Microarray Chip Research Articles

Accurate molecular identification of different meat adulterations without carryover contaminations on a microarray chip PCR-directed microfluidic lateral flow strip device

Meat adulteration-based food fraud has recently become one of the global major economical, illegal, religious, and public health concerns. In this work, we developed a microarray chip polymerase chain reaction (PCR)-directed microfluidic lateral flow strip (LFS) device that facilitates the accurate and simultaneous identification of beef adulterated with chicken, duck, and pork, especially in processed beef products. To realize this goal, four pairs of amplification primers were designed and applied for specifically amplifying genomic DNA extracted from mixed meat powders in microarray chip. With the prominent advantage of this device lies in the flexible combination and integration of sample loading, detection, and reporting in microstructures, all the DNA amplicons can be individually visualized on the LFS unit, leading to the appearance of test lines (TC line, TD line, TP line, or TB line) as well as the control line (C line) for the species identification and quantification in beef products. Based on this new method, the adulterants were successfully distinguished and identified in mixtures down to 0.01% (wt.%) while the carryover aerogel contamination in routine molecular diagnostic laboratories was effectively avoided. The practicability, accuracy, and reliability of the device were further confirmed by using real-time PCR as a gold standard control on the successful identification of 50 processed ground meat samples sourced from local markets. The method and device proposed herein could be a useful tool for on-site identification of food authentication.

Three-phase contact line confined dense nanoparticle array for high-capacity DNA synthesis

This paper presents a facile and cost-effective fabrication method of microreactor array chip for high-throughput DNA synthesis with three orders of mangnitude enhancement in synthesis capacity. Inkjet printing was used to dispense a massive droplet array of silica nanoparticle slurry on chemically-modified surface. Dense microreactor array can be simply obtained by following the procedure of three-phase contact line (TCL)-confined nanoparticle aggregating, which is dominated by the receding contact angle (RCA) of the modified substrates. Chip with RCAs greater than 90° transfers the resultant force to a lifting statu as well as enhances the inward force effect, which leading to a dense and compact packing synergistically on limited chip area. Herein, a consequential increasement in effective reaction area contributes to the significant enhancement in synthesis capacity as compared to a planar or porous substtrate. The proposed microarray chip demonstrates great prospects for both high-throughput and high-capacity DNA synthesis.

Fabrication and Validation of a 3D Portable PEGDA Microfluidic Chip for Visual Colorimetric Detection of Captured Breast Cancer Cells.

To guide therapeutic strategies and to monitor the state changes in the disease, a low-cost, portable, and easily fabricated microfluidic-chip-integrated three-dimensional (3D) microchamber was designed for capturing and analyzing breast cancer cells. Optimally, a colorimetric sensor array was integrated into a microfluidic chip to discriminate the metabolites of the cells. The ultraviolet polymerization characteristic of poly(ethylene glycol) diacrylate (PEGDA) hydrogel was utilized to rapidly fabricate a three-layer hydrogel microfluidic chip with the designed structure under noninvasive 365 nm laser irradiation. 2-Hydroxyethyl methacrylate (HEMA) was added to the prepolymer in order to increase the adhesive capacity of the microchip's surface for capturing cells. 1-Vinyl-2-pyrrolidone (NVP) was designed to improve the toughness and reduce the swelling capacity of the hydrogel composite. A non-toxic 3D hydrogel microarray chip (60 mm × 20 mm × 3 mm) with low immunogenicity and high hydrophilicity was created to simulate the real physiological microenvironment of breast tissue. The crisscross channels were designed to ensure homogeneous seeding density. This hydrogel material displayed excellent biocompatibility and tunable physical properties compared with traditional microfluidic chip materials and can be directly processed to obtain the most desirable microstructure. The feasibility of using a PEGDA hydrogel microfluidic chip for the real-time online detection of breast cancer cells' metabolism was confirmed using a specifically designed colorimetric sensor array with 16 kinds of porphyrin, porphyrin derivatives, and indicator dyes. The results of the principal component analysis (PCA), the hierarchical cluster analysis (HCA), and the linear discriminant analysis (LDA) suggest that the metabolic liquids of different breast cells can be easily distinguished with the developed PEGDA hydrogel microfluidic chip. The PEGDA hydrogel microfluidic chip has potential practicable applicability in distinguishing normal and cancerous breast cells.

Cold exposure protects against medial arterial calcification development via autophagy

Medial arterial calcification (MAC), a systemic vascular disease different from atherosclerosis, is associated with an increased incidence of cardiovascular events. Several studies have demonstrated that ambient temperature is one of the most important factors affecting cardiovascular events. However, there has been limited research on the effect of different ambient temperatures on MAC. In the present study, we showed that cold temperature exposure (CT) in mice slowed down the formation of vitamin D (VD)-induced vascular calcification compared with room temperature exposure (RT). To investigate the mechanism involved, we isolated plasma-derived exosomes from mice subjected to CT or RT for 30 days (CT-Exo or RT-Exo, respectively). Compared with RT-Exo, CT-Exo remarkably alleviated the calcification/senescence formation of vascular smooth muscle cells (VSMCs) and promoted autophagy by activating the phosphorylation of AMP-activated protein kinase (p-AMPK) and inhibiting phosphorylation of mammalian target of rapamycin (p-mTOR). At the same time, CT-Exo promoted autophagy in β-glycerophosphate (β-GP)-induced VSMCs. The number of autophagosomes and the expression of autophagy-related proteins ATG5 and LC3B increased, while the expression of p62 decreased. Based on a microRNA chip microarray assay and real-time polymerase chain reaction, miR-320a-3p was highly enriched in CT-Exo as well as thoracic aortic vessels in CT mice. miR-320a-3p downregulation in CT-Exo using AntagomiR-320a-3p inhibited autophagy and blunted its anti-calcification protective effect on VSMCs. Moreover, we identified that programmed cell death 4 (PDCD4) is a target of miR-320a-3p, and silencing PDCD4 increased autophagy and decreased calcification in VSMCs. Treatment with CT-Exo alleviated the formation of MAC in VD-treated mice, while these effects were partially reversed by GW4869. Furthermore, the anti-arterial calcification protective effects of CT-Exo were largely abolished by AntagomiR-320a-3p in VD-induced mice. In summary, we have highlighted that prolonged cold may be a good way to reduce the incidence of MAC. Specifically, miR-320a-3p from CT-Exo could protect against the initiation and progression of MAC via the AMPK/mTOR autophagy pathway.Graphic

DNA microarray chip assay in new use: early diagnostic value in cutaneous mycobacterial infection.

The clinical practicability of DNA microarray chip in detecting the presence of mycobacterial species/isolates directly in the skin tissues has not been evaluated, nor the efficacy of DNA microarray chip as a novel diagnostic tool for the early diagnosis of cutaneous mycobacterial infections is known. The present study analyzed the incidence of cutaneous mycobacterial infections in Shanghai and explored the efficacy of a novel DNA microarray chip assay for the clinical diagnosis of the disease from skin tissue specimens compared to traditional detection methods. A total of 60 participants fulfilling the defined diagnostic criteria and confirmed positive for cutaneous mycobacterial infections from 2019 to 2021 were enrolled in the study. Subsequent to recording the participants' medical history and clinical characteristics, the skin tissue specimens were collected for analyses. The specimens underwent histopathological analyses, skin tissue culture, and DNA microarray chip assay. Increased incidence of cutaneous mycobacterial infection was detected from 2019 to 2021. The most common infecting pathogen was M. marinum followed by M. abscessus. The sensitivity, specificity and accuracy of the skin tissue culture method were 70%, 100% and 76.62%, respectively, while that of the DNA microarray chip assay were 91.67%, 100% and 93.51%, respectively. The sensitivity and accuracy of the DNA microarray chip assay were significantly higher than those of the skin tissue culture method. The positive likelihood and diagnostic odds ratio were >10 and >1, respectively for both the methods. The negative likelihood ratio was significantly higher (30% vs 8.33%) and the Youden's index was significantly lower (70.00% vs 91.67%) in the skin culture method compared to that of the DNA microarray chip assay. There was a significant association of false negative results with a history of antibiotic use in the skin tissue culture method. Given the increasing incidence of cutaneous mycobacterial infections, early diagnosis remains a prime clinical focus. The DNA microarray chip assay provides a simple, rapid, high-throughput, and reliable method for the diagnosis of cutaneous mycobacterial infections with potential for clinical application.

Jiedu Recipe, a compound Chinese herbal medicine, inhibits cancer stemness in hepatocellular carcinoma via Wnt/β-catenin pathway under hypoxia

ObjectiveJiedu Recipe (JR), a Chinese herbal remedy, has been shown to prolong overall survival time and decrease recurrence and metastasis rates in patients with hepatocellular carcinoma (HCC). This work investigated the mechanism of JR in HCC treatment. MethodsThe chemical constituents of JR were detected using liquid chromatography-mass spectrometry. The potential anti-HCC mechanism of JR was screened using network pharmacology and messenger ribonucleic acid (mRNA) microarray chip assay, followed by experimental validation in human HCC cells (SMMC-7721 and Huh7) in vitro and a nude mouse subcutaneous transplantation model of HCC in vivo. HCC cell characteristics of proliferation, migration and invasion under hypoxic setting were investigated using thiazolyl blue tetrazolium bromide, wound healing and Transwell assays, respectively. Image-iT™ Hypoxia Reagent was added to reveal hypoxic conditions. Stem cell sphere formation assay was used to detect the stemness. Epithelial-mesenchymal transition (EMT) markers like E-cadherin, vimentin and α-smooth muscle actin, and pluripotent transcription factors including nanog homeobox, octamer-binding transcription factor 4, and sex-determining region Y box protein 2 were analyzed using Western blotting and real-time polymerase chain reaction. Western blot was performed to ascertain the anti-HCC effect of JR under hypoxia involving the Wnt/β-catenin pathway. ResultsAccording to network pharmacology and mRNA microarray chip analysis, JR may potentially act on hypoxia and inhibit the Wnt/β-catenin pathway. In vitro and in vivo experiments showed that JR significantly decreased hypoxia, and suppressed HCC cell features of proliferation, migration and invasion; furthermore, the hypoxia-induced increases in EMT and stemness marker expression in HCC cells were inhibited by JR. Results based on the co-administration of JR and an agonist (LiCl) or inhibitor (IWR-1-endo) verified that JR suppressed HCC cancer stem-like properties under hypoxia by blocking the Wnt/β-catenin pathway. ConclusionJR exerts potent anti-HCC effects by inhibiting cancer stemness via abating the Wnt/β-catenin pathway under hypoxic conditions.Please cite this article as: Guo BJ, Ruan Y, Wang YJ, Xiao CL, Zhong ZP, Cheng BB, Du J, Li B, Gu W, Yin ZF. Jiedu Recipe, a compound Chinese herbal medicine, inhibits cancer stemness in hepatocellular carcinoma via Wnt/β-catenin pathway under hypoxia. J Integr Med. 2023; 21(5): 474–486.

PCA-WRKNN-assisted label-free SERS serum analysis platform enabling non-invasive diagnosis of Alzheimer’s disease

Alzheimer’s disease (AD) is a progressive and irreversible neurodegenerative brain disorder with significant economic and societal impacts, whereas early AD diagnosis remains a considerable challenge. Here, a robust and convenient surface-enhanced Raman scattering (SERS) analysis platform was fabricated on a microarray chip to dissect the variation in serum composition for AD diagnosis, eliminating the invasive cerebrospinal fluid (CSF)-based and costly instrument-dependent diagnostic methods. AuNOs array prepared by self-assembly at liquid-liquid interface enabled the acquirement of SERS spectra with excellent reproducibility. Moreover, a finite-difference time-domain (FDTD) simulation suggested the significant plasmon hybridization generated by AuNOs aggregation, resulting in high signal-to-noise ratio SERS spectra. We established an AD mice model with Aβ1-40 induction followed by recording the serum SERS spectra at different stages. A multivariate analysis method of principal component analysis (PCA)-weighted representation-based k-nearest neighbor (WRKNN) was applied for the characteristics extraction to improve the classification performance, with an accuracy of over 95 %, an AUC of over 90 %, a sensitivity of over 80 %, and a specificity of over 96.7 %. The results of this study demonstrate the potential of SERS application as a diagnostic screening method, following further validation and optimization, which may open up new exciting opportunities for future biomedical applications.

KDM6B Negatively Regulates the Neurogenesis Potential of Apical Papilla Stem Cells via HES1.

Stem cells from the apical papilla (SCAPs) are used to regulate the microenvironment of nerve defects. KDM6B, which functions as an H3K27me3 demethylase, is known to play a crucial role in neurogenesis. However, the mechanism by which KDM6B influences the neurogenesis potential of SCAPs remains unclear. We evaluated the expression of neural markers in SCAPs by using real-time RT-PCR and immunofluorescence staining. To assess the effectiveness of SCAP transplantation in the SCI model, we used the BBB scale to evaluate motor function. Additionally, toluidine blue staining and Immunofluorescence staining of NCAM, NEFM, β-III-tubulin, and Nestin were used to assess nerve tissue remodeling. Further analysis was conducted through Microarray analysis and ChIP assay to study the molecular mechanisms. Our results show that KDM6B inhibits the expression of NeuroD, TH, β-III tubulin, and Nestin. In vivo studies indicate that the SCAP-KDM6Bsh group is highly effective in restoring spinal cord structure and motor function in rats suffering from SCI. Our findings suggest that KDM6B directly binds to the HES1 promoter via regulating H3K27me3 and HES1 expression. In conclusion, our study can help understand the regulatory role of KDM6B in neurogenesis and provide more effective treatments for nerve injury.

Microarray biochip fabricated on silicon nanowires/carbon dots heterostructures for enhanced viral DNA detection

Recent studies have shown that human oncoviruses are responsible for 10% of cancer cases worldwide. While PCR assays are highly sensitive and specific, microarrays offer outstanding performance for detecting multiple targets simultaneously. However, in microarray systems, accurate detection of DNA viruses relies on the type of microarray platform, while obtaining high-quality, fluorescent-labelled single-stranded DNA bares an equal contribution.Our study demonstrates a proof-of-concept of a microarray platform for enhanced DNA detection. First, we assembled 3D microarray chips on silicon nanowires (SiNWs) substrates using a one-step metal-assisted chemical etching (1-MACE) technique, coated them with SU-8 polymer, and ornated with carbon quantum dots (CDs) in either poly(diallyldimethylammonium) PDDA or poly(ethyleneimine) PEI solutions. Second, we obtained high-quality labelled HPV 16 target ssDNA through classic PCR and asymmetric PCR with a nested primer labelled with Cy5, then hybridised the ssDNA on the SiNWs/SU-8/CDs platforms.The fluorescent signal of hybridised DNA was strongest on the SiNWs/SU-8 substrates, and adding CDs further enhanced the signal. The best signal intensities (4.303, 3.7) and coefficients of variation (3.12%, 2.59%) were achieved by combining HPV 16 probes co-immobilised with CDs functionalised with PDDA. Our study conclusively demonstrates the vast potential of this microarray platform for improved DNA detection.

OligoHydrogelArray (OHA) for Parallelized Solid‐Phase Extraction of Oligonucleotides

AbstractImmobilization of oligonucleotides on solid surfaces is an important step in many experimental workflows in biology, such as gene expression analysis, genotyping, and drug discoveries. Capturing oligonucleotides in a highly efficient miniaturized format is still challenging. In this work, preparation of functionalized miniaturized acrylamide hydrogels on a droplet microarray (DMA) chip is reported. By further modification of these hydrogels through the Cu‐catalyzed alkyne‐azide cycloaddition, oligonucleotides are attached covalently, creating the OligoHydrogelArray (OHA). OHA enables the hybridization of oligonucleotides with defined sequences in a parallelized, miniaturized, and high‐throughput manner with an overall loading capacity and extraction efficiency suitable for most biological and chemical applications. This system enables the parallelized solid‐phase extraction of target oligonucleotides out of a mixture for purification and enrichment of DNA/RNA/PNA for application in fields such as transcriptomics. In the current study, are establish the chemical procedure for reproducible preparation of OHA and determine key characteristics, such as height, diameter, and shape of miniaturized gel pads as well as the loading capacity of oligonucleotides within the material. Finally, the ability to extract complementary oligonucleotide strands out of solution through hybridization is demonstrated to set the course for future applications.

Flow-Based CL-SMIA for the Quantification of Protein Biomarkers from Nasal Secretions in Comparison with Sandwich ELISA.

Protein biomarkers in nasal secretions can be used as a measure to differentiate between allergies, airway diseases and infections for non-invasive diagnostics. The point-of-care quantification of biomarker levels using flow-based microarray facilitates precise and rapid diagnosis and displays the potential for targeted and effective treatment. For the first time, we developed a flow-based chemiluminescence sandwich microarray immunoassay (CL-SMIA) for the quantification of nasal interferon-beta (IFN-β) on the Microarray Chip Reader-Research (MCR-R). Polycarbonate foils are used as a cost-effective surface for immobilizing capture antibodies. By using a commercially available set of anti-human IFN-β antibodies, the CL-SMIA can be compared directly to an enzyme-linked immunosorbent assay (ELISA) performed in microtiter plates concerning the bioanalytical performance and economic issues. Pre-incubation of the sample with detection antibodies facilitates the lower consumption of detection antibodies, as this allows for a longer interaction time between the antibody and the biomarker. The direct injection of pre-incubated samples into the microarray chips eliminates the adsorption of proteins in the tubing as well as the contamination of the tubing and valves of the MCR-R with clinical samples. The small flow cell allows for a low sample volume of 50 μL. The limit of detection of 4.53 pg mL-1 was slightly increased compared to a sandwich ELISA performed on microtiter plates which were 1.60 pg mL-1. The possibility to perform the CL-SMIA in a multiplexed mode makes it a promising assay for the rapid and cost-effective non-invasive detection of biomarkers in nasal secretions.

Genetic factors for differentiated thyroid cancer in French Polynesia: new candidate loci.

Populations of French Polynesia (FP), where France performed atmospheric tests between 1966 and 1974, experience a high incidence of differentiated thyroid cancer (DTC). However, up to now, no sufficiently large study of DTC genetic factors in this population has been performed to reach definitive conclusion. This research aimed to analyze the genetic factors of DTC risk among the native FP populations. We analyzed more than 300000 single nucleotide polymorphisms (SNPs) genotyped in 283 DTC cases and 418 matched controls born in FP, most being younger than 15 years old at the time of the first nuclear tests. We analyzed the genetic profile of our cohort to identify population subgroups. We then completed a genome-wide analysis study on the whole population. We identified a specific genetic structure in the FP population reflecting admixture from Asian and European populations. We identified three regions associated with increased DTC risk at 6q24.3, 10p12.2, and 17q21.32. The lead SNPs at these loci showed respective p-values of 1.66×10-7, 2.39×10-7, and 7.19×10-7 and corresponding odds ratios of 2.02, 1.89, and 2.37. Our study results suggest a role of the loci 6q24.3, 10p12.2 and 17q21.32 in DTC risk. However, a whole genome sequencing approach would be better suited to characterize these factors than genotyping with microarray chip designed for the Caucasian population. Moreover, the functional impact of these three new loci needs to be further explored and validated.

Microarray Chip and Method for Simultaneous and Highly Consistent Electroporation of Multiple Cells of Different Sizes.

Cell electroporation is an important cell manipulation technology to artificially transfer specific extracellular components into cells. However, the consistency of substance transport during the electroporation process is still an issue due to the wide size distribution of the natural cells. In this study, a cell electroporation microfluidic chip based on a microtrap array is proposed. The microtrap structure was optimized for single-cell capture and electric field focusing. The effects of the cell size on the cell electroporation in the microchip were investigated through simulation and experiment methods using the giant unilamellar vesicle as the simplified cell model, and a numerical model of a uniform electric field was used as a comparison. Compared with the uniform electric field, a lower threshold electric field is required to induce electroporation and produces a higher transmembrane voltage on the cell under a specific electric field in the microchip, showing an improvement in cell viability and electroporation efficiency. The larger perforated area produced on the cells in the microchip under a specific electric field allows a higher substance transfer efficiency, and the electroporation results are less affected by the cell size, which is beneficial for improving substance transfer consistency. Furthermore, the relative perforation area increases with the decrease of the cell diameter in the microchip, which is exactly opposite to that in a uniform electric field. By manipulating the electric field applied to the microtrap individually, a consistent proportion of substance transfer during electroporation of cells with different sizes can be achieved.

Assessment of cytotoxic and apoptotic activities of the Cassia angustifolia aqueous extract against SW480 colon cancer

Abstract The current natural extract modalities for colorectal cancer are limited. This research seeks to assess the process of extracting the plant’s bioactive constituents from Cassia angustifolia and to show the anticancer role played by the plant’s aqueous extract at 0°C by identifying the genes that alter in expression after the Cassia angustifolia treatment in colon cancer cells. The bioactive components of Cassia angustifolia extract were revealed using gas chromatography-mass spectrometry analysis. The colon carcinoma cell lines (SW480) were treated with Cassia angustifolia macrophages at concentrations of 50, 150, and 200 µg/mL for 48 h. Apoptosis was examined by fluorescence-activated cell sorting analysis of Cassia angustifolia-treated and -untreated cells. Microarray analysis was performed by using human microarray chips (HG-U95A) for untreated and treated SW480 cells. Microarray data were confirmed by the reverse transcription polymerase chain reaction. The findings showed that the Cassia angustifolia aqueous extract at 0°C/24 h contained the entire absolute phenolic content of 28.43 mg/g and the entire absolute flavonoid content of 9.16 mg/g. Cassia angustifolia enhanced the hindrance of cell development and apoptosis and decreased glucose uptake. Western blot analysis showed induction in the expression of cleaved caspases 3 and 9 in SW480 cells. Microarray data identified 11 genes and 7 expressed sequence tags (ESTs) markedly altered in treated vs non-treated SW480 cells. Several of these genes have been embroiled in multiple malignancies. In conclusion, the current study provides remarkable new data for Cassia angustifolia extracted at 0°C/24 h. We discovered 7 ESTs and 11 genes that are significantly altered in the progression of SW480 cells treated with Cassia angustifolia therapy versus no treatment, with anticancer and apoptosis inducer effects.

The Development of 3D Atomic Force Microscopy with Magnetically Driven-Orthogonal Cantilever Probes

This paper presents a three-dimensional (3D)-atomic force microscopy (AFM) method based on magnetically driven (MD)-orthogonal cantilever probes (OCPs), in which two independent scanners with three degrees of freedom are used to achieve the vector tracking of a sample surface with a controllable angle. A rotating stage is integrated into the compact AFM system, which helps to achieve 360° omnidirectional imaging. The specially designed MD-OCP includes a horizontal cantilever, a vertical cantilever, and a magnetic bead that can be used for the mechanical drive in a magnetic field. The vertical cantilever, which has a protruding tip, can detect deep grooves and undercut structures. The design, simulation, fabrication, and performance analysis of the MD-OCP are described first. Then, the amplitude compensation and home positioning for 360° rotation are introduced. A comparative experiment using an AFM step grating verifies the ability of the proposed method to characterize steep sidewalls and corner details, with a 3D topography reconstruction method being used to integrate the images. The effectiveness of the proposed 3D-AFM based on the MD-OCP is further confirmed by the 3D characterization of a micro-electromechanical system (MEMS) device with microcomb structures. Finally, this technique is applied to determine the critical dimensions (CDs) of a microarray chip. The experimental results regarding the CD parameters show that, in comparison with 2D technology, from which it is difficult to obtain sidewall information, the proposed method can obtain CD information for 3D structures with high precision and thus has excellent potential for 3D micro–nano manufacturing inspection.

Development of a novel microarray data analysis tool without normalization for genotyping degraded forensic DNA

Since the arrest of the Golden State Killer in the US in April 2018, forensic geneticists have been increasingly interested in the investigative genetic genealogy (IGG) method. While this method has already been in practical use as a powerful tool for criminal investigation, we have yet to know well the limitations and potential risks. In this current study, we performed an evaluation study focusing on degraded DNA using the Affymetrix Genome-Wide Human SNP Array 6.0 platform (Thermo Fisher Scientific). We revealed one of the potential problems that occur during SNP genotype determination using a microarray-based platform. Our analysis results indicated that the SNP profiles derived from degraded DNA contained many false heterozygous SNPs. In addition, it was confirmed that the total amount of probe signal intensity on microarray chips derived from degraded DNA decreased significantly. Because the conventional analysis algorithm performs normalization during genotype determination, we concluded that noise signals could be genotype-called. To address this issue, we proposed a novel microarray data analysis method without normalization (nMAP). Although the nMAP algorithm resulted in a low call rate, it substantially improved genotyping accuracy. Finally, we confirmed the usefulness of the nMAP algorithm for kinship inferences. These findings and the nMAP algorithm will make a contribution to the advance of the IGG method.

Construction of circRNA-miRNA-mRNA Network Reveal Functional circRNAs and Key Genes in Acute Myeloid Leukemia.

CircRNA is closely correlated with a wide variety of processes of acute myeloid leukemia (AML), whereas the novel circRNAs, their molecular mechanism and the specific function they played in AML should be explored in depth. The microarray chip data of AML patients and normal samples in the Gene Expression Omnibus (GEO) database were selected to differentially expressed (DE) circRNA, miRNA, and mRNA genes. The miRNA gene was the intersection of the circRNA target gene predicted using CSCD and the miRNA gene screened from AML patients, while the mRNA gene was the intersection of the target gene mRNA of miRNA predicted using miRanda and miRTarBase software and the mRNA gene screened from AML patients. The hub mRNAs related to survival were further screened through Cox proportional hazard regression. CircRNA/miRNA/mRNA interaction network was constructed by using Cytoscape software.10 circRNAs and 6 miRNAs in bone marrow mononuclear cells (BMMNCs) of AML patients (n=43) and healthy controls (n=35) were determined by RT-qPCR. Correlations between them were analyzed by Pearson correlation coefficient. 10 circRNAs, 6 miRNAs, and 33 mRNAs were identified. Subsequently, the network of circRNAs, miRNAs, and hub genes was built using Cystoscope. Four key circRNAs, seven hub genes and their regulatory pathways were identified. The result of RT-qPCRs showed that hsa_circ_0009581 and hsa_circ_0005273 were significantly upregulated in AML patients while hsa_circ_0000497 and hsa_circ_0001947 were significantly downregulated. Hsa-miR-150-5p was significantly downregulated; hsa-miR-454-3p was upregulated in AML patients. Hsa_circ_0009581 and hsa-miR-150-5p; hsa_ circ_0001947 and hsa-miR-454-3p were inversely correlated using Pearson's correlation coefficient. This study suggests that differentially expressed circRNAs take on a critical significance to AML development and may be the effective therapeutic targets. We suppose that hsa_circ_0009581 promotes leukemia development through hsa-miR-150-5p and hsa_circ_0001947 through hsa-miR-454-3p. hsa_circ_0001947 and hsa_circ_0009581 may provide new directions in the pathogenesis of AML.

Network pharmacology and bioinformatics study on the treatment of renal fibrosis with persicae semen-carthami flos drug pair.

To use network pharmacology and bioinformatics technology to reveal the mechanism of persicae semen-carthami flos drug pair in the treatment of renal fibrosis (RF). Compounds in traditional Chinese medicine were obtained through the Herb database. Appropriate compounds and corresponding drug targets were screened out based on the 5 rules of Lipinski and pharmacokinetics. Screening of suitable disease miRNAs by microarray chips in the GEO database. Find differentially expressed genes by analyzing miRNAs. Protein-protein interaction analysis and enrichment analysis of therapeutic targets were performed using String database and Omicshare platform. Molecular docking via the DockThor platform. A total of 28 drug compounds and 228 drug targets were screened in this study. A total of 9 miRNAs and 6649 disease targets were obtained by GEO2R software analysis. Finally, 97 therapeutic targets were obtained. A total of 1124 Gene Ontology enrichment analysis results were obtained. Therapeutic targets play multiple roles in biological processes, molecular functions, and cellular organization. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the persicae semen-carthami flos drug pair played a role in the treatment of RF mainly through calcium signaling pathway, pathways in cancer, cAMP signaling pathway, and other pathways. Molecular docking showed that the traditional Chinese medicine compounds had good binding ability to the target. Persicae semen and carthami flos play a role in the treatment of RF through multiple targets and multiple pathways. It provides ideas and references for follow-up research and new drug development.

Single-Cell Microarray Chip with Inverse-Tapered Wells to Maintain High Ratio of Cell Trapping.

A single-cell microarray (SCM) influenced by gravitational force is expected to be one of the simple methods in various fields such as DNA analysis and antibody production. After trapping the cells in the SCM chip, it is necessary to remove the liquid from the SCM to wash away the un-trapped cells on the chip and treat the reagents for analysis. The flow generated during this liquid exchange causes the trapped cells to drop out of conventional vertical wells. In this study, we propose an inverse-tapered well to keep trapped cells from escaping from the SCM. The wells with tapered side walls have a reduced force of flow toward the opening, which prevents trapped cells from escaping. The proposed SCM chip was fabricated using 3D photolithography and polydimethylsiloxane molding techniques. In the trapping experiment using HeLa cells, the cell residual rate increased more than two-fold for the SCM chip with the inverse-tapered well with a taper angle of 30° compared to that for the conventional vertical SCM chip after multiple rounds of liquid exchanges. The proposed well structure increases the number of trapped cells and decreases the cell dropout rate to improve the efficiency of cellular analysis.

Application potential of chicken DNA chip in domestic pigeon species – Preliminary results

Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.