Functional Analysis Research Articles

Construct dysregulated miRNA-mRNA interaction networks to conjecture possible pathogenesis for Stomach adenocarcinomas.

Post-transcriptional regulation of mRNA induced by microRNA is known crucial in tumor occurrence, progression, and metastasis. This study aims at identifying significant miRNA-mRNA axes for stomach adenocarcinomas (STAD). RNA expression profiles were collected from The Cancer Genome Atlas (TCGA) and GEO database for screening differently expressed RNAs and miRNAs (DE-miRNAs/DE-mRNAs). Functional enrichment analysis was conducted with Hiplot and DAVID-mirPath. Connectivity MAP was applied in compounds prediction. MiRNA-mRNA axes were forecasted by TarBase and MiRTarBase. Real-time reverse transcription polymerase chain reaction (RT-qPCR) of stomach specimen verified these miRNA-mRNA pairs. Diagnosis efficacy of miRNA-mRNA interactions was measured by Receiver operation characteristic curve and Decision Curve Analysis. Clinical and survival analysis were also carried out. CIBERSORT and ESTIMATE was employed for immune microenvironment measurement. Totally 228 DE-mRNAs (105 upregulated and 123 downregulated) and 38 DE-miRNAs (22 upregulated and 16 downregulated) were considered significant. TarBase and MiRTarBase identified 18 miRNA-mRNA pairs, 12 of which were verified in RT-qPCR. The network of miR-301a-3p/ELL2 and miR-1-3p/ANXA2 were established and verified in external validation. The model containing all 4 signatures showed better diagnosis ability. Via interacting with M0 macrophage and resting mast cell, these miRNA-mRNA axes may influence tumor microenvironment. This study established a miRNA-mRNA network via bioinformatic analysis and experiment validation for STAD.

Sci-tech innovation, industrial structure transformation and economic development: An empirical study based on province panel data of China

Based on panel data of 31 provinces in China from 2000 to 2019, this study explores the complex dynamic interaction between scientific and technological innovation, industrial structure transformation and economic development by building PVAR model. After GMM estimation, impulse response function analysis and variance decomposition analysis, the following conclusions are drawn: Technological innovation has a significant promoting effect on economic development, and economic development can also promote technological innovation; Technological innovation has a positive impact on industrial structure transformation, while industrial structure transformation has a slight negative impact on technological innovation; Economic development can lead to industrial structure transformation, but the impact of industrial structure transformation on economic development is not significant.

Exploring the molecular mechanisms network of breast cancer by multi-omics analysis.

Breast cancer (BC), the most prevalent malignancy in women globally, still lacks comprehensive research on its molecular targets and necessitates further investigation into the underlying molecular mechanisms driving its initiation and progression. The GSE20685 Series Matrix File downloaded from the Gene Expression Omnibus database was divided into a high-risk group (n=49) and a low-risk group (n=278) to construct the co-expression network. Four hub genes were identified based on the Weighted Gene Co-expression Network Analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses were performed. Hub gene immune infiltration was investigated using the Tumor Immune Estimation Resource database, and CD4+ T cell expression levels were substantially correlated with hub gene expression. Based on the CancerRxGene database (Genomics of Drug Sensitivity in Cancer database), it was found that the hub genes were highly sensitive to common chemotherapy drugs such as AKT inhibitor VIII and Erlotinib. The expression of Secreted Frizzled-Related Protein 1, melanoma-inhibiting activity (MIA), and Keratin 14 was related to tumor mutation burden, and the expression of MIA also affected the microsatellite instability of the tumor. This study employs multi-omics analysis to investigate the molecular network associated with the prognosis of BC, highlighting its intricate connection with the immune microenvironment. These findings pinpoint four crucial genes in BC progression, offering targets for further research and therapy. Their connections to immune infiltration and chemotherapy sensitivity underscore complex interactions in the tumor microenvironment.

Functional support vector machine.

Linear and generalized linear scalar-on-function modeling have been commonly used to understand the relationship between a scalar response variable (e.g. continuous, binary outcomes) and functional predictors. Such techniques are sensitive to model misspecification when the relationship between the response variable and the functional predictors is complex. On the other hand, support vector machines (SVMs) are among the most robust prediction models but do not take account of the high correlations between repeated measurements and cannot be used for irregular data. In this work, we propose a novel method to integrate functional principal component analysis with SVM techniques for classification and regression to account for the continuous nature of functional data and the nonlinear relationship between the scalar response variable and the functional predictors. We demonstrate the performance of our method through extensive simulation experiments and two real data applications: the classification of alcoholics using electroencephalography signals and the prediction of glucobrassicin concentration using near-infrared reflectance spectroscopy. Our methods especially have more advantages when the measurement errors in functional predictors are relatively large.

Alaska Pollock-derived Gelatin Sealant has Higher Sealing Strength than, and Comparable Biocompatibility with, Fibrin Sealant in Porcine and Rat Dural Injury Models.

Burst strength study in porcine dural models and functional and histological study in rat dural models. This study aimed to investigate the sealing strength and biocompatibility of Alaska pollock-derived gelatin (ApGltn) and fibrin sealants in disrupted dural injuries. Disruption of the dura mater occurs during spine surgery, leading to cerebrospinal fluid leakage. Fibrin sealant is usually applied to ruptured sites; however, it lacks sealing strength. A novel biocompatible sealant composed of ApGltn was recently demonstrated to have good burst strength and biocompatibility in the porcine aorta. Ten porcine dura maters with central holes were covered with ApGltn and fibrin sealants (five samples per group). The maximum burst strength of each sealant was measured, and histological examination was performed after burst testing. Twenty-seven dura maters of male Wistar rats were used for functional and histopathological evaluations. The rats were treated with three surgical interventions: defect + ApGltn sealant; defect + fibrin sealant; defect alone (nine rats per group). Macroscopic confirmation of the sealant, hindlimb motor function analysis, and histopathological examination were performed at 2, 4, and 8 weeks after the procedure. The maximum burst strength of the ApGltn sealant was approximately 4.4 times higher than that of the fibrin sealant (68.1±12.1 vs. 15.6±8.7mmHg; P<0.001). Histological examination confirmed that the ApGltn sealant showed tight adhesion to the dural surface, whereas a gap was observed between the fibrin sealant and the dura mater. In the rat model, the ApGltn sealant resulted in spinal function and dural histological findings similar to those of the fibrin sealant. The ApGltn sealant had a higher sealing strength than, and comparable effect on dura regeneration with, the fibrin sealant.

Description of Fuscovulum ytuae sp. nov, a facultative autotroph isolated from the intertidalite of Yangma island, China.

In this study, we reported a Gram-stain-negative, ovoid to rod-shaped, atrichous, and facultative anaerobe bacteria strain named YMD61T, which was isolated from the intertidal sediment of Yangma island, China. Growth of strain YMD61T occurred at 10.0-45.0°C (optimum, 30.0°C), pH 7.0-10.0 (optimum, 8.0) and with 0-3.0% (w/v) NaCl (optimum, 2.0%). Phylogenetic tree analysis based on 16S rRNA gene or genomic sequence indicated that strain YMD61T belonged to the genus Fuscovulum and was closely related to Fuscovulum blasticum ATCC 33,485T (96.6% sequence similarity). Genomic analysis indicated that strain YMD61T contains a circular chromosome of 3,895,730bp with DNA G + C content of 63.3%. The genomic functional analysis indicated that strain YMD61T is a novel sulfur-metabolizing bacteria, which is capable of fixing carbon through an autotrophic pathway by integrating the processes of photosynthesis and sulfur oxidation. The predominant respiratory quinone of YMD61T was ubiquinone-10 (Q-10). The polar lipids of YMD61T contained phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unidentified lipids, unidentified aminolipid and unidentified aminophospholipid. The major fatty acids of strain YMD61T contained C18:1ω7c 11-methyl and summed feature 8 (C18:1 ω 7c or/and C18:1 ω 6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD61T represents a novel species of the genus Fuscovulum, and the name Fuscovulum ytuae sp. nov. is proposed. The type strain is YMD61T (= MCCC 1K08483T = KCTC 43,537T).

The bidirectional connection between family functioning and psychopathology: A network analysis in a large sample of adolescents with anorexia nervosa and their parents.

Family functioning is a risk and maintaining factor for anorexia nervosa (AN). This study aims to identify specific areas of family functioning according to adolescents and parental perspectives associated with eating and general psychological symptoms in people with AN. Four-hundred-forty-five adolescents with AN or atypical AN and their parents were enrolled. Adolescents completed the Eating Disorder Inventory-3, the Youth Self-Report questionnaire, and the Family Assessment Device (FAD). Their parents filled in the FAD. A network analysis was conducted including all subscales. The bridge function analysis was applied to identify the bridge nodes connecting each community constituted of family functioning perception with the communities of adolescents' eating and general psychological symptoms. Family communication was the node most strongly connecting fathers and mothers' perception of family functioning and adolescents' eating symptoms. Problem solving was the node with the highest bridge expected influence between mothers' family functioning and adolescents' general psychopathology. General functioning and problem solving were the bridge nodes between adolescents' view of family functioning and eating and general psychopathology. Maturity fear, interpersonal insecurity, and interpersonal alienation were the bridge nodes between adolescents' eating symptoms and mothers, fathers, and adolescents' family functioning communities respectively. Family members must be involved in the therapeutic process to improve family communication and problem solving diverting their attention toward emotional needs and interpersonal difficulties of adolescents with AN. Developing autonomy and independence from parents and building trustworthy relationships with peers may be favored by improving familiar dynamics and may contribute to prevent the maintenance of AN.

Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence.

The regulation of carbon metabolism and virulence is critical for the rapid adaptation of pathogenic bacteria to host conditions. In Pseudomonas aeruginosa, RccR is a transcriptional regulator of genes involved in primary carbon metabolism and is associated with bacterial resistance and virulence, although the exact mechanism is unclear. Our study demonstrates that PaRccR is a direct repressor of the transcriptional regulator genes mvaU and algU. Biochemical and structural analyses reveal that PaRccR can switch its DNA recognition mode through conformational changes triggered by KDPG binding or release. Mutagenesis and functional analysis underscore the significance of allosteric communication between the SIS domain and the DBD domain. Our findings suggest that, despite its overall structural similarity to other bacterial RpiR-type regulators, RccR displays a more complex regulatory element binding mode induced by ligands and a unique regulatory mechanism.

Functional outcomes and rates of return to sport activities in a non-athlete population after the open Brostrom-Gould repair: a seven-year follow-up.

After an ankle sprain, up to 20% of patients may develop chronic lateral ankle instability (CLAI) requiring surgical treatment. The objective of this study was to investigate the functional outcomes and rates of return to sport activities in a cohort of non-athlete patients with chronic lateral ankle instability (CLAI) who underwent the opened Brostrom-Gould technique (BGT). Seventy-nine patients (seventy-nine feet) from three different centers undergoing BGT were reviewed. For clinical and functional analysis, the AOFAS ankle-hindfoot scale was applied and rates of return to sport activities were assessed. Correlation of Δ-AOFAS and rates of return to sport activities with all variables analyzed was performed. Mean AOFAS score improved from 64.6 to 97.2 (p < 0.001). Sixty-one (77.2%) returned to preinjury activities and 18 (22.8%) changed to a lower-level modality. Symptoms of instability were related to Δ-AOFAS (p = 0.020). Change in the sport activity was related to pain and symptoms of instability (p = 0.41 and p < 0.001). Recreational athlete patients who underwent the BGT demonstrated excellent functional outcomes after a mean follow-up of 7years. Residual pain and symptoms of instability after surgery were the main complaints associated with limitations in physical activities.

Cyanobacterial Proteomics: Diversity and Dynamics.

Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.

Prognostic gene landscapes and therapeutic insights in sepsis-induced coagulopathy

BackgroundSepsis is a common and critical condition encountered in clinical practice that can lead to multi-organ dysfunction. Sepsis-induced coagulopathy (SIC) significantly affects patient outcomes. However, the precise mechanisms remain unclear, making the identification of effective prognostic and therapeutic targets imperative. MethodsThe analysis of transcriptome data from the whole blood of sepsis patients, facilitated the identification of key genes implicated in coagulation. Then we developed a prognostic model and a nomogram to predict patient survival. Consensus clustering classified sepsis patients into three subgroups for comparative analysis of immune function and immune cell infiltration. Single-cell sequencing elucidated alterations in intercellular communication between platelets and immune cells in sepsis, as well as the role of the coagulation-related gene FYN. Real-time quantitative PCR determined the mRNA levels of critical coagulation genes in septic rats' blood. Finally, administration of a FYN agonist to septic rats was observed for its effects on coagulation functions and survival. ResultsThis study identified four pivotal genes—CFD, FYN, ITGAM, and VSIG4—as significant predictors of survival in patients with sepsis. Among them, CFD, FYN, and ITGAM were underexpressed, while VSIG4 was upregulated in patients with sepsis. Moreover, a nomogram that incorporates the coagulation-related genes (CoRGs) risk score with clinical features of patients accurately predicted survival probabilities. Subgroup analysis of CoRGs expression delineated three molecular sepsis subtypes, each with distinct prognoses and immune profiles. Single-cell sequencing shed light on heightened communication between platelets and monocytes, T cells, and plasmacytoid dendritic cells, alongside reduced interactions with neutrophils in sepsis. The collagen signaling pathway was found to be essential in this dynamic. FYN may affect platelet function by modulating factors such as ELF1, PTCRA, and RASGRP2. The administration of the FYN agonist can effectively improve coagulation dysfunction and survival in septic rats. ConclusionsThe research identifies CoRGs as crucial prognostic markers for sepsis, highlighting the FYN gene's central role in coagulation disorders associated with the condition and suggesting novel therapeutic intervention strategies.

The potential crosstalk genes and molecular mechanisms between glioblastoma and periodontitis.

Despite clinical and epidemiological evidence suggestive of a link between glioblastoma (GBM) and periodontitis (PD), the shared mechanisms of gene regulation remain elusive. In this study, we identify differentially expressed genes (DEGs) that overlap between the GEO datasets GSE4290 [GBM] and GSE10334 [PD]. Functional enrichment analysis was conducted, and key modules were identified using protein-protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA). The expression levels of CXCR4, LY96, and C3 were found to be significantly elevated in both the test dataset and external validation dataset, making them key crosstalk genes. Additionally, immune cell landscape analysis revealed elevated expression levels of multiple immune cells in GBM and PD compared to controls, with the key crosstalk genes negatively associated with Macrophages M2. FLI1 was identified as a potential key transcription factor (TF) regulating the three key crosstalk genes, with increased expression in the full dataset. These findings contribute to our understanding of the immune and inflammatory aspects of the comorbidity mechanism between GBM and PD.

Distinct neural signatures of pulvinar in C9orf72 amyotrophic lateral sclerosis mutation carriers and noncarriers.

Thalamic alterations have been reported as a major feature in presymptomatic and symptomatic patients carrying the C9orf72 mutation across the frontotemporal dementia-amyotrophic lateral sclerosis (ALS) spectrum. Specifically, the pulvinar, a high-order thalamic nucleus and timekeeper for large-scale cortical networks, has been hypothesized to be involved in C9orf72-related neurodegenerative diseases. We investigated whether pulvinar volume can be useful for differential diagnosis in ALS C9orf72 mutation carriers and noncarriers and how underlying functional connectivity changes affect this region. We studied 19 ALS C9orf72 mutation carriers (ALSC9+) accurately matched with wild-type ALS (ALSC9-) and ALS mimic (ALSmimic) patients using structural and resting-state functional magnetic resonance imaging data. Pulvinar volume was computed using automatic segmentation. Seed-to-voxel functional connectivity analyses were performed using seeds from a pulvinar functional parcellation. Pulvinar structural integrity had high discriminative values for ALSC9+ patients compared to ALSmimic (area under the curve [AUC] = 0.86) and ALSC9- (AUC = 0.77) patients, yielding a volume cutpoint of approximately 0.23%. Compared to ALSmimic, ALSC9- showed increased anterior, inferior, and lateral pulvinar connections with bilateral occipital-temporal-parietal regions, whereas ALSC9+ showed no differences. ALSC9+ patients when compared to ALSC9- patients showed reduced pulvinar-occipital connectivity for anterior and inferior pulvinar seeds. Pulvinar volume could be a differential biomarker closely related to the C9orf72 mutation. A pulvinar-cortical circuit dysfunction might play a critical role in disease progression and development, in both the genetic phenotype and ALS wild-type patients.

Hsa_circ_0008360 promotes high glucose-induced damage in HK-2 cells via miR-346/WNT2B axis.

Diabetic nephropathy (DN) is a leading cause of end-stage renal disease worldwide. Recent researches have shown that circular RNAs (circRNAs) could affect the progress of DN, but the mechanism isstill indistinct. In this work, we explored the roles of hsa_circ_0008360 in DN. The levels of hsa_circ_0008360, microRNA-346 (miR-346) and Winglesstype family member 2B (WNT2B) were indicated by quantitative real-time polymerase chain reaction (qRT-PCR) in DN tissues and HK2 cells. Meanwhile, the protein level of WNT2B was quantified by Western blot analysis. Besides, the function of cells was examined by Cell Counting Kit-8 (CCK8) assay, flow cytometry assay, western blot, and ELISA kit. Furthermore, the interplay between miR-346 and hsa_circ_0008360 or WNT2B was detected by dual-luciferase reporter assay. The levels of hsa_circ_0008360 and WNT2B were increased, and the miR-346 level was decreased in the serum of DN patients and HG-treated HK2 cells. For functional analysis, hsa_circ_0008360 deficiency promoted cell viability, inhibits cell apoptosis, inflammatory response, and the synthesis of related fibrotic proteins in HG-treated HK2 cells. Moreover, overexpression of miR-346 induced the proliferation and inhibit apoptosis of HG-induced HK2 cells by inhibiting WNT2B expression. In mechanism, hsa_circ_0008360 acted as a miR-346 sponge to regulate the level of WNT2B. Hsa_circ_0008360 can regulate miR-346/WNT2B axis in HG-induced HK2 cells, providing an underlying targeted therapy for DN patients.

Identifying immune-related prognostic biomarkers in osteosarcoma: Development and validation of the tumor immune microenvironment risk model based on analysis of TCGA.

Osteosarcoma is a rare and aggressive malignancy with limited effective therapeutic options. This study aimed to identify immune-related prognostic biomarkers and develop a prognostic model for osteosarcoma. We performed integrated analysis of transcriptomic data and immune cell infiltration profiles of 84 osteosarcoma samples from the Cancer Genome Atlas (TCGA) database. Time-dependent receiver operating characteristic (ROC) curve analysis was used to assess the prognostic value of the TIMErisk model. We also performed functional annotation and pathway enrichment analyses to explore the potential mechanisms underlying the TIMErisk model. We identified a seven-gene TIMErisk model (C2, APBB1IP, BST2, TRPV2, CCL5, GBP1, and F13A1) that was independently associated with overall survival of osteosarcoma patients. The TIMErisk model showed significant associations with immune cell infiltration and immunosuppressive gene expression. In addition, the TIMErisk model was associated with drug sensitivity, and we found that several immune checkpoint genes were significantly differentially expressed between high- and low-TIMErisk groups. Functional annotation and pathway enrichment analyses revealed that the TIMErisk model was associated with multiple immune-related pathways, including antigen processing and presentation, cytokine-cytokine receptor interaction, and T cell receptor signaling pathway. Our study identified a novel TIME-based prognostic model for osteosarcoma that incorporates immune-related genes and can be used to predict patient prognosis and response to immunotherapy. Our findings highlight the importance of the TIME microenvironment in osteosarcoma progression and suggest that immune-related biomarkers may have clinical significance in the management of osteosarcoma.

Asymptotic analysis of three-parameter Mittag-Leffler function with large parameters, and application to sub-diffusion equation involving Bessel operator

Asymptotic analysis of three-parameter Mittag-Leffler function with large parameters, and application to sub-diffusion equation involving Bessel operator

COP9 signalosome complex is a prognostic biomarker and corresponds with immune infiltration in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is among the most common deadly tumors but still lacks specific biomarkers for diagnosis, prognosis, and treatment guidance. The COP9 signalosome (COPS) is an essential regulator of the ubiquitin conjugation pathway upregulated in various cancers. We evaluated the contributions of COPS subunits to HCC tumorigenesis and their utility for prognosis. We comprehensively evaluated the tumor expression pattern and tumorigenic functions of COPS subunits using The Cancer Genome Atlas (TCGA), The Human Protein Atlas and immunohistochemistry. Kaplan-Meier, Cox regression, ROC curve, and nomogram analyses were used to assess the predictive values of COPS subunits for clinical outcome. Expression levels of COPS subunits were significantly upregulated in HCC tissues, which predicted shorter overall survival (OS). Further, Cox regression analysis identified COPS5, COPS7B, and COPS9 as independent prognostic biomarkers for OS. High mutation rates were also found in COPS subunits. Functional network analysis indicated that COPS and neighboring genes regulate 'protein neddylation', 'protein deneddylation', and 'protein ubiquitination'. The COPS PPI included strong interactions with p53, CUL1/2/3/4, and JUN. Moreover, the correlations between COPS subunit expression levels and tumor immune cell infiltration rates were examined using TIMER, TISIDB, ssGSEA, and ESTIMATE packages. COPS subunits expression levels were positively correlated with specific tumor immune cell infiltration rates, immunoregulator expression levels, and microsatellite instability in HCC. Finally, knockout of COPS6 and COPS9 in HCC cells reduced while overexpression enhanced proliferation rate and metastasis capacity. Our study revealed that COPS potential biomarker for unfavorable HCC prognosis and indicators of immune infiltration, tumorigenicity, and metastasis.

Hippocampal subfields and their neocortical interactions during autobiographical memory

Abstract Advances in ultra-high field 7 Tesla functional magnetic resonance imaging (7 T fMRI) have provided unprecedented opportunities to gain insights into the neural underpinnings supporting human memory. The hippocampus, a heterogeneous brain structure comprising several subfields, plays a central role during vivid re-experiencing of autobiographical memories (AM). However, due to technical limitations, how hippocampal subfields differentially support AM, whether this contribution is specific to one portion along the hippocampal long-axis, and how subfields are functionally connected with other brain regions typically associated with AM retrieval remains elusive. Here, we leveraged technical advances of parallel imaging and employed a submillimeter Echo Planar Imaging sequence over the whole brain while participants re-experienced vivid, detail-rich AM. We found that all hippocampal subfields along the long-axis were engaged during AM retrieval. Nonetheless, only the pre/parasubiculum within the anterior body of the hippocampus contributed over and above to AM retrieval. Moreover, whole-brain functional connectivity analyses of the same data revealed that this part of the hippocampus was the only one that was strongly connected to other brain regions typically associated with AM, such as the ventromedial prefrontal cortex (vmPFC) and medial/lateral parietal regions. In the context of the broader literature, our results support recent proposals that the anterior body of the pre/parasubiculum may play an important role in scene-based cognition, such as its engagement during the re-experiencing of personal past events.

Nobiletin alleviates atherosclerosis by inhibiting lipid uptake via the PPARG/CD36 pathway

BackgroundAtherosclerosis (AS) is a persistent inflammatory condition triggered and exacerbated by several factors including lipid accumulation, endothelial dysfunction and macrophages infiltration. Nobiletin (NOB) has been reported to alleviate atherosclerosis; however, the underlying mechanism remains incompletely understood.MethodsThis study involved comprehensive bioinformatic analysis, including multidatabase target prediction; GO and KEGG enrichment analyses for function and pathway exploration; DeepSite and AutoDock for drug binding site prediction; and CIBERSORT for immune cell involvement. In addition, target intervention was verified via cell scratch assays, oil red O staining, ELISA, flow cytometry, qRT‒PCR and Western blotting. In addition, by establishing a mouse model of AS, it was demonstrated that NOB attenuated lipid accumulation and the extent of atherosclerotic lesions.Results(1) Altogether, 141 potentially targetable genes were identified through which NOB could intervene in atherosclerosis. (2) Lipid and atherosclerosis, fluid shear stress and atherosclerosis may be the dominant pathways and potential mechanisms. (3) ALB, AKT1, CASP3 and 7 other genes were identified as the top 10 target genes. (4) Six genes, including PPARG, MMP9, SRC and 3 other genes, were related to the M0 fraction. (5) CD36 and PPARG were upregulated in atherosclerosis samples compared to the normal control. (6) By inhibiting lipid uptake in RAW264.7 cells, NOB prevents the formation of foam cell. (7) In RAW264.7 cells, the inhibitory effect of oxidized low-density lipoprotein on foam cells formation and lipid accumulation was closely associated with the PPARG signaling pathway. (8) In vivo validation showed that NOB significantly attenuated intra-arterial lipid accumulation and macrophage infiltration and reduced CD36 expression.ConclusionsNobiletin alleviates atherosclerosis by inhibiting lipid uptake via the PPARG/CD36 pathway.

Hydrophilicity of Organically Modified Montmorillonite and Effect on Benzene Adsorption by the Molecular Dynamics Method.

Interlayer modification of layered materials with organocations has been known to endow the nanocomposite with hydrophobicity, and adsorption of aromatic compounds in the aqueous phase has been investigated for decades by using montmorillonite, a representative layered clay mineral, as the host material. Usage of the organocation has been believed to be effective due to the π-π interaction with the aromatic adsorbate, the presence of which is not verified spectroscopically in the water-immersed state. Considering that the organocation is generally regarded as a pillar to keep the interlayer space, the interaction between the organocation and adsorbate has not yet been clarified sufficiently. In the present study, we revealed the role of the organocation by the molecular dynamics method, where tetramethylammonium (TMA) and trimethylphenylammonium (TMPA) ions were selected as the representative and simple organocations, and benzene was the adsorbate to exclude the effect of the substitution group. Both H2O and benzene molecules were introduced in the interlayer of TMA- or TMPA-modified montmorillonite to model the water-immersed adsorption structure. It was found that H2O is preferentially distributed on the clay surface, followed by the center of the interlayer when the amount of H2O is large. In the adsorption model, benzene was vertically adsorbed on the clay surface. Radial distribution function analysis revealed that benzene is distributed around both the methyl and the phenyl groups in the TMA and TMPA cations, but the orientation of the phenyl ring is not consistent with that of benzene. Thus, benzene was found not to form the π-π interaction in montmorillonite modified with the TMPA cations in the water-immersed state. Furthermore, the surface was partly covered with the phenyl group in the TMPA cation, decreasing the adsorption area. Therefore, the experimental suggestion that benzene is adsorbed on the clay surface was reproduced by our simulation, and the interaction between the organocation and benzene and surface occupancy should be paid attention to maximize the adsorption property.