Showing 3 results for Askari
A Askari Rad, J Fayazi, M Nazari, Mr Hajjari,
Volume 13, Issue 1 (10-2018)
Abstract
Recent advances in DNA sequencing and computational algorithms revealed the SNPs of highest value. Laboratory study of gene and its alleles is difficult and time consuming. In this study, we used several computational algorithms to demonstrate the effects of gene structure and function of heat shock protein 70 (HSP70) in buffalo. HSP70 is a chaperone molecule that expressed in response to stress. On the other hand, buffalo is one of the resistant animals to heat stress. In this study from Affymetrix 90K SNP chip in 112 Khuzestan buffalo and published sequence information is used for Hindi buffalo. In Khuzestan buffalo dataset, snp was not found, but one snp was recognized in Hindi buffalo. Snp analysis (Methionine/Threonine) was done using SIFT,PROVEAN.SIFT with calculate factor 1 and PROVEAN algorithm with calculate factor 0.33 which showed this mutation or SNP effect is non-destructive and with the normal protein operation. I-mutant algorithm was used to check mutant hsp70 protein stability, and predict SNP impacts on the stability of the protein using regression based on the changes in free energy (DDG=0.47) showed that "met5thr" snp at 25 ºC ,PH=7 decrease the protein stability. Validation of the model by Ramachandran and ProSA Zscore maps indicates a slight deviation in the mutated protein compared to the normal model. Molecular docking and how to hsp70 connect to its ligand adenosine diphosphate (ADP) indicates in both the natural and mutated models that mutation leads to decrease in protein stability and change its structure, which also changes the structure of ligand binding site. But generally in this study the mutation does not show significant and destructive effect on protein structure.
Nahid Askari, Morteza Hadizadeh,
Volume 17, Issue 3 (11-2022)
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is a leading cause of cancer-related death worldwide. Many studies confirm that the interaction between microRNAs and mRNAs plays an important role in the incipience and progression of HCC. Accordingly, to better appreciate the miRNA-mRNA interaction, gene expression data from liver tissue (GSE39791) was analyzed. Finally, six up-regulated and 62 down-regulated genes were identified using the LIMMA package in R. After that, significant mRNAs were analyzed by the miRNet database based on liver tissue; significant interactions of 56 microRNAs were found that targeted mRNAs, miRNA-mRNA network was visualized by Cytoscape software. Pathways analysis and biological processes of significant mRNAs with clusterProfiler and Goplot packages showed that the retinol metabolism, drug metabolism and chemical carcinogens pathways were the most significantly affected in HCC. But, the detoxification of inorganic compounds, retinol metabolism and terpenoid metabolism were the most meaningful in biological processes. Examination of signalling pathways revealed that the metabolic pathway is a critical biomarker in both of these two types of gastrointestinal cancer, which may serve a role in the pathogenesis. Examination of signaling pathways revealed that, the metabolic pathway as a critical biomarker in both of these two types of gastrointestinal cancer, which may serve a role in the pathogenesis. In summary, the present survey provided evidence that could support the prognosis of liver tumors in the future.
Mahboobeh Dehghan, Masoud Tohidfar, Seyed Omid Ranaei Siadat, Hossein Askari, Fataneh Fatemi, Yahya Sefidbakht,
Volume 19, Issue 1 (5-2024)
Abstract
RBD plays a major role in causing SARS-COV-2 infection, because the entry of the virus into the host cell occurs by binding RBD to the receptor of angiotansin-converting enzyme 2(ACE2). RBD is also an important immunogenic candidate in the development of protein subunit vaccines. In this study, expression of recombinant RBD in Pichia pink yeast was done easily and at low cost. Recombinant RBD and adjuvants such as sodium alginate, alum and the combination of the two were tested in a mouse model in increasing the level of neutralizing antibodies and increase the stability of the vaccine. The results showed that the use of an alternative natural adjuvant system instead of alum adjuvant increases the immunogenicity of RBD antigen and its stability, so that RBD formulated with sodium alginate alone and RBD formulated with sodium alginate and alum showed higher antibody titer and stability compared to RBD formulated with alum alone. The increase in immunogenicity of RBD antigen with RBD:SA:AL formulation was determined by serological assays that included direct ELYSA and surrogate Virus Neutralization Test (sVNT). High levels of IgGs and neutralizing antibodies were shown in serum of mice immunized with the RBD:SA:AL formulation. Collectively, our results showed that sodium alginate is as an effective natural adjuvant compare with the alum adjuvant. In ,addition, according to the obtained results, the combination of sodium alginate and Alum is more effective than sodium alginate alone .In order to, visualize, RBD-FC vaccine structure, molecular dynamics simulation was done for RBD-FC with glycan and without glycan modification. The analysis of root mean square deviation (RMSD), radius of gyration (RG), and root mean square fluctuation (RMSF) showed that the construct has stable fold and suitable conformation due to the used linker.
