Golzar Farhadi, J. Fayazi, H. Roshanfekr, M. Nazari, E. Behdani
Background: Oocyte maturation begins at the embryonic stage and continues throughout life. The effect of Follicle- Stimulating hormone (FSH) on gene of genes was evaluated using GEO access codes for the data set GSE38345. Materials and Methods: The microarray data containing the gene expression information from cow oocytes show that their maturation is influenced by FSH. Data analysis was performed using GEO2R. After identifying the genes and examining the different genes expressed, two gene groups with increased and decreased expression were identified. The interaction of each of the gene groups was examined using the STRING database, based on the co-expression information. The meaningful sub networks were explored using the Clusterone software. Gene ontology was performed using the comparative GO database. The miRNA-mRNA interaction network was also studied based on the miRWalk database. Finally, meaningful networks and subnets obtained by the Cytoscape software, were designed. Results: Comparison of oocyte gene expression data between the pre-maturation and postmaturation stages after treatment with FSH revealed 5958 genes with increased expression and 4275 genes with decreased expression. Examination of the protein interaction network among the set of increased and decreased expression genes based on string information revealed 262 genes with increased expression and 147 genes with decreased expression (high confidence (0.7) data). RPS3, NUSAP1, TBL3, and ATP5H showed increased expression and were effective in the positive regulation of rRNA processing, cell division, mitochondrial ATP synthesis coupled proton, and in oxidative phosphorylation and progesterone-mediated functions. WDR46 and MRPL22 showed decreased expression, which were important in the regulation of SRP-dependent co-translational proteins targeting the membrane, RNA secondary structure, unwinding, and functional pathways of ribosomal and RNA polymerase. The most important miRNA genes in the protein network of increased and decreased gene expression were bta-miR-10b-5p and miR-29b-2-5p. Conclusion: Examination of the genes expressed in the oocyte maturation pathway revealed nuclear, mitochondrial, and miRNA genes. Increasing and decreasing gene expression helps maintain equilibrium, which can be a biological marker.
{"title":"Use of Protein-Protein Interaction Network for Biomarker Identification in Oocyte Maturation","authors":"Golzar Farhadi, J. Fayazi, H. Roshanfekr, M. Nazari, E. Behdani","doi":"10.18502/RMM.V6I3.4611","DOIUrl":"https://doi.org/10.18502/RMM.V6I3.4611","url":null,"abstract":"Background: Oocyte maturation begins at the embryonic stage and continues throughout life. The effect of Follicle- Stimulating hormone (FSH) on gene of genes was evaluated using GEO access codes for the data set GSE38345. Materials and Methods: The microarray data containing the gene expression information from cow oocytes show that their maturation is influenced by FSH. Data analysis was performed using GEO2R. After identifying the genes and examining the different genes expressed, two gene groups with increased and decreased expression were identified. The interaction of each of the gene groups was examined using the STRING database, based on the co-expression information. The meaningful sub networks were explored using the Clusterone software. Gene ontology was performed using the comparative GO database. The miRNA-mRNA interaction network was also studied based on the miRWalk database. Finally, meaningful networks and subnets obtained by the Cytoscape software, were designed. Results: Comparison of oocyte gene expression data between the pre-maturation and postmaturation stages after treatment with FSH revealed 5958 genes with increased expression and 4275 genes with decreased expression. Examination of the protein interaction network among the set of increased and decreased expression genes based on string information revealed 262 genes with increased expression and 147 genes with decreased expression (high confidence (0.7) data). RPS3, NUSAP1, TBL3, and ATP5H showed increased expression and were effective in the positive regulation of rRNA processing, cell division, mitochondrial ATP synthesis coupled proton, and in oxidative phosphorylation and progesterone-mediated functions. WDR46 and MRPL22 showed decreased expression, which were important in the regulation of SRP-dependent co-translational proteins targeting the membrane, RNA secondary structure, unwinding, and functional pathways of ribosomal and RNA polymerase. The most important miRNA genes in the protein network of increased and decreased gene expression were bta-miR-10b-5p and miR-29b-2-5p. Conclusion: Examination of the genes expressed in the oocyte maturation pathway revealed nuclear, mitochondrial, and miRNA genes. Increasing and decreasing gene expression helps maintain equilibrium, which can be a biological marker.","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48955246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sepideh Khalili-Savadkouhi, A. K. Malekshah, Mehri Mirhoseini, M. Moosazadeh, M. Shahidi
Background: In vitro culture of mammalian embryos can slow or stop growth completely. This may be due to the medium used, pH, temperature, or light. There is considerable concern about the harmful effect of light in the laboratory environment. Cell number and apoptosis are useful parameters that indicate embryonic development and health. In this study, we assessed these two factors in the blastocyst. Materials and methods: A total of 128 embryos were extracted from NMRI mice at the 2-cell stage and were divided into 4 groups. The embryos were exposed to light for 0, 5, 15, and 30 min, and then cultured for 96 h. The degree of embryonic development were recorded every 24 h. Furthermore, several morphologically normal blastocysts were evaluated using the TUNEL assay. Results: There was no significant difference in developmental stages between the experimental and control groups. An evaluation of the percentage of blastomeres and apoptotic cells revealed significant differences among the four groups. The maximum number of apoptotic blastomeres was observed in the group exposed to light for 30 minutes. Conclusion: Up to thirty minutes of white fluorescent light can induce apoptosis in blastomeres, but it does not prevent embryo development.
{"title":"The Influence of Light on Apoptosis in Preimplantation Mouse Embryos In Vitro","authors":"Sepideh Khalili-Savadkouhi, A. K. Malekshah, Mehri Mirhoseini, M. Moosazadeh, M. Shahidi","doi":"10.18502/RMM.V6I3.4607","DOIUrl":"https://doi.org/10.18502/RMM.V6I3.4607","url":null,"abstract":"Background: In vitro culture of mammalian embryos can slow or stop growth completely. This may be due to the medium used, pH, temperature, or light. There is considerable concern about the harmful effect of light in the laboratory environment. Cell number and apoptosis are useful parameters that indicate embryonic development and health. In this study, we assessed these two factors in the blastocyst. Materials and methods: A total of 128 embryos were extracted from NMRI mice at the 2-cell stage and were divided into 4 groups. The embryos were exposed to light for 0, 5, 15, and 30 min, and then cultured for 96 h. The degree of embryonic development were recorded every 24 h. Furthermore, several morphologically normal blastocysts were evaluated using the TUNEL assay. Results: There was no significant difference in developmental stages between the experimental and control groups. An evaluation of the percentage of blastomeres and apoptotic cells revealed significant differences among the four groups. The maximum number of apoptotic blastomeres was observed in the group exposed to light for 30 minutes. Conclusion: Up to thirty minutes of white fluorescent light can induce apoptosis in blastomeres, but it does not prevent embryo development.","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45071823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Faezeh Namazi, Nasrin Hadi, M. Moghimi, Amir Eshaghiyan, Behnaz Nateghi
Background: Chronic lymphocytic leukemia (CLL) is the most common adult human leukemia. Studies revealed that microRNAs (miRNAs) can function as oncogenes or tumor suppressors in CLL and that the expression of miRNAs, such as miR-193b-3p and miR-376a-3p change in several diseases. We aimed to elucidate the changes in miR- 193b-3p and miR-376a-3p expression in CLL and determine their potential as diagnostic biomarkers for this disease. Materials and Methods: We investigated miR-193b-3p and miR-376a-3p expression by quantitative real-time PCR in peripheral blood mononuclear cells of 30 patients with CLL and 30 healthy individuals. Moreover, in silico molecular enrichment analysis was conducted on predicted and validated targets of miR-193b-3p and miR-376a-3p from the miRecords and miRTarBase databases. Results: The expression of miR-193b-3p and miR-376a-3p was significantly different between the two groups (P<0.0001 and P < 0.0001, respectively). Conclusion: Based on these findings, miR-193b-3p and miR-376a-3p could be novel biomarkers for the early diagnosis of CLL and could be used to design new CLL control strategies.
{"title":"Down-regulation of miR-193b-3p and miR-376a-3p in Chronic Lymphocytic Leukemia","authors":"Faezeh Namazi, Nasrin Hadi, M. Moghimi, Amir Eshaghiyan, Behnaz Nateghi","doi":"10.18502/RMM.V6I3.4609","DOIUrl":"https://doi.org/10.18502/RMM.V6I3.4609","url":null,"abstract":"Background: Chronic lymphocytic leukemia (CLL) is the most common adult human leukemia. Studies revealed that microRNAs (miRNAs) can function as oncogenes or tumor suppressors in CLL and that the expression of miRNAs, such as miR-193b-3p and miR-376a-3p change in several diseases. We aimed to elucidate the changes in miR- 193b-3p and miR-376a-3p expression in CLL and determine their potential as diagnostic biomarkers for this disease. Materials and Methods: We investigated miR-193b-3p and miR-376a-3p expression by quantitative real-time PCR in peripheral blood mononuclear cells of 30 patients with CLL and 30 healthy individuals. Moreover, in silico molecular enrichment analysis was conducted on predicted and validated targets of miR-193b-3p and miR-376a-3p from the miRecords and miRTarBase databases. Results: The expression of miR-193b-3p and miR-376a-3p was significantly different between the two groups (P<0.0001 and P < 0.0001, respectively). Conclusion: Based on these findings, miR-193b-3p and miR-376a-3p could be novel biomarkers for the early diagnosis of CLL and could be used to design new CLL control strategies.","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42437626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leili Sadeghi-Amiri, A. Barzegar, A. Rafiei, Omolbanin Amjadi
The five leading causes of cancer-related deaths are lung (1,760,000 deaths), colorectal (862,000 deaths), stomach (783,000 deaths), liver (782,000 deaths), and breast (627,000 deaths) cancers. Epigenetic changes can alter chromatin compaction, leading to the regulation of gene expression without changing the primary DNA sequence. Epigenetic mechanisms are normally involved in cellular processes such as genomic stability, chromosome X inactivation, and embryonic development and differentiation. Similar to other types of chromatin modifications, DNA methylation has been verified to affect the expression of various genes. Any impairment in these mechanisms alters the regulation of gene expression and can contribute to malignant cell transformation. Over the past few years, extensive innovations within the field of epigenetics have encouraged its application as a major strategy for the treatment of important diseases such as cancer.
{"title":"An Overview of the Epigenetic Modifications of Gene Expression in Tumorigenesis","authors":"Leili Sadeghi-Amiri, A. Barzegar, A. Rafiei, Omolbanin Amjadi","doi":"10.18502/RMM.V6I3.4606","DOIUrl":"https://doi.org/10.18502/RMM.V6I3.4606","url":null,"abstract":"The five leading causes of cancer-related deaths are lung (1,760,000 deaths), colorectal (862,000 deaths), stomach (783,000 deaths), liver (782,000 deaths), and breast (627,000 deaths) cancers. Epigenetic changes can alter chromatin compaction, leading to the regulation of gene expression without changing the primary DNA sequence. Epigenetic mechanisms are normally involved in cellular processes such as genomic stability, chromosome X inactivation, and embryonic development and differentiation. Similar to other types of chromatin modifications, DNA methylation has been verified to affect the expression of various genes. Any impairment in these mechanisms alters the regulation of gene expression and can contribute to malignant cell transformation. Over the past few years, extensive innovations within the field of epigenetics have encouraged its application as a major strategy for the treatment of important diseases such as cancer.","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46141262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jaber Zafari, H. Vazini, Fatemeh Javani-jouni, P. Abdolmaleki, R. Monajemi, Elahe Shams, M. Satari
Background: Expansion of the use of magnetic fields in metals, mining, transport, research, and medicine industries has led to a discussion about the effects of magnetic fields and whether their strength is negligible. The aim of this study was to investigate the effects of magnetic field on the viability and proliferation rate of HeLa cells. Materials and Methods: We studied the effects of magnetic field on the viability, proliferation rate and membrane lipid peroxidation of cells, thus, HeLa cells (cancer cells) and human fibroblast cells (normal cells) were used. Initially, the cells were cultured in DMEM and to determine the impact of the magnetic field, the cells were treated with magnetic field at 4 specific intensity levels (0, 7, 14 and 21 mT) and 2 exposure times (24 h and 48 h). The viability percentage and inhibition of cell proliferation were calculated by MTT assay and Trypan blue staining, respectively. Results: Lipid peroxidation of the cell membrane was examined by malondialdehyde (MDA) method. As the intensity and exposure time of the static magnetic field (SMF) increased, the viability percentage and proliferation rate decreased and the lipid peroxidation levels increased in the Hela cells. Conclusion: In this study, we have shown the anticancer effects of static magnetic field and propose a suitable intensity range that can be effective for the treatment of cancer.
{"title":"Anticancer Effects of Moderate Static Magnetic Field on Cancer Cells In Vitro","authors":"Jaber Zafari, H. Vazini, Fatemeh Javani-jouni, P. Abdolmaleki, R. Monajemi, Elahe Shams, M. Satari","doi":"10.18502/RMM.V6I3.4610","DOIUrl":"https://doi.org/10.18502/RMM.V6I3.4610","url":null,"abstract":"Background: Expansion of the use of magnetic fields in metals, mining, transport, research, and medicine industries has led to a discussion about the effects of magnetic fields and whether their strength is negligible. The aim of this study was to investigate the effects of magnetic field on the viability and proliferation rate of HeLa cells. Materials and Methods: We studied the effects of magnetic field on the viability, proliferation rate and membrane lipid peroxidation of cells, thus, HeLa cells (cancer cells) and human fibroblast cells (normal cells) were used. Initially, the cells were cultured in DMEM and to determine the impact of the magnetic field, the cells were treated with magnetic field at 4 specific intensity levels (0, 7, 14 and 21 mT) and 2 exposure times (24 h and 48 h). The viability percentage and inhibition of cell proliferation were calculated by MTT assay and Trypan blue staining, respectively. Results: Lipid peroxidation of the cell membrane was examined by malondialdehyde (MDA) method. As the intensity and exposure time of the static magnetic field (SMF) increased, the viability percentage and proliferation rate decreased and the lipid peroxidation levels increased in the Hela cells. Conclusion: In this study, we have shown the anticancer effects of static magnetic field and propose a suitable intensity range that can be effective for the treatment of cancer.","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49532956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C. Taghadosi, G. Kojouri, A. Ahadi, Mohammad Hashemi-Bahremani, A. Kojouri
{"title":"Bovine Leukaemia Virus Tax Antigen Identification in Human Lymphoma Tissue: Possibility of onco-protein Gene Ttransmission","authors":"C. Taghadosi, G. Kojouri, A. Ahadi, Mohammad Hashemi-Bahremani, A. Kojouri","doi":"10.32598/RMM.7.2.75","DOIUrl":"https://doi.org/10.32598/RMM.7.2.75","url":null,"abstract":"","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42073525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mansoureh Taghizadeh, Behzad Javadian, A. Rafiei, Azadeh Taraghian, M. Moosazadeh
{"title":"Antimicrobial resistance and virulence of Salmonella spp. from foods in Mazandaran","authors":"Mansoureh Taghizadeh, Behzad Javadian, A. Rafiei, Azadeh Taraghian, M. Moosazadeh","doi":"10.32598/RMM.7.2.59","DOIUrl":"https://doi.org/10.32598/RMM.7.2.59","url":null,"abstract":"","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46655118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Farinaz Khosravian, F. Ketabchi, Nasrin Hadi, Faezeh Namazi, Mansoor Salehi
{"title":"Expression Profiles of IGF1, EGF, and FGF2 Genes in Patients With Prostate Cancer in Isfahan Province, Iran","authors":"Farinaz Khosravian, F. Ketabchi, Nasrin Hadi, Faezeh Namazi, Mansoor Salehi","doi":"10.32598/RMM.7.2.39","DOIUrl":"https://doi.org/10.32598/RMM.7.2.39","url":null,"abstract":"","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45772091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Faezeh Namazi, Nasrin Hadi, Fatemeh Parnian, M. Moghimi
{"title":"Evaluation of IL-2 and IL-7 expression in patients with prostate cancer","authors":"Faezeh Namazi, Nasrin Hadi, Fatemeh Parnian, M. Moghimi","doi":"10.32598/RMM.7.2.83","DOIUrl":"https://doi.org/10.32598/RMM.7.2.83","url":null,"abstract":"","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41768106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evaluation of Iead Effects on Laccase Enzyme Activity in Bacillus Subtilis WPI","authors":"P. Moghadam, Hassan Mahmoudi","doi":"10.32598/RMM.7.2.69","DOIUrl":"https://doi.org/10.32598/RMM.7.2.69","url":null,"abstract":"","PeriodicalId":30778,"journal":{"name":"Research in Molecular Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45101116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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