Introduction: DNA extraction from the ancient bones tissues is currently very difficult. Phenol chloroform silica method is one of the methods currently used for this aim. The purpose of this study was to optimize the assessment method.Methods: DNA of 62 bone tissues (average 3-11 years) was first extracted with phenol chloroform silica methods and then with changing of some parameters of the methods the extracted DNA was amplified in eight polymorphisms area including FES, F13, D13S317, D16, D5S818, vWA and CD4. Results from samples gained by two methods were compared in acrylamide gel.Results: The average of PCR yield for new method and common method in eight polymorphism regions was 75%, 78%, 81%, 76%, 85%, 71%, 89%, 86% and 64%, 39%, 70%, 49%, 68%, 76%, 71% and 28% respectively. The average of DNA in optimized (in 35l silica density) and common method were 267.5 μg/ml with 1.12 purity and 192.76 g/ml with 0.84 purity respectively.Conclusions: According to the findings of this study, it is estimated that longer EDTA attendance is an efficient agent in removing calcium and also adequate density of silica particles can be efficient in removal of PCR inhibitors.

Background & Aim: DNA Typing methods offer great help in identification of single deceased individuals, war and mass disaster victims. It has been a challenge to extract DNA from bones previously soaked in water, burned or buried for a long time, due to the reduced quality and quantity of DNA in the bone samples. The aim of this investigation is the comparison and evaluation of two different DNA extraction methods, namely the phenol-chloroform-silica and the guanidinium thiocyanate-Silica for DNA analysis of old bones.Materials & Methods: DNA was extracted from twenty randomly chosen bone samples, with 8 years passing of their death, from unknown human remains by using of phenol-chloroform-silica and guanidinium thiocyanate-Silica methods. Spectrophotometer was used to estimate the quantity and quality of DNA. Then, extracted DNA was profiled by a set of eight short tandem repeats (STRs) loci named CD4, vWA, LPL, D5S818, D16S539, D13S317, F13 and FES. The successfulness of the DNA profiling of the specimens was measured by counting all type able electrophoretic results in each case.Findings: DNA quantification results showed that the phenol-chloroform-silica extracted on average 256.27 mg/ml of DNA with the average purity degree of 1.07, compared with the DNA concentration of 170.86 mg/ml and purity of 0.94 by the guanidinium thiocyanate-Silica. Our results on the overall success rate of polymerase chain reaction (PCR) amplification in eight STRs loci mentioned above indicates that phenol-chloroform-silica method (76%) was more effective than guanidinium thiocyanate-Silica (64%).Conclusions: Although the phenol-chloroform-silica showed better results in STR Typing from degraded bone samples than guanidinium thiocyanate-Silica, we suggest using both methods in analysis of old bone tissue simultaneously to improve the interpretation of results.

Most molecular genetic tests begin by extracting DNA and RNA. To achieve this, obtaining a suitable, reliable, and repeatable extraction method is of great importance. In this regard, optimization of the extraction of nucleic acids from the Iranian cyclamen plant (Cyclamen coum Miller) and the introduction and expression of housekeeping genes was performed. After collecting plant samples from the three organs of leaf, petal and hypocotyl, modified CTAB and SDS methods were used for DNA isolation and modified Trizol, CTAB-LiCl and RNX-Plus methods were used for RNA isolation. The quality of isolated DNA and RNA was checked by electrophoresis and their concentration was measured with nanodrop. The presence of 18S ribosomal, actin (ACT), tubulin (TUB) and elongation factor (EF-1a) gene fragments was investigated using polymerase chain reaction (PCR). Based on the results, the lowest DNA concentration was related to the CTAB method. The DNA concentration and quality of Iranian cyclamen leaf, petal and hypocotyl samples were higher in the modified SDS method than in the CTAB method. The isolation of DNA using the modified SDS method not only had a high purity but also had relatively high performance. According to quality analysis of the RNA isolated from leaf, petal, and hypocotyl samples using Trizol, CTAB-LiCl, and RNX-Plus protocols, all three strategies may be used to isolate RNA from Iranian cyclamen tissues. However, the Trizol method is superior to other methods in terms of high band resolution and RNA concentration. The production of cDNA from RNA isolated from three Iranian cyclamen tissues was successfully performed only by Trizol and RNX-Plus methods. Based on the results, cDNA made from RNA isolated by Trizol method had better quality. To check the efficiency of RNA samples in RT-PCR reaction and the expression of housekeeping genes, RT-PCR test was performed. Based on the results, the presence of the bands related to the housekeeping genes fragment in the electrophoresis stage confirmed the good quality of the produced cDNA and also indicated the high quality of the isolated RNA from the Trizol and RNX-Plus methods. RT-PCR results showed that the expression of actin, EF-1a, 18S and tubulin gene was positive in most Iranian cyclamen organs. Among housekeeping genes, tubulin and 18S genes, had higher band resolution and higher quality in all samples and tissues.

Background and Aim: Isolation of genomic DNA from bacterial cells is one of the processes typically performed in most biological laboratories and there are different methods to do it. In this study, two methods including phenol-chloroform, and magnetic nanoparticles, were used to extract genomic DNA of Staphylococcus aureus. Materials and Methods: In the present study, the standard strain of Staphylococcus aureus ATCC 25923 was used for extraction of genomic DNA by phenol-chloroform and magnetic nanoparticles methods. Nanodrop and electrophoresis on agarose gel were used to evaluate the quality and concentration of extracted DNA. Results: The concentration of extracted DNA by phenol-chloroform and magnetic nanoparticle) SiO2/Fe3O4) methods were obtained 550. 4 and 131. 6 µ, g/ml respectively. Conclusion: From the findings of this study it can be concluded that due to the thick wall of Staphylococcus aureus, genomic DNA extraction by magnetic nanoparticles (Fe3O4/SiO2) have acceptable concentration and purity for molecular processes such as PCR, and can be used as an alternative to other extraction methods.

Background: The most important researches in molecular and genetic engineering fields are the finding of optimal methods for extraction of the genomic content of microorganisms and cells using them, can achieve the most amount and purity with the least time and cost. There are several methods for the extraction of bacterial DNA and the use of magnetic nanoparticles is one of the novel methods of nucleic acid isolation. The aim of this study  is to compare DNA extracted from Escherichia coli using two techniques including phenol-chloroform and magnetic nanoparticles. Methods: In this study, Escherichia coli strain ATCC25922 was used to compare the two extraction methods. For genomic DNA extraction  the phenol-chloroform methods as well as the technique of using bilayer SiO2/Fe3O4 magnetic nanoparticles were used. Both products were analyzed by nanodrop and following agarose gel electrophoresis. Results: The results of optical density (OD) evaluation with nanodrop spectrophotometer showed that the concentration of extracted DNA with conventional phenol-chloroform method and magnetic nanoparticle extraction technique were 761. 4 µ g/ml and 531 µ g/ml respectively. Conclusion: According to the obtained results by comparing the optical absorption of the two products and comparative evaluation with control groups in magnetic nanoparticle extraction method, also by comparing different factors such as the amount of time required, costs, ease of use, it can be concluded that due to the time-consuming and dangerous nature of the phenol-chloroform method, the using magnetic nanoparticles is an appropriated method for extracting the genomic content.

The extraction-precipitation method has been a desired method of synthesizing silica particles. In this work, silica particles were synthesized from sugarcane bagasse using this method. The identity of the particles was determined with Fourier Transform Infra-Red (FT-IR), and the particle size was measured with a Scanning Electron Microscope (SEM). Smaller-sized silica particles were obtained by extracting silica with sodium hydroxide from the sugarcane bagasse and obtaining the precipitate by bringing the pH down. In order to increase the size, sodium hydroxide was again added to the silicate solution before the pH was brought down, and the obtained precipitate was heated to a higher degree Celsius. Its hydroxyl content was also reduced. Previous studies have revealed the potential of sodium hydroxide addition for silica particle increment using the Stober method. We reported here an increase in silica particle size with the aid of sodium hydroxide as a catalyst through a greener technique, the extraction-precipitation method.

Introduction: Haemophilus influenzae type b (Hib) is a Gram negative bacterium and one of the causative agents of acute bacterial meningitis, especially in infants and children less than 5 years old. Lipooligosaccharide (LOS), one of the virulence factors which plays an important role in pathogenesis of Hib, has multiple applications in diagnosis and conjugate vaccines. In this study, LOS extracted from two Hib standard strains (ATCC 39930 and ATCC 10214) were compared. Methods: LOS was extracted by a modified hot phenol method from the aqueous and phenol phase and its concentration and purity assayed. Protein contaminations of the samples were determined spectrophotometrically and their endotoxin contents were assayed by the Limulus amebocyte lysate (LAL). Result: The yield of the extracted LOS from strain ATCC10214 was about 475 mg/ml and the protein contaminations of the samples were approximately 0.07 mg/ml, whereas strain ATCC39930 yielded 520 mg/ ml of LOS with protein contamination of 0.08 mg/ml. The results showed that the production of LOS by both strains was similar and the variation observed was not statistically significant (p<0.001).

Phenolic compounds are important environmental pollutants, whose separation and removal from water and industrial wastewater, especially in the oil industry, is essential. In the present research, the efficiency of an adsorbent silica aerogel in removing 4- Chlorophenol(4-CP) and 4-Bromophenol(4-BP), as phenolic compounds, from an aqueous solution, is studied, and the effects of various factors, such as contact time, pH and initial concentration, are analyzed. It was observed that the amount of adsorption increases at low pH, and this amount increases by incrementing the concentration of the emissions. Additionally, increasing the amount of adsorbent causes a decrease in halophenols. Results show that 4-BP is much better than 4-CP for adsorbtion onto the silica aerogel. Langmuir and Freundlich adsorption isotherms have been applied to model the equilibrium adsorption data. The study on the adsorption isotherms of these contaminants shows that adsorption of these emissions follows the Freundlich isotherm. In addition, adsorption kinetics using pseudo-first-order and pseudo-second order equations, elovich, and an intra-particle diffusion model, were analyzed. The results showed that the uptake of these compounds follows the intra-particle diffusion model and pseudo-second order equation.