Comparison of DNA Extraction Efficiency and Reproducibility of Different Aeration Diffuser Biofilms Using Bead-Beating Protocol

2018 ◽  
Vol 28 (6) ◽  
pp. 293-304
Author(s):  
Pitiporn Asvapathanagul ◽  
Manel Garrido-Baserba ◽  
Betty H. Olson ◽  
Hee-Deung Park ◽  
Deqiang Chen ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Extraction Efficiency ◽  
Quantitative Polymerase Chain Reaction ◽  
E Coli ◽  
Bead Beating ◽  
Copy Numbers ◽  
Total Dna ◽  
Polymerase Chain ◽  
Gordonia Amarae

An existing bead-beating DNA extraction protocol was employed to compare the DNA extraction recovery and fragment quality of 6 different aeration diffuser biofilms. <i>Escherichia coli</i>, <i>Gordonia amarae</i>, and mixed liquor were used as controls. The fraction of total DNA<sub>biofilm</sub> decreased monotonically with increasing number of beat beatings (BB) when the amount of DNA present was sufficient (&#x3e;4 μg<sub>DNA</sub>/cm<sup>2</sup>), excluding the ceramic disk. While controls required only 2 BBs, 3 out of 5 BBs achieved ≥70% of total DNA (70.3 ± 1.7%) for 5 out of 6 biofilms. Quantitative polymerase chain reaction (PCR) analyses of 353 and 1,505 basepair (bp) amplicons from pure culture extracts showed target copy numbers were not degraded for the first 2 BBs, but the third BB decreased amplicon concentrations by 0.65 and 1.12 log for <i>E. coli</i>, and 0.39 and 0.40 log for <i>G. amarae</i>, respectively. The 353 bp fragment amplification from biofilm samples showed minimal degradation for the first 3 BBs. PCR and gel electrophoresis confirmed integrity of amplified 1,505 bp DNA fragments over the 5 BBs, except in the EDPM (75 mm diameter, tube) diffuser biofilm (4.98 ± 0.62 μg<sub>DNA</sub>/cm<sup>2</sup>). Taken together, this study showed type of diffuser membrane biofilms had no effects on extraction efficiency, but low DNA concentrations reduced extraction performance.

AN IMPROVED METHOD FOR INHIBITOR FREE NUCLEIC ACIDS FROM POLYPHENOL RICH LEAVES OF MUSA SPP

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
N.NANDHA KUMAR ◽  
K. SOURIANATHA SUNDARAM ◽  
D. SUDHAKAR ◽  
K.K. KUMAR
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Proteinase K ◽  
Chain Reaction ◽  
Banana Plant ◽  
High Molecular Weight Dna ◽  
Musa Spp ◽  
Leaf Tissues ◽  
Polymerase Chain

Excessive presence of polysaccharides, polyphenol and secondary metabolites in banana plant affects the quality of DNA and it leads to difficult in isolating good quality of DNA. An optimized modified CTAB protocol for the isolation of high quality and quantity of DNA obtained from banana leaf tissues has been developed. In this protocol a slight increased salt (NaCl) concentration (2.0M) was used in the extraction buffer. Polyvinylpyrrolidone (PVP) and Octanol were used for the removal of polyphenols and polymerase chain reaction (PCR) inhibitors. Proteins like various enzymes were degraded by Proteinase K and removed by centrifugation from plant extract during the isolation process resulting in pure genomic DNA, ready to use in downstream applications including PCR, quantitative polymerase chain reaction (qPCR), ligation, restriction and sequencing. This protocol yielded a high molecular weight DNA isolated from polyphenols rich leaves of Musa spp which was free from contamination and colour. The average yields of total DNA from leaf ranged from 917.4 to 1860.9 ng/ìL. This modified CTAB protocol reported here is less time consuming 4-5h, reproducible and can be used for a broad spectrum of plant species which have polyphenol and polysaccharide compounds.

Quality Improvement of the DNA extracted by boiling method in Gram negative bacteria

2017 ◽  
Vol 6 (04) ◽  
pp. 5347 ◽  
Author(s):  
Omar B. Ahmed* ◽  
Anas S. Dablool
Keyword(s):  
Dna Extraction ◽  
Control Method ◽  
Extraction Procedure ◽  
Cost Effective ◽  
High Yield ◽  
Gram Negative Bacteria ◽  
Bacterial Dna ◽  
Gram Negative ◽  
E Coli

Several methods of Deoxyribonucleic acid (DNA) extraction have been applied to extract bacterial DNA. The amount and the quality of the DNA obtained for each one of those methods are variable. The study aimed to evaluate bacterial DNA extraction using conventional boiling method followed by alcohol precipitation. DNA extraction from Gram negative bacilli was extracted and precipitated using boiling method with further precipitation by ethanol. The extraction procedure performed using the boiling method resulted in high DNA yields for both E. coli and K. pneumoniae bacteria in (199.7 and 285.7μg/ml, respectively) which was close to control method (229.3 and 440.3μg/ml). It was concluded that after alcohol precipitation boiling procedure was easy, cost-effective, and applicable for high-yield quality of DNA in Gram-negative bacteria.

scholarly journals Eliminating false positives in a qPCR assay for the detection of the uidA gene in Escherichia coli

2013 ◽  
Vol 11 (3) ◽  
pp. 382-386 ◽  
Author(s):  
Richard Kibbee ◽  
Natalie Linklater ◽  
Banu Örmeci
Keyword(s):  
Escherichia Coli ◽  
Quantitative Polymerase Chain Reaction ◽  
Qpcr Assay ◽  
Uida Gene ◽  
Chain Reaction ◽  
Taq Polymerase ◽  
E Coli ◽  
Gene Copies ◽  
Polymerase Chain ◽  
Low Levels

Due to contaminant Escherichia coli DNA present in recombinant Taq polymerase reagents, it is not possible to reliably detect low levels of E. coli in samples using the quantitative polymerase chain reaction (qPCR) assay. Native Taq polymerase was successfully used in this study to detect five uidA gene copies (5 fg of genomic DNA) of the uidA gene.

scholarly journals Photoelectrocatalytic disinfection of water and wastewater: performance evaluation by qPCR and culture techniques

2012 ◽  
Vol 11 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Danae Venieri ◽  
Efthalia Chatzisymeon ◽  
Eleonora Politi ◽  
Spiridon S. Sofianos ◽  
Alexandros Katsaounis ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Charge Carriers ◽  
Treated Wastewater ◽  
Bacterial Inactivation ◽  
Culture Techniques ◽  
E Coli ◽  
Log Reduction ◽  
Water Matrix ◽  
Water And Wastewater ◽  
Polymerase Chain

Photoelectrocatalytic oxidation (PEC) was evaluated as a disinfection technique using water and secondary treated wastewater spiked with Escherichia coli and Enterococcus faecalis. PEC experiments were carried out using a TiO2/Ti-film anode and a zirconium cathode under simulated solar radiation. Bacterial inactivation was monitored by culture and quantitative polymerase chain reaction (qPCR). Inactivation rates were enhanced when the duration of the treatment was prolonged and when the bacterial density and the complexity of the water matrix were decreased. E. coli cells were reduced by approximately 6 orders of magnitude after 15 min of PEC treatment in water at 2V of applied potential and an initial concentration of 107 CFU/mL; pure photocatalysis (PC) led to about 5 log reduction, while electrochemical oxidation alone resulted in negligible inactivation. The superiority of PEC relative to PC can be attributed to a more efficient separation of the photogenerated charge carriers. Regarding disinfection in mixed bacterial suspensions, E. coli was more susceptible than E. faecalis at a potential of 2V. The complex composition of wastewater affected disinfection efficiency, yielding lower inactivation rates compared to water treatment. qPCR yielded lower inactivation rates at longer treatment times than culture techniques, presumably due to the fact that the latter do not take into account the viable but not culturable state of microorganisms.

scholarly journals Use of Fluorescence Quantitative Polymerase Chain Reaction (PCR) for the Detection of Escherichia coli Adhesion to Pig Intestinal Epithelial Cells

2016 ◽  
Vol 19 (3) ◽  
pp. 619-625 ◽  
Author(s):  
C.H. Dai ◽  
L.N. Gan ◽  
W.U. Qin ◽  
C. Zi ◽  
G.Q. Zhu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Epithelial Cells ◽  
Intestinal Epithelial Cells ◽  
Quantitative Polymerase Chain Reaction ◽  
Relative Number ◽  
Intestinal Epithelial ◽  
Chain Reaction ◽  
E Coli ◽  
Polymerase Chain

AbstractAn efficient and accurate method to testEscherichia coli(E. coli) adhesion to intestinal epithelial cells will contribute to the study of bacterial pathogenesis and the function of genes that encode receptors related to adhesion. This study used the quantitative real-time polymerase chain reaction (qPCR) method. qPCR primers were designed from thePILINgene ofE. coliF18ab, F18ac, and K88ac, and the pig β-ACTINgene. Total deoxyribonucleic acid (DNA) fromE. coliand intestinal epithelial cells (IPEC-J2 cells) were used as templates for qPCR. The 2−ΔΔCtformula was used to calculate the relative number of bacteria in cultures of different areas. We found that the relative numbers of F18ab, F18ac, and K88ac that adhered to IPEC-J2 cells did not differ significantly in 6-, 12-, and 24-well culture plates. This finding indicated that there was no relationship between the relative adhesion number ofE. coliand the area of cells, so the method of qPCR could accurately test the relative number ofE. coli. This study provided a convenient and reliable testing method for experiments involvingE. coliadhesion, and also provided innovative ideas for similar detection methods.

scholarly journals MiR-145-5p Inhibits the Invasion of Prostate Cancer and Induces Apoptosis by Inhibiting WIP1

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Jianming Sun ◽  
Linggang Deng ◽  
Ye Gong
Keyword(s):  
Prostate Cancer ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Luciferase Reporter Gene ◽  
Anticancer Effects ◽  
Polymerase Chain

Prostate cancer (PCa) is a common malignant tumor of the male genitourinary system that seriously affects the quality of life of patients. Studying the pathogenesis and therapeutic targets of PCa is important. In this study, we investigated the role of miR-145-5p in PCa and its potential molecular mechanisms. The expression levels of miR-145-5p in PCa tissues and adjacent control tissues were detected by real-time quantitative polymerase chain reaction. The effects of miR-145-5p overexpression on PCa were studied using cell proliferation, migration, and invasion experiments. Furthermore, WIP1 was the target gene of miR-145-5p through the bioinformatics website and dual-luciferase reporter gene experiment. Further studies found that WIP1 downregulation could inhibit the proliferation, invasion, and cloning of PCa cells. Overexpression of WIP1 reversed the anticancer effects of miR-145. The anticancer effect of miR-145 was achieved by inhibiting the PI3K/AKT signaling pathway and upregulating ChK2 and p-p38MAPK. Taken together, these results confirmed that miR-145-5p inhibited the growth and metastasis of PCa cells by inhibiting the expression of proto-oncogene WIP1, thereby playing a role in tumor suppression in PCa and may become a potential therapeutic target for the treatment of PCa.

scholarly journals PCR detection of Vibrio cholerae, Escherichia coli, and Salmonella sp. from bottled drinking water in Iran

2018 ◽  
Vol 12 (09) ◽  
pp. 700-705
Author(s):  
Mojtaba Bonyadian ◽  
Hamdallah Moshtaghi ◽  
Hanie Nadi
Keyword(s):  
Escherichia Coli ◽  
Drinking Water ◽  
Vibrio Cholerae ◽  
Screening Method ◽  
Chain Reaction ◽  
Culture Methods ◽  
E Coli ◽  
Drinking Waters ◽  
Polymerase Chain

Introduction: The quality of drinking water has an important role in human health. This study was aimed to detect Escherichia. coli, Salmonella sp. and Vibrio cholerae from bottled drinking waters produced in Iran. Methodology: A total of 240 samples of bottled water of different brands were collected for testing between March 2015 to December 2015 in Shahrekord-Iran. Samples were examined by polymerase chain reaction (PCR) combined with culture methods for the detection of E. coli, Salmonella sp., and V. cholerae. Results: The results of PCR revealed that the uidA gene from E. coli, IpaB gene from Salmonella sp, and epsM gene from V. cholerae were detected in 6 (2.5%), 1 (0.4 %), 0 (0%) of the samples, respectively. But in culture methods, only E. coli 5 (2.1%) were isolated from the samples. The contamination with E. coli was significantly higher (P < 0.05) in water produced during the hot seasons than the cold seasons. Conclusions: This study confirmed the presence of Escherichia coli as the main microorganism in bottle drinking water in Iran. Also, our study showed that PCR can be used as a screening method for monitoring the enteric pathogens in drinking water.

scholarly journals Sources of microbiological contamination in sachet water from Ghana

2020 ◽  
Vol 10 (2) ◽  
pp. 202-208
Author(s):  
Asli Aslan ◽  
Haresh Rochani ◽  
Oghenekpaobor Oyibo ◽  
J. Edward Dotherow ◽  
Kendall W. Anderson ◽  
...  
Keyword(s):  
Drinking Water ◽  
Quantitative Polymerase Chain Reaction ◽  
Microbiological Quality ◽  
Total Coliform ◽  
Primary Sources ◽  
Source Tracking ◽  
E Coli ◽  
Sewage Contamination ◽  
Sachet Water

Abstract Sachet water is one of the primary sources of drinking water in rapidly growing countries. A study to assess the microbiological quality of sachet water in 21 different brands was conducted in Ghana. Culturable total coliform was positive in 87% of the samples collected, where Escherichia coli colonies were absent. The analysis of quantitative polymerase chain reaction results indicated the presence of E. coli genes in 44.6% of the samples, with the highest concentration up to 3,166 CCE/100 ml. Microbial source tracking analyses showed that the source of E. coli genes did not originate from sewage contamination because the human-associated HF183 marker was not detected. Of the 175 samples tested, 71% did not mention any water treatment before filling the packages. These results suggest non-human sources of contamination, such as biofilm formation in the pipelines used to fill these packages due to poor disinfection. Our study shows an urgent need for increased regulation and standardized manufacturing of sachet water to ensure safe drinking water.

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