Tahereh Yahya, Shohreh Zare Karizi, Ali Jahanian,
Volume 20, Issue 9 (12-2017)
Abstract
Abstract
Background: DNA-based computing is an emerging research aspect that enables the in-vivo computation and decision making with significant correctness. Recent papers show that the expression level of miRNAs are related to the progress status of some diseases such as cancers and DNA computing is introduced as a low cost and concise technique for detection of these biomarkers. In this paper, DNA-based logic gates are implemented in the laboratory to detect the level of miR-21 as the biomarker of cancer.
Materials and Methods: At the first, required strands for designing DNA gates are synthesized. Then, double stranded gate is generated in laboratory using a temperature gradient that followed by electrophoresis process. This double strand is the computation engine for detecting the miR-21 biomarker. miR-21 is as input in designed gate. At the end, the expression level of miR-21 is identified by measuring the generated fluorescent.
Results: at the first stage, the proposed DNA-based logic gate is evaluated by using the synthesized input strands and then it is experimented on a tumor tissue. Experimental results on synthesized strands show that its detection quality/correctness is 2.5x better than conventional methods.
Conclusion: Experimental results on the tumor tissues are successful and are matched with those are extracted from real time PCR results. Also, the results show that this method is significantly more suitable than real time PCR in view of time and cost.
Ali Reza Morad Abadi, Mohammad Arjomandzadegan, Navid Emami, Manijeh Kahbazi, Azam Ahmadi, Saeed Falahat, Seyyed Hossein Hosseini, Mehdi Kargaran, Parisa Khosravi,
Volume 21, Issue 4 (8-2018)
Abstract
Background and Aim: Ziehl Nelson staining, fluorescent and also culture are the standard methods for the diagnosis of tuberculosis. In this study, the performance of conventional cultivation methods was compared with Flash PCR.
Materials and Methods: A total of 56 sputum samples from patients with suspected tuberculosis in Tuberculosis Center of Arak city were collected and Ziehl–Neelsen and culture in Löwenstein–Jensen medium were accomplished. Moreover, DNA from all of the 56 sputum samples was extracted by Chelex100 method. Molecular evaluation was accomplished by Flash PCR kit containing probes and primers for gene amplification IS6110. Positive and negative controls together with samples were used in a MTC410 apparatus for amplification. FD-12 apparatus was used to evaluate the results. In addition, electrophoresis on agarose was used for confirmation of the results.
Findings: From 56 sputum samples of suspected TB patients, 20 samples were positive and 36 samples were negative on microscopic evaluation and culture methods. FLASH-PCR molecular analysis showed that all of 20 positive samples were positive in molecular methods, too. On the other hand, three of sputum samples that were negative by culture and staining were positive in FLASH-PCR method. One of these 3 patients, received Isoniazid, pyrazinamide and ethambutol antibiotic by responsible medicine. All results were confirmed using conventional electrophoresis.
Conclusion: In some negative samples, possibly because of the small number of bacteria in sample or a defect in the sampling, the Flash PCR may due good advantages. Therefore, due to the low cost, this method is recommended for routine use.
Abolfazl Morad, Mehdi Zeinoddini,
Volume 23, Issue 6 (11-2020)
Abstract
Background and Aim: In the microbial contamination of food and water, identifying the trace amounts of contaminating bacteria has always been of researchers’ interest and concern. The most frequent approach to resolve this problem is using culture-based methods to increase and enrich bacteria samples; accordingly, it extends the bacterial detection process to several hours or days. One of the smart strategies to solve this problem is the concentration of bacteria using physical methods. The present study aimed to enrich Vibrio cholerae as the most essential water-polluting germs. Accordingly, we used the filtration method and evaluated its function by culture method and two detection approaches of Adenosine Triphosphate (ATP) and PCR assay.
Methods & Materials: A certain concentration of V. Cholerae was artificially added to a specified volume of sterile water. Then, the bacteria were extracted from the medium and filtered using 0.450 µm separable filters. Finally, the performance of the pre- and post-filtration processes was compared using bacterial cell culture (CFU), ATP, and PCR assay with the specific primers for the ompW gene of V. cholerae.
Ethical Considerations: This article is a meta-analysis with no human or animal sample.
Results: The present research results indicated that the applied method presented high efficiency and recovery performance. In other words, samples provided no positive response before filtration in both methods; however, after filtration in isolated and recovered samples, the presence of bacteria was detected in the ATP and PCR methods.
Conclusion: In conclusion, the employed strategy can detect V. cholerae in non-culture and in the shortest time in contaminated water samples.
