scholarly journals Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

2021 ◽  
Author(s):  
Melody A Vachon ◽  
Katja Engel ◽  
Rachel C Beaver ◽  
Greg W Slater ◽  
Jeffrey Binns ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Bentonite Clay ◽  
Starting Material ◽  
Nucleic Acid Detection ◽  
Resistant Bacteria ◽  
Acid Extraction ◽  
Swelling Properties ◽  
Sulfate Reducing ◽  
Abundance And Diversity ◽  
Bentonite Clays

Characterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.

scholarly journals Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Melody A. Vachon ◽  
Katja Engel ◽  
Rachel C. Beaver ◽  
Greg F. Slater ◽  
W. Jeffrey Binns ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Bentonite Clay ◽  
Starting Material ◽  
Nucleic Acid Detection ◽  
Resistant Bacteria ◽  
Acid Extraction ◽  
Swelling Properties ◽  
Sulfate Reducing ◽  
Abundance And Diversity ◽  
Bentonite Clays

AbstractCharacterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.

scholarly journals Rapid Bedside Inactivation of Ebola Virus for Safe Nucleic Acid Tests

2016 ◽  
Vol 54 (10) ◽  
pp. 2521-2529 ◽  
Author(s):  
Maiken Worsøe Rosenstierne ◽  
Helen Karlberg ◽  
Karoline Bragstad ◽  
Gunnel Lindegren ◽  
Malin Lundahl Stoltz ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Ebola Virus ◽  
Storage Temperature ◽  
Nucleic Acid Detection ◽  
Blood Collection ◽  
Acid Extraction ◽  
Simple Method ◽  
Virus Rna ◽  
Vacuum Tubes ◽  
Nucleic Acid Tests

Rapid bedside inactivation of Ebola virus would be a solution for the safety of medical and technical staff, risk containment, sample transport, and high-throughput or rapid diagnostic testing during an outbreak. We show that the commercially available Magna Pure lysis/binding buffer used for nucleic acid extraction inactivates Ebola virus. A rapid bedside inactivation method for nucleic acid tests is obtained by simply adding Magna Pure lysis/binding buffer directly into vacuum blood collection EDTA tubes using a thin needle and syringe prior to sampling. The ready-to-use inactivation vacuum tubes are stable for more than 4 months, and Ebola virus RNA is preserved in the Magna Pure lysis/binding buffer for at least 5 weeks independent of the storage temperature. We also show that Ebola virus RNA can be manually extracted from Magna Pure lysis/binding buffer-inactivated samples using the QIAamp viral RNA minikit. We present an easy and convenient method for bedside inactivation using available blood collection vacuum tubes and reagents. We propose to use this simple method for fast, safe, and easy bedside inactivation of Ebola virus for safe transport and routine nucleic acid detection.

Fast and Accurate Control Strategy for Portable Nucleic Acid Detection (PNAD) System Based on Magnetic Nanoparticles

2021 ◽  
Vol 17 (3) ◽  
pp. 407-415
Author(s):  
Yile Fang ◽  
Haoran Liu ◽  
Yue Wang ◽  
Xiangyi Su ◽  
Lian Jin ◽  
...  
Keyword(s):  
Magnetic Nanoparticles ◽  
Nucleic Acid ◽  
Control Strategy ◽  
Melting Curve ◽  
Circuit Board ◽  
Nucleic Acid Detection ◽  
Amplification Efficiency ◽  
Acid Extraction ◽  
Sample Processing ◽  
Temperature Controller

Portable nucleic acid detection (PNAD) systems are performed for sample processing, amplification and detection automatically in an individual device realizing "sample in, answer out." For this goal, numerous function modules should be integrated in a diminutive device, in which temperature controller is one of the most important modules. In a nucleic acid detection process, both sample processing and polymerase chain reaction (PCR) require fast and accurate temperature control to increase concentration and purity of the extraction product and to improve amplification efficiency. In this paper, a dual-channel temperature controller for PNAD systems is developed, which contains a printed circuit board (PCB) and an integrated control program with a fast and accurate control strategy. According to the principle of nucleic acid detection based on magnetic nanoparticles, the controller can work in different modes such as high-precision heating control for nucleic acid extraction, rapid thermal cycle control for PCR, and rate adjustable constant heating/cooling control for melting curve. Evaluatively, the average heating/cooling rate of the module can exceed about 6 C/s, while the temperature fluctuation was less than ± 0.1°C, which can meet the demands of PNAD systems very well.

Nucleic acid detection on DNA chips using highly reactive and stable diazo-biotins

2008 ◽  
Author(s):  
Alain Laurent ◽  
Arnaud Burr ◽  
Thibault Martin ◽  
Frédéric Lasnet ◽  
Sébastien Hauser ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Detection ◽  
Dna Chips

scholarly journals Differing Effects of Standard and Harsh Nucleic Acid Extraction Procedures on Diagnostic Helminth Real-Time PCRs Applied to Human Stool Samples

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 188
Author(s):  
Tanja Hoffmann ◽  
Andreas Hahn ◽  
Jaco J. Verweij ◽  
Gérard Leboulle ◽  
Olfert Landt ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Pcr Assay ◽  
Bead Beating ◽  
Stool Samples ◽  
Pcr Assays ◽  
Human Stool

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen’s kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

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