Search Results (105)

Pear (Pyrus pyrifolia) is an important deciduous fruit tree that requires a specific period of low-temperature accumulation to trigger spring flowering. The warmer winter caused by global warming has led to insufficient winter chilling, disrupting floral initiation and significantly reducing pear yields in Southern China. In this study, we integrated targeted phytohormone metabolomics, full-length transcriptomics, and proteomics to explore the regulatory mechanisms of dormancy in ‘Mixue’, a pear cultivar with an extremely low chilling requirement. Comparative analyses across the multi-omics datasets revealed 30 differentially abundant phytohormone metabolites (DPMs), 2597 differentially expressed proteins (DEPs), and 7722 differentially expressed genes (DEGs). Integrated proteomic and transcriptomic expression clustering analysis identified five members of the dormancy-associated MADS-box (DAM) gene family among dormancy-specific differentially expressed proteins (DEPs) and differentially expressed genes (DEGs). Phytohormone correlation analysis and cis-regulatory element analysis suggest that DAM genes may mediate dormancy progression by responding to abscisic acid (ABA), gibberellin (GA), and salicylic acid (SA). A dormancy-associated transcriptional regulatory network centered on DAM genes and phytohormone signaling revealed 35 transcription factors (TFs): 19 TFs appear to directly regulate the expression of DAM genes, 18 TFs are transcriptionally regulated by DAM genes, and two TFs exhibit bidirectional regulatory interactions with DAM. Within this regulatory network, we identified a novel pathway involving REVEILLE 6 (RVE6), DAM, and CONSTANS-LIKE 8 (COL8), which might play a critical role in regulating bud dormancy in the ‘Mixue’ low-chilling pear cultivar. Furthermore, lncRNAs ONT.19912.1 and ONT.20662.7 exhibit potential cis-regulatory interactions with DAM1/2/3. This study expands the DAM-mediated transcriptional regulatory network associated with bud dormancy, providing new insights into its molecular regulatory mechanisms in pear and establishing a theoretical framework for future investigations into bud dormancy control. Full article

Compelling evidence has demonstrated a bidirectional relationship between Sjögren’s syndrome (SS) and periodontitis (PD). Nevertheless, the underlying mechanisms driving their co-occurrence remain unclear, highlighting the need for finding the hub gene. This study sought to examine the common genes and any connections between SS and PD. Differently expressed genes (DEGs) were analyzed by means of gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO) methods. The test and validation sets were used to depict the receiver operating characteristic (ROC) curves. The immune cell infiltration was performed via the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) methodology. The relationships between immune infiltrating cells and the common gene were examined. Ninety-five common genes with similar expression trends were obtained after DEGs analysis, which were enriched in cytokine—cytokine receptor interaction, chemokine signaling pathway, proteasome, intestinal immune network for IgA production, and cytosolic DNA sensing pathway. Thirty-nine common genes were obtained after WGCNA. Sixteen shared genes of DEGs analysis and WGCNA were incorporated into the LASSO model to obtain the unique shared gene, C-C motif chemokine receptor 1 (CCR1), which overexpressed and owned predictable ROC curves in test and validation sets. The examination of immune cell infiltration underscored its crucial roles in the disturbance of immune homeostasis and the emergence of pathogenic circumstances with the simultaneous occurrence of SS and PD. CCR1 overexpresses and serves as a critical pathogenic hub linking SS and PD, which may play a role through immune cell infiltration. Full article

Background/Objectives: The regulatory SNPs (rSNPs) that disturb the binding of transcription factors (TFs) and alter the transcription levels of genes play a paramount role in the formation of different traits and are associated with many pathologies. The search for allele-specific events in RNA-seq and ChIP-seq data is a powerful genome-wide approach to detect rSNPs. Using this approach, we have identified the T → A rs2072580 substitution in the bidirectional SART3/ISCU promoter as a potential rSNP and demonstrated its association with colorectal cancer, relying on International Cancer Genome Consortium data. The goal of this work was to identify the TF binding site that is affected by the T → A substitution and to study the effect of this substitution on reporter gene expression in different plasmid constructs. Methods: Electrophoretic mobility shift assay (EMSA), cross-competition analysis and supershift assay, plasmid construction, and dual luciferase reporter assay. Results: The T → A rs2072580 substitution is shown to damage the binding site for ubiquitous TF CREB1 and to significantly decrease the activity of the heterologous promoter carrying the cassettes of two or three repeated CREB binding sites inserted upstream of it. However, the substitution disturbing the CREB1 binding site within the bidirectional promoter shared by SART3 and ISCU inhibits the promoter activity of only the SART3 gene but has no effect on the activity of the ISCU promoter. Conclusions: The performed comprehensive functional analysis of the T → A rs2072580 in the bidirectional SART3/ISCU promoter unambiguously implies it is an rSNP. These results form the background for further studies of this rSNP and its potential significance for various pathologies. Full article

Hidradenitis suppurativa (HS) and atopic dermatitis (AD) are both inflammatory dermatoses that can significantly impact patient quality of life, however, limited research exists regarding their association. The purpose of this comprehensive review is to compare the inflammatory pathogenesis of HS and AD, explore the associations between these diseases, and discuss standalone and concomitant disease treatment options. Although HS and AD are understood to be primarily driven by the Th1 and Th2 inflammation pathways, respectively, these conditions both utilize the Janus Kinase/Signal transducer and activator of transcription (JAK/STAT) pathway to promote inflammation. Newer research also suggests that IL-36 and IL-1 receptor-associated kinase 4 (IRAK4) may be two additional inflammatory signals shared between the HS and AD disease pathways. These shared mechanisms are reflected in patient presentations as HS and AD are often concomitantly present and demonstrate a bidirectional association in the current literature. Treatment options for concomitant disease are limited, but leverage the shared immune pathogenesis of both diseases. Dupilumab has been reported to improve both HS and AD symptoms in select patients. JAK inhibitors are currently FDA-approved for the treatment of AD, and early trials have suggested benefits from JAK inhibitors such as upadacitinib, povorcitinib, and topical ruxolitinib for HS. Possible future avenues for research on treating both HS and AD include IRAK-4 inhibitors such as zabedosertib and BAY1830839, and diet and gut microbiome modifications. Full article

Metabolic reprogramming and epigenetic alterations are fundamental hallmarks of cancer cells, contributing to adaptation, progression, and resistance. In melanoma, high metabolic-epigenetic plasticity enables the rapid modulation of cell states in response to environmental and therapeutic pressures. Recent studies have highlighted a bidirectional crosstalk between cellular metabolism and epigenetic regulation. Epigenetic modifications influence the transcriptional control of metabolic genes, thereby shaping metabolic phenotypes. Conversely, specific metabolites are essential cofactors or substrates for epigenetic enzymes, directly modulating the epigenome. Understanding the intricate mechanisms of this interaction offers opportunities for the development of innovative tumor management that combines epigenetic, metabolic, and therapy interventions. In this review, we summarize the latest evidence on the role of the metabolism–epigenetics axis in melanoma and discuss its potential clinical implications, aiming to provide a comprehensive overview of metabolic/epigenetic interconnections. Full article

The Nuclear factor erythroid 2-related factor 2 (NRF2) Neurogenic locus NOTCH homolog protein (NOTCH) crosstalk has emerged as a critical regulatory axis in the progression of solid cancers, especially lung, affecting tumor growth and resistance to therapy. NRF2 is a master transcription factor that orchestrates the cellular antioxidant response, while NOTCH signaling is involved in the cell–cell communication processes by influencing the patterns of gene expression and differentiation. Although frequently altered independently, genetic and epigenetic dysregulation of both NRF2 and NOTCH pathways often converge to deregulate oxidative stress responses and promote tumor cell survival. Recent findings reveal that the NRF2/NOTCH interplay extends beyond canonical signaling, contributing to metabolic reprogramming and reshaping the tumor microenvironment (TME) to promote cancer malignancy. Emerging scientific evidences highlight the key role of biochemical and metabolomic changes within NRF2–NOTCH crosstalk, in contributing to cancer progression and metabolic reprogramming, beyond facilitating the adaptation of cancer cells to the TME. Actually, the effects of the NRF2–NOTCH bidirectional interaction in either supporting or suppressing lung tumor phenotypes are still unclear. This review explores the molecular mechanisms underlying NRF2–NOTCH crosstalk in lung cancer, highlighting the impact of genetic and epigenetic deregulation mechanisms on neoplastic processes, modulating the TME and driving the metabolic reprogramming. Furthermore, we discuss therapeutic opportunities for targeting this regulatory network, which may open new avenues for overcoming drug resistance and improving clinical outcomes in lung cancer. Full article

As the construction industry shifts from an extensive development model to one characterized by intelligent structural systems, the imperative to enhance productivity and management efficiency has emerged as a critical challenge. Conventional rebar construction processes heavily rely on manual operations—such as on-site rebar cutting, manual transcription of material lists, and decentralized processing—which are susceptible to subjective errors and often result in significant material waste. This issue is particularly pronounced in large-scale projects, where disorganized management of rebar quantities and placements exacerbates inefficiencies. To address these challenges, this study proposes an integrated approach that synergistically combines a genetic algorithm-based rebar-cutting optimization model with BIM technology, thereby optimizing rebar management throughout the construction process. The research is structured into two primary components. Firstly, a one-dimensional mathematical model for rebar-cutting optimization is developed, incorporating an innovative real-number encoding strategy within the genetic algorithm framework to maximize material utilization. A case study conducted on a pump station project reveals that the utilization rates for 32 mm and 16 mm rebar reach 86.76% and 93.90%, respectively, significantly exceeding the industry standard of 80%. Secondly, an automated batch modeling tool is developed using C# and the Revit API, which enables the efficient generation of rebar components; a unique coding system is employed to establish a bidirectional mapping between the digital model and the physical rebar, ensuring precise positioning and effective information management. Overall, this integrated method—encompassing rebar-cutting optimization, digital modeling, and on-site intelligent management—not only mitigates material waste and reduces production costs but also markedly enhances construction efficiency and accuracy in complex projects, thereby providing robust technical support for the seamless integration of intelligent construction and industrialized building practices. Full article

Transcription factors (TFs) are fundamental regulators of gene expression and perform diverse functions in cellular processes. The management of 3-dimensional (3D) genome conformation and gene expression relies primarily on TFs. TFs are crucial regulators of gene expression, performing various roles in biological processes. They attract transcriptional machinery to the enhancers or promoters of specific genes, thereby activating or inhibiting transcription. Identifying these TFs is a significant step towards understanding cellular gene expression mechanisms. Due to the time-consuming and labor-intensive nature of experimental methods, the development of computational models is essential. In this work, we introduced a two-layer prediction framework based on a support vector machine (SVM) using the latent space representation of a protein language model, ProtBert. The first layer of the method reliably predicts and identifies transcription factors (TFs), and in the second layer, the proposed method predicts and identifies transcription factors that prefer binding to methylated deoxyribonucleic acid (TFPMs). In addition, we also tested the proposed method on an imbalanced database. In detecting TFs and TFPMs, the proposed model consistently outperformed state-of-the-art approaches, as demonstrated by performance comparisons via empirical cross-validation analysis and independent tests. Full article

The rising prevalence of mental health disorders, particularly depression, highlights the need for improved approaches in therapeutic interventions. Traditional psychotherapy relies on subjective assessments, which can vary across therapists and sessions, making it challenging to track emotional progression and therapy effectiveness objectively. Leveraging the advancements in Natural Language Processing (NLP) and domain-specific Large Language Models (LLMs), this study introduces nBERT, a fine-tuned Bidirectional Encoder Representations from the Transformers (BERT) model integrated with the NRC Emotion Lexicon, to elevate emotion recognition in psychotherapy transcripts. The goal of this study is to provide a computational framework that aids in identifying emotional patterns, tracking patient-therapist emotional alignment, and assessing therapy outcomes. Addressing the challenge of emotion classification in text-based therapy sessions, where non-verbal cues are absent, nBERT demonstrates its ability to extract nuanced emotional insights from unstructured textual data, providing a data-driven approach to enhance mental health assessments. Trained on a dataset of 2021 psychotherapy transcripts, the model achieves an average precision of 91.53%, significantly outperforming baseline models. This capability not only improves diagnostic accuracy but also supports the customization of therapeutic strategies. By automating the interpretation of complex emotional dynamics in psychotherapy, nBERT exemplifies the transformative potential of NLP and LLMs in revolutionizing mental health care. Beyond psychotherapy, the framework enables broader LLM applications in the life sciences, including personalized medicine and precision healthcare. Full article

BC is the most commonly diagnosed cancer and the second leading cause of cancer death among women worldwide. Cellular stress is a condition that leads to disrupted homeostasis by extrinsic and intrinsic factors. Among other stressors, hypoxia is a driving force for breast cancer (BC) progression and a general hallmark of solid tumors. Thus, intratumoral hypoxia is an important determinant of invasion, metastasis, treatment failure, prognosis, and patient mortality. Acquisition of the epithelial–mesenchymal transition (EMT) phenotype is also a consequence of tumor hypoxia. The cellular response to hypoxia is mainly regulated by the hypoxia signaling pathway, governed by hypoxia-inducible factors (HIFs), mainly HIF1α. HIFs are a family of transcription factors (TFs), which induce the expression of target genes involved in cell survival and proliferation, metabolic reprogramming, angiogenesis, resisting apoptosis, invasion, and metastasis. HIF1α cooperates with a large number of other TFs. In this review, we focused on the crosstalk and cooperation between HIF1α and other TFs involved in the cellular response to hypoxia in BC. We identified a cluster of TFs, proposed as the HIF1α-TF interactome, that orchestrates the transcription of target genes involved in hypoxia, due to their post-translational modifications (PTMs), including phosphorylation/dephosphorylation, ubiquitination/deubiquitination, SUMOylation, hydroxylation, acetylation, S-nitrosylation, and palmitoylation. PTMs of these HIF1α-related TFs drive their stability and activity, degradation and turnover, and the bidirectional translocation between the cytoplasm or plasma membrane and nucleus of BC cells, as well as the transcription/activation of proteins encoded by oncogenes or inactivation of tumor suppressor target genes. Consequently, PTMs of TFs in the HIF1α interactome are crucial regulatory mechanisms that drive the cellular response to oxygen deprivation in BC cells. Full article

Arbuscular mycorrhizal (AM) symbiosis, a mutually beneficial interaction between plant roots and AM fungi, plays a key role in plant growth, nutrient acquisition, and stress tolerance, which make it a major focus for sustainable agricultural strategies. This intricate association involves extensive transcriptional reprogramming in host plant cells during the formation of arbuscules, which are specialized fungal structures for nutrient exchange. The symbiosis is initiated by molecular signaling pathways triggered by fungal chitooligosaccharides and strigolactones released by plant roots, which act as chemoattractants and signaling molecules to promote fungal spore germination, colonization, and arbuscule development. Calcium spiking, mediated by LysM domain receptor kinases, serves as a critical second messenger in coordinating fungal infection and intracellular accommodation. GRAS transcription factors are key components that regulate the transcriptional networks necessary for arbuscule development and maintenance, while small RNAs (sRNAs) from both plant and fungi, contribute to modifications in gene expression, including potential bidirectional sRNA exchange to modulate symbiosis. Understanding the molecular mechanisms related to AM symbiosis may provide valuable insights for implementation of strategies related to enhancing plant productivity and resilience. Full article

Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, as many regulatory proteins need to be expressed in small quantities, and excessive expression can have harmful effects on cells and organisms. Therefore, it is important to select the right promoter when creating transgenic organisms for research and practical applications. Methods: In this study, we used the Drosophila melanogaster genome as a source of natural promoter sequences for RNA polymerase II. These sequences were extracted and used to create a set of promoters that are suitable for practical application. The promoters were tested in a model system using fluorescent reporter genes in S2 cells and transgenic lines of Drosophila. Results: We assessed the expression levels of fluorescent reporter genes to rank the tested promoters from strongest to weakest. Six individual promoters of different sizes were established and compared. Additionally, we designed and tested three pairs of bidirectional promoters that could be used to simultaneously express two proteins. Conclusions: Based on our findings, we grouped the tested promoters into three categories: strong, moderate, and weak. These promoters can be utilized in transgenic model systems for protein production at different levels, from high to low. Bidirectional promoters, constructed “head-to-head”, meaning oppositely directed with the minimum distance between them, represent a novel tool for the co-expression of proteins. Full article

Bidirectional promoters (BDPs) regulate the transcription of two adjacent, oppositely oriented genes, offering a compact structure with significant potential for multigene expression systems. Although BDPs are evolutionarily conserved, their regulatory roles and sequence characteristics vary across species, with limited studies in fish. Here, we systematically analyzed the distribution, sequence features, and expression patterns of BDPs in the medaka (Oryzias latipes) genome. A total of 1737 divergent gene pairs, representing 13% of medaka genes, were identified as potentially regulated by BDPs. These genes are enriched in essential biological processes, including organelle function, RNA processing, and ribosome biogenesis. Transcriptomic analysis revealed that co-regulation (co-expression and co-silencing) is a prominent feature of these gene pairs, with variability influenced by tissue and sex. Sequence analysis showed that medaka BDPs are compact, with most fragments under 400 bp and an average GC content of 42.06%. Validation experiments confirmed the bidirectional transcriptional activity of three histone-related BDPs in both medaka SG3 cells and embryos, demonstrating effective and robust regulatory efficiency. This study enhances our understanding of the genomic organization and transcriptional regulation in fish and provides a valuable reference for developing species-specific multigene expression systems in fish genetic engineering. Full article

Background/Objectives: Aging is a natural physiological process involving biological and genetic pathways. Growing evidence suggests that alterations in the epigenome during aging result in transcriptional changes, which play a significant role in the onset of age-related diseases, including cancer, cardiovascular disease, diabetes, and neurodegenerative disorders. For this reason, the epigenetic alterations in aging and age-related diseases have been reviewed, and the major extrinsic factors influencing these epigenetic alterations have been identified. In addition, the role of the gut microbiome and its metabolites as epigenetic modifiers has been addressed. Results: Long-term exposure to extrinsic factors such as air pollution, diet, drug use, environmental chemicals, microbial infections, physical activity, radiation, and stress provoke epigenetic changes in the host through several endocrine and immune pathways, potentially accelerating the aging process. Diverse studies have reported that the gut microbiome plays a critical role in regulating brain cell functions through DNA methylation and histone modifications. The interaction between genes and the gut microbiome serves as a source of adaptive variation, contributing to phenotypic plasticity. However, the molecular mechanisms and signaling pathways driving this process are still not fully understood. Conclusions: Extrinsic factors are potential inducers of epigenetic alterations, which may have important implications for longevity. The gut microbiome serves as an epigenetic effector influencing host gene expression through histone and DNA modifications, while bidirectional interactions with the host and the underexplored roles of microbial metabolites and non-bacterial microorganisms such as fungi and viruses highlight the need for further research. Full article

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2–17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect–fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution. Full article