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Appl. Environ. Microbiol. 76, 3590–9. Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy. 2010

Nishino, S.F., Shin, K.A., Payne, R.B. and Spain, J.C.

Notes: The authors identified a bacterial strain that can use the toxin 3-nitropropionic acid (3NPA) as its sole carbon and nitrogen sources and cloned the genes that encode the enzymes responsible for the initial steps in the 3NPA degradation pathway. The Pseudomonas library used to clone these genes was created using genomic DNA isolated using the Wizard® SV Genomic DNA Purification System. Closely related genes were amplified from other bacterial species for phylogenetic analysis. PCRs were performed using the GoTaq® Hot Start Polymerase. (4164)

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Genetics 182, 133–144. A proximal centriole-like structure is present in Drosophila spermatids and can serve as a model to study centriole duplication. 2009

Blachon, S., Cai, X., Roberts, K.A., Yang, K., Polyanovsky, A., Church, A. and Avidor-Reiss, T.

Notes: These authors studied the formation of centrioles in Drosophila spermatids. Genomic DNA was extracted from whole flies using the Wizard® SV Genomic DNA Purification System. The DNA was then subjected to PCR, purified and sequenced. RNA was purified from whole flies using the SV Total RNA Isolation System. After RNA extraction, the samples were used in RT-PCR. (4064)

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Drug Metab. Dispos. 37, 1726–1732. Characterizing the effects of common UDP glucuronosyltransferase (UGT) 1A6 and UGT1A1 polymorphisms on cis- and trans-resveratrol glucuronidation. 2009

Iwuchukwu, O.F., Ajetunmobi, J., Ung, D. and Nagar, S.

Notes: This study examined the genotype-phenotype correlation of the two major UGT isoforms, UGT1A1 and UGT1A6, involved in resveratrol metabolism. Genomic DNA was isolated from 30mg human liver tissue samples (normal and metastatic) using the Wizard® SV Genomic DNA Purification System. The purified DNA was eluted with 65°C water and 200–400ng of eluted DNA was used in a PCR-RFLP UGT1A6 genotyping assay. Amplification was carried out using PCR Master Mix in a final volume of 50µl, and the amplimers digested with appropriate restriction enzymes. (4018)

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J. Nutr. 139, 1054–1060. Folic acid supplementation during the juvenile-pubertal period in rats modifies the phenotype and epigenotype induced by prenatal nutrition. 2009

Burdge, G.C., Lillycrop, K.A., Phillips, E.S., Slater-Jefferies, J.L., Jackson, A.A. and Hanson, M.A.

Notes: This study examined the effects of folic acid supplementation on the offspring of pregnant rats fed a protein-restricted diet. Genomic DNA was extracted from rat adipose tissue using the Wizard® SV Genomic DNA Purification System. The purified DNA was then incubated with methylation-sensitive restriction enzymes and then used in real-time PCR. (4066)

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Nucl. Acids Res. 37, 5343–5352. Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. 2009

Oberto, J., Breuil, N., Hecker, A., Farina, F., Brochier-Armanet, C., Culetto, E. and Forterre, P.

Notes: In this paper, the role of the KAE1/osgep/ygjD gene family, a universally conserved gene set without an assigned function, was investigated in yeast and Caenorhabditis elegans. Genomic DNA was isolated from Saccharomyces cerevisiae using the Wizard® SV Genomic DNA Purification System. This purified DNA was then used in PCR. (4065)

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Proc. Natl. Acad. Sci. USA 105, 18314–18319. Non-DNA-binding platinum anticancer agents: Cytotoxic activities of platinum-phosphato complexes towards human ovarian cancer cells. 2008

Bose, R.N., Maurmann, L., Mishur, R.J., Yasui, L., Gupta, S., Grayburn, W.S., Hofstetter, H. and Salley, T.

Notes: The authors were interested in testing platinum (Pt) anticancer drugs that do not bind to DNA to see how they worked in cisplatin- and carboplatin-resistant cells. The human ovarian cancer cells, A2780 and A2780/C30, were seeded in T75 cm2 flasks with 1.0 × 107 cells. After 24 hours, the cells were treated with 0, 10, 20, 30 and 50µM Pt compounds for 24 hours. Medium was removed, the cells washed, trypsinized and centrifuged. Genomic DNA was isolated using the Wizard® SV Genomic DNA Purification System and quantitated using absorbance at 260nm. This DNA was using in DNA-Pt binding assessment. (4019)

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Proc. Natl. Acad. Sci. USA 105, 12445-12450. Oncogenic bystander radiation effects in Patched heterozygous mouse cerebellum. 2008

Mancuso, M., Pasquali, E., Leonardi, S., Tanori, M., Rebessi, S., Di Majo, V., Pazzaglia, S., Toni, M.P., Pimpinellam M., Covelli, V. and Saran, A.

Notes: To examine radiation-bystander responses in neonatal mouse cerebellum, heterozygous radiosensitive Patched-1 (Ptch1) mice were exposed to either whole body (WB) x-rays or shielded head/rest of body (SH) irradiation. Genomic DNA was isolated from tumors and normal tissue using the Wizard® SV Genomic DNA Purification System. Loss of heterozygosity was tested using PCR and sequencing of exon 23 of the Ptch1 gene. (3940)

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BMC Genomics 9, 315. The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola). 2008

Carapelli, A., Comandi, S., Convey, P., Nardi, F. and Frati, F.

Notes: To sequence the mitochondrial genome one of the most widespread and common collembolan species of Antarctica, springtail Cryptopygus antarcticus. Specimens were collected from Killingbeck I during a 2002 polar expedition and frozen in liquid nitrogen. The Wizard® SV Genomic Purification System was used to extract total DNA from the samples and the complete mitochondrial genome was amplified twice, first with universal primers and sequenced, and then using long PCR with specific primers. The long PCR products were mechanically sheared, blunt end repaired and purified using the Wizard® SV Gel and PCR Clean-Up System. The fragments were then cloned, transformed and sequenced. (3976)

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Am. J. Pathol. 171, 1153-1167. Dissecting the impact of chemotherapy on the human hair follicle: a pragmatic in vitro assay for studying the pathogenesis and potential management of hair follicle dystrophy. 2007

Bodó, E., Tobin, D.J., Kamenisch, Y., Bíró, T., Berneburg, M., Funk, W. and Paus, R.

Notes: To study how chemotherapy affects hair follicles (HF), the researchers microdissected and cultured human anagen VI scalp follicles and treated the cells with 4-Hydroperoxycyclophosphamide (4-HC) at similar concentrations to those received during therapy. After incubation for 24 hours with 30µmol/L of 4-HC, the HFs were homogenized and genomic DNA was purified using the Wizard® SV Genomic DNA Purification System. To determine if the treatment induced the mitochondrial common DNA deletion, the isolated DNA was subjected to real-time PCR. Further examination of gene expression was performed by isolating total RNA from two HF samples, reverse transcribing 3µg of the RNA using 15U of AMV Reverse Transcriptase and 0.025 µg/µl random primers, and amplifying seven human genes in a TaqMan® Assay. (3746)

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Genome Res. 17, 1286-1295. Domain-wide regulation of gene expression in the human genome. 2007

Gierman, H.J., Indemans, M.H., Koster, J., Goetze, S., Seppen, J., Geerts, D., van Driel, R. and Versteeg, R.

Notes: The authors explored the possibility of a domain-based level of gene expression regulation for chromosomes by integrating the green fluorescent protein (GFP) reporter in 90 different locations in cultured human cells. This integration was accomplished by infecting human embryonic kidney cells (HEK293) with a lentiviral construct carrying the GFP gene under the control of the ubiquitously expressed human phosphoglycerate kinase (PGK), sorting GFP-positive cells by FACS and selecting clones for expansion. Genomic DNA was isolated from the various clones using the Wizard® SV Genomic DNA Purification System and analyzed by PCR or restriction digested for Southern blotting. (3743)

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Toxicol. Sci. 89, 314-324. Exposure to diazinon alters in vitro retinogenesis: retinospheroid morphology, development of chicken retinal cell types, and gene expression. 2007

Paraoanu, L.E., Mocko, J.B., Becker-Roeck, M., Smidek-Huhn, J., and Layer, P.G.

Notes: To examine gross changes in DNA content, genomic DNA was isolated from chicken retinospheroid cultures treated with diazinon, an organophosphate pesticide. DNA purified with the Wizard® SV Genomic DNA Purification System was used to determine changes in total DNA content after pesticide exposure. (3586)

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Proc. Natl. Acad. Sci. USA 104, 12796-12800. Metabolic plasticity during mammalian development is directionally dependent on early nutritional status. 2007

Gluckman PD, Lillycrop KA, Vickers MH, Pleasants AB, Phillips ES, Beedle AS, Burdge GC, Hanson MA.

Notes: To examine how exposure to leptin in utero affects hepatic gene expression and epigenetic status in adulthood, pregnant Wistar rats were fed a standard diet or 30% undernutrition. The three-day-old pups were exposed to saline or leptin for 10 days, weaned and either fed a standard or high-fat diet. On day 170, the rats were sacrificed and tissues snap frozen. Five micrograms of genomic DNA was isolated from rat liver using the Wizard® SV Genomic DNA Purification System. Then 25ng of the purified DNA was digested with methylation-sensitive restriction enzymes, and the glucocorticoid receptor (GR) and peroxisome proliferator-activated receptor alpha (PPARα) fragments were amplified by real-time PCR. (3744)

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J. Clin. Microbiol. 45, 651-655. Recurrent disseminated skin lesions due to Metarrhizium anisopliae in an adult patient with acute myelogenous leukemia. 2007

Osorio, S., de la Cámara, R., Monteserin, M.C., Granados, R., Oña, F., Rodriguez-Tudela, J.L. and Cuenca-Estrella, M.

Notes: To identify the infectious organism present in human skin biopsy samples, genomic DNA was isolated using the Wizard® SV Genomic DNA Purification System. Two microliters of purified DNA was amplified and then sequenced for determination of fungal species. (3745)

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Mol. Cancer Ther. 6, 856-865. The glycotope-specific RAV12 monoclonal antibody induces oncosis in vitro and has antitumor activity against gastrointestinal adenocarcinoma tumor xenografts in vivo. 2007

Loo, D., Pryer, N., Young, P., Liang, T., Coberly, S., King, K.L., Kang, K., Roberts, P., Tsao, M., Xu, X., Potts, B. and Mather, J.P.

Notes: The authors examined the effectiveness of a monoclonal antibody treatment to human tumor-derived cells implanted under the kidney capsule of male athymic mice. These tumors were recovered from mouse kidney and the total genomic DNA isolated using the Wizard® SV Genomic DNA Purification System. The human tumor DNA was quantified using a TaqMan® qPCR method. (3748)

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Jpn. J. Clin. Oncol. 36, 351-356. Expression and mutation statuses of epidermal growth factor receptor in thymic epithelial tumors. 2006

Suzuki, E., Sasaki, H., Kawano, O., Endo, K., Haneda, H., Yukiue, H., Kobayashi, Y., Yano, M., and Fujii, Y.

Notes: In this study, genomic DNA was extracted from 99 frozen thymic epithelial tumor samples using the Wizard® SV Genomic DNA Purification System. Purified DNA was used in TaqMan SNP genotyping assays for 13 epidermal growth factor receptor (EGFR) gene mutations. (3585)

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FASEB J. 20, 1131 - 1141. Overexpression of SUR2A generates a cardiac phenotype resistant to ischemia. 2006

Du, Q., Jovanovic, S., Clelland, A., Sukhodub, A., Budas, G., Phelan, K., Murray-Tait, V., Malone, L., and Jovanovic, A.

Notes: To study sarcolemmal ATP-sensitive K+ (KATP) channels, transgenic mice were generated that express SUR2A, the proposed regulatory protein of the complex. Genomic DNA was extracted from mouse ears using the Wizard® SV Genomic DNA Purification System and used for genotyping transgenic animals.
(3584)

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J. Clin. Microbiol. 44, 2750–2759. Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification. 2006

Zucol, F., Ammann, R.A., Berger, C., Aebi, C., Altwegg, M., Niggli, F.K., and Nadal, D.

Notes: A panel of 11 Gram-negative and 11 Gram-positive bacterial species was used to develop a real-time PCR detection method. Initially DNA was purified from 1ml of various dilutions of bacteria resuspended in a saline solution using either the QIAamp DNA blood mini kit or the Wizard® SV Genomic DNA Purification System. The results suggested that the Wizard® SV Genomic DNA Purification System extraction protocol was superior in disrupting the bacterial cell wall (especially of Gram-positive bacteria), to allow release of bacterial DNA. Using DNA purified with the Wizard® SV Genomic DNA Purification System, detection of S. aureus and E. coli at concentrations as low as 101 CFU per PCR was achieved. The Wizard® SV Genomic DNA Purification System purification protocol provided in eNotes online (www.promega.com/enotes/applications/ap0051_tabs.htm) was used with the following modifications: The bacterial pellet was resuspended in 400µl of enzymatic lysis solution (47mM EDTA, 25mg/ml lysozyme, 20µg/ml lysostaphin) and incubated for 2 hours at 37°C. Next, 19.2mg/ml proteinase K was added (final concentration 0.4mg/ml), and the mixture was incubated for 1 hour at 55°C. Finally, the Nuclei Lysis Solution and RNase Solution were added, mixed and incubated for 10 minutes at 80°C. For real-time PCR analysis, 2µl of genomic DNA was used. (3676)

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J. Clin. Invest. 116, 735–742. The latency-associated nuclear antigen of Kaposi sarcoma-associated herpesvirus induces B cell hyperplasia and lymphoma. 2006

Fakhari, F.D., Jeong, J.H., Kanan, Y. and Dittmer, D.P.

Notes: To examine possible Ig gene rearrangement of B-cell neoplasias after Kaposi sarcoma–associated herpesvirus infection, transgenic mice expressing KSHV latency-associated nuclear antigen (LANA) were created. Genomic DNA was isolated from murine spleens using the Wizard® SV Genomic DNA Purification System, and 1.7ng of the purified genomic DNA was used in PCR analysis. (3414)

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Clin. Can. Res. 11, 2924-2929. EGFR Mutation status in Japanese lung cancer patients: genotyping analysis using LightCycler. 2005

Sasaki, H., Endo, K., Konishi, A., Takada, M., Kawahara, M., Iuchi, K., Matsumura, A., Okumura, M., Tanaka, H., Kawaguchi, T., Shimizu, T., Takeuchi, H., Yano, M., Fukai, I., and Fujii, Y.

Notes: To rapidly characterize somatic mutations in the EGF receptor in lung cancer tissues, genomic DNA was extracted from lung biopsies using the Wizard® SV Genomic DNA Purification System. The extracted DNA was used in a LightCycler SNP genotyping assay to determine the genotype of common loci associated with improved patient response to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. (3588)

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Clin. Can. Res. 11, 8699-8705. Methylation of the DPYD promoter: an alternative mechanism for dihydropyrimidine dehydrogenase deficiency in cancer patients. 2005

Ezzeldin, H.H., Lee, A.M., Mattison, L.K., and Diasio, R.B.

Notes: To examine the methylation status of the DPYD promoter, genomic DNA was extracted from an RKO cell line and from peripheral blood mononuclear cells using the Wizard® SV Genomic DNA Purification System. The isolated DNA was treated by sodium bisulfate modification followed by amplification and sequencing, or by DHPLC to determine CpG island methylation state. (3587)

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J. Virol. 78, 9936-9946. Poly(ADP-Ribose) polymerase 1 binds to Kaposi's sarcoma-associated Herpesvirus (KSHV) terminal repeat sequence and modulates KSHV replication in latency. 2005

Ohsaki, E., Ueda, K., Sakakibara, S., Do, E., Yada, K. and Yamanishi, K.

Notes: Three terminal repeat sequences (TR) from Kaposi's sarcoma-associated herpesvirus (KSHV) were PCR amplified and then purified using the Wizard® PCR Preps DNA Purification System. The PCR products were 386, 424, and 307 base pairs in size.  These TR products were used in PARP1-DNA ELISA assays.  The authors also used the Wizard® SV Genomic DNA Purification System to isolate DNA from a BC3 cell line infected with KSHV. The isolated DNA was used in real-time PCR to assess KSHV copy number in cells. (3232)

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J. Virol. 79, 245-256. The Epstein-Barr virus replication protein BBLF2/3 provides an origin-tethering function through interaction with the zinc finger DNA binding protein ZBRK1 and the KAP-1 corepressor. 2005

Liao, G., Huang, J., Fixman, E.D. and Hayward, S.D.

Notes: The Wizard® SV Genomic DNA Purification System was used to purify total DNA from plasmid-electroporated EBV-positive D98-HR1 cells. The isolated DNA was digested by two different restriction enzyme combinations and used in Southern blots to identify electroporated plasmid levels. (3231)

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Int. J. Syst. Evol. Microbiol. 54, 2241-2244. Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine. 2004

Santini, J.M., Streimann, I.C.A. and vanden Hoven, R.N.

Notes: The Wizard® SV Genomic DNA Purification System was used to isolate genomic DNA from a novel arsenate-respiring bacterial strain (JMM-4T). The isolated DNA was used in hybridization studies with B. arseniciselenatis DNA to help characterize the new strain.  (3235)

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J. Immunol. 173, 1240-1248. Schistosoma mansoni worms induce anergy of T cells via selective up-regulation of programmed death ligand 1 on macrophages. 2004

Smith, P., Walsh, C.M., Mangan, N.E., Fallon, R.E., Sayers, J.R., McKenzie, A.N.J. and Fallon, P.G.

Notes: The Wizard® SV Genomic DNA Purification System was used to purify genomic DNA from blood fluke Schistosoma mansoni worm cercariae shed from Biomphalaria glabrata snails. The genomic DNA was used in PCR to type each individual S. mansoni worm in a cercariae. (3230)

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J. Bacteriol. 185, 5815–5821. Role of 2-Phosphoglycolate Phosphatase of Escherichia coli in Metabolism of the 2-Phosphoglycolate Formed in DNA Repair. 2004

Pellicer, M.T., Nunez, M.F., Aguilar, J., Badia, J., and Baldoma, L.

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)

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