Modares Journal of Biotechnology

Abstract Mnemiopsin 2 is a Ca2+ regulated photo protein with 207 residues and a molecular weight of 24722 Daltons. In the structure of this photoprotein, the EF-hand I-III-IV motifs have retained their function in binding to Ca2+, while the EF-hand II has lost its activity during evolution. Each EF-hand has a helix-loop-helix (HLH) structure. Loops with length of 12 residues are responsible for Ca2+ binding. In this study, in order to recovery the structural and functional of the EF-hand loop II, a Photoprotein Mnemiopsin Chimeric (PMC) was designed using direct evolution and rational design. The mutant structure were modeled by Modeller v2.10 software. Then the best model was evaluated using the Chimera x.8.1 software and Modeval and SAVES and ModEval server for RMSD, RRDistance, Z-Dope, Errat and Verify 3D parameters were investigated. Also, the secondary structure, free energy of folding and accessible surface of the models were investigated by the VADAR server. The hydrophobicity and instability index were evaluated by Protscale and ProtParam servers. The Prosite results indicate the formation of EF-hand II loop in PMC. It is worth mentioning that Changes in the surface hydrophobicity of the recovered EF-hand II motif may affect the interaction with Ca2+. That means, due to the increase the Ca2+ binding sites, sensitivity to Ca2+ and activity were predicted to change.
 

Abstract Background:
HIV has at least six regulatory genes among which the Vif protein can control HIV replication. This study, as the first report, investigated the important mutations in VIF protein in sequences from Iranian patients and using immunoinformatics, conserved regions of this protein and B-Cell, T-Cell and CTL epitopes to stimulate the immune system, were determined.
Methods:
VIF sequences were obtained from NCBI GenBank, and tertiary structures, B-Cell, T-Cell and CTL epitopes were predicted by bioinformatics tools; besides, their antigenic and allergenic properties were studied.
Results:
The most prevalent mutations in Vif protein were related to S 49 P (90%), S 140 N and N 186 S (80%). Two substitutions at positions 41 and 42 were introduced which have effect on Vif binding to host factor. In addition, three regions were identified as the best epitope sequences with high potential to induce immune system and the lowest allergic properties, among which 5-32 region was suggested as the best vaccine candidate regions.
Conclusion:
This study as the first study from Iran using immunoinformatics tools to introduced a region with the high potential to induce humoral and cellular immune systems and lowest allergenic properties which can be used for further studies on HIV vaccines.

Abstract
Chitinases are essential enzymes in crustaceans that play an important role in the molting cycle and digestion of chitin. Based on the present study, the chitinase encoding cDNA of Penaeus mergueinsis with a length of 1440 bp containing 467 amino acids was sequenced by PCR and then its phylogenetic and bioinformatics analysis was performed. The new sequence was registered in the gene bank with the accessition number MT250539 and the molecular weight of the protein resulting from this sequence was predicted to be 51.84 KDa and the theoretical isoelectric point of 4.79. Comparison of amino acid sequences among penaeid chitinases showed the highest identification (about 97 to 92%) with P. mondon chi-3, F. chinensis, P. vannamei and P. japonicus chi-3, respectively. Phylogenetic studies showed that chitinase in the present study belongs to group 3 chitinases. Revealed protein pattern analyzes showed that chitinase from P. mergueinsis contained the catalytic domain Glyco-18 at position 2-347, a chitin-binding site of pritrophin A at position 403-456, a disulfide bridge formed by two cysteines at position 436-421 is a chitin-binding domain type 2, active site (¹¹7FDGLDMDWE¹²⁵), a proline / threonine-rich region at positions 376-412, and a putative N-glycosylation site at position 427-424 (NTSG). The present study shows that the P. mergueinsis sequence contains active chitinase motifs similar to previously sequenced chitinases, and in the case of cloning, expression and purification probably has functional and structural features similar to the enzymes of the above species.

Abstract In most cancers, the expression level of heat shock proteins is increased, which makes cancer cells resistant to drug therapy and has a poor prognosis. They have also been linked to cell proliferation, invasion and metastasis. Lycopene, as a carotenoid, is an effective antioxidant used to prevent the growth of cancerous glands. Prostate cancer is one of the most common cancers seen in men. To treat this disease, surgery and chemotherapy are mostly used, which have many complications after treatment and are costly. In this study, prostate cancer was treated with lycopene and raw microarray big data were received from GEO section of NCBI database. Then, the expression changes of heat shock proteins (hsp27) were determined using bioinformatics tools and methods, and comparing the expression levels of lycopene-treated genes with non-treated ones showed that the expression level of HSPB8 gene was drastically reduced and also, no significant changes were observed in the expression level of other gene families in this group. Results show that lycopene can cause stress in cancer cells and this stress predisposes the cell to apoptosis.

Abstract Objective: Premature ovarian failure (POF) is one of the most important reproductive diseases in women under 40 years of age, which affects the quality of life and longevity of these people by causing short-term and long-term complications.
The incidence of POF is a chronic process that takes several years to develop. The patient went through stages such as premature ovarian insufficiency (POI) and decreased ovarian reserve (DOR), in the early stages of the disease decreased ovarian function efficiency (POI) and then with further progression of the disease, the patient decreased ovarian reserve and further reduce their performance. As the disease progresses, the person eventually develops premature and complete ovarian failure, or POF studies have shown that many factors, including surgical trauma, autoimmune diseases, certain drugs, vaccines, and genetic factors, play a role. Genetic studies have shown that several genes are involved in the development of this disease. Part of the regulation of the expression of these genes is the responsibility of small genetic factors called miRNAs.
Materials and Methods: In the present study, bioinformatics information of miRNAs involved in this disease was investigated. For this purpose, genetic databases such as UCSC, NCBI, KEGG, MIRBASE, TARGET SCAN, STRING, etc. were used to access the genes involved in this disease, structural and functional communication, messaging pathways and regulatory miRNA.
Results and Conclusion: The results of this study indicate that three factors, miRNA-187, miRNA-33b and miRNA-33a, are very effective in the development and progression of this disease.

Abstract MicroRNAs are a group of small non-coding RNAs that regulate gene expression in eukaryotes at the post-transcriptional level. MicroRNAs, through regulating the expression of large numbers of mRNAs, act as major regulators of various biological processes such as embryonic development, cell proliferation, differentiation, and apoptosis. Therefore, the identification of microRNAs and their target genes is very effective in finding the mechanisms of embryonic development, growth, and also the processes underlying the induction and progression of various diseases. Because of the high costs of molecular experiments, the identification of effective microRNAs through bioinformatics tools and computational biology is faster and cheaper than the experimental methods. Several online bioinformatics tools and databases have been developed and are freely available for predicting microRNAs target genes. The available online tools use a broad range of information, including sequencing data, gene expression data, and computational algorithms for predicting microRNAs target genes. Some of the most important of these online tolls are miRWalk, TargetScan, RNAhybrid, Diana-microT, miRanda, and MirTarget. The four main features of the interaction between a microRNA and an mRNA, including seed pairing, sequence conservation, free energy, and access to the binding site in a target are used in the algorithm of all of these prediction tools. This stud aimed to review the latest findings on the characteristics and capabilities of microRNA target prediction tools, comparing the performance of these tools, and finally introducing the most efficient tool in the field of target gene prediction for bioinformatics, biomedicine, and molecular medicine studies.

Abstract Escherichia coli is a Gram-negative bacterium, the second most common bacteria in the intestine and the main indicator of urban water pollution, is the most common cause of urinary tract infection and also is one of the main factors in food poisoning and diarrhea. Drug resistance of this bacterium to antibiotics is a global challenge. Horizontal gene transfer (HGT) is the movement of genetic material between unicellular and other gene transfer pathways which is an important factor in the evolution of many organisms, antibiotic resistance in bacteria, gene function. Antibiotic resistance in E. coli can be transferred to another species of bacteria through HGT mechanisms. Today, Bioinformatics methods have been used to understand of gene transfer from HGT mechanism. In this study, we used bioinformatics tools such as PredictBias, ACLAME, Mobil Genetic Elements (MGEs) PAI-ID, and Alien_Hunter in order to genes analysis that related from antibiotic resistance in E. coli. Bioinformatics and MIC assays result show that from 26 to 30 genes have been identified in all safthwers. Most of genes that identified show over 50 percent of GC content. put P gene with 178, blaCMY with 62, BlaTEM with 43, and aac-6 with 66 homology in the PredictBias website identified. Also in the ACLAME website, mob (A-C) and rep (A-C) gene family are highest number of horizontal gene transfer from infection bacteria strain. Those cluster genes are the highest resistant of laboratory tests which carries resistant genes such as blaSHV and blaCHV on the blaCMY plasmid.

Abstract A biological network represents the interaction between a set of macromolecules to drive a particular biological process. In a biological environment, abnormalities happen not only in one molecule but also through a biological network. One of the most effective methods to detect anomaly is the comparison between healthy and diseased networks. In this regard, biological network alignment is one of the most efficient ways to find the difference between healthy and diseased cells. This problem, protein-protein interaction network alignment, has been raised in two main types: Local network alignment and Global network alignment. According to the NP-completeness of this problem, different non-deterministic approaches have been proposed to tackle the Global network alignment problem. Recently, NetAl has been introduced as a common algorithm to align two networks. Although this algorithm can align two networks at the appropriate time, it does not consider biological features. In this study, we present a new framework called PRAF to improve the results of network alignment algorithms such as NetAl by considering some biological features like gene ontology (GO).

Abstract Aims: Antioxidants in sesame oil, including tocopherols and sesamin have greatly increased the shelf life of it against heat. Following the increase in the expression of the cytochrome P450 enzyme encoder (CYP81Q1), the content of sesame is increased in different stages of development of sesame seeds. The aim of this study was cloning, sequencing, and bioinformatics study of CYP81Q1 gene of Iranian sesame (Seamum indicum L.) cultivar.
Materials and Methods: In the present experimental research, DNA was extracted from leaves and stems of Karaj1 sesame cultivar and the target gene was amplified by PCR. Gene was cloned in binary vector pBI121 and confirmed by 3 methods, including enzymatic digestion, PCR, and sequencing. Then bioinformatics characterization of this gene was studied and the Ramachandran plot was drawn on the three-dimensional structure of the gene.
Findings: Cloning was confirmed. DNA sequencing results confirmed the cloned segment. Molecular weight and predicted isoelectric point of the protein were 57021.3 Dalton and 8.46, respectively. The three-dimensional structure of the protein had a good stroke chain. The sequencing result of this gene showed a difference in the 23 nucleotides of this gene in sesame seeds of Karaj 1 (access number KP771974.1) with a reported sequence in the NCBI gene bank (access number AB194714.1), which resulted in the sequencing of the CYP81Q1 gene in Iranian sesame (Karaj 1) at this database.
Conclusion: Based on nucleotide sequencing, the target gene has 1521 base pairs, and differs from 23 nucleotides with the sample registered at the NCBI World Bank. This gene encodes a protein length of 506 amino acids. This protein is very similar with the registered protein in NCBI.

Abstract With the instrumentation of Mass Spectrometry (MS) and advances carried out in bioinformatic tools and databases, along with birth of nanotechnology in 1990s, biology experienced a dramatic revolution and new perspectives were found in molecular biology and medicine, agriculture, environmental sciences and pharmatiuticals. The most important one is systematic look at the entire organism and solving biological problems at the level of entire system viewed as an integrated and interacting network of genes, proteins and biochemical reactions (Systems Biology). In addition, :union: of biology and nanotechnology result in creation of nanobiotechnology. This paper provides an easy-to-read guide to the concepts of some of the major topics in today’s biology. Topics discussed here, include fundamentals of proteomics and systematic descriptions of the various types of studies in proteomics. After a brief review on the physical principles of nanotechnology, the application of one of its products, known as quantum dot in biology and particularly, proteomics studies, were discussed. This account covers the general principles and applications of new emerging fields in biology.