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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.

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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.       

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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.
 

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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.

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In an in silico investigation, genome sequences of three RNA viruses were identified in the crown imperial Fritillaria imperialis L. transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these three novel viruses belong to the genus Amalgavirus. They were tentatively named Crown imperial amalgavirus (CIAV), Iranian amalgavirus (IrAV), and Koohrang amalgavirus (KAV). The RNA-dependent RNA polymerases (RdRps) of CIAV, IrAV, and KAV showed 69.53%, 42.26%, and 37.46% amino acid sequence identities with the homologous RdRp of the most closely related virus, respectively, suggesting that they are novel viruses. Also, the conserved motifs of RdRp were detected in the RdRp of each CIAV, IrAV, and KAV. Genomes of both CIAV and IrAV were complete and contained two overlapping Open Reading Frames (ORFs). A + 1 programmed ribosomal frameshifting (PRF) motif, which matches the conserved amalgaviruses consensus sequence UUU_CGN was found at the ORF1/ORF2 boundary of CIAV and IrAV. The current study reports three novel viruses for the first time from crown imperial, and these findings enrich our understanding of new plant dsRNA virus species, which may also be helpful for the study of amalgaviruses.


 

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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.

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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.

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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. 

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Newcastle disease virus (NDV) causes one of the most dangerous infections in birds. High economic losses and high mortality are outcomes of this virus, which does not have any immediate cure. The natural reservoir of this virus can remain among bird and non-bird animals like farm animals. In Iran, this virus has reached a steady situation. Also, it should be mentioned that migrating birds can transfer the virus. The F protein of the virus is essential in pathogenicity and determination of pathogenic strain of NDVs, which has the regions that are essential in pathogenicity, immunogenicity, cell fusibility, and tissue necrosis. In this study, with computational analysis of this protein, some features related to this protein such as protein cleavage site, the conserved region in immunogenicity, infected species in Middle Eastern countries, and physicochemical properties of protein were determined. Results showed that the F protein of NDV consists of highly conserved regions that show a high rate of similarity and identity. Despite the majority of strains characterized as pathogenic, there were still non-pathogenic strains circulating in the Middle East. In this comprehensive study, protein regions essential in immunogenicity and epitope formation were identified, which may be used in the development of recombinant vaccines against this virus.
 

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Objective: Prostate cancer is the fifth most common cancer. In 2012, it was the second leading cause of cancer death for men worldwide. The PI3K/AKT pathway plays an essential role in pathogenesis of prostate cancer; the key role of this pathway in cancer progression makes it an attractive target for prostate cancer therapy. MicroRNAs (miRNAs) that regulate gene expression have a special ability to simultaneously control multiple genes and pathways which make them candidates for therapeutics. This study aims to determine miRNAs which target the PI3K/AKT pathway and evaluate them in prostate cancer cell lines. Methods: In order to determine an effective miRNA for the PI3K/AKT pathway, we assessed six genes from this pathway which have been proposed as drug targets in ten different prediction algorithms. Next, the candidate miRNAs were analyzed in expression profile and pathway analysis databases. Expression of candidate miRNAs in control and prostate cancer cell lines were subsequently evaluated. Results: According to bioinformatics, the miR-29 family could target the most genes from this list. Other bioinformatic estimates confirmed these results. The miR-29 family showed significant downregulation in prostate cancer cell lines LNCAP, PC3 and DU-145 compared to control samples. Conclusion: These results propose the possibility of using the miR-29 family to inhibit the PI3K/AKT pathway in prostate cancer.

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Although more than 98% of the human genome is transcribed, most of these transcripts are not translated into proteins. Rather, they are considered as non-coding RNAs. MicroRNAs (miRNAs) are very short non-coding RNAs approximately 22 nucleotides in length which regulate many key processes of cells such as growth, proliferation, differentiation, cell cycle, apoptosis (programmed cell death) and metabolism. On the other hand, it is known that these small regulatory molecules are involved in many human diseases such as different cancers and cardiovascular disorders. Therefore, discovery and functional characterization of novel miRNAs is a prominent achievement. Low abundance and spatiotemporal expression of these mediator molecules make their discovery difficult by conventional methods. Therefore, bioinformatics software have been designed for the prediction of stem-loop structures capable of producing miRNA precursors in the human genome. On the other hand, there are several bioinformatics tools for prediction of miRNA target genes. Prediction of miRNA target genes helps to characterize the function of a miRNA. In this paper, we have reviewed some of the common efficient bioinformatics tools and experimental approaches used for prediction and identification of the miRNA genes and their target genes. 

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Objective: The TcpA colonization factor of pili A and the cholera toxin are the most important pathogenesis factors of Vibrio cholera that have the ability to stimulate the immune system. The aim of this study is a bioinformatics analysis of the expression of CtxB-TcpA recombinant chimeric protein in E. coli, and production of antibody against it in mice.
Methods: We designed a gene cassette that contained the CtxB and TcpA genes, and a spacer linker by using bioinformatics. Characteristics that include the structure of the chimer protein and epitopes were studied. In order to build a gene cassette, TcpA and CtxB genes were proliferated and cloned in pET28a(+). CtxB-TcpA gene expression was induced by IPTG. The produced CtxB-TcpA recombinant protein was confirmed by SDS-PAGE and Western blot analyses. Antibody produced from mice serum was isolated and confirmed by ELISA.
Results: The codon adaptation index of the optimized gene was 0.9. The prevalence ratio codons increased to 74% through codon optimization. Enzyme analysis verified the chimeric gene CtxB-TcpA cloning in the pET28a (+) expression vector. A protein with a molecular weight of 35 kDa was seen on SDS-PAGE. Its reaction with anti-histidine antibodies was confirmed by Western blot. The purified protein was 33.100 mg/l. Immunization of mice induced a serum antibody response.
Conclusion: The chimeric protein can be considered a good candidate for effective immunity against cholera.

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Salt stress, as the most important abiotic stress, limits growth of plants and causes extensive damage to agricultural production worldwide. Therefore, it is necessary to identify genes that play a key role in tolerance to salt stress in plants through the analysis of transcriptome data such as microarray and High-Throughput Sequencing (HTS or NGS). In the present research, the combined analysis of microarray data by R packages for Hordeum vulgare L. under salinity stress identified 685 upregulated meta-DEGs (differentially expressed genes) and 766 downregulated meta-DEGs. The upregulated genes mostly belong to abiotic stress tolerance and hormone biosynthesis, and the downregulated genes pertain to late embryogenesis abundant protein and salinity stress response. GO terms in the upregulated genes are mostly associated with response to external and internal stresses; and in the downregulated genes, they are mostly associated with cellular metabolism. In the up and down meta-DEGs by KEGG, most of the genes connected to salinity stress included PP2C, ABF, AGT, and ChiB and F-box connected to the downregulated genes. Moreover, Transcription Factors (TFs) in the up and downregulated meta-DEGs with high frequency included AP2, ERF, bZIP, and bHLH. Most of the hub upregulated genes acquired from this research were metabolite biosynthesis and photosynthesis-related; and the hub downregulated genes were mainly the tricarboxylic acid cycle and glycolysis processes-related. Finally, a comparison was made between this meta-analysis and data obtained from other investigations. The findings validated their up and down expression. Our results give a new understanding about the molecular mechanism and present many TFs and candidate genes for salt stress tolerance in barley breeding programs.

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Introduction: Iron is an essential element that works as a cofactor in mitochondrial respiration, neurotransmitter biosynthesis, and myelination enzymes. Several pieces of evidence reveal that iron accumulates in demyelinating lesions in patients with multiple sclerosis (MS), and its intracellular homeostasis is disrupted, which exacerbates inflammation and demyelination.
Methods: We reanalyzed a microarray human MS dataset from GEO DataSests, under accession number GSE108000. We examined differentially expressed genes involved in iron metabolism between different types of MS lesions and peri-lesional normal-appearing white matter (PL-NAWM). We used GEO2R for differential expression analysis and created volcano plots, Venn diagrams, and pie charts for data visualization using RStudio software.
Results: We identified 58 genes involved in iron metabolism within the dataset. The expression of key iron-regulating genes, responsible for iron uptake, storage, and export, including CYBRD1, STEAP3, SLC39A14, FTL, FTH1, and CP were significantly changed. We also indicated significant alterations in the iron regulatory pathways in MS lesions and the PL-NAWM. The most prominent alterations were related to the iron uptake pathway, which showed enhanced activity.
Conclusion: Significant changes in iron regulatory gene expressions across MS lesions and the PL-NAWM may lead to dysregulation in iron homeostasis. This imbalance likely contributes to neurodegenerative processes associated with MS. The modifications in the PL-NAWM can be regarded as early-disease indicators. Recognizing these molecular changes provides valuable insights for facilitating timely MS diagnosis and developing targeted therapeutic strategies.