Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci

Designing and Expression of Recombinant Chimeric Spike Protein from SARS-CoV-2 in Escherichia coli and Its Immunogenicity Assessment

Since December 2019, the world has been grappling with an ongoing global COVID-19 pandemic. Various virus variants have emerged over the past two years, each posing a greater threat than its predecessors. The recent appearance of the omicron variant (B.1.1.529) has raised significant alarm within the field of epidemiology due to its highly contagious nature and rapid transmission rate. The omicron variant possessed mutations in the key receptor-binding domain (RBD) region, the S region, and these modifications have shown a notable impact on the strain's susceptibility to neutralizing antibodies. Developing safe and efficient vaccines to prevent a future severe acute respiratory outbreak of coronavirus syndrome 2 (SARS-CoV-2) is significant. Viral surface spike proteins are ideal targets for vaccines. This study aimed to find a multi-subunit chimeric vaccine. After conducting bioinformatics analysis, the recombinant spike (RS) protein of SARS-CoV-2 was deliberately designed and subsequently produced using E. coli expression systems. The immunogenicity of RS and neutralizing antibody responses were evaluated on immunized BALB/c mice. There was a significant difference in antibody titers between RS-immunized mice and control groups. The endpoint of the serum antibody titer of mice immunized with our chimeric protein was 2.5 times higher than that of the negative control. The chimeric construct could present multiple antigens simultaneously, influentially affecting immunization. Sera from mice vaccinated by RS could recognize the SARS-CoV-2 virus and neutralize antibodies. Our chimeric peptide could bind to antibodies in the serum of patients infected with different serotypes of the SARS-CoV-2 virus, such as alpha, delta, and omicron variants. The results indicated that the RS protein would be a potential novel antigenic candidate for subunit vaccine development and could be used as a useful alternative to generate diagnostic serological tests for SARS-CoV-2 infection.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.

MicroRNA Databases and Tools

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.

The animal nuclear factor Y: an enigmatic and important heterotrimeric transcription factor

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor with the ability to bind to CCAAT boxes in nearly all eukaryotes and has long been a topic of interest since it is first identified. In plants, due to each subunit of NF-Y is encoded by multiple gene families, there are a wide variety NF-Y complex combinations that fulfill many pivotal functions. However, the animal NF-Y complex usually has only one type of combination, as each subunit is generally encoded by a single gene. Even though, mounting evidence points to that the animal NF-Y complex is also essential for numerous biological processes involved in proliferation and apoptosis, cancer and tumor, stress responses, growth and development. Therefore, a relatively comprehensive functional dissection of animal NF-Y will enable a deeper comprehension of how lesser combinations of the NF-Y complex regulate diverse aspects of biology processes in animal. Here, we focus mainly on reviewing recent advances related to NF-Y in the animal field, including subunit structural characteristics, expression regulation models and biological functions, and we also discuss future directions.

Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

MicroRNAs (miRNAs) are short (~22 nucleotides) noncoding RNAs and disseminated throughout the genome, either in the intergenic regions or in the intronic sequences of protein-coding genes. MiRNAs have been proved to play important roles in regulating gene expression. Hence, understanding the transcriptional mechanism of miRNA genes is a very critical step to uncover the whole regulatory network. A number of miRNA promoter prediction models have been proposed in the past decade. This review summarized several most popular miRNA promoter prediction models which used genome sequence features, or other features, for example, histone markers, RNA Pol II binding sites, and nucleosome-free regions, achieved by high-throughput sequencing data. Some databases were described as resources for miRNA promoter information. We then performed comprehensive discussion on prediction and identification of transcription factor mediated microRNA regulatory networks.

NF-Y in cancer: Impact on cell transformation of a gene essential for proliferation

NF-Y is a ubiquitous heterotrimeric transcription factor with a binding affinity for the CCAAT consensus motif, one of the most common cis-acting element in the promoter and enhancer regions of eukaryote genes in direct (CCAAT) or reverse (ATTGG) orientation. NF-Y consists of three subunits, NF-YA, the regulatory subunit of the trimer, NF-YB, and NF-YC, all required for CCAAT binding. Growing evidence in cells and animal models support the notion that NF-Y, driving transcription of a plethora of cell cycle regulatory genes, is a key player in the regulation of proliferation. Proper control of cellular growth is critical for cancer prevention and uncontrolled proliferation is a hallmark of cancer cells. Indeed, during cell transformation aberrant molecular pathways disrupt mechanisms controlling proliferation and many growth regulatory genes are altered in tumors. Here, we review bioinformatics, molecular and functional evidence indicating the involvement of the cell cycle regulator NF-Y in cancer-associated pathways. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.