Gene Expression Patterns Research Articles

Identification and expression analysis of four sHsp genes in Sogatella furcifera under abiotic stress

Sogatella furcifera is a typical r-strategist insect with strong adaptability and one of the major pests in rice cultivation. Small heat shock proteins (sHsp) play a vital role in insects responding to external abiotic stress. However, little is known about the role of sHsp in the defense against abiotic stress in S. furcifera. In this study, four sHsp genes (SofHsp20.7, SofHsp21.6, SofHsp21.7, and SofHsp21.8) were identified from S. furcifera, and their gene expression patterns were analyzed at different developmental stages, temperature stress, insecticide exposure, and UV-A irradiation. The results indicated that four sHsp were expressed at various developmental stages of the S. furcifera, with the highest transcription levels in the first-instar nymphs, fourth day fifth instar nymphs, third-day adult females, and eggs, respectively. High-temperature stress (30 °C and 40 °C) significantly induced the expression of all four sHsp genes, while low-temperature stress (10 °C) reduced their expression. Sublethal concentrations (LC10 and LC25) of buprofezin increased the expression levels of SofHsp20.7 and SofHsp21.8. Under UV-A irradiation, the S. furcifera also significantly induced the expression of all four sHsp genes, with the highest expression observed at 90 min after exposure to the stress. These results suggest that sHsp genes are essential for the resistance or tolerance of S. furcifera to high temperature, buprofezin, and UV-A irradiation. This research provides a foundation for understanding the molecular mechanisms underlying the S. furcifera adaptation to abiotic stress.

Effect of Quorum Sensing Systems on Biofilm Formation and Virulence in Salmonella

In recent years, as the paradigm of communication between cells has been clarified, the ability of bacteria to change their gene expression patterns in response to various extracellular signals has attracted great interest. In particular, intracellular and intercellular communication between bacterial populations, called quorum sensing (QS), is essential for coordinating physiological and genetic activities. QS studies are critical, particularly in elucidating the regulatory mechanisms of infectious processes in food-borne pathogens. Elucidating the QS mechanisms in Salmonella is effective in silencing the virulence factors in the fight against this bacterium. The aims of this study were; to create luxS gene mutants that play a vital role in the QS activity of Salmonella and to determine the effect of this mutation on the expression of virulence genes in the bacteria and to determine the impact of synthetic N-hexanoyl-homoserine lactone (C6HSL) on biofilm formation and AI-2 signaling pathway of Salmonella wild strain and luxS gene mutants. luxS gene mutants were constructed by recombining the gene region with the chloramphenicol gene cassette based on homologous region recombination. In the luxS mutants obtained in this way, the expression of eight different virulence genes (hilA, invA, inv, glgC, fimF, fliF, lpfA, gyrA), which have essential roles in Salmonella pathogenicity, was determined by quantitative real-time reverse transcriptase polymerase chain reaction (rRT-qPCR) method and compared with natural strains. As a result of these studies, it was determined that the expression of each gene examined was significantly reduced in luxS mutant strains. The relative AI-2 activities of Salmonella strains were analyzed depending on time. It was determined that the highest activity occurred at the fourth hour and the AI-2 activities of luxS mutants were reduced compared to the wild strain. Finally, it was determined that C6HSL increased the biofilm activity of Salmonella Typhimurium DMC4, SL1344 wild strains, and mutants, mainly at the 72nd hour. In conclusion, our results proved that C6HSL stimulated QS communication in all strains and increased biofilm of Salmonella formation and autoinducer activity. This situation determines that Salmonella responds to external signals by using QS systems. In addition, this research contributed to provide additional information on interspecies communication mechanisms to develop strategies to prevent biofilm formation of this pathogen.

Gene Expression Patterns and Phenotypic Associations in Chondrogenesis: Insights into Skeletal Dysplasia Nosology

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes, known as chondrogenesis, is a complex process that plays a fundamental role in cartilage formation and skeletal development. This study elucidates the transcriptional dynamics and phenotypic correlations at various stages of chondrogenesis (early, mid, and late) using RNA-seq data. We focused on the differential expression of transcription factors (TFs) and RNA-binding proteins (RBPs). We identified critical genes during their highest expression periods and generated heatmaps to visualize these temporal patterns. Additionally, we conducted a comprehensive analysis of skeletal dysplasia nosology genes, determining their highest expression periods and phenotypic implications using the DisGeNET database. Our findings reveal that early-stage (D1) gene expression is linked to craniofacial development and limb formation anomalies, primarily involving genes responsible for extracellular matrix (ECM) organization and signal transduction. Mid-stage (D7) genes are associated with cartilage matrix composition and skeletal growth, highlighting roles in chondrocyte proliferation and matrix deposition. Late-stage (D21) genes are implicated in bone mineral density, cartilage integrity, and joint formation, ensuring the maturation and functionality of cartilage tissue. This study provides a detailed analysis of gene expression regulators and their phenotypic correlations during chondrogenesis, offering insights into the molecular mechanisms driving cartilage development and skeletal dysplasias. Understanding these temporal gene expression patterns enhances our knowledge of chondrogenesis and aids in developing targeted therapies for cartilage-related diseases. These findings underscore the significance of time-point analyses in capturing the dynamic regulation of gene expression throughout the differentiation process.

Gene Expression Patterns and Phenotypic Associations in Chondrogenesis: Insights into Skeletal Dysplasia Nosology

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes, known as chondrogenesis, is a complex process that plays a fundamental role in cartilage formation and skeletal development. This study elucidates the transcriptional dynamics and phenotypic correlations at various stages of chondrogenesis (early, mid, and late) using RNA-seq data. We focused on the differential expression of transcription factors (TFs) and RNA-binding proteins (RBPs). We identified critical genes during their highest expression periods and generated heatmaps to visualize these temporal patterns. Additionally, we conducted a comprehensive analysis of skeletal dysplasia nosology genes, determining their highest expression periods and phenotypic implications using the DisGeNET database. Our findings reveal that early-stage (D1) gene expression is linked to craniofacial development and limb formation anomalies, primarily involving genes responsible for extracellular matrix (ECM) organization and signal transduction. Mid-stage (D7) genes are associated with cartilage matrix composition and skeletal growth, highlighting roles in chondrocyte proliferation and matrix deposition. Late-stage (D21) genes are implicated in bone mineral density, cartilage integrity, and joint formation, ensuring the maturation and functionality of cartilage tissue. This study provides a detailed analysis of gene expression regulators and their phenotypic correlations during chondrogenesis, offering insights into the molecular mechanisms driving cartilage development and skeletal dysplasias. Understanding these temporal gene expression patterns enhances our knowledge of chondrogenesis and aids in developing targeted therapies for cartilage-related diseases. These findings underscore the significance of time-point analyses in capturing the dynamic regulation of gene expression throughout the differentiation process.

Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.

DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.

Tick-Borne pathogens and defensin genes expression: A closer look at Ixodes ricinus and Dermacentor reticulatus

The immune system of ticks, along with that of other invertebrates, is comparatively simpler than that of vertebrates, relying solely on innate immune responses. Direct antimicrobial defence is provided by the synthesis of antimicrobial peptides (AMPs), including defensins. The aim of this study was to investigate the differences in defensin genes expression between questing and engorged Ixodes ricinus (def1 and def2) and Dermacentor reticulatus (defDr) ticks, in the presence of selected pathogens: Borrelia spp., Rickettsia spp., Babesia spp., Anaplasma phagocytophilum, and Neoehrlichia mikurensis in the natural environment. After pathogen screening by PCR/qPCR, the expression of defensin genes in pathogen positive ticks and ticks without any of the tested pathogens, was analysed by reverse transcription qPCR. The results showed an increased expression of defensin genes in I. ricinus ticks after blood feeding and I. ricinus and D. reticulatus ticks during in cases of co-infection. In particular, the expression of defensins genes was higher in questing D. reticulatus than in questing and engorged I. ricinus ticks, when borreliae were detected. This study contributes to uncovering the expression patterns of defensin genes in the presence of several known tick pathogens, the occurrence of these pathogens and possible regulatory mechanisms of defensins in tick vector competence.

Deciphering endometrial dysfunction in patients with uterine myoma using endometrial organoids: a pilot study

Research QuestionWhat kind of influence does intramural myoma have on the endometrium, and how does it take action? DesignEndometrium was collected from 13 patients with noncavity-distorting intramural myomas (diameter ≤4cm) (FIGO type 4) and 13 patients without myoma receiving hysterectomy due to benign cervical diseases with a similar clinical baseline. Endometrial organoids were established in vitro and induced to the secretory phase by estrogen and progesterone. Transcriptome sequencing was conducted on endometrial organoids at both untreated and secretory stages from 3 myoma patients and 3 control patients. Immunofluorescence and RT-qPCR were performed on endometrial organoids from another 10 myoma patients and 10 control patients for validation. ResultsOur data revealed abnormally increased hormone receptor (PGR, PRLR and ESR2) levels in the untreated endometrial organoids with myoma, resulting in abnormal glandular and vascular development. The aberrant responses to estrogen and progestogen prompted further investigation into the secretory phase. The secretory endometrial organoids with myoma exhibited greater abnormalities characterized by decreased cilia (marked by acetyl-α-tubulin, ODF2 and TPPP) and increased ECM remodeling (marked by COL6A1). Both untreated and secretory endometrial organoids with myoma showed upregulated ECM mechano-transduction related genes and pathways. The expression pattern of receptivity-related genes was disturbed in endometrial organoids with myoma. ConclusionOur study is the first to reveal that intramural myomas create an abnormal hormonal and mechanical environment whether in the untreated or secretory endometrial organoids. The intramural myomas negatively impact gene expression relating to endometrial glands, blood vessels, cilia, and ECM, indicating that intramural myomas impair endometrial decidualization and receptivity.

Region-specific gene expression profile in the epididymis of high- and low-fertile dromedary camels.

The scenario of the fertile spermatozoa with high fertilizing capability is basically dependent on gene expression-based epididymal function. The current investigation aimed to declare the varied expression of different candidate genes (PLA2G4D, LCN15, CLUAP1, SPP1, AQP12B, DEFB110 and ESR1) relevant to spermatozoa features between the different epididymal segments in the mature dromedary camels (n = 30). Scrotal contents were collected post-slaughtering, during the breeding season and the epididymis was separated from the testicles and divided into three segments (caput, corpus and cauda) based on its morphology and anatomical characteristics. Epididymal spermatozoa were harvested from each epididymal portion and evaluated for motility, count, viability and morphology. Samples were grouped depending on their epididymal sperm cells features into high-fertile (n = 15) and low-fertile (n = 15) groups. The gene expression of the candidate genes was defined in the isolated RNA from each epididymal portion tissue. The segmental sperm motion and count were significantly (p < .05 and p < .01) higher in the three epididymal parts of high-fertile camels than the lower ones. There were some candidate genes markedly up-regulated in its expression in epididymal head of high-fertile camels (PLA2G4D and LCN15) and low fertile (CLUAP1), while others in the body region of the high-fertile group (SPP1, AQP12B and DEFB110). Nevertheless, ER1 did not differ in the expression among the epididymal segments. In conclusion, the variant expression patterns of these epididymal genes in relation to the regional spermatozoa features might suggest important roles of these genes in sperm maturation process in the epididymis and focusing more interest on their potential utility as markers for male camel fertility prediction.

The transcriptomic landscape of Botrytis cinerea infection on postharvest grapes sheds light on the biological function of the Bcnrps1 gene

Botrytis cinerea, a prevalent necrotrophic fungal pathogen, causes significant postharvest infections including fruits. This pathogen exploits senescent tissues, resulting in significant economic losses. During the Botrytis-plant interaction, a molecular cross-talk is established between the host and the pathogen, mediated by the interplay of the plant's defense pathways and the phytopathogenic fungus's virulence pathways, which are modulated by abiotic and biotic factors.The Bcnrps1 genes is secondary metabolims gene that encodes a non-ribosomal peptide synthetase. This family enzyme is responsible for the synthesis of natural peptides with a wide range of biological activities. Although the function of the majority of these peptides remains elusive, they could evolve in plant-pathogen interaction during infection process. Deletion of the Bcnrps1 gene increases the virulence of the pathogen otherwise, a reduction in sensitivity to toxic compounds such as spermidine and the fungicide pyrimethanil is observed. A transcriptome analysis was performed in this study to comprehensively elucidate the behavior of this mutant and to assess the molecular dynamics both in Bcnrps1 mutant and wild-type strains during the infection process of harvested white grapes. The number of differentially expressed genes (DEGs) during infection differs significantly between the B. cinerea B05.10 strain and the ΔBcnrps1 strain. The results demonstrate that, during white grape infection, the mutant induces genes related to five main functional groups: detoxification, transcription factors, CAZymes, virulence factors, and secondary metabolism. These findings underscore the crucial role of the Bcnrps1 gene in mediating the fungal response to environmental stressors and plant-derived substances during plant-pathogen interactions, as supported by observed gene expression patterns.

Lack of Bmal1 leads to changes in rhythmicity and impairs motivation towards natural stimuli.

Maintaining proper circadian rhythms is essential for coordinating biological functions in mammals. This study investigates the effects of daily arrhythmicity using Bmal1-knockout (KO) mice as a model, aiming to understand behavioural and motivational implications. By employing a new mathematical analysis based on entropy divergence, we identified disrupted intricate activity patterns in mice derived by the complete absence of BMAL1 and quantified the difference regarding the activity oscillation's complexity. Changes in locomotor activity coincided with disturbances in circadian gene expression patterns. Additionally, we found a dysregulated gene expression profile particularly in brain nuclei like the ventral striatum, impacting genes related to reward and motivation. Further investigation revealed that arrhythmic mice exhibited heightened motivation for food and water rewards, indicating a link between circadian disruptions and the reward system. This research sheds light on how circadian clock alterations impact the gene expression regulating the reward system and how this, in turn, can lead to altered seeking behaviour and motivation for natural rewards. In summary, the present study contributes to our understanding of how reward processing is under the regulation of circadian clock machinery.

The effect of parental age on the quantity and quality of offspring in Syngnathus typhle, a species with male pregnancy.

Parental age impacts offspring quantity and quality. Most prior research focused on maternal age. Since in most organisms the mother produces the costly eggs plus provides all or most parental care, it is difficult to distinguish maternal effects mediated via the egg from later maternal care. Here, we addressed the effects of parental age on offspring in Syngnathus typhle, a pipefish with male pregnancy. The divide between one parent producing the eggs and the second parent being the exclusive provider of parental care facilitates a distinction between the effects of parental age on egg quality versus parental age on early development. We fully reciprocally crossed young and old mothers and young and old fathers and assessed impact of parental age combination on offspring number, offspring size, and offspring gene expression patterns. Neither parental combination significantly influenced offspring size or male gestation duration; however, they influenced the number of offspring. Paternal, but not maternal, age strongly affected the offspring gene expression. Offspring from old fathers exhibited substantial changes in the expression of genes related to cell cycle regulation, protein synthesis, DNA repair, and neurogenesis. Our findings thus highlight the importance of gestation, as opposed to gamete production, in shaping the parental contribution to offspring development.

Pharmacological activation of mesenchymal stem cells increases gene expression pattern of cell adhesion molecules and fusion with neonatal cardiomyocytes.

Cellular therapy is considered a better option for the treatment of degenerative disorders. Different cell types are being used for tissue regeneration. Despite extensive research in this field, several issues remain to be addressed concerning cell transplantation. One of these issues is the survival and homing of administered cells in the injured tissue, which depends on the ability of these cells to adhere. To enhance cell adherence and survival, Rap1 GTPase was activated in mesenchymal stem cells (MSCs) as well as in cardiomyocytes (CMs) by using 8-pCPT-2'-O-Me-cAMP, and the effect on gene expression dynamics was determined through quantitative reverse transcriptase-polymerase chain reactionanalysis. Pharmacological activation of MSCs and CMsresulted in the upregulation of connexin-43 and cell adhesion genes, which increased the cell adhesion ability of MSCs and CMs, and increased the fusion of MSCs with neonatal CMs. Treating stem cells with a pharmacological agent that activates Rap1a before transplantation can enhance their fusion with CMs and increase cellular regeneration.

Gene expression patterns associated with PFOA exposure in Czech Young men and women

Perfluorooctanoic acid (PFOA), a member of per- and polyfluoroalkyl substances (PFASs), has been widely used in manufacturing for decades. Currently, PFOA is strictly regulated, but due to its high stability and persistence, it is detected in both environmental as well as in human matrices. To elucidate mechanisms of PFOA toxicity in humans, we determined the genome-wide transcriptomic changes of peripheral blood mononuclear cells (PBMC) responding to PFOA exposure in a sex-stratified analysis. This work employed samples from 145 female and 143 male participants of the CELSPAC: YA study to characterize PFOA-associated transcripts in a broader context using computational analysis. PFOA-associated gene expression differed significantly between men and women, as only 2% of mapped genes were expressed in both sexes. Disease-specific enrichment analysis revealed cancer and immune-related disease terms as those most enriched in male and female populations. Patterns of enriched terms within the gene set enrichment analysis indicated three main targets of PFOA toxicity: i) lipid metabolism for women; ii) cell cycle regulation for men; and iii) immune system response for both sexes. In summary, our genome-wide transcriptomics analysis described sex-specific differences in PFOA-associated gene expression and provided evidence about biological pathways underlying PFOA toxicity in humans.

The transcriptomic landscape of Botrytis cinerea infection on postharvest grapes sheds light on the biological function of the Bcnrps1 gene.

Botrytis cinerea, a prevalent necrotrophic fungal pathogen, causes significant postharvest infections including fruits. This pathogen exploits senescent tissues, resulting in significant economic losses. During the Botrytis-plant interaction, a molecular cross-talk is established between the host and the pathogen, mediated by the interplay of the plant's defense pathways and the phytopathogenic fungus's virulence pathways, which are modulated by abiotic and biotic factors.The Bcnrps1 genes is secondary metabolims gene that encodes a non-ribosomal peptide synthetase. This family enzyme is responsible for the synthesis of natural peptides with a wide range of biological activities. Although the function of the majority of these peptides remains elusive, they could evolve in plant-pathogen interaction during infection process. Deletion of the Bcnrps1 gene increases the virulence of the pathogen otherwise, a reduction in sensitivity to toxic compounds such as spermidine and the fungicide pyrimethanil is observed. A transcriptome analysis was performed in this study to comprehensively elucidate the behavior of this mutant and to assess the molecular dynamics both in Bcnrps1 mutant and wild-type strains during the infection process of harvested white grapes. The number of differentially expressed genes (DEGs) during infection differs significantly between the B. cinerea B05.10 strain and the ΔBcnrps1 strain. The results demonstrate that, during white grape infection, the mutant induces genes related to five main functional groups: detoxification, transcription factors, CAZymes, virulence factors, and secondary metabolism. These findings underscore the crucial role of the Bcnrps1 gene in mediating the fungal response to environmental stressors and plant-derived substances during plant-pathogen interactions, as supported by observed gene expression patterns.

RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma

Ocular melanoma, including uveal melanoma (UM) and conjunctival melanoma (CM), is the most common ocular cancer among adults with a high rate of recurrence and poor prognosis. Loss of epigenetic homeostasis disturbed gene expression patterns, resulting in oncogenesis. Herein, we comprehensively analyzed the DNA methylation, transcriptome profiles, and corresponding clinical information of UM patients through multiple machine-learning algorithms, finding that a methylation-driven gene RBMS1 was correlated with poor clinical outcomes of UM patients. RNA-seq and single-cell RNA-seq analyses revealed that RBMS1 reflected diverse tumor microenvironments, where high RBMS1 expression marked an immune active TME. Furthermore, we found that tumor cells were identified to have the higher communication probability in RBMS1+ state. The functional enrichment analysis revealed that RBMS1 was associated with pigment granule and melanosome, participating in cell proliferation as well as apoptotic signaling pathway. Biological experiments were performed and demonstrated that the silencing of RBMS1 inhibited ocular melanoma proliferation and promoted apoptosis. Our study highlighted that RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma, contributing to the therapeutic customization and clinical decision-making.

Hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

Uncovering PheCLE1 and PheCLE10 Promoting Root Development Based on Genome-Wide Analysis.

Moso bamboo (Phyllostachys edulis), renowned for its rapid growth, is attributed to the dynamic changes in its apical meristem. The CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) family genes are known to play crucial roles in regulating meristem and organ formation in model plants, but their functions in Moso bamboo remain unclear. Here, we conducted a genome-wide identification of the CLE gene family of Moso bamboo and investigated their gene structure, chromosomal localization, evolutionary relationships, and expression patterns. A total of 11 PheCLE genes were identified, all of which contained a conserved CLE peptide core functional motif (Motif 1) at their C-termini. Based on Arabidopsis classification criteria, these genes were predominantly distributed in Groups A-C. Collinearity analysis unveiled significant synteny among CLE genes in Moso bamboo, rice, and maize, implying potential functional conservation during monocot evolution. Transcriptomic analysis showed significant expression of these genes in the apical tissues of Moso bamboo, including root tips, shoot tips, rhizome buds, and flower buds. Particularly, single-cell transcriptomic data and in situ hybridization further corroborated the heightened expression of PheCLE1 and PheCLE10 in the apical tissue of basal roots. Additionally, the overexpression of PheCLE1 and PheCLE10 in rice markedly promoted root growth. PheCLE1 and PheCLE10 were both located on the cell membrane. Furthermore, the upstream transcription factors NAC9 and NAC6 exhibited binding affinity toward the promoters of PheCLE1 and PheCLE10, thereby facilitating their transcriptional activation. In summary, this study not only systematically identified the CLE gene family in Moso bamboo for the first time but also emphasized their central roles in apical tissue development. This provides a valuable theoretical foundation for the further exploration of functional peptides and their signaling regulatory networks in bamboo species.

Exercise Rescues Obesogenic-Related Genes in the Female Hypothalamic Arcuate Nucleus: A Potential Role of miR-211 Modulation.

Obesity is a major public health concern that is associated with negative health outcomes. Exercise and dietary restriction are commonly recommended to prevent or combat obesity. This study investigates how voluntary exercise mitigates abnormal gene expression in the hypothalamic arcuate nucleus (ARC) of diet-induced obese (DIO) rats. Using a transcriptomic approach, novel genes in the ARC affected by voluntary wheel running were assessed alongside physiology, pharmacology, and bioinformatics analysis to evaluate the role of miR-211 in reversing obesity. Exercise curbed weight gain and fat mass, and restored ARC gene expression. High-fat diet (HFD) consumption can dysregulate satiety/hunger mechanisms in the ARC. Transcriptional clusters revealed that running altered gene expression patterns, including inflammation and cellular structure genes. To uncover regulatory mechanisms governing gene expression in DIO attenuation, we explored miR-211, which is implicated in systemic inflammation. Exercise ameliorated DIO overexpression of miR-211, demonstrating its pivotal role in regulating inflammation in the ARC. Further, in vivo central administration of miR-211-mimic affected the expression of immunity and cell cycle-related genes. By cross-referencing exercise-affected and miR-211-regulated genes, potential candidates for obesity reduction through exercise were identified. This research suggests that exercise may rescue obesity through gene expression changes mediated partially through miR-211.

Immunological Signatures for Early Detection of Human Head and Neck Squamous Cell Carcinoma through RNA Transcriptome Analysis of Blood Platelets.

Although there has been a reduction in head and neck squamous cell carcinoma occurrence, it continues to be a serious global health concern. The lack of precise early diagnostic biomarkers and postponed diagnosis in the later stages are notable constraints that contribute to poor survival rates and emphasize the need for innovative diagnostic methods. In this study, we employed machine learning alongside weighted gene co-expression network analysis (WGCNA) and network biology to investigate the gene expression patterns of blood platelets, identifying transcriptomic markers for HNSCC diagnosis. Our comprehensive examination of publicly available gene expression datasets revealed nine genes with significantly elevated expression in samples from individuals diagnosed with HNSCC. These potential diagnostic markers were further assessed using TCGA and GTEx datasets, demonstrating high accuracy in distinguishing between HNSCC and non-cancerous samples. The findings indicate that these gene signatures could revolutionize early HNSCC identification. Additionally, the study highlights the significance of tumor-educated platelets (TEPs), which carry RNA signatures indicative of tumor-derived material, offering a non-invasive source for early-detection biomarkers. Despite using platelet and tumor samples from different individuals, our results suggest that TEPs reflect the transcriptomic and epigenetic landscape of tumors. Future research should aim to directly correlate tumor and platelet samples from the same patients to further elucidate this relationship. This study underscores the potential of these biomarkers in transforming early diagnosis and personalized treatment strategies for HNSCC, advocating for further research to validate their predictive and therapeutic potential.

Long-Term In Vitro Culture Alters Gene Expression Pattern of Genes Involved in Ontological Groups Representing Cellular Processes.

The oviduct provides an optimal environment for the final preparation, transport, and survival of gametes, the fertilization process, and early embryonic development. Most of the studies on reproduction are based on in vitro cell culture models because of the cell's accessibility. It creates opportunities to explore the complexity of directly linked processes between cells. Previous studies showed a significant expression of genes responsible for cell differentiation, maturation, and development during long-term porcine oviduct epithelial cells (POECs) in vitro culture. This study aimed at establishing the transcriptomic profile and comprehensive characteristics of porcine oviduct epithelial cell in vitro cultures, to compare changes in gene expression over time and deliver information about the expression pattern of genes highlighted in specific GO groups. The oviduct cells were collected after 7, 15, and 30 days of in vitro cultivation. The transcriptomic profile of gene expression was compared to the control group (cells collected after the first day). The expression of COL1A2 and LOX was enhanced, while FGFBP1, SERPINB2, and OVGP1 were downregulated at all selected intervals of cell culture in comparison to the 24-h control (p-value < 0.05). Adding new detailed information to the reproductive biology field about the diversified transcriptome profile in POECs may create new future possibilities in infertility treatments, including assisted reproductive technique (ART) programmes, and may be a valuable tool to investigate the potential role of oviduct cells in post-ovulation events.