DNA was extracted from whole blood using a Puregene® Blood Core Kit B (Lot No. 8510944, Germantown, MD, USA). The extraction process was performed according to the manufacturer’s instructions. Assessment of the DNA yield was completed by NanoDrop (Thermo Scientific, ND-2000 UV-Vis Spectrophotometer, Waltham, MA, USA). The extracted DNA was stored −20 °C until further use in genotyping of the different SNPs [22 (link)].
Nd 2000 uv vis spectrophotometer
Manufactured by Thermo Fisher Scientific
Sourced in United States
The ND-2000 UV-Vis spectrophotometer is a laboratory instrument designed to measure the absorbance or transmittance of light through a sample. It operates in the ultraviolet and visible light spectrum, typically between 190 and 1100 nanometers. The ND-2000 can be used to quantify the concentration of specific compounds in a solution by analyzing the absorption spectrum.
Automatically generated - may contain errors
Lab products found in correlation
Fraction recovery system, by Beckman Coulter (4 mentions)
Quick seal polyallomer tubes, by Beckman Coulter (3 mentions)
Optima l 100 xp, by Beckman Coulter (3 mentions)
Nanodrop, by Thermo Fisher Scientific (2 mentions)
Miseq pe300 sequencer, by Illumina (1 mentions)
Hiseq 2500 platform, by Illumina (1 mentions)
Powersoil dna extraction kit, by Qiagen (1 mentions)
Ar200, by Leica (1 mentions)
Quick seal polypropylene tubes, by Beckman Coulter (1 mentions)
Mobio powersoil dna isolation kit, by Qiagen (1 mentions)
Beckman ultracentrifuge, by Beckman Coulter (1 mentions)
8 protocols using nd 2000 uv vis spectrophotometer
1
DNA Extraction from Whole Blood
2
Antimicrobial Susceptibility Testing Optimization
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Trypticase soy agar (TSA) + 5% sheep’s blood containing antimicrobials representing four drug classes (pleuromutilin-tiamulin, macrolide-tylosin, β-lactam-ampicillin and quinolone-nalidixic acid) were prepared. For each antimicrobial, plates containing a series of dilutions from 0.25–128 μg/ml were made and MICs were determined for B. pilosicoli, B. hyodysenteriae and B. hampsonii. The organism concentration of each BHIS broth culture was determined by measuring (Thermo Scientific ND-2000 UV-Vis Spectrophotometer) the OD600nm. A 1:5 dilution series (undiluted broth culture, 1:5, 1:25, 1:625, 1:3125) was made of each broth culture, and 2 μl was spotted onto the antimicrobial-containing plates in triplicate. Plates were incubated anaerobically for 2 days at 42°C and the lowest concentrations at which no hemolysis was observed were recorded.
By comparing our results (how MIC changes in different species with different inoculum concentrations and the repeatability of observations between replicates for each inoculum density) and conventions of the discipline (CLSI standards), an optimal starting inoculum concentration was selected.
By comparing our results (how MIC changes in different species with different inoculum concentrations and the repeatability of observations between replicates for each inoculum density) and conventions of the discipline (CLSI standards), an optimal starting inoculum concentration was selected.
3
Soil Metagenomics with Hg Contamination
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Approximately 0.5 g of soil was weighed before adding exogenous Hg and after aging. Thereafter, DNA was extracted using a Fast DNA SPIN Kit according to the manufacturer’s instructions. The extracted soil DNA was subsequently amplified by PCR, using universal primers with different TAG tags. The cut gel was purified using a NanoDrop® (Thermo Fisher Scientific, Waltham, MA, USA). The DNA concentration was determined using an ND-2000 UV-Vis spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and the purified DNA was sequenced using a MiSeq PE 300 sequencer (Illumina Inc., San Diego, CA, USA) from Shanghai Meiji Biomedical Technology Co., Ltd. (Shanghai, China) After sequencing, low-quality sequences were removed, effective sequences were distinguished, and the sequence direction was adjusted according to the barcode and primer sequences.
4
Soil Microbiome Profiling via 16S rRNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Soil DNA was extracted using PowerSoil DNA extraction kit (MoBio, United States) according to manufacturer’s instructions. DNA concentration was determined using an ND-2000 UV-Vis spectrophotometer (NanoDrop Technologies, United States). The hypervariable V4 region of 16S rRNA gene was subsequently amplified by polymerase chain reaction (PCR) using the primer pair of 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACVSGGGTATCTAAT-3′) with barcode (Sengupta and Dick, 2017 ). Purified PCR amplicons were sequenced by an Illumina HiSeq2500 platform (Novogene, China). Reads were chosen after the quality filtering, and the reads were discarded if the barcodes were uncorrectable. Chimeras were removed and the sequences with high quality were clustered into different operational taxonomic units (OTUs) based on 97% similarity using Uparse1 . The representative OTU sequences were chosen for taxonomical classification using QIIME pipeline and Ribosomal Database Project (RDP) (Xu et al., 2017 (link)). The sequences were archived at Genbank (BioSample accession: SAMN12734515 ; BioProject ID, PRJNA565100 ).
5
Soil Metagenome Extraction and Density Gradient Centrifugation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA extraction was conducted on two soil samples from each treatment that were incubated for 3, 6, and 9 days, using a Powersoil DNA extraction kit (MO BIO Laboratories, Inc. Carlsbad, CA, USA) following the manufacturer’s instructions. The DNA content was quantified with an ND-2,000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Thereafter, about 10,000-ng DNA was added to Quick-Seal polyallomer tubes (13 × 51 mm, 5.1 mL, Beckman Coulter, Pasadena, CA, USA) and spun in Tris-EDTA (TE, pH 8.0)/CsCl solution. Prior to sealing the tubes with one cordless quick-seal tube topper (Beckman Coulter), the average buoyant density (BD) of all prepared gradients was confirmed with a digital refractometer (model AR200, Leica Microsystems Inc., Buffalo Grove, IL, USA), and adjusted by adding small volumes of CsCl solution or Tris-EDTA buffer. The tubes were transferred to an ultracentrifuge (Optima L-100XP, Beckman Coulter). Centrifugation was performed at 45,000 g (20°C) for 48 h. Subsequently, the centrifuge tubes were placed onto a fraction recovery system (Beckman Coulter) and fractions (150 μL for each) were collected. The BD of each fraction was then measured, and CsCl was removed by introducing concentrated ethanol [30 (link)].
6
Density Gradient Centrifugation of Microbial DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
After centrifuging 100 mL of each water sample from the 12 C-PHE and 13 C-PHE treatments, total nucleic acids were extracted from the resulting cell pellets using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer's instructions. 39 DNA content was quantified using the ND-2,000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Approximately 5 µg DNA were added to Quick-Seal polyallomer tubes (13 × 51 mm, 5.1 mL; Beckman Coulter, Pasadena, CA, USA) and mixed with Tris-EDTA (pH 8.0)-CsCl solution at a final buoyant density (BD) of ~1.77 g/mL. The BD was determined using a digital refractometer (model AR200; Leica Microsystems Inc., Buffalo Grove, IL, USA). After balancing and sealing, the tubes were transferred to an ultracentrifuge (Optima L-100XP, Beckman Coulter) at 45,000 g (20°C) for 48 h. Subsequently, DNA in the tube was fractioned (400 µL each) and collected using a fraction recovery system (Beckman Coulter). After the BD measurements, the DNA fractions were purified using the method described by Sun et al. 40 The relationships between BD and the fraction number or DNA concentration are listed in Figure S1 and Figure S2, respectively.
Approximately 5 µg DNA were added to Quick-Seal polyallomer tubes (13 × 51 mm, 5.1 mL; Beckman Coulter, Pasadena, CA, USA) and mixed with Tris-EDTA (pH 8.0)-CsCl solution at a final buoyant density (BD) of ~1.77 g/mL. The BD was determined using a digital refractometer (model AR200; Leica Microsystems Inc., Buffalo Grove, IL, USA). After balancing and sealing, the tubes were transferred to an ultracentrifuge (Optima L-100XP, Beckman Coulter) at 45,000 g (20°C) for 48 h. Subsequently, DNA in the tube was fractioned (400 µL each) and collected using a fraction recovery system (Beckman Coulter). After the BD measurements, the DNA fractions were purified using the method described by Sun et al. 40 The relationships between BD and the fraction number or DNA concentration are listed in Figure S1 and Figure S2, respectively.
7
Density Gradient Centrifugation of Activated Sludge DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Activated sludge samples were collected at the beginning and end of PHE degradation. Total nucleic acids were extracted from the cell pellets harvested via centrifugation of 15 mL of each sample from the 12 C-PHE and 13 C-PHE treatments, using a PowerSoil DNA Isolation Kit (MoBio, Carlsbad, CA, USA) according to the manufacturer's instructions. DNA was quantified with an ND-2000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Approximately 5 μg of DNA was added to Quick-Seal polypropylene tubes (13 × 51 mm, 5.1 mL; Beckman Coulter, Pasadena, CA, USA) and mixed with Tris-EDTA (TE; pH 8.0)/CsCl solution at a final buoyant density (BD) of ~1.77 g/mL. The BD was determined using a digital refractometer (model AR200; Leica Microsystems Inc., Buffalo Grove, IL, USA) and adjusted using CsCl solution or Tris-EDTA buffer. After balancing and sealing, the tubes were transferred to an ultracentrifuge (Optima L-100XP; Beckman Coulter) at 45,000 g (20°C) for 48 h.
After centrifugation, DNA was collected from each 400-μL fraction using a fraction recovery system (Beckman Coulter). The BD of each fraction was then measured, and the DNA fractions were purified following a published method (Song et al. 2015) . The relationships between BD and the fraction number or DNA concentration are listed in Fig. S1 andS2, respectively.
Approximately 5 μg of DNA was added to Quick-Seal polypropylene tubes (13 × 51 mm, 5.1 mL; Beckman Coulter, Pasadena, CA, USA) and mixed with Tris-EDTA (TE; pH 8.0)/CsCl solution at a final buoyant density (BD) of ~1.77 g/mL. The BD was determined using a digital refractometer (model AR200; Leica Microsystems Inc., Buffalo Grove, IL, USA) and adjusted using CsCl solution or Tris-EDTA buffer. After balancing and sealing, the tubes were transferred to an ultracentrifuge (Optima L-100XP; Beckman Coulter) at 45,000 g (20°C) for 48 h.
After centrifugation, DNA was collected from each 400-μL fraction using a fraction recovery system (Beckman Coulter). The BD of each fraction was then measured, and the DNA fractions were purified following a published method (Song et al. 2015) . The relationships between BD and the fraction number or DNA concentration are listed in Fig. S1 andS2, respectively.
8
Isopycnic Ultracentrifugation of PAH-Amended DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
On Day 3, 9 and 14, samples amend with 13 C labeled and unlabeled PAHs (ANT, PHE and FLA) were sacrificed for DNA extraction. Total genomic DNA was extracted using a MoBio power soil DNA isolation kit (MO BIO Laboratories, Inc.
Carlsbad, CA) according to the manufacturer's instruction. DNA concentrations were determined using an ND-2000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE). Then DNA was prepared as previously for isopycnic ultracentrifugation and gradient fractionation [32, 33] . Briefly, approximately 10,000-ng DNA was added to Quick-Seal polyallomer tubes (13×51 mm, 5.1 ml, Beckman Coulter), along with a Tris-EDTA (TE, pH 8.0)/CsCl solution with a final buoyant density of ∼1.77 g mL -1 . After sealed with a cordless quick-seal tube topper, the tubes were transferred to a Beckman ultracentrifuge and centrifuged at 178,000 × g (20°C) for 48 h. Following centrifugation, 150-μL fractions were collected from each tube using a fraction recovery system (Beckman). The BD value of each fraction was then measured. CsCl was removed by glycogen-assisted ethanol precipitation [35] .
Carlsbad, CA) according to the manufacturer's instruction. DNA concentrations were determined using an ND-2000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE). Then DNA was prepared as previously for isopycnic ultracentrifugation and gradient fractionation [32, 33] . Briefly, approximately 10,000-ng DNA was added to Quick-Seal polyallomer tubes (13×51 mm, 5.1 ml, Beckman Coulter), along with a Tris-EDTA (TE, pH 8.0)/CsCl solution with a final buoyant density of ∼1.77 g mL -1 . After sealed with a cordless quick-seal tube topper, the tubes were transferred to a Beckman ultracentrifuge and centrifuged at 178,000 × g (20°C) for 48 h. Following centrifugation, 150-μL fractions were collected from each tube using a fraction recovery system (Beckman). The BD value of each fraction was then measured. CsCl was removed by glycogen-assisted ethanol precipitation [35] .
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!