Showing 8 results for Khansarinejad
Mahdi Paryan, Mahdieh Mondanizadeh, Samira Mohammadi-Yeganeh , Behzad Khansarinejad,
Volume 14, Issue 5 (11-2011)
Abstract
Background: HIV-1 and HCV are two of the most important blood-borne infectious agents. Hence, reliable, precise, and sensitive detection of these viruses in infected patients and donated blood units is highly important. Noticing the limitations of serological assays in detection of these infectious agents, this study was to use fast and sensitive molecular assays like real-time PCR.
Materials and Methods: In this trial, a home-brewed SYBR green-based multiplex real time PCR, on the basis of melting curve analysis, was developed for the single or simultaneous detection of HCV and HIV-1 infections in plasma samples. Data were analyzed using SPSS software version 16.
Results: The results obtained from different reactions on several clinical samples showed that the analytical sensitivities of the developed assay for HIV-1 and HCV were 200 and 100 copies/ml, respectively. It was also shown that the primers designed for each virus had no interaction with each other and other interfering agents.
Conclusion: Noticing the good level of sensitivity and specificity, easy handling, relatively low cost, and rapid analysis of samples, this method can be a useful and rapid approach for simple and effective detection of HCV and HIV-1 in plasma samples.
Mahdieh Mondanizadeh, Ghasem Mosayebi, Ehsan Arefian, Massoud Saidijam, Behzad Khansarinejad,
Volume 17, Issue 2 (5-2014)
Abstract
Background: Although miR-124 molecule has been known as an inducer of neurogenesis, few researches have been done on the targets of this molecule and its functional mechanisms in differentiation toward neurons and maintaining neuronal state. The microarray technique has been established as the reference method for studying the genes under the control of miRNAs. However, the high cost of this method has hampered its use in most research centers. On the other hand, the improvement of bioinformatical algorithms and computer modeling systems has led to the development of the bioinformatical softwares that can predict mRNA targets for miRNAs. Therefore, the aim of this theoretical study was to bioinformatically evaluate the effect of miR-124 on transcription factors that can be involved in neurogenesis and neuronal cell amplification, by using various specific softwares. Materials and Methods: Using different algorithms in TargetScan, DIANA and miRWalk databases, the potential transcription factors targets of miR-124 were identified. Then, a score table was prepared from the candidate genes, based on the affinity of the seed region of miR-124 and the number of targets in the 3`-UTR region of transcription factors. Finally, transcription factors with higher scores were chosen as candidates for practical analysis.
Results: The results of bioinformaical analysis showed that the LAMC1, ITGB1, PTBP1, SOX9, SP1, and EFNB1 molecules are the most potential factors that might be affected by miR-124 during neurogenesis.
Conclusion: It seems that transcription factor SP1 is under the control of the miR-124 and plays a crucial role in neurogenesis process. Therefore, this protein can be considered as a suitable new candidate for experimental evaluation.
Behzad Khansarinejad, Mahdieh Mondanizadeh, Mohammad Rafeie, Siamak Mirab Samiee,
Volume 17, Issue 4 (7-2014)
Abstract
Background: The Real-time PCR assay has been established as the standard method for Human Cytomegalovirus (HCMV) quantitation in immunocompromised patients. However, the question of which one of whole blood or plasma specimens is better for viral quantitation is still unresolved for many clinical laboratories. To answer this question, the current study compares HCMV DNA load in whole blood and plasma samples.
Materials and Methods: In this prospective study, the whole blood and plasma samples were obtained from 41 transplantated patients and the viral load was detected using a validated, in-house Real-time PCR assay.
Results: Of the total 193 examined specimens, 174 were negative and 19 samples, from 16 patients, were positive in at least one of whole blood or plasma samples. Based on the results of linear regression analysis, the cytomegalovirus viral load was correlated in whole blood and plasma samples (R2: 0.872). However, the regression equation shows that the HCMV load in whole blood samples is higher than load of this virus in plasma. The validity of the quantitative results was confirmed by repeating the tests and analyzing the results using the repeated measure analysis.
Conclusion: Based on the results of the present study, HCMV quantitation in whole blood samples has a higher analytical sensitivity than in plasma samples.
Pegah Parvaee, Mahdieh Mondanizadeh, Behzad Khansarinejad, Amir Nader Emami Razavi,
Volume 19, Issue 5 (8-2016)
Abstract
Background: Circulating microRNAs are promising biomarkers in diagnosis and assessment of cancerous patients. Quantitative Real-time PCR assay is a sensitive test for evaluating the levels of miRNAs expression. Nevertheless, there is no concurrence on selecting appropriate reference genes for qPCR analysis of miRNAs in circulation. Therefore, the current study aimed to select a suitable reference gene for normalizing the RT-qPCR assay results in plasma samples of patients with gastric cancer.
Materials and Methods: Based on previously published studies, three molecules SNORD47, U6 RNA, and miR-103 were selected as the candidate reference genes. After RNA extraction from plasma samples of 40 patients with gastric cancer and 40 healthy individuals, expression levels of these molecules were evaluated using Real-time PCR method.
Results: The results showed that the developed assays are able to diagnose their specified targets by a suitable linear range. By comparing patients and control groups, although the expression levels of miR-103 molecule were not equal between the two groups (p= 0.017), SNORD47 and U6 RNAs had similar expression levels. However, the variations of SNORD47 expression were lower that U6 RNA.
Conclusion: Based on the results of the current study, the SNORD47 molecule has a stable expression levels in plasma samples of patients with gastric cancer and normal individuals and can be used as an appropriate reference gene for normalizing the quantitative data of qPCR assay.
Mina Zolfaghari, Behzad Khansarinejad, Ali Ganji, Zeinab Hamzehloo, Hamid Abtahi,
Volume 19, Issue 11 (2-2017)
Abstract
Abstract
Background: Ureaplasma and M. genitalium species belong to a kind of bacteria that are sexually transmitted and are the possible cause of pelvic inflammatory disease and nongonococcal urethritis, and et al. The aim of this study was to determine the urea plasma and Mycoplasma genitalium species frequency in women with vaginal infection and various sexual partners who referred to women, s health promotion and treatment center in Arak.
Materials and Methods: Endocervical swab samples from 110 women with vaginal infections referred to women’s health promotion and treatment center in Arak, were prepared. Patients’ personal information and identities during reception process were registered. The samples were transferred to the laboratory in the transport environment and after DNA extraction, were evaluated according to Real-time PCR assay.
Results: Urea plasma and Mycoplasma genitalium bacteria existed in 96(87.27%) and 4(3.63%) of patients, respectively. Among them, 4 cases had both bacteria infections. The amount of isolation in young women between 30-39 years old was more than others.
Conclusion: The results show that the colonization of urea plasma species in adult women is 40-80% and in studied group is 87.27%. These results indicate that with due attention to the increasing number of sexual partners and the increase of sexual activity, the urea plasma colonization of women will increase. In view of the potential influence of mycoplasma species on side effects resulted from pregnancy infection of mothers and mortality, on-time diagnosis and treatment will be increasingly essential.
Niloofar Moradi, Mehdi Paryan, Behzad Khansarinejad, Mohammad Rafiei, Mahdieh Mondanizadeh,
Volume 19, Issue 12 (3-2017)
Abstract
Abstract
Background: Hepatocellular carcinoma (HCC) is the third major cause of cancer death worldwide. Hepatitis B virus (HBV) and HBx gene play an important role in the development of HCC by influencing signaling pathways. Since there is no detectable symptom in the early phase of HCC, there is need to find new HCC-specific markers with high sensitivity for early detection and diagnosis of HCC. On the other hand, by the advent and development of bioinformatic sciences, it is now possible to predict miRNAs as biomarkers, and their targets. Therefore, in the present study, based on the results of the bioinformatic software applications with different algorithm, we selected the miRNA targeting HBx and NOTCH1 mRNAs according to higher score, suitable connection with target gene and confirming them in more softwares.
Materials and Methods: First, the sequences of NOTCH1 and HBx genes were retrieved from NCBI. Afterwards, several software applications such as TargetScan, mirWalk, miRBase, Miranda, PicTar, miRVir, and DIANA were applied to predict miRNAs.
Results: Based on the high scoring by bioinformatics softwares and suitable targeting, miR-34a were selected to target NOTCH1 and miR-6510, miR-5193 and miR-214 were chosen to targetHBX gene.
Conclusion: Because of tumor suppression roles of miR-214 and miR-34a, they probably could be used as therapeutic strategy in cancer researches. It is also seems that the miR-5193 could act as a specific marker in Hepatocellular carcinoma.
Mahdieh Mondanizadeh, Niloofar Moradi, Razieh Amini, Behzad Khansarinejad, Ghasem Mosayebi,
Volume 22, Issue 5 (11-2019)
Abstract
Background and Aim Chronic Lymphocytic Leukemia (CLL) is the most commonly occurring leukemia in adults, accounting for about 30-25% of total leukemia. One of the important etiological causes of this leukemia is the disruption of the Nuclear Factor Kappa B (NF-kB) signaling pathway. The two proteins of Apoptosis-Inducing Ligand (APRIL) and B-Cell Activating Factor (BAFF) play a role in the pathogenesis of this leukemia by affecting the NF-kB signaling pathway. In this study, due to the effect of miRNAs in regulating many cellular processes, the prediction of the prominent miRNAs targeting APRIL and BAFF transcripts in B-cell CLL patients was evaluated using specific and different bioinformatics programs.
Methods & Materials Afterwards retrieving the sequences of APRIL and BAFF proteins from the NCBI website, by using several programs including miRanda, TargetScan, miRWalk, DIANA and miRDB with different algorithms, the prediction of miRNAs targeting these genes was investigated.
Ethical Considerations This study was approved by the Research Ethics Committee of Arak University of Medical Sciences.
Results Based on the scoring system of bioinformatics programs, “hsa-miR-145-5p” and “hsa-miR-185-5p” were identified as miRNAs targeting APRIL gene, while “hsa-miR-424” and “hsa-miR-497”were miRNAs targeting BAFF gene. They were suggested for the practical studies in future.
Conclusion Based on the important role of APRIL and BAFF genes in the normal process of cell death and B-cell evolution, it seems that the mi-RNAs predicted by bioinformatics programs using different algorithms can be used as a diagnostic molecular biomarker to identify B-cell CLL patients.
Tahere Azimi, Malihe Bagheri, Mahdi Pariyan, Behzad Khansarinejad, Ashraf Zamani, Mahdieh Mondanizadeh,
Volume 23, Issue 3 (August & September 2020)
Abstract
Background and Aim: Cervical Cancer (CC) is the third most common malignancy in the women, the main cause of which is human papillomavirus (HPV). Both E6 and E7 oncogenes of the virus play an important role in its tumorigenesis. Today, methods available for screening CC are not capable of detecting the disease at an early stage. Therefore, it is important to identify new biomarkers for early detection of this cancer. For this purpose, in the present study, miRNAs targeting the two oncogenes E6 and E7 of human papillomavirus (types 16 and 18) were studied in CC by bioinformatics.
Methods & Materials: First, using the NCBI database, the E6 and E7 gene sequences were obtained for both human papillomavirus types 16 and 18. Then, using the miRBase and RNA22 bioinformatics databases, the most appropriate targeting miRNAs for these genes were selected.
Ethical Considerations: This study was approved by Ethics Committee of Arak University of Medical Sciences.
Results: Based on the P obtained from bioinformatics databases, miRNA including miR-92a-5p (P=7.51e-2), miR-195-3p (P=2.24e-1), miR-34a-5p (P=2.73e-1) and miR-155-5p (P=4.95e-2) were introduced for the two genes E6 and E7.
Conclusion: Results from bioinformatics studies revealed that of the four miRNAs identified, miR-155-5p and miR-92a-5p are probably the targeting miRNAs specific for the E6 and E7 genes, respectively. Therefore, it seems that these miRNAs can be a suitable candidate for in vitro studies in CC patients.
