. Methods and Results: This paper aims to identify Tregs associated with the diagnosis of sepsis. For this purpose, transcriptional data from the GEO database for sepsis and its controls were downloaded and subjected to differential expression analysis. Immuno-infiltration analysis of the obtained DEGs revealed that Tregs were significantly different in sepsis and its controls. To further explore the cellular landscape and interactions in sepsis, single-cell RNA sequencing (scRNA-seq) data were analyzed. We identified key cell types and their interactions, including Tregs, using cell–cell communication analysis tools such as CellChat. This analysis provided in-sights into the dynamic changes in immune cell populations and their communication networks in sepsis. Thus, we utilized multiple machine learning algorithms to screen and extract Treg-related genes associated with sepsis diagnosis. We then performed both in-ternal and external validation tests. The final diagnostic model was constructed with high diagnostic accuracy (accuracy of 0.9615). Furthermore, we verified the diagnostic gene via a qPCR experiment. Conclusions: This paper elucidates the potential diagnostic targets associated with Tregs in sepsis progression and provides comprehensive understanding of the immune cell interactions in sepsis through scRNA-seq analysis. Full article
(This article belongs to the Collection Feature Papers in Immunology and Immunotherapy)
23 pages, 14601 KiB  
Article
Deciphering the Olfactory Mechanisms of Sitotroga cerealella Olivier (Lepidoptera: Gelechiidae): Insights from Transcriptome Analysis and Molecular Docking
by Hui Li, Sheng Qiao, Xiwen Hong and Yangyang Wei
Insects 2025, 16(5), 461; https://doi.org/10.3390/insects16050461 - 27 Apr 2025
Viewed by 190
Abstract
Olfaction is crucial for insect activities such as host seeking, foraging, oviposition, and predator avoidance. While olfactory proteins have been identified across several insect species, their specific functions are largely enigmatic. In this study, we investigated the olfactory proteins of the Angoumois grain [...] Read more.
Olfaction is crucial for insect activities such as host seeking, foraging, oviposition, and predator avoidance. While olfactory proteins have been identified across several insect species, their specific functions are largely enigmatic. In this study, we investigated the olfactory proteins of the Angoumois grain moth, Sitotroga cerealella Olivier. A total of 165 presumptive olfactory genes were identified in the antennal transcriptome of S. cerealella, encompassing 33 odorant-binding proteins (OBPs), 10 chemosensory proteins (CSPs), 58 odorant receptors (ORs), 41 ionotropic receptors (IRs), 21 gustatory receptors (GRs), and 2 sensory neuron membrane proteins (SNMPs). BLASTX and a phylogenetic analysis showed a high similarity of these genes to the orthologs in other model insects. A qRT-PCR analysis demonstrated that ScerOBP15 and ScerOBP23 are specifically and highly expressed in antennae, exhibiting male-biased expression patterns. Moreover, molecular docking revealed their strong binding affinity to the wheat volatiles n-heptadecane and geranyl acetone. Also, the potential active sites within ScerOBP15 and ScerOBP23 that engage with these volatiles have been identified, implying a possible role in host localization. Our findings shed light on the mechanisms underlying the behavioral responses of S. cerealella to wheat odors, enhance our comprehension of their olfactory processes, and pave the way for the development of highly specific and sustainable pest management strategies. Full article
(This article belongs to the Special Issue Research on Insect Molecular Biology)
Show Figures

Graphical abstract

30 pages, 115122 KiB  
Article
A Comprehensive Analysis of Chemical Composition and Anti-Inflammatory Effects of Cassava Leaf Extracts in Two Varieties in Manihot esculenta Crantz
by Jie Cai, Wenli Zhu, Jingjing Xue, Yanqing Ma, Kaimian Li, Lanyue Zhang, Oluwaseun Olayemi Aluko, Songbi Chen, Xiuqin Luo and Feifei An
Int. J. Mol. Sci. 2025, 26(9), 4140; https://doi.org/10.3390/ijms26094140 - 27 Apr 2025
Viewed by 97
Abstract
Cassava is a tropical tuberous root crop, feeding over a billion people globally. However, research on the chemical composition and bioactive effects of cassava leaves remains scarce. Two specific varieties of South China No. 9 (green leaves (G.L.)) and South China No. 20 [...] Read more.
Cassava is a tropical tuberous root crop, feeding over a billion people globally. However, research on the chemical composition and bioactive effects of cassava leaves remains scarce. Two specific varieties of South China No. 9 (green leaves (G.L.)) and South China No. 20 (purple leaves (P.L.)) were investigated in this study. The components of G.L. and P.L. were analyzed under different extraction methods using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-Q-TOF/MS). Results showed that cassava leaf extracts are rich in bioactive metabolites such as D-(+)-mannose, trigonelline, rutin, kaempferol-3-O-rutinoside, and oleamide. To assess the anti-inflammatory efficacy of bioactive compounds, animal models were established. Compared to the histamine group (NA), the group treated with the extracts had reduced epidermal thickness in hematoxylin and eosin (HE) staining. Further analysis revealed a drastic reduction in the number of mast cells in toluidine blue (TB) staining and expression levels of inflammatory cytokines (IL-17 and TNF-α) in immunohistochemistry (IHC) staining. The ethanolic extracts from the leaves demonstrated potent anti-inflammatory activities, with the extract from G.L. surpassing that from P.L. Transcriptomic analyses propose that the anti-inflammatory effects of cassava leaves may be related to the modulation of genes involved in mast cell activation, such as Cma1, Cpa3, and Fn1, among others. Network pharmacology unveiled that the extract of cassava leaves modulates pathways associated with apoptosis, inflammation, and metabolism. Molecular docking revealed strong binding interactions between 1-stearoylglycerol and oleamide from cassava leaves extracts and the proteins of AKT1, TNF, and BRAF. Overall, cassava leaf extracts seem to be a promising natural anti-inflammatory agent. Full article
(This article belongs to the Section Bioactives and Nutraceuticals)
Show Figures

Figure 1

21 pages, 4470 KiB  
Article
Ethylene Signaling Modulates Dehydrin Expression in Arabidopsis thaliana Under Prolonged Dehydration
by Irina I. Vaseva, Heorhii Balzhyk, Maria Trailova, Tsvetina Nikolova, Zornitsa Katerova, Simona Galabova, Dessislava Todorova, Iskren Sergiev and Valya Vassileva
Int. J. Mol. Sci. 2025, 26(9), 4148; https://doi.org/10.3390/ijms26094148 - 27 Apr 2025
Viewed by 163
Abstract
Dehydrins are stress-inducible proteins with protective functions, characterized by high hydrophilicity, thermostability, and a low degree of secondary structure. They stabilize cellular membranes, preserve macromolecule conformation, and support enzymatic and structural protein functions. Their accumulation in plant tissues under drought is regulated by [...] Read more.
Dehydrins are stress-inducible proteins with protective functions, characterized by high hydrophilicity, thermostability, and a low degree of secondary structure. They stabilize cellular membranes, preserve macromolecule conformation, and support enzymatic and structural protein functions. Their accumulation in plant tissues under drought is regulated by abscisic acid (ABA)-dependent and ABA-independent pathways. Ethylene plays a key role in stress adaptation, but its relationship with dehydrin accumulation remains unclear. This study investigates how ethylene influences dehydrin expression in Arabidopsis thaliana during prolonged dehydration using transcript profiling and immunodetection in wild-type (Col-0), ethylene-constitutive (ctr1-1), and ethylene-insensitive (ein3eil1) mutants. Comparative analyses showed increased survival of ctr1-1 plants under dehydration stress, likely due to reduced oxidative damage. Analysis of dehydrin-coding genes identified multiple Ethylene Response Factor (ERF) binding sites, flanking the transcription start sites, which suggests a fine-tuned ethylene-dependent regulation. The ability of ethylene signaling to either suppress or stabilize particular dehydrins was demonstrated by RT-qPCR and immunodetection experiments. Under drought stress, ethylene signaling appeared to suppress root-specific dehydrins. A Y-segment-containing protein with approximate molecular weight of 20 kDa showed decreased levels in ctr1-1 and higher accumulation in ein3eil1, indicating that ethylene signaling acts as a negative regulator. These results provide new information on the dual role of ethylene in dehydrin control, highlighting its function as a molecular switch in stress adaptive responses. Full article
(This article belongs to the Special Issue The Role of Cytokinins and Other Phytohormones in Plant Life)
Show Figures

Graphical abstract

27 pages, 8482 KiB  
Article
Comparative Analysis of ANN, GEP, and Water Advance Power Function for Predicting Infiltrated Water Volume in Furrow of Permeable Surface
by A A Alazba, Mohamed A. Mattar, Ahmed El-Shafei, Farid Radwan, Mahmoud Ezzeldin and Nasser Alrdyan
Water 2025, 17(9), 1304; https://doi.org/10.3390/w17091304 - 27 Apr 2025
Viewed by 111
Abstract
The present investigation utilized artificial neural networks (ANN) and gene expression programming (GEP) in comparison with the two-point method (TPM) to develop a generalized solution for predicting infiltrated water volume (∀Z) across various soil types under furrow conditions. This work assesses [...] Read more.
The present investigation utilized artificial neural networks (ANN) and gene expression programming (GEP) in comparison with the two-point method (TPM) to develop a generalized solution for predicting infiltrated water volume (∀Z) across various soil types under furrow conditions. This work assesses infiltration behavior with respect to experimental data from several temporal contexts. Data distribution and model performance are evaluated via descriptive statistics and correlation tests. Artificial intelligence (AI) models (ANN and GEP) trained and evaluated utilizing input variables—inflow rate (Qin); furrow length (L); waterfront advance time at the end of the furrow (TL); infiltration opportunity time (To); and cross-sectional area of the inflow (Ao) are compared with TPM performance. More precisely and consistently than the water advance power function, AI-based algorithms hope to be invading water volume. Statistical analysis shows that ANN and GEP have lower error metrics, increased generalizability, and better representation of complex infiltration dynamics. The determination coefficient (R2) of ANN data produced 98.1% for testing and 97.8% for validation, while TPM showed accuracy reductions of 2.5% and 4.6%, respectively. On the other side, the R2 of GEP produced 95.7% for testing and 96.1% for validation, while TPM showed accuracy reductions of 0.7% and 3%, respectively. During ANN model computation, TPMs root mean square error (RMSE) of 0.0135 m3/m exceeded all mean values. Errors within 10% relative deviation were displayed using the ANN model Z. Particularly, ANN and GEP, the study revealed that AI techniques predict furrow irrigation penetration of water volume better than the water advance power function. These models advance soil and furrow adaptation, extrapolation, and accuracy. Results show that AI-driven modeling may maximize hydrological assessments and irrigation control. Full article
Show Figures

Figure 1

21 pages, 10131 KiB  
Article
Development and Experimental Validation of Machine Learning-Based Disulfidptosis-Related Ferroptosis Biomarkers in Inflammatory Bowel Disease
by Yongchao Liu, Jing Shao, Jie Zhang, Mengmeng Sang, Qiuyun Xu and Liming Mao
Genes 2025, 16(5), 496; https://doi.org/10.3390/genes16050496 - 27 Apr 2025
Viewed by 162
Abstract
Background: Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract, defined by intestinal epithelial cell death. While ferroptosis and disulfidptosis have been linked to IBD pathogenesis, the functional significance of disulfidptosis-related ferroptosis genes (DRFGs) in this disease remains poorly [...] Read more.
Background: Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract, defined by intestinal epithelial cell death. While ferroptosis and disulfidptosis have been linked to IBD pathogenesis, the functional significance of disulfidptosis-related ferroptosis genes (DRFGs) in this disease remains poorly characterized. This investigation sought to pinpoint DRFGs as diagnostic indicators and clarify their mechanistic contributions to IBD progression. Methods: Four IBD datasets (GSE65114, GSE87473, GSE102133, and GSE186582) from the GEO database were integrated to identify differentially expressed genes (DEGs) (|log2FC| > 0.585, adj. p < 0.05). A Pearson correlation analysis was used to link disulfidptosis and ferroptosis genes, followed by machine learning (LASSO and RF) to screen core DRFGs. The immune subtypes and single-cell sequencing (GSE217695) results were analyzed. A DSS-induced colitis Mus musculus (C57BL/6) model was used for validation. Results: Transcriptomic profiling identified 521 DEGs, with 16 defined as DRFGs. Nine hub genes showed diagnostic potential (AUC: 0.71–0.91). Functional annotation demonstrated that IBD-associated genes regulate diverse pathways, with a network analysis revealing their functional synergy. The PPI networks prioritized DUOX2, NCF2, ACSL4, GPX2, CBS, and LPCAT3 as central hubs. Two immune subtypes exhibited divergent DRFG expression. Single-cell mapping revealed epithelial/immune compartment specificity. The DSS-induced murine colitis model confirmed differential expression patterns of DRFGs, with concordant results between qRT-PCR and RNA-seq, emphasizing their pivotal regulatory roles in disease progression and potential for translational application. Conclusions: DRFGs mediate IBD progression via multi-signal pathway regulation across intestinal cell types, demonstrating diagnostic and prognostic potential. Full article
(This article belongs to the Special Issue Machine Learning in Cancer and Disease Genomics)
Show Figures

Figure 1

31 pages, 4089 KiB  
Article
A Pilot Investigation of Circulating miRNA Expression in Individuals Exposed to Aluminum and Welding Fumes
by Gözde Öztan, Halim İşsever, Tuğçe İşsever, Fatma Oğuz, Sevgi Canbaz, Canan Küçükgergin and Kazım Yalçın Arga
Curr. Issues Mol. Biol. 2025, 47(5), 306; https://doi.org/10.3390/cimb47050306 - 26 Apr 2025
Viewed by 140
Abstract
The objectives of this study comprise the identification of key miRNAs and their target genes associated with severe tolerance in individuals exposed to aluminum and welding fumes, and the elucidation of the underlying regulatory mechanisms. In this study, the levels of seven miRNAs [...] Read more.
The objectives of this study comprise the identification of key miRNAs and their target genes associated with severe tolerance in individuals exposed to aluminum and welding fumes, and the elucidation of the underlying regulatory mechanisms. In this study, the levels of seven miRNAs (hsa-miR-19a-3p, hsa-miR-130b-3p, hsa-miR-25-3p, hsa-miR-363-3p, hsa-miR-92a-3p, hsa-miR-24-3p, and hsa-miR-19b-3p) were analyzed using both hsa-miR-16-5p and RNU6 (U6 snRNA) as reference miRNAs to validate normalization reliability. The qRT-PCR method was used on blood serum samples from 16 workers who were exposed to aluminum, 16 workers who were exposed to welding fumes, and 16 healthy controls who were not exposed to aluminum or welding fumes. We determined heavy metal levels from serum samples of workers exposed to aluminum and welding fumes and control groups using the ICP-OES method. The expression levels of hsa-miR-19a-3p and hsa-miR-19b-3p in aluminum-exposed and control groups were found to be statistically significant (p < 0.05). When workers exposed to welding fumes were compared with the those in the control groups, the expression levels of hsa-miR-19a-3p, hsa-miR-130b-3p, hsa-miR-92a-3p, and hsa-miR-24-3p were observed to be statistically significant (p < 0.05). This study shows that the identification of miRNAs and target genes in different biological functions and pathways plays an important role in understanding the molecular mechanisms of responses to heavy metal toxicity. We share the view that the study will make a significant contribution to the literature in that seven candidate miRNAs can be used as possible biomarkers for exposure to aluminum and welding fumes in humans. Full article
(This article belongs to the Collection Bioinformatics Approaches to Biomedicine)
Show Figures

Figure 1

Back to TopTop