Bioinformatics
Masoud Tohidfar; Yousef Saeedi Honar; Naser Farrokhi
Abstract
Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of ...
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Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients.
Bioinformatics
Maryam Mehdizadeh hakkak; Masoud Tohidfar; Mohammad Hossein Mirjalili
Abstract
Squalane is an unsaturated triterpene that has wide applications in pharmaceuticals. In this research, the production of squalene and its bioinformatic analysis in four species of unicellular and multicellular eukaryotes and prokaryotes were investigated in order to determine the difference of this gene ...
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Squalane is an unsaturated triterpene that has wide applications in pharmaceuticals. In this research, the production of squalene and its bioinformatic analysis in four species of unicellular and multicellular eukaryotes and prokaryotes were investigated in order to determine the difference of this gene in eukaryotes and prokaryotes. The results of phylogenetic analysis showed that algae as multicellular eukaryotes, yeast as single-celled eukaryote and bacteria as single-celled prokaryote were placed in one group and plants were placed in a separate group. GC percentage of SQS protein was evaluated by GC Content Calculator, as well as aliphatic index and instability index by protparam. The results showed that the SQS gene is in a range from unstable to stable. The analysis of the presence of signal sequences and the analysis of the detection of the final location of the protein showed that the possibility of transferring the SQS protein to the mitochondria, chloroplast and secretory pathway is very low and it is not among the signal proteins. It was also found in Gymnema sylvestre that this protein has three protected domains. The comparison of the secondary structure of the protein confirmed the existence of alpha sheets. 3D modeling of this protein in plant was done by homology modeling method and using Swiss Model database after selecting a suitable model with high similarity which was extracted from PDB database. In order to validate the structure of the drawn three-dimensional model and stereochemical analysis, the Ramachandran diagram was drawn and the dihedral angles were calculated. The results of structural quality evaluation showed that the proposed models have good quality and stability. The study of the protein structure can help to understand the function of the protein, and studying the details of its structure can be useful in the studies of the active site of the protein and docking.
Genetic Engineering and Gene Transformation
Masoumeh Fallah Ziarani; Masoud Tohidfar
Volume 8, Issue 21 , June 2018, , Pages 71-79
Abstract
Today, Change the color of the flower due to its commercial importance is one of the goals of the researchers. Creation of the variation in flower color of ornamental plants can be highly profitable for the country and facilitate the way for export to other parts of the world. In the past, efforts have ...
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Today, Change the color of the flower due to its commercial importance is one of the goals of the researchers. Creation of the variation in flower color of ornamental plants can be highly profitable for the country and facilitate the way for export to other parts of the world. In the past, efforts have been do in the traditional way and genetic engineering for change the color of the flower, but with slowdown. With the discovery of Crispr's system, the ability to make targeted changes at the genome level took less time. In order to target change by Crispr, the target gene and area must be identified, that is done by bioinformatic tools. The desired change through the design of gRNA is done. In following, the normal protein and mutated protein were checked for the function. Today, donor DNA is used to enhance the performance of the Crispr system. In this system, by homologous recombination can be enhanced Crisper's performance by replaces a healthy gene or knocked out and prevented the creation of non-specific changes in the genome.
Bioinformatics
Masoumeh Fallah Ziarani; Masoud Tohidfar; Zahra Aminfar
Volume 7, Issue 17 , July 2017, , Pages 15-29
Abstract
The biosynthesis pathway of fatty acids is one of the important pathways in the body of most organisms that an enzyme Acyl carrier protein (ACP) plays an important role in it. The purpose of this study is phylogenetic and in silico analysis of gene ACP. More analysis indicate that ACP gene has 4 exons, ...
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The biosynthesis pathway of fatty acids is one of the important pathways in the body of most organisms that an enzyme Acyl carrier protein (ACP) plays an important role in it. The purpose of this study is phylogenetic and in silico analysis of gene ACP. More analysis indicate that ACP gene has 4 exons, 3 introns and and 2 mRNA in prokaryotes and 13 exons, 12 introns and 9 mRNA in eukaryotes. This protein has target mitochondrial in plant eukaryotes and non-mitochondrial target in prokaryotes and it is not also included of secreted proteins. The results of multiple alignments by T-Coffee server showed that the ACP genes between bacterial species are more protected than plant species. Phylogenetic analysis of ACP proteins in prokaryotes is revealed that except for a cluster, in other case Gram-positive bacteria are in one cluster and gram-negative bacteria are in another cluster. In eukaryotes, different plant species are scattered in different clusters. These results indicated that clustering in eukaryotes are not relate to species. In addition, the study of ACP proteins in eukaryotes and prokaryotes revealed that both eukaryotes and prokaryotes are placed together in some clusters that is due to the similarities of sequences in species. Comparison of the secondary structure of the protein in eukaryotes and prokaryotes showed that the number of alpha and beta sheets in prokaryotes are more than of eukaryotes. Three-dimensional modeling of this protein was done by homology modeling using Swiss Model database in wheat (as representative of eukaryotic) and bacteria Clostridioides difficile 630 (as represented prokaryotes). The best templates were extracted with high similarity from PDB database. To validation of modeled structure and esterochemical analysis, Ramachandran plot was drawn and dihydral angles were calculated. Structural quality evaluation results showed that the proposed models are good quality and stability. The study of protein structure may help to understand protein function and the details of its structure can be useful in studies of the active site of the protein and docking.
Biotic and Abiotic stress
Behnam Bakhshi; Mohmmad Reza Bihamta; Ghasem Hosseini Salekdeh; Masoud Tohidfar
Volume 3, Issue 5 , February 2013, , Pages 93-102
Abstract
Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating ...
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Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating plant gene expression in biotic and abiotic stress. In this study, we selected five miRNAs for promoter analysis and evaluation of differential expression of them under drought stress in roots. Three of them including miR162, miR169 and miR172 are conserved in many plants and the others including miR1425 and miR1880 are rice specific miRNAs. In addition, upstream screening of MIRNA genes showed that upstream region of some MIRNA genes like MIR172 are enriched with important regulatory elements like DRE and ABRE. Quantitative Realtime-PCR was used in this study for analyzing differential expression of evaluated miRNAs. Studying the differential expression of miRNAs in roots under drought condition showed that miR169 was up-regulated but conversely, miR172 was down-regulated. The rest of miRNAs in our study did not show significant differential expression under drought stress. It can be concluded that NF-YA and AP2 as the most important target genes for miR169 and miR172 respectively can play critical roles in response to drought stress. .
