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The aim of this study was to evaluate the performances of methods such as sequencing of the internal transcribed spacer (ITS) and 26S (D1/D2) regions of ribosomal DNA, RFLP analysis of the ITS region and commercial biochemical test kit for the identification of the yeasts isolated during spontaneous fermentation of fresh crushed pineapple juice. The experiments were conducted in Thailand and Australia. The yeast isolates in Thailand were identified by sequencing the ITS and 26S (D1/D2) regions of ribosomal DNA and RFLP analysis of the ITS region. The yeast isolates in Australia were identified by sequencing analysis of the two DNA regions and commercial biochemical test kit. The identification results conducted in both countries were relatively similar. Mainly, the yeast isolates could be identified by the use of 26S rDNA in combination with ITS sequencing analysis. In Thailand, approximately 80% of the yeast isolates identified by sequencing analysis of the two regions gave similar identities and included Rhodotolula mucilaginosa, Issatchenkia orientalis, Hanseniaspora uvarum, Hanseniaspora opuntiae, Pichia guilliermondii, Aureobasidium pullulans, Saccharomycodes ludwigii, Candida tropicalis, Pichia fermentans, Zygosaccharomyces bailii, Candida stellata and Erythrobasidium hasegawianum.In Australia, 86% of the yeast isolates gave similar identifications by the sequencing analysis of the two regions and included P. guilliermondii, Pichia membranifaciens, P. fermentans, H. uvarum, H. opuntiae, I. orientalis, Candida sp., Yarrowia lipolytica, Tremella globispora, R. mucilaginosa and A. pullulans.

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DNA sequence determination is a tremendous human achievement. DNA sequencing includes several methods and technologies in use for determining the order of the nucleotide bases (adenine, guanine, cytosine, and thymine) in a molecule of DNA. Knowledge of DNA sequences has become indispensable for basic biological research, other research branches utilizing DNA sequencing, and in numerous applied fields such as diagnostic, biotechnology, forensic biology and biological systematics. The advent of DNA sequencing has significantly accelerated biological research and discovery. Rapid sequencing, the result of modern DNA sequencing technology, is instrumental in the sequencing of the human genome for the Human Genome Project. Related projects, often by scientific collaboration across continents, have generated complete DNA sequences of humans as well as numerous animals, plants and microbial genomes. DNA sequencing methods currently under development include labeling DNA polymerase and reading the sequence as a DNA strand transits through nanopores. Additional methods include microscopy-based techniques such as atomic force microscopy or transmission electron microscopy that are used to identify the positions of individual nucleotides within long DNA fragments (>5000 bp) by nucleotide labeling with heavier elements (e.g., halogens) for visual detection and recording. Third generation technologies aim to increase throughput and decrease the time to result and cost by eliminating the need for excessive reagents and harnessing the processivity of DNA polymerase. Researchers in the field of genetics in Iran use this technology in their studies, but unfortunately our literature lack proper Persian language resources. The authors intend to write a series of review articles in this field. The present paper is an introduction to the summary of important techniques in DNA sequencing.

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DNA is made up of molecules called nucleotides. There are four different nucleotides in DNA which are called Adenine, Guanine, Cytosine, and Thymine, or simply A, G, C and T. Determining the order of these bases is called DNA sequencing. This sequence determines the genes and these genes specify an individual’s unique traits. Therefore, the genetic research plays an important role in detection, prevention and treatment of diseases which are caused by genetic abnormalities and mutations. Common DNA sequencing methods are usually based on chemical reactions. These methods have some disadvantages for example they are expensive and also they cause losing DNA. So, in recent years the progress in molecular scale simulation methods has made various approaches for DNA sequencing. In this paper, a suitable method for DNA sequencing has been presented and its accuracy is investigated by molecular dynamics simulations. In this method, DNA molecule passes through the carbon nanotube first, and then the graphene nanopore, with a specific speed. Different bases are determined by analyzing the required force for passing DNA. In this proposed method, the speed and cost of sequencing are improved.

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Tarkhineh is one of the traditional foods in Iran and a rich source of probiotic bacteria. The objective of this study was to identify the probiotic bacteria isolated from Tarkhineh using 16S rRNA gene sequencing and molecular typing with repetitive extragenic palindromic–PCR (REP-PCR). In total, 20 different bacteria were isolated from traditional dairy products and Tarkhineh. Molecular identification of the isolates was carried out by 16S rRNA gene sequencing, and DNA sequences of isolates deposited in GenBank. The REP-PCR reaction by REP1R-I, REP2-I and REP1R-I+REP2-I markers was performed for fingerprinting and characterization of the isolates. Un-weighted pair group method with arithmetic mean (UPGMA) clustering methods were performed based on Dice similarity. The REP1R-I primer grouped isolates into three, and REP2-I and REP1R-I+REP2-I grouped all isolates into four main clusters in dendrograms. In all analyses, isolates of Lactobacillus casei, Lactobacillus brevis, Lactobacillus plantarum, and Entrococcus facium formed separate clusters. The results of sequencing corresponded to clustering in the dendrogram. According to the results, REP-PCR is an accurate technique for determining the genetic diversity of lactic acid bacteria species.