Structural and functional characterization of SARS-CoV-2 nucleocapsid protein mutations identified in Turkey by using in silico approaches.

Missense mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus may cause changes in the structure of proteins. The nucleocapsid (N) protein is an important target for drugs and vaccines. The main purpose of this study is to detect missense mutations in the SARS-CoV-2 N protein and to reveal the effects of these mutations on protein structure by using in silico approaches. 161 missense mutations of the N protein were determined in 2286 SARS-CoV-2 genomes derived from the GISAID EpiCoV database in the Turkish population. Identified 161 missense mutations were analyzed by using sequence and structure-based methods to predict effects of mutation on function and structure of SARS-CoV-2 N protein. These analyzes revealed that some mutations showed deleterious effects and change of stability and flexibility of nucleocapsid protein. D3L, S194L, S235F, and P13L (Omicron variant) mutations were further analyzed in our study due to their importance in the literature and in our results. Even though, our findings are essential for research of SARS-CoV-2 virus, in vitro and in vivo validations are necessary. Keywords: nucleocapsid protein; SARS-CoV-2; missense mutations; protein stability; protein flexibility.

A comprehensive in silico analysis of multiple sclerosis related non-synonymous SNPs and their potential effects on protein structure and function.

BACKGROUND: Multiple Sclerosis (MS) is an autoimmune and central nervous system disease characterized by an inflammatory demyelinating process in the brain. Although the exact cause of MS is still unclear, environmental, and genetic factors are known to play a role in the development of disease. New molecular markers must be identified to understand the mechanism of disease formation and progression. We investigated the effects of MS-related non-synonymous single-nucleotide polymorphisms (nsSNPs) on the structure and function of identified proteins in this study. METHODS: Missense variations associated with MS were extracted from the NHGRI-EBI GWAS database. Functional and structural analysis of nsSNPs on mapped genes was performed using g:Profiler, Wikipathway, KEGG, Reactome and Gene ontology programs (p < 0.05 was accepted statistically significant). Amino acid sequence-based analysis was performed to identify deleterious variants by using PROVEAN and PredictSNP tools. Finally, protein structure analyzes were performed on deleterious protein variants by DynaMut, Mutabind2 and Missense3D servers to identify changes in protein stability and flexibility. RESULTS: 10 target nsSNPs were identified. Among these rs34536443, rs10936599, rs2293152, rs11808092, rs1129183 were found deleterious according to amino acid sequence-based analysis. Furthermore, structure-based analyses show that TYK2 (P1104A), MYNN (H6Q), EVI5 (Q612H), and LZTFL1 (D246N) substitutions increase protein stability and decrease structure flexibility, whereas STAT3 (R426G) substitution decreases protein stability and increases structure flexibility. CONCLUSION: We revealed that identified nsSNPs have potential effects on stability and flexibility of the target proteins. The prominent target genes are thought to have significant impacts on the pathogenesis of MS. Further in vitro and in vivo studies are required to validate our in silico results.

Investigation of the effects of the royal jelly on genomic demethylation and tumor suppressor genes in human cancer cells.

Royal jelly is a gelatinous nutrient secretion produced by the mandibular glands of young worker honey bees and has a critical role in honey bee life. In the honey bee colonies, queen and worker honey bees have very different morphologies and behaviors due to their diet in the larval period, despite having the same genome. In comparison, queen bees formed from larvae that feed royal jelly exclusively, and worker bees formed from larvae that feed on much less royal jelly. DNA methylation has been shown to play a critical role in the development of queen and worker honeybees. Alterations in DNA methylation, one of the epigenetic mechanisms defined as hereditable nucleotide modifications that occur in gene expression without changes in the DNA sequence, are closely related to many diseases, especially cancer. Hypermethylation of CpG islands located in the promoter regions of genes causes gene silencing and tumor suppressor genes epigenetically have silenced in cancer. The inactivation of tumor suppressor genes disrupts nearly all cellular pathways in cancer. In contrast to genetic alterations, gene silencing by epigenetic modifications may potentially be reversed and used in cancer treatment. Royal jelly, which causes epigenetic changes in bee colonies, has the potential to cause a change in cancer cells. In our study, royal jelly's effects on DNA methyltransferase enzyme and gene methylation of RASSF1A tumor suppressor were investigated in human cancer cell lines (HeLa, HT29, and A549), and modifications in the gene expression profile of royal jelly were determined by next generation sequencing.

Identification of miRNAs and their potential effects on multiple sclerosis related pathways using in silico analysis.

BACKGROUND: MicroRNAs (miRNAs) regulate gene expression post-transcriptionally via mRNA degradation. As a result, they have an impact on a variety of pathways in organisms that are important for both health and disease. miRNAs can be used as potential diagnostic, prognostic and therapeutic biomarkers for immune and nervous system-related diseases such as MS. METHOD: Differentially expressed miRNAs from peripheral blood samples of patient and control groups were selected from NCBI GEO Datasets using GEO2R. Common miRNAs and their related pathways were analyzed using miRNet, miRWalk, DIANA mirpath, KEGG pathway. Target genes and their protein-protein interactions were also evaluated using STRING and GeneMANIA. RESULTS: We found 12 common miRNAs, four of which were determined to be more important in MS-related pathways such as the immune and neural signaling networks. These include pathways neurotrophin, JAK-STAT, B cell receptor, ErbB, MAPK, Fc gamma R-mediated phagocytosis, Chemokine and T cell receptor signaling pathways. Moreover, target gene analyses were performed and MAPK1, PIK3CD, PIK3R1, PIK3R2, PIK3R3, PIK3R5, AKT2, SOS2, RAF1 genes were found. Further analysis showed that the identified genes and related pathways have interactions at multiple points, and that the overlapping points are commonly found in the PI3K-Akt signaling pathway. CONCLUSION: In this paper, MS-related miRNAs and their potential effects on related pathways were evaluated. This study can be used for understanding MS pathogenesis and provides new tools for the discovery of new therapies.

Association between occurrence of ossicular chain defect and osteoprotegerin gene expression in patients with chronic otitis media.

OBJECTIVE: Chronic otitis media (COM) is an important debilitating public problem causing hearing loss due to irreversible resorption of the ossicular chain. Activation of osteoprotegerin (OPG) during an acute attack of COM prevents bone resorption.The aim of the study was to investigate the role of OPG gene expression level on ossicular chain resorption in chronic otitis media. MATERIALS AND METHODS: Fifty operated COM patients were included in the study. While 20 patients underwent ossiculoplasty, 30 patients underwent type 1 tympanoplasty. For RNA isolation and OPG gene expression analysis, middle ear swabs were taken from nasopharynx in the ostium of the Eustachian tube. RNA was isolated with mRNA easy kit and kept at - 85 °C till the cDNA and expression analysis. Expression levels were analyzed with real-time quantitative PCR in comparison with PDGB gene expression level as an internal control. RESULTS: Sample Cq measurements of type 1 tympanoplasty group were higher than Cq measurements of the internal control group (p = 0.027; p < 0.05). In contrast, there was no statistically significant difference between sample Cq measurements of ossiculoplasty group and Cq measurements of the internal control group (p = 0.293; p > 0.05). CONCLUSION: Since OPG gene expression level was significantly higher in type 1 tympanoplasty group, OPG gene regulation system may have an effect on ossicular chain destruction in COM.

The Effect of PAI-1 Gene Variants and PAI-1 Plasma Levels on Development of Thrombophilia in Patients With Klinefelter Syndrome.

Klinefelter syndrome (KS) is a common sex chromosome-related abnormality seen among men. KS negatively affects spermatogenesis and testosterone production. It increases the risk of thrombosis but its molecular mechanism has not been well described yet. Elevated PAI-1 is a risk factor for thrombosis. The rs1799889 polymorphism located in the promoter region of the PAI-1 gene was detected in patients with deep venous thrombosis. In this study, the PAI-1 gene variant and its plasma levels in KS patients were examined. Forty-one KS patients (47, XXY) and 50 age-matched healthy controls participated. DNA was isolated from peripheral blood and a real-time PCR method was used to detect known SNPs in the PAI-1 gene. In addition, PAI-1 plasma levels were measured by using ELISA method. There was no significant difference between PAI-1 gene polymorphisms of KS patients and controls ( p > .05). The significant difference was observed in PAI-1 plasma levels between two groups (high PAI-1 plasma level in KS patients compared to controls). The patients' group mean was 55.13 and control group mean in PAI-1 level was 29.89 ng/ml ( p = .020). Clinical features related to thromboembolism especially varicose veins were detected in KS patients frequently ( p = .04). These results suggest that thromboembolism related to clinical features is seen more frequently in cases with KS, but it may not be dependent only on the PAI-1 gene polymorphism structure.