Notes: These authors used DNA typing to identify human skeletal remains found in mass graves. DNA was isolated using standard phenol/chloroform extraction, the DNA IQ™ System or other methods. A modified DNA IQ™ System protocol was developed using 2g of pulverized bone. DNA was quantitated using the AluQuant^® Human DNA Quantitation System or Quanti-Blot™ Human DNA quantitation kit. DNA typing was performed using several STR amplification kits, including the PowerPlex^® 16 System. In some cases mitochondrial DNA testing was necessary due to the degree of nuclear DNA degradation. Of the 481 samples, 385 were amplified successfully and 109 sets of remains were identified. (3640)

Notes: The authors identified a gene, trkA, in Vibrio vulnificus that is responsible for serum resistance and characterized this gene by genetic analysis. Total RNA was isolated from wild-type V. vulnificus CKM-1 using the SV Total RNA Isolation System. Subsequently, 0.1 µg RNA was used in a two-step RT-PCR to amplify three regions of interest both in trkA and downstream of trkA. The products were analyzed on a 2% agarose gel stained with ethidium bromide. (3072)

Notes: The authors of this article describe using the SV 96 Total RNA Isolation System on the Beckman-Coulter BioMek^® FX automated laboratory instrument to purify total RNA from 96 separate 2 x 10⁵ HUVEC cell cultures. To demonstrate the quality and consistency of RNA yield, the isolated RNA was reverse transcribed and used in real-time PCR.  (3090)

Notes: These authors used a new DNA purification method that combines cetyltrimethylammonium bromide (CTAB) and isoamyl alcohol/chloroform extraction to isolate DNA from bones soaked in water, burned bones, or bones that had been buried for a long time. Following the CTAB and isoamyl alcohol/chloroform extraction, PCR inhibitors were removed using the DNA IQ™ System or the QIAquick PCR Purification Kit. The authors preferred the DNA IQ™ System because of its speed and ease-of-use. (3642)

Notes: Researchers used the Wizard^® Genomic DNA Purification Kit to isolate genomic DNA from non-Agrobacterium field bacteria samples. The isolated genomic DNA was used in PCR to amplify regions of the 16S rRNA gene. The PCR products were cleaned up using the Wizard^® SV Gel and PCR Clean-Up System and used in sequencing reactions. The paper also mentions the use of the Wizard^® Magnetic DNA Purification System for Food to isolate Agrobacterium radiobacter from cucumber root mats grown in the lab. (3190)

Notes: The authors generated population data for 244–546 unrelated individuals from Antioquia in Columbia. DNA was extracted from whole blood samples using a salting out protocol, then amplified as directed by the manufacturer. Amplified fragments were detected using the ABI PRISM^® 310 Genetic Analyzer. (3857)

Notes: GoTaq^® DNA Polymerase was used in PCR amplifications to genotype zfarnt2 -/- zebrafish mutants with a specific set of primers. The zfarnt2 gene encodes a receptor that is important for mediating chemical toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in zebrafish. (3192)

Notes: In this study, GoTaq^® DNA Polymerase was used to PCR amplify a region of the Disrupted-in-Schizophrenia-1 (DISC1) gene from patient samples. Specific primers were used in the amplification reactions to test for polymorphisms in the region. (3128)

Notes: Researchers used GoTaq^® DNA polymerase to amplify 139bp and 815bp regions of hOST-PTP cDNA for detection and probe synthesis. The full-length 4006bp cDNA was amplified with Pfu DNA Polymerase. Fragments were gel purified using the Wizard^® SV Gel and PCR Clean-Up System prior to cloning into the pGEM^®-T Easy Vector.  The Prime-a-Gene^® Labeling System was used to make ³²P-dCTP labeled probes, which were used to screen cDNA clones. (3111)

Notes: The Wizard^® Genomic DNA Purification Kit was used to purify genomic DNA from Burkholderia thailandensis and Burkholderia pseudomallei.  The genomic DNA was used in PCR to amplify the arabinose assimilation operon.  (3104)

Notes: Two genes (CzcR and CzcS) encoding the CzcCBA (cobalt/zinc/cadmium) heavy metal efflux pump were cloned using  Pfu DNA Polymerase and genomic DNA from PT5 and PT1105 strains of Pseudomonas aeruginosa. The products were 900 and 1,600 bp, respectively. RNA from 5 different strains of Pseudomonas aeruginosa was isolated and treated with RQ1 RNase-Free DNase.  The RNA was used in reverse transcription reactions with the ImProm-II™ Reverse Transcriptase and random primers.  Copy-DNAs produced from the reaction were stored at -20°C until use in real-time PCR.  (3044)

Notes: cDNA was synthesized from 5μg total RNA from patient skin fibroblasts using the specific ALG1 β1,4 mannosyltransferase primer in the presence of 5% DMSO and 1 unit of ImProm-II™ Reverse Transcriptase. Reverse transcription reactions were performed at 42°C for one hour.  PCR amplification of the cDNA produced ~1,200bp amplimers.  (3180)

Notes: Using the SV Total RNA Isolation System before RT-PCR, expression levels of AtGGT-IB were compared in flowers, leaves, stems, and root tissues of wildtype and era1-2 Arabidopsis plants. First-strand synthesis was performed with M-MLV Reverse Transcriptase using 500ng of RNA and an equal amount of oligo(dT). A 1:10 dilution of this product was used for amplification. (2855)

Notes: This paper describes the use of RQ1 RNase-Free DNase to remove DNA from TRIZOL- purified total RNA. The researchers describe stopping RQ1 RNase-Free DNase reactions with RQ1 RNase-Free DNase Stop Solution and heating the reactions at 64°C before using the samples in RT-PCR.  (3187)

Notes: DNA was purified from blood stains and buccal swabs with DNA IQ™ System and two other comparative methods. A high throughput AluQuant^® assay on the BioMek^® 2000 was compared to a quantiblot method for quantifying human genomic DNA. DNA samples extracted with the DNA IQ™ System had less variability than the quantiblot method. The AluQuant^® System showed a similar level of sensitivity, reproducibility and precision compared to the quantiblot method.  (3007)

Notes: MCF-7 cells were incubated for 24 hours in PRF-SFM and then detached and plated on uncoated dishes or dishes coated with 2μg/cm² poly-L-Lysine (P-Lys) in PBS, 30μg/ml fibronectin (Fn) in PBS or 30μg/ml type IV Collagen (Col) in 10mM acetic acid. The cells plated on uncoated dishes were treated both with and without 10nM estradiol (E2). After 24 hours, total cellular RNA was extracted and reverse transcribed using M-MLV reverse transcriptase. Briefly, reverse transcription was performed on 1μg of total RNA in a final volume of 10μl by incubation at 37°C for 30 min with 200U of M-MLV reverse transcriptase, 0.4μg oligo-dT, 0.5μM dNTP and 24U RNasin^® Ribonuclease Inhibitor, followed by heat denaturation for 5 minutes at 95°C. Subsequent PCR analysis was performed on 1μl of the RT product in a final volume of 25μl. Primers were used to amplify the 210bp fragment of PS2 and the 304 bp fragment of cathepsin D. Amplification of 408bp of ribosomal RNA 36B4 was performed as control. The PCR mixture consisted of 1.25U GoTaq^® DNA Polymerase, 1X PCR buffer (10mM Tris-HCl, 50mM KCl), 2.5mM MgCl₂, 0.2mM each dNTP, 0.6μM of each PS2 primer or cathepsin D primer and 0.2μM of each 36B4 primer. PCR was performed for 20 cycles at 95°C for 1 minute, 59°C for 2 minutes and 72°C for 1 minute. Ten microliters of the PCR products were separated on a 1.2% agarose gel. (3377)

Notes: The Wizard^® Genomic DNA Purification Kit was used to purify genomic DNA from Yersinia pestis Kimberley53 strain.  The isolated genomic DNA was digested with restriction endonucleases and then used in PCR amplifications. The amplified products were sequenced to verify the presence of a transposon insertion site.  (3103)

Notes: The researchers used pGEM®-T Easy Vectors (Cat.# A1360) to clone Zika virus PCR products. (4651)

Notes: GoTaq^® DNA Polymerase was used to amplify a portion of Human Papillomavirus 16 (HPV 16) from cervical carcinoma-derived genomic DNA. The amplified region of HPV 16 was then purified and used in sequencing reactions. (3358)

Notes: The AccessQuick™ RT-PCR System was used to analyze mRNA expression of Hypoxia Inducible Factor-1α (HIF-1α) in HCT116 cells. RT-PCR was performed using 0.5μg of Trizol-isolated total RNA and HIF-1α specific primers. (3060)

Notes: GoTaq^® DNA Polymerase was used to amplify Green Fluorescent Protein and β-actin cDNA. This paper describes use of a “Touchdown” PCR procedure for amplification of the β-actin cDNA. Gels are presented displaying the amplification products from the reporter constructs and cells used in the experiments. (3129)

Notes: The authors used real-time quantitative PCR to characterize cytokine response after HIV infection of human lymphoid tissues. To synthesize first-strand cDNA, total RNA was reverse transcribed using the ImProm-II™ Reverse Transcription System: 200U of ImProm-II Reverse Transcriptase, 2µg of total RNA, 500ng of oligo(dT) primer, 500µM dNTPs 3mM MgCl₂ and 24U of RNase inhibitor in 1x ImProm-II™ reaction buffer. To obtain viral stocks for infection, 293T cells were transfected with the proviral plasmids pNL4-3 and pYU-2 using the ProFection^® Mammalian Transfection System—Calcium Phosphate. (3455)

Notes: A fusion protein construct was made using the Monster Green™ Fluorescent Protein phMGFP Vector and the PCR-amplified Open Reading Frame E (ORF-E) from Bovine herpesvirus 1. The construct was transfected into mouse neuroblastoma (Neuro-2A) cells (ATCC CCL131), human neuroblastoma (SK-N-SH) cells, rabbit skin cells and bovine kidney cells. Transfected cells were visualized using an Olympus FW500/BX60 confocal microscope with 488nm excitation laser and 522nm emission filter set. The ORF-E-MGFP protein was localized in discreet domains within the nucleus of Neuro-2A and SK-N-SH cells. In rabbit skin cells and bovine kidney cells the ORF-E-MGFP protein was detected in the cytoplasm and nucleus. (3029)

Notes: The SV 96 Total RNA Isolation System was use to purify total RNA from stably transfected MCF-7 cell clones expressing deletion mutants of SEL1L, a protein implicated in breast tumor formation. One microgram of total RNA purified with the SV 96 Total RNA Isolation System was then used in RT-PCR. (2846)

Notes: The authors identified a TERMINAL FLOWER homolog, CsTFL, in Washington navel oranges (Citrus sinensis) and investigated its role and the role of other genes in juvenility and flower production. The CsTFL gene was amplified from genomic DNA using PCR and degenerate primers, and amplification products were cloned into the pGEM^®-T Easy Vector. The resulting clones were sequenced using the fmol^® DNA Cycle Sequencing System. The CsTFL cDNA was amplified by RT-PCR, using 4 µg of total RNA from whole flowers and ImProm-II™ Reverse Transcriptase. The amplified cDNA was then cloned into the pGEM^®-T Easy Vector. To evaluate CsTFL gene copy number and allele origins, the authors performed a Southern blot with 10 µg of genomic DNA and a CsTFL probe labeled with the Prime-a-Gene^® Labeling System. To characterize CsTFL expression in various citrus tissues, RT-PCR was performed with 2 µg of total RNA and ImProm-II™ Reverse Transcriptase. The levels of CsTFL RNA and other RNAs were determined by cDNA synthesis using ImProm-II™ Reverse Transcriptase, followed by real-time PCR. Amplification products were quantitated by SYBR^® Green fluorescence. Standard curves for each real-time PCR target were generated using known amounts of in vitro transcribed RNA. Prior to reverse transcription and real-time PCR, total RNA samples were treated with RQ1 RNase-Free DNase to remove DNA contaminants. (3650)