The Experts below are selected from a list of 73830 Experts worldwide ranked by ideXlab platform
Tatyana A. Sysoeva - One of the best experts on this subject based on the ideXlab platform.
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Benchmarking DNA Isolation kits used in analyses of the urinary microbiome.
Scientific reports, 2021Co-Authors: Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. SysoevaAbstract:The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA Isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA Isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA Isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
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Benchmarking DNA Isolation kits used in analyses of the urinary microbiome
2020Co-Authors: Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. SysoevaAbstract:Abstract The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA Isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA Isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA Isolation kits result in significantly different DNA yields from urine samples but non-significant differences in the number of reads recovered, alpha, or beta diversity. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. The Promega kit recovered fewer Gram positive bacteria compared to other kits. The Promega and DNeasy PowerSoil kits also appear to have some important biases towards over-representing certain Gram negative bacteria of biologic relevance within the urinary microbiome.
Bohuslav Rittich - One of the best experts on this subject based on the ideXlab platform.
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Silica-coated La0.75Sr0.25MnO3 nanoparticles for magnetically driven DNA Isolation.
Journal of separation science, 2011Co-Authors: Štěpánka Trachtová, Ondřej Kaman, Alena Španová, Pavel Veverka, E. Pollert, Bohuslav RittichAbstract:Magnetic La0.75Sr0.25MnO3 nanoparticles possessing an approximately 20 nm thick silica shell (LSMO(0.25)@SiO2) were characterised and tested for the Isolation of PCR-ready bacterial DNA. The results presented here show that thenanoparticles do not interfere in PCR. DNA was reversibly adsorbed on their silica shell from the aqueous phase system (16 % PEG 6000 – 2 M NaCl). The method proposed was used for DNA Isolation from complex food samples (dairy products and probiotic food supplements). The isolated DNA was compatible with PCR. The main advantages of the nanoparticles tested for routine use were their high colloidal stability allowing a more precise dosage and therefore high reproducibility of DNA Isolation.
Lisa Karstens - One of the best experts on this subject based on the ideXlab platform.
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Benchmarking DNA Isolation kits used in analyses of the urinary microbiome.
Scientific reports, 2021Co-Authors: Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. SysoevaAbstract:The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA Isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA Isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA Isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
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Benchmarking DNA Isolation kits used in analyses of the urinary microbiome
2020Co-Authors: Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. SysoevaAbstract:Abstract The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA Isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA Isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA Isolation kits result in significantly different DNA yields from urine samples but non-significant differences in the number of reads recovered, alpha, or beta diversity. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. The Promega kit recovered fewer Gram positive bacteria compared to other kits. The Promega and DNeasy PowerSoil kits also appear to have some important biases towards over-representing certain Gram negative bacteria of biologic relevance within the urinary microbiome.
Alejandro Sánchez Alvarado - One of the best experts on this subject based on the ideXlab platform.
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Planarian High Molecular Weight DNA Isolation by Spooling.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Shasha Zhang, Alejandro Sánchez AlvaradoAbstract:High-quality large molecular weight genomic DNA is important for genomic studies. Most commercial available genomic DNA purification kits have failed to generate high molecular weight DNA of sufficient quality from planarians. Here, we describe a simple and efficient genomic DNA Isolation method, which has worked for several different planarian species, including Schmidtea mediterranea. This phenol-chloroform based method can be used to obtain genomic DNA of up to 150 kb and can be used for bacterial artificial chromosome (BAC) library construction, next-generation sequencing and PCR cloning.
Ali Tuncel - One of the best experts on this subject based on the ideXlab platform.
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comparative DNA Isolation behaviours of silica and polymer based sorbents in batch fashion monodisperse silica microspheres with bimodal pore size distribution as a new sorbent for DNA Isolation
Artificial Cells Nanomedicine and Biotechnology, 2018Co-Authors: Gulcin Gunal, Eda S Ogut, Hasan Ilhan, Gunes Kibar, Ali TuncelAbstract:AbstractMonodisperse silica microspheres with bimodal pore-size distribution were proposed as a high performance sorbent for DNA Isolation in batch fashion under equilibrium conditions. The proposed sorbent including both macroporous and mesoporous compartments was synthesized 5.1 μm in-size, by a “staged shape templated hydrolysis and condensation method”. Hydrophilic polymer based sorbents were also obtained in the form of monodisperse-macroporous microspheres ca 5.5 μm in size, with different functionalities, by a developed “multi-stage microsuspension copolymerization” technique. The batch DNA Isolation performance of proposed material was comparatively investigated using polymer based sorbents with similar morphologies. Among all sorbents tried, the best DNA Isolation performance was achieved with the monodisperse silica microspheres with bimodal pore size distribution. The collocation of interconnected mesoporous and macroporous compartments within the monodisperse silica microspheres provided a hig...
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comparative DNA Isolation behaviours of silica and polymer based sorbents in batch fashion monodisperse silica microspheres with bimodal pore size distribution as a new sorbent for DNA Isolation
Artificial Cells Nanomedicine and Biotechnology, 2018Co-Authors: Gulcin Gunal, Eda S Ogut, Hasan Ilhan, Gunes Kibar, Cigdem Kip, Ali TuncelAbstract:Monodisperse silica microspheres with bimodal pore-size distribution were proposed as a high performance sorbent for DNA Isolation in batch fashion under equilibrium conditions. The proposed sorbent including both macroporous and mesoporous compartments was synthesized 5.1 μm in-size, by a "staged shape templated hydrolysis and condensation method". Hydrophilic polymer based sorbents were also obtained in the form of monodisperse-macroporous microspheres ca 5.5 μm in size, with different functionalities, by a developed "multi-stage microsuspension copolymerization" technique. The batch DNA Isolation performance of proposed material was comparatively investigated using polymer based sorbents with similar morphologies. Among all sorbents tried, the best DNA Isolation performance was achieved with the monodisperse silica microspheres with bimodal pore size distribution. The collocation of interconnected mesoporous and macroporous compartments within the monodisperse silica microspheres provided a high surface area and reduced the intraparticular mass transfer resistance and made easier both the adsorption and desorption of DNA. Among the polymer based sorbents, higher DNA Isolation yields were achieved with the monodisperse-macroporous polymer microspheres carrying trimethoxysilyl and quaternary ammonium functionalities. However, batch DNA Isolation performances of polymer based sorbents were significantly lower with respect to the silica microspheres.