Exploring the common mechanisms and biomarker ST8SIA4 of atherosclerosis and ankylosing spondylitis through bioinformatics analysis and machine learning.

Background: Atherosclerosis (AS) is a major contributor to cerebrovascular and cardiovascular events. There is growing evidence that ankylosing spondylitis is closely linked to AS, often co-occurring with it; however, the shared pathogenic mechanisms between the two conditions are not well understood. This study employs bioinformatics approaches to identify common biomarkers and pathways between AS and ankylosing spondylitis. Methods: Gene expression datasets for AS (GSE100927, GSE28829, GSE155512) and ankylosing spondylitis (GSE73754, GSE25101) were obtained from the Gene Expression Omnibus (GEO). Differential expression genes (DEGs) and module genes for AS and ankylosing spondylitis were identified using the Limma R package and weighted gene co-expression network analysis (WGCNA) techniques, respectively. The machine learning algorithm SVM-RFE was applied to pinpoint promising biomarkers, which were then validated in terms of their expression levels and diagnostic efficacy in AS and ankylosing spondylitis, using two separate GEO datasets. Furthermore, the interaction of the key biomarker with the immune microenvironment was investigated via the CIBERSORT algorithm, single-cell analysis was used to identify the locations of common diagnostic markers. Results: The dataset GSE100927 contains 524 DEGs associated with AS, whereas dataset GSE73754 includes 1,384 genes categorized into modules specific to ankylosing spondylitis. Analysis of these datasets revealed an overlap of 71 genes between the DEGs of AS and the modular genes of ankylosing spondylitis. Utilizing the SVM-RFE algorithm, 15 and 24 central diagnostic genes were identified in datasets GSE100927 and GSE73754, respectively. Further validation of six key genes using external datasets confirmed ST8SIA4 as a common diagnostic marker for both conditions. Notably, ST8SIA4 is upregulated in samples from both diseases. Additionally, ROC analysis confirmed the robust diagnostic utility of ST8SIA4. Moreover, analysis through CIBERSORT suggested an association of the ST8SIA4 gene with the immune microenvironment in both disease contexts. Single-cell analysis revealed that ST8SIA4 is primarily expressed in Macrophages, Monocytes, T cells, and CMPs. Conclusion: This study investigates the role of ST8SIA4 as a common diagnostic gene and the involvement of the lysosomal pathway in both AS and ankylosing spondylitis. The findings may yield potential diagnostic biomarkers and offer new insights into the shared pathogenic mechanisms underlying these conditions.

Exploring therapeutic targets and molecular mechanisms for treating diabetes mellitus-associated heart failure with Qishen Yiqi dropping pills: A network pharmacology and bioinformatics approach.

Diabetes mellitus (DM) and heart failure frequently coexist, presenting significant public health challenges. QiShenYiQi Dropping Pills (QSDP) are widely employed in the treatment of diabetes mellitus concomitant with heart failure (DM-HF). Nevertheless, the precise mechanisms underlying their efficacy have yet to be elucidated. Active ingredients and likely targets of QSDP were retrieved from the TCMSP and UniProt databases. Genes associated with DM-HF were pinpointed through searches in the GeneCards, OMIM, DisGeNET, and TTD databases. Differential genes connected to DM-HF were sourced from the GEO database. Enrichment analyses via gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways, as well as immune infiltration assessments, were conducted using R software. Further analysis involved employing molecular docking strategies to explore the interactions between the identified targets and active substances in QSDP that are pertinent to DM-HF treatment. This investigation effectively discerned 108 active compounds and 257 targets relevant to QSDP. A protein-protein interaction network was constructed, highlighting 6 central targets for DM-HF treatment via QSDP. Gene ontology enrichment analysis predominantly linked these targets with responses to hypoxia, metabolism of reactive oxygen species, and cytokine receptor interactions. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways demonstrated that these targets mainly participate in pathways linked to diabetic complications, such as AGE-RAGE signaling, dyslipidemia, arteriosclerosis, the HIF-1 signaling pathway, and the tumor necrosis factor signaling pathway. Further, immune infiltration analysis implied that QSDP's mechanism in treating DM-HF might involve immune-mediated inflammation and crucial signaling pathways. Additionally, molecular docking studies showed that the active substances in QSDP have strong binding affinities with these identified targets. This research presents a new model for addressing DM-HF through the use of QSDP, providing novel insights into incorporating traditional Chinese medicine (TCM) principles in the clinical treatment of DM-HF. The implications of these findings are substantial for both clinical application and further scientific inquiry.

Identification of common mechanisms and biomarkers for dermatomyositis and atherosclerosis based on bioinformatics analysis.

BACKGROUND: Dermatomyositis (DM) manifests as an autoimmune and inflammatory condition, clinically characterized by subacute progressive proximal muscle weakness, rashes or both along with extramuscular manifestations. Literature indicates that DM shares common risk factors with atherosclerosis (AS), and they often co-occur, yet the etiology and pathogenesis remain to be fully elucidated. This investigation aims to utilize bioinformatics methods to clarify the crucial genes and pathways that influence the pathophysiology of both DM and AS. METHOD: Microarray datasets for DM (GSE128470, GSE1551, GSE143323) and AS (GSE100927, GSE28829, GSE43292) were retrieved from the Gene Expression Omnibus (GEO) database. The weighted gene co-expression network analysis (WGCNA) was used to reveal their co-expressed modules. Differentially expression genes (DEGs) were identified using the "limma" package in R software, and the functions of common DEGs were determined by functional enrichment analysis. A protein-protein interaction (PPI) network was established using the STRING database, with central genes evaluated by the cytoHubba plugin, and validated through external datasets. Immune infiltration analysis of the hub genes was conducted using the CIBERSORT method, along with Gene Set Enrichment Analysis (GSEA). Finally, the NetworkAnalyst platform was employed to examine the transcription factors (TFs) responsible for regulating pivotal crosstalk genes. RESULTS: Utilizing WGCNA analysis, a total of 271 overlapping genes were pinpointed. Subsequent DEG analysis revealed 34 genes that are commonly found in both DM and AS, including 31 upregulated genes and 3 downregulated genes. The Degree Centrality algorithm was applied separately to the WGCNA and DEG collections to select the 15 genes with the highest connectivity, and crossing the two gene sets yielded 3 hub genes (PTPRC, TYROBP, CXCR4). Validation with external datasets showed their diagnostic value for DM and AS. Analysis of immune infiltration indicates that lymphocytes and macrophages are significantly associated with the pathogenesis of DM and AS. Moreover, GSEA analysis suggested that the shared genes are enriched in various receptor interactions and multiple cytokines and receptor signaling pathways. We coupled the 3 hub genes with their respective predicted genes, identifying a potential key TF, CBFB, which interacts with all 3 hub genes. CONCLUSION: This research utilized comprehensive bioinformatics techniques to explore the shared pathogenesis of DM and AS. The three key genes, including PTPRC, TYROBP, and CXCR4, are related to the pathogenesis of DM and AS. The central genes and their correlations with immune cells may serve as potential diagnostic and therapeutic targets.

Development of double-layer poly (amino acid) modified electrochemical sensor for sensitive and direct detection of betamethasone in cosmetics.

Screening for illegal use of glucocorticoids (GCs) in cosmetics by electrochemical methods is extremely challenging due to the poor electrochemical activity of GCs. In this study, poly-L-Serine/poly-Taurine modified electrode (P(Tau)/P(L-Ser)/GCE) was prepared for sensitive and direct determination of betamethasone in cosmetics by a simple two-step in situ electropolymerization reaction. The relevant parameters of preparation and electroanalytical conditions were respectively studied, including the concentration of polymerization solution, the number of scanning circles and the scanning rate. The SEM and EDS mapping demonstrated successful preparation of P(Tau)/P(L-Ser)/GCE. The electro-catalytic properties of the obtained electrodes were investigated using cyclic voltammetry and differential pulse voltammetry methods, showing a remarkable improvement of sensitivity for the detection of betamethasone due to the synergic effect of both P(L-Ser) and P(Tau). In addition, we investigated the electrochemical reduction of betamethasone on the surface of modified electrode. It was found that the process was controlled by diffusion effect and involved the transfer of two electrons and two protons. Then the electrochemical sensor method based on P(Tau)/P(L-Ser)/GCE was established and delivered a linear response to betamethasone concentration from 0.5 to 20 µg mL-1 with a limit of detection of 32.2 ng mL-1, with excellent recoveries (98.1%-106.8%) and relative standard deviations (＜4.8%). Furthermore, the established electrochemical sensor method was compared with conventional HPLC method. The results showed that both of them were comparable. Moreover, the established electrochemical sensor method was with the merits of short analysis time, environmentally friendly, low cost and easy to achieve in-site detection.

Multi-template imprinted solid-phase microextraction coupled with UPLC-Q-TOF-MS for simultaneous monitoring of ten hepatotoxic pyrrolizidine alkaloids in scented tea.

Pyrrolizidine alkaloids (PAs) are a series of ubiquitous natural toxins in flowering plants, which are associated with serious hepatic disease in humans. However, the simultaneously fast and sensitive monitoring of different PAs are still challenge because of the diversity of PAs and huge amount of interference in complex samples, such as scented tea samples. In this study, molecularly imprinted solid phase microextraction (MIP-SPME) fibers were fabricated by using multi-template imprinting technique for selective recognition and efficient enrichment of different PAs from scented teas. MIP-SPME could be used for selective adsorption of ten types of PAs through specific recognition cavity and strong ionic interaction, including senecionine, lycopsamine, retrorsine, heliotrine, lasiocarpine, monocrotaline, echimidine, erucifoline, europine and seneciphylline. The extraction parameters were also optimized including extraction time, elution solvent and elution time. Then, ultra performance liquid chromatography- quadrupole-time of flight mass spectrometry (UPLC-Q-TOF-MS) coupled with MIP-SPME method was developed for fast, simple, sensitive and accurate determination of ten PAs in scented teas. The established method was validated and presented satisfactory accuracy and high precision. It was also successfully applied for simultaneous determination of ten PAs in different scented tea samples. PAs were found in most of these scented tea samples, which suggest the cautious use of scented tea for consumers.

Poly(caffeic acid)-coated molecularly imprinted magnetic nanoparticles for specific and ultrasensitive detection of glycoprotein.

Molecularly imprinted polymers (MIPs) are artificial chemical receptors, and can recognize template molecules with a high selectivity and affinity. As "antibody mimics", MIPs have been widely studied in various fields. However, the general applicability of MIPs is limited by the type of functional monomers. Herein, we developed caffeic acid (CA, a natural polyphenol) as novel a functional monomer. An innovative poly(caffeic acid)-coated molecularly imprinted magnetic nanoparticles (PCA-MIMN) with transferrin (TRF) as a model glycoprotein template was fabricated by autoxidation of CA with hexamethylenediamine (HMDA) in an aerobic environment as imprinted layer. The successful fabrication of PCA-MIMN was proved in detail by diversified characterization. The PCA-MIMN exhibited not only outstanding binding affinity and specificity for target glycoprotein, but also excellent hydrophilicity due to the externally generous hydrophilic groups. To evaluate the preeminent performance, the PCA-MIMN was linked with pH-triggered allochroic-graphene oxide (AGO), which was used for determination of TRF in real samples. The proposed PCA-MIMN linked AGO strategy exhibited ultrahigh sensitivity with limit of detection of 0.38 pg mL-1 for TRF. Finally, the proposed strategy was successfully applied in determination of TRF in spiked human serum sample with recovery and relative standard deviation in the range of 97.2%-103.9% and 4.6%-5.8%, respectively. This work demonstrates that the "autoxidation of CA with HMDA" may be a universal tool for synthesis of highly specific MIPs, and the type of functional monomers will increase exponentially due to the presence of numerous polyphenols in nature.

Preparation of phenyl-boronic acid polymeric monolith by initiator-free ring-opening polymerization for microextraction of sulfonamides prior to their determination by ultra-performance liquid chromatography-tandem mass spectrometry.

In this study, a novel phenyl-boronic acid polymeric monolith (PBAPM) in polyether ether ketone (PEEK) tube was fabricated. The inner wall of PEEK tube was modified with mussel inspired polydopamine layer to firmly bond PBAPM, so as to avoid the outflow of PBAPM from PEEK tube and improve the service life and application scope of PBAPM. The PBAPM was synthesized by initiator-free ring-opening polymerization based on our previous work. The boric acid groups provided B-N coordination sites, as well as the hydrophobic amino and epoxy monomers provided hydrophobic interaction sites. Due to the synergistic effect of hydrophobic interaction and B-N coordination, the PBAPM exhibited excellent binding amounts for nitrogen-containing sulfonamides (SAs). In addition, the PBAPM possessed excellent stability, rigidity and permeability. Therefore, the PBAPM was used as solid phase microextraction (SPME) material for enrichment and separation of SAs from aqueous samples. The PBAPM SPME was optimized in detail, and combined with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis for simultaneous determination of 10 kinds of SAs from tap, lake and river water. Using only 1 mL of water samples, limit of quantitation of SAs could reach 0.54-4.5 ng L-1. Recoveries of standard spiked SAs from water samples were between 82.0% and 105.4%, with intra-day and inter-day relative standard deviation ranging from 3.3% to 5.6% and 4.2% to 8.1%, respectively. The PBAPM SPME combined with UPLC-MS/MS method shown better or similar recoveries, and used fewer samples than previous methods. These results demonstrated that the PBAPM could selectively separate and enrich ultra-trace nitrogen-containing SAs from aqueous samples.

Increasing the homologous recombination efficiency of eukaryotic microorganisms for enhanced genome engineering.

In recent years, eukaryotic microorganisms have been widely applied to offer many solutions for everyday life and have come to play important roles in agriculture, food, health care, and the fine-chemicals industry. However, the complex genetic background and low homologous recombination efficiency have hampered the implementation of large-scale and high-throughput gene editing in many eukaryotic microorganisms. The low efficiency of homologous recombination (HR) not only makes the modification process labor-intensive but also completely precludes the application of many otherwise very useful genome editing techniques. Thus, increasing the efficiency of HR is clearly an enabling technology for basic research and gene editing in eukaryotic microorganisms. In this review, we summarize the current strategies for enhancing the efficiency of HR in eukaryotic microorganisms (particularly yeasts and filamentous fungi), list some small molecules and candidate genes associated with homologous and non-homologous recombination, and briefly discuss the further development prospects of these strategies.

Advances in the metabolic engineering of Yarrowia lipolytica for the production of terpenoids.

Terpenoids are a large class of natural compounds based on the C5 isoprene unit, with many biological effects such activity against cancer and allergies, while some also have an agreeable aroma. Consequently, they have received extensive attention in the food, pharmaceutical and cosmetic fields. With the identification and analysis of the underlying natural product synthesis pathways, current microbial-based metabolic engineering approaches have yielded new strategies for the production of highly valuable terpenoids. Yarrowia lipolytica is a non-conventional oleaginous yeast that is rapidly emerging as a valuable host for the production of terpenoids due to its own endogenous mevalonate pathway and high oil production capacity. This review aims to summarize the status and strategies of metabolic engineering for the heterologous synthesis of terpenoids in Y. lipolytica in recent years and proposes new methods aiming towards further improvement of terpenoid production.

Dirac potential in a rotational dissipative quantum system.

This study proposes the usage of an effective potential to investigate a dissipative quantum system with rotational velocity. After gauge transformation, a Doebner- Goldin equation (DGE) that describes the dissipative quantum system with a Dirac potential is obtained. The DGE is solved based on constraint of vertical relation between the rotational velocity field and density gradient when a harmonic oscillator model is considered. It is observed that the dissipative quantum system is directly equivalent to a monopole system and that the two gauge potentials that are given by Wu and Yang in the north and south hemispheres can be reproduced. Furthermore, a set of gauge-invariant parameters is obtained to discuss the dissipation characteristics of the system.