Computational aptamer design for spike glycoprotein (S) (SARS CoV-2) detection with an electrochemical aptasensor.

A new bioinformatic platform (APTERION) was used to design in a short time and with high specificity an aptamer for the detection of the spike protein, a structural protein of SARS-CoV-2 virus, responsible for the COVID-19 pandemic. The aptamer concentration on the carbon electrode surface was optimized using static contact angle and fluorescence method, while specificity was tested using differential pulse voltammetry (DPV) associated to carbon screen-printed electrodes. The data obtained demonstrated the good features of the aptamer which could be used to create a rapid method for the detection of SARS-CoV-2 virus. In fact, it is specific for spike also when tested against bovine serum albumin and lysozyme, competitor proteins if saliva is used as sample to test for the virus presence. Spectrofluorometric characterization allowed to measure the amount of aptamer present on the carbon electrode surface, while DPV measurements proved the affinity of the aptamer towards the spike protein and gave quantitative results. The acquired data allowed to conclude that the APTERION bioinformatic platform is a good method for aptamer design for rapidity and specificity. KEY POINTS: • Spike protein detection using an electrochemical biosensor • Aptamer characterization by contact angle and fluorescent measurements on electrode surface • Computational design of specific aptamers to speed up the aptameric sequence time.

Comprehensive analyses of brain cell communications based on multiple scRNA-seq and snRNA-seq datasets for revealing novel mechanism in neurodegenerative diseases.

AIMS: Complex cellular communications between glial cells and neurons are critical for brain normal function and disorders, and single-cell level RNA-sequencing datasets display more advantages for analyzing cell communications. Therefore, it is necessary to systematically explore brain cell communications when considering factors such as sex and brain region. METHODS: We extracted a total of 1,039,459 cells derived from 28 brain single-cell RNA-sequencing (scRNA-seq) or single-nucleus RNA-sequencing (snRNA-seq) datasets from the GEO database, including 12 human and 16 mouse datasets. These datasets were further divided into 71 new sub-datasets when considering disease, sex, and region conditions. In the meanwhile, we integrated four methods to evaluate ligand-receptor interaction score among six major brain cell types (microglia, neuron, astrocyte, oligodendrocyte, OPC, and endothelial cell). RESULTS: For Alzheimer's disease (AD), disease-specific ligand-receptor pairs when compared with normal sub-datasets, such as SEMA4A-NRP1, were identified. Furthermore, we explored the sex- and region-specific cell communications and identified that WNT5A-ROR1 among microglia cells displayed close communications in male, and SPP1-ITGAV displayed close communications in the meninges region from microglia to neurons. Furthermore, based on the AD-specific cell communications, we constructed a model for AD early prediction and confirmed the predictive performance using multiple independent datasets. Finally, we developed an online platform for researchers to explore brain condition-specific cell communications. CONCLUSION: This research provided a comprehensive study to explore brain cell communications, which could reveal novel biological mechanisms involved in normal brain function and neurodegenerative diseases such as AD.

SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics.

Soybean (Glycine max (L.) Merr.) is a globally significant crop, widely cultivated for oilseed production and animal feeds. In recent years, the rapid growth of multi-omics data from thousands of soybean accessions has provided unprecedented opportunities for researchers to explore genomes, genetic variations, and gene functions. To facilitate the utilization of these abundant data for soybean breeding and genetic improvement, the SoybeanGDB database (https://venyao.xyz/SoybeanGDB/) was developed as a comprehensive platform. SoybeanGDB integrates high-quality de novo assemblies of 39 soybean genomes and genomic variations among thousands of soybean accessions. Genomic information and variations in user-specified genomic regions can be searched and downloaded from SoybeanGDB, in a user-friendly manner. To facilitate research on genetic resources and elucidate the biological significance of genes, SoybeanGDB also incorporates a variety of bioinformatics analysis modules with graphical interfaces, such as linkage disequilibrium analysis, nucleotide diversity analysis, allele frequency analysis, gene expression analysis, primer design, gene set enrichment analysis, etc. In summary, SoybeanGDB is an essential and valuable resource that provides an open and free platform to accelerate global soybean research.

Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma.

Background: Detection of SHOX2 methylation has been used to assist in the early diagnosis of lung cancer in many hospitals as SHOX2 may be important in the tumorigenesis of lung cancer. However, there are few studies on the mRNA expression, methylation, and molecular mechanism of SHOX2 in lung cancer. We aimed to explore the role of SHOX2 in lung adenocarcinoma (LUAD). Methods: First, we examined the differential expression of SHOX2 mRNA and methylation in cancerous and normal tissues using databases. Second, we analyzed the relationship between SHOX2 expression and common clinical parameters in LUAD patients. Third, we further explored the methylated level and its specific location of SHOX2 and the mainly factors of SHOX2 gene expression. Finally, we screened the correlatively expressed genes to analyze the pathways from the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes using DAVID. Results: We found that the mRNA expression of SHOX2 was higher in multiple cancers, including LUAD and lung squamous cell carcinoma (LUSC), than in normal tissues. Among LUAD patients, SHOX2 expression was higher in patients of middle-young age, with smoking history, in advanced stages, and with nodal distant metastasis. In addition, our results showed that patients with high expression of SHOX2 are prone to recurrence, poor differentiation, and poor prognosis. Thus, we identified that SHOX2 might be an oncogene for LUAD progression. The main factor influencing the high expression of SHOX2 mRNA may be DNA methylation, followed by copy number variation (CNV), but not by gene mutations in LUAD. Unexpectedly, we found that SHOX2 undergoes hypomethylation in the gene body instead of hypermethylation in the promoter. Additionally, SHOX2 has cross talk in the PI3K-Akt signaling pathway and ECM-receptor interaction. Conclusion: SHOX2 is highly expressed in most cancers. SHOX2 gene expression might be mainly regulated by methylation of its gene body in LUAD, and its high expression or hypomethylation indicates poor differentiation and poor prognosis. SHOX2 could be involved in PI3K-Akt and other important cancer-related signaling pathways to promote tumorigenesis.