Comparative analysis of the DNA isolated from thyme leaves using different methods

Background. The base for a molecular analysis is DNA of high quality. For DNA isolation, different kits or classical methods are used. For mass analysis, isolation with kits is a very expensive process. So, the objective of our investigation was to find a cheap method for high-quality DNA isolation from leaves of various thyme cultivars.Materials and methods. Leaves cut from thyme accessions (Thymus mastichina L. cv. ‘Svetliachok’, T. striatus Vahl. cv. ‘Jubileiniy’, T. vulgaris L. cv. ‘Fantasia’, and T. vulgaris cv. ‘Jalos’.) maintained ex situ in the collection of the Nikita Botanical Gardens were used as the material for the analysis. Light microscopy was used to study leaf anatomy and localize essential oil on leaf cross sections. Essential oil was extracted on Ginsberg devices, and phenolic content was measured with The Folin–Ciocâlteu reagent (FCR). Commercial kits (DiamondDNATM, PureLink® Plant Total DNA Purification Kit) and classical methods (CTAB, CTAB with 2% polyvinylpyrrolidone) were used for DNA isolation. DNA quality was evaluated spectrophotometrically, with electrophoresis (horizontal, automated system Agilent 4200 TapeStation) and PCR.Results. The analysis showed that the leaf blade mesophyll of four thyme cultivars had inclusions with essential oil. The content of essential oil and phenolic compounds was measured biochemically. Since the plants were characterized by the presence of secondary metabolites, DNA was isolated by different methods. Spectrophotometry demonstrated that the classical CTAB method and CTAB with 2% PVP provided the best results. Using an automated electrophoresis system, the presence of high-molecularweight DNA (more than 52000 bp) in significant amounts was detected in the samples isolated with DiamondDNATM kit and CTAB + 2% PVP.Conclusion. Among the tested kits and methods, CTAB + 2% PVP provided thyme DNA suitable for PCR and, presumably, for genome library preparation. The low cost of reagents for this technique makes it applicable for future mass analysis of plant material.

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EFFICIENT METHOD OF DNA ISOLATION FROM BULKING SAMPLES OF SEEDLINGS

Adaptive Fodder Production ◽

10.33814/afp-2222-5366-2021-3-29-48 ◽

2021 ◽

Vol 2021 (3) ◽

pp. 29-48

Author(s):

Irina Klimenko ◽

Alexey Antonov ◽

Vladimir Dushkin ◽

Anastasia Shamustakimova ◽

Yulian Mavlyutov

Keyword(s):

Dna Isolation ◽

Low Cost ◽

Leaf Tissue ◽

Perennial Grasses ◽

Genetic Studies ◽

Modified Method ◽

Extraction Buffer ◽

Low Efficiency ◽

Commercial Kits ◽

The Individual

Forage annual and perennial grasses are the difficult subject for molecular and genetic studies because of the problem with obtaining qualitative genomic DNA for PCR, due of high content of proteins, polysaccharides and polyphenols. The known methods of DNA extraction or the numerous commercial kits allow isolating purified nucleic acids from the leaf tissue, but characterized by low efficiency at seedlings using. The modified method of DNA isolation, based on the SDS-extraction buffer (sodium dodecil sulfate), is presented in this study. Significant modifications were introduced in the reagents compound and the steps of procedure accordingly to used type of plant tissue and the result was positive at usage on the bulking samples, as well as on the individual genotypes (the only seedling). Reliability of this method and the functionality of the obtained DNA samples were tested in PCR with different molecular markers (SSR, SRAP and PawS) in researches on revealing of forage legume grasses DNA polymorphism. The general advantages of the proposed method are simplicity and effectiveness, the possibility to isolate qualitative DNA without toxic reagents application, as well as relatively low cost and availability of reagents. This method can be useful for studying the genetic biodiversity and for decision the different tasks, required the rapid analysis of large plant populations.

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An improved and low-cost protocol for high-quality DNA isolation for the Chagas disease vectors

Infection Genetics and Evolution ◽

10.1016/j.meegid.2020.104201 ◽

2020 ◽

Vol 80 ◽

pp. 104201

Author(s):

Daryl David Cruz ◽

Elizabeth Nava-García ◽

Elizabeth Arellano

Keyword(s):

Chagas Disease ◽

Dna Isolation ◽

Low Cost ◽

Disease Vectors ◽

High Quality ◽

Chagas Disease Vectors

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A simple and rapid method for isolating high-quality RNA from kenaf containing high polysaccharide and polyphenol contents

10.1101/2020.07.06.189506 ◽

2020 ◽

Author(s):

Xiaofang Liao ◽

Hongwei Li ◽

Aziz Khan ◽

Yanhong Zhao ◽

Wenhuan Hou ◽

...

Keyword(s):

Low Cost ◽

Rna Extraction ◽

Rna Isolation ◽

Cost Effective ◽

Spectrophotometric Analysis ◽

Rt Pcr ◽

High Quality ◽

Time Saving ◽

Ctab Method ◽

Commercial Kits

AbstractThe isolation of high-quality RNA from kenaf is crucial for genetic and molecular biology studies. However, high levels of polysaccharide and polyphenol compounds in kenaf tissues could irreversibly bind to and coprecipitate with RNA, which complicates RNA extraction. In the present study, we proposed a simplified, time-saving and low-cost extraction method for isolating high quantities of high-quality RNA from several different kenaf tissues. RNA quality was measured for yield and purity, and the proposed protocol yielded high quantities of RNA (10.1-12.9 μg/g·FW). Spectrophotometric analysis showed that A260/280 ratios of RNA samples were in the range of 2.11 to 2.13, and A260/230 ratios were in the range of 2.04-2.24, indicating that the RNA samples were free of polyphenols, polysaccharides, and protein contaminants after isolation. The method of RNA extraction presented here was superior to the conventional CTAB method in terms of RNA isolation efficiency and was more sample-adaptable and cost-effective than commercial kits. Furthermore, to confirm downstream amenability, the high-quality RNA obtained from this method was successfully used for RT-PCR, real-time RT-PCR and Northern blot analysis. We provide an efficient and low-cost method for extracting high quantities of high-quality RNA from plants that are rich in polyphenols and polysaccharides, and this method was also validated for the isolation of high-quality RNA from other plants.

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A Low-Cost, High Quality MRI Breast Scanner Using Prepolarization

10.21236/ada390614 ◽

1999 ◽

Author(s):

Albert Macovski

Keyword(s):

Low Cost ◽

High Quality

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Low-cost synthesis of high quality graphene oxide with large electrical and thermal conductivities

Materials Letters ◽

10.1016/j.matlet.2021.129649 ◽

2021 ◽

pp. 129649

Author(s):

Shalik Ram Joshi ◽

Jaekyo Lee ◽

Gun-Ho Kim

Keyword(s):

Graphene Oxide ◽

Low Cost ◽

High Quality ◽

Thermal Conductivities

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Urban Air Quality Modeling Using Low-Cost Sensor Network and Data Assimilation in the Aburrá Valley, Colombia

Atmosphere ◽

10.3390/atmos12010091 ◽

2021 ◽

Vol 12 (1) ◽

pp. 91

Author(s):

Santiago Lopez-Restrepo ◽

Andres Yarce ◽

Nicolás Pinel ◽

O.L. Quintero ◽

Arjo Segers ◽

...

Keyword(s):

Air Quality ◽

Data Assimilation ◽

Transport Model ◽

Cost Model ◽

Low Cost ◽

Model Performance ◽

Monitoring Network ◽

Correlation Factor ◽

Chemical Transport Model ◽

High Quality

The use of low air quality networks has been increasing in recent years to study urban pollution dynamics. Here we show the evaluation of the operational Aburrá Valley’s low-cost network against the official monitoring network. The results show that the PM2.5 low-cost measurements are very close to those observed by the official network. Additionally, the low-cost allows a higher spatial representation of the concentrations across the valley. We integrate low-cost observations with the chemical transport model Long Term Ozone Simulation-European Operational Smog (LOTOS-EUROS) using data assimilation. Two different configurations of the low-cost network were assimilated: using the whole low-cost network (255 sensors), and a high-quality selection using just the sensors with a correlation factor greater than 0.8 with respect to the official network (115 sensors). The official stations were also assimilated to compare the more dense low-cost network’s impact on the model performance. Both simulations assimilating the low-cost model outperform the model without assimilation and assimilating the official network. The capability to issue warnings for pollution events is also improved by assimilating the low-cost network with respect to the other simulations. Finally, the simulation using the high-quality configuration has lower error values than using the complete low-cost network, showing that it is essential to consider the quality and location and not just the total number of sensors. Our results suggest that with the current advance in low-cost sensors, it is possible to improve model performance with low-cost network data assimilation.

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Linum usitatisimum L. is the most important crop in Russia for the production of high-quality oil with low cost (review)

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/640/4/042014 ◽

2021 ◽

Vol 640 (4) ◽

pp. 042014

Author(s):

E N Turin ◽

A N Susskiy ◽

R S Stukalov ◽

M V Shestopalov ◽

E L Turina ◽

...

Keyword(s):

Low Cost ◽

High Quality ◽

Important Crop

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Evaluation of a New Immunochromatography Technology Test (LDBio Diagnostics) To Detect Toxoplasma IgG and IgM: Comparison with the Routine Architect Technique

Journal of Clinical Microbiology ◽

10.1128/jcm.01106-17 ◽

2017 ◽

Vol 55 (12) ◽

pp. 3395-3404 ◽

Cited By ~ 7

Author(s):

Caroline Mahinc ◽

Pierre Flori ◽

Edouard Delaunay ◽

Cécile Guillerme ◽

Sana Charaoui ◽

...

Keyword(s):

Western Blot ◽

Sensitivity And Specificity ◽

Blot Analysis ◽

False Positive ◽

Automated System ◽

University Hospitals ◽

Content Type ◽

Automated Screening ◽

Commercial Kits ◽

Fully Automated System

ABSTRACTA study comparing the ICT (immunochromatography technology)ToxoplasmaIgG and IgM rapid diagnostic test (LDBio Diagnostics, France) with a fully automated system, Architect, was performed on samples from university hospitals of Marseille and Saint-Etienne. A total of 767 prospective sera and 235 selected sera were collected. The panels were selected to test various IgG and IgM parameters. The reference technique,ToxoplasmaIgGII Western blot analysis (LDBio Diagnostics), was used to confirm the IgG results, and commercial kits Platelia Toxo IgM (Bio-Rad) and Toxo-ISAgA (bioMérieux) were used in Saint-Etienne and Marseille, respectively, as the IgM reference techniques. Sensitivity and specificity of the ICT and the Architect IgG assays were compared using a prospective panel. Sensitivity was 100% for the ICT test and 92.1% for Architect (cutoff at 1.6 IU/ml). The low-IgG-titer serum results confirmed that ICT sensitivity was superior to that of Architect. Specificity was 98.7% (ICT) and 99.8% (Architect IgG). The ICT test is also useful for detecting IgM without IgG and is both sensitive (100%) and specific (100%), as it can distinguish nonspecific IgM from specificToxoplasmaIgM. In comparison, IgM sensitivity and specificity on Architect are 96.1% and 99.6%, respectively (cutoff at 0.5 arbitrary units [AU]/ml). To conclude, this new test overcomes the limitations of automated screening techniques, which are not sensitive enough for IgG and lack specificity for IgM (rare IgM false-positive cases).

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