Notes: Thrombomodulin (TM) expression was examined by isolating genomic DNA from biopsies of human malignant mesothelioma and normal mesothelial tissue, and cultured cell lines with or without PARP1 silencing treated with 5-aza-2´-deoxycytidine and trichostatin alone or in combination and then subjected to biosulfide modification. To analyze methylation of TM, a CpG island in the promoter, 5´ UTR and an exon region containing 44 CpG dinucleotides were PCR amplified, cloned into the pGEM^®-T Easy Vector, transformed and positive clones selected using IPTG/X-Gal and analyzed by PCR. Colonies were cultured, the plasmids isolated using the Wizard^® Plus SV Minipreps DNA Purification System then 10 clones
from each sample type were sequenced. (4132)

Notes: This study investigated the effect of teichoic acid alanylation on biofilm formation, adhesion, sensitivity to antimicrobial peptides and resistance to neutrophil killing in Enterococcus faecalis. The dlt operon in E. faecalis controls D-alanylation of teichoic acids. A deletion mutant lacking a portion of the dltA gene, which encodes a putative D-alanine activating enzyme, was created. Compared to the wildtype strain, the E. faecalis dltA deletion mutant produced less biofilm, exhibited reduced adhesion to cultured epithelial cells, was more sensitive to various antimicrobial peptides and less sensitive to opsonic killing. Plasmids used during the mutagenesis procedure and for complementation studies were purified from E. coli or Enterococci using the PureYield™ Plasmid Midipreps System or the Wizard^® Plus SV Minipreps System. (3526)

Notes: In the process of demonstrating the role of IN in HIV-1 integration in yeast, the authors purified all DNA vectors and PCR products with the Wizard® Plus SV Miniprep System and Wizard® SV Gel System. PCR products were generated using Taq DNA Polymerase. The pGEM®-T Vector was used to clone amplification products. Sequencing was performed using BamHI, religated with T4 DNA Ligase. (3704)

Notes: To purify stolbur phytoplasma DNA from total DNA of infected periwinkle plants, two rounds of suppression subtractive hybridization (SSH) were performed, followed by amplification with Taq DNA polymerase. The resultant PCR products (1µl) were ligated into 50ng of pGEM^®-T Easy Vector using 3 units T4 DNA Ligase. After transformation of DH10B cells, ampicillin-resistant colonies were grown and the plasmids purified using the Wizard^® Plus SV Minipreps DNA Purification System. The insert lengths were estimated after EcoR I digestion and agarose gel electrophoresis prior to amplification and labeling with digoxigenin. These probes were used for dot hybridization with denatured healthy or infected plant DNA (10µg) and the corresponding plasmid as a positive control (100 ng). (3436)

Notes: The authors demonstrated that transient penicillin-induced cell wall loss in S. aureus mediates high-level resistance to beta-lactam antibiotics and that, following cell wall recovery, the penicillin resistance is inherited in a stable manner. Also, cells that had previously been cell wall defective had a propensity to lose their cell wall on further penicillin exposure. To examine possible alterations in the penicillin-binding proteins, pbp genes were sequenced. The Wizard® Plus SV Minipreps DNA Purification System was used to isolate DNA from liquid cultures after cloning. (3540)

Notes: The authors infected Vero cells with the rickettsial agent, then recovered bacterial DNA from the infected cells using the Wizard^® Plus SV Minipreps DNA Purification System, and amplified this DNA by PCR. (3541)

Notes: The Wizard® SV Genomic DNA Purification System was used to isolate genomic DNA from the E. coli K-12 derivative, MC4100.  The isolated genomic DNA was used as a template to PCR clone the Escherichia coli 2-phosphoglycolate phosphatase (gph) gene.  The PCR plasmid constructs were also purified with the Wizard® Plus SV Minipreps DNA Purification System. (3218)

Notes: These authors performed gel shift (EMSA) assays to determine whether purified VirA binds to the vapA promoter. Radiolabeled DNA fragments for the EMSA assays were prepared using DNA Polymerase I Large (Klenow) Fragment. Primer extension using ImProm-II™ Reverse Transcriptase localized the transcription start site within the vapA promoter. To characterize the transcriptional organization of the virR gene cluster, the authors performed reverse transcription using ImProm-II™ Reverse Transcriptase and Random Primers, followed by PCR using a combinations of primers in opposite orientations throughout the gene cluster. The plasmids used in this study were purified by alkaline lysis method or using the Wizard^® Plus SV Minipreps DNA Purification System.
(3563)

Notes: In this paper, the Wizard^® Plus SV Minipreps DNA Purification System was used to isolate plasmid DNA. (2556)

Notes: This study investigated the effect of aberrant expression of EAAT2 mRNA on expression of the EAAT2 protein in human glioma cells. EAAT2 encodes an excitatory amino acid transporter that helps to clear glutamate from synaptic cleft. In transfection-based studies on human U251 gliomal cells,  transient transfection efficiency was evaluated using a luciferase reporter gene, and luciferase activity was detected with the Luciferase Assay System. In separate experiments, RTPCR products were cloned into plasmid vectors. Plasmid DNAs containing PCR products were isolated from bacteria using the Wizard^® Plus SV Minipreps DNA Purification System. (2607)

Notes: Total RNA was isolated from various rat tissues with the SV Total RNA Isolation System. Yields are reported as 10µg from 16 whole cochlea, 8µg from 16 modiola, 10.4µg from 48 cochlear sensorineural epithelial/lateral walls and 50µg from the substantia nigra region of four brains. The isolated RNA was used for RT-PCR in the presence of RNasin^® Ribonuclease Inhibitor. The resulting amplimer was subcloned into the pGEM^®-T Easy Vector and clones were purified with the Wizard^® Plus SV Minipreps System. (2176)

Notes: The Wizard^® Plus SV Minipreps DNA Purification System was used to prepare plasmid DNA for fluorescent sequencing on an ABI 373 machine. The plasmids were isolated from 10ml cultures in LB media. (0663)

Notes: Authors use the Wizard^® Plus SV Minipreps DNA Purification System to purify plasmid DNA for fluorescent sequencing. (1136)

Notes: The Wizard^® Plus SV Minipreps DNA Purification System was used to prepare plasmid templates for fluorescent sequencing on an ALF system. (0592)

Notes: The authors used the Wizard^® Plus SV Minipreps DNA Purification System to isolate plasmid DNA. (1474)