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J. Biol. Chem. 278, 1784-1793. Alternate activation of two divergently transcribed mouse genes from a bidirectional promoter is linked to changes in histone modification. 2003

Schuettengruber, B., Doetzlhofer, A., Kroboth, K., Wintersberger, E. and Seiser, C.

Notes: The acetylation status of histones was explored as an indicator of functional gene expression. The acetylation status of core histones H3 and H4 were assessed in treated and untreated cells by crosslinking chromatin, immunoprecipitating the chromatin with acetyl-H3 and acetyl-H4 specific antibodies. The crosslinking was reversed and the immunoprecipitated were phenol chloroform extracted then amplified for the mouse histone H4 gene. Amplifications were also set up with untreated genomic DNA to insure the amplification was within the linear range and to supply standards for gel-based quantitation.  All amplifications were performed with the PCR Master Mix. (2611)

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Reprod. Biol. Endocrinol. 1, epublished. Analysis and characterization of differential gene expression during rapid trophoblastic elongation in the pig using suppression subtractive hybridization. 2003

Ross, J.W., Ashworth, M.D., Hurst, A.G., Malayer, J.R. and Geisert, R.D.

Notes: The Wizard® SV 96 Plasmid DNA Purification System was used to purify random subtractive PCR clones from DH5α cells.  The subtractive PCR clones were made from porcine spherical and tubular conceptuses.  Purified clones were denatured and screened with a DIG High Prime DNA Labeling and Detection Starter Kit (Roche Applied Science). (2748)

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J. Biol. Chem. 278 (39), 37937–37947. Cellular prostaglandin E2 production by membrane-bound prostaglandin E synthase-2 via both cyclooxygenases-1 and -2. 2003

Murakami, M., Nakashima, K., Kamei, D., Masuda, S., Ishikawa, Y., Ishii, T., Ohmiya, Y., Watanabe, K. and Kudo, I.

Notes: The Wizard® SV Gel and PCR Clean-Up System was used to purify a mutant ~870bp prostaglandin E synthase (PGES) PCR product. The purified fragment was then subcloned into the pLenti6/V4-D-TOPO vector and sequenced. (2749)

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Proc. Natl. Acad. Sci. USA 100, 9422-9427. Cloning and characterization of the Drosophila U7 small nuclear RNA. 2003

Dominski, Z., Yang, X.C., Purdy, M. and Marzluff, W.F.

Notes: Improm-II™ Reverse Transcriptase was used to clone U7T snRNA isolated from Drosophila nuclear extracts. The authors used 1ng of extracted U7T snRNA, 30ng of a U7T primer, and 1μl of the Improm-II™ Reverse Transcriptase. cDNAs from the reaction were PCR-amplified and cloned. The resultant clones were used to make probes for Northern blot analysis. (2723)

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J. Clin. Microbiol. 41, 2440-2443. Comparison of commercial DNA extraction kits for extraction of bacterial genomic DNA from whole-blood samples. 2003

Smith, K., Diggle, M.A., and Clarke, S.C.

Notes: The authors of this paper describe testing and comparing five genomic DNA purification kits for their ability to isolate bacterial DNA from Neisseria meningitidis-, Streptococcus pneumoniae-, and Haemophilus influenzae-inoculated whole blood samples. The Wizard® SV 96 Genomic DNA Purification System was considered to be the best kit for its ease of use and ability to be automated on a Roboseq 4200 PE liquid-handling robot. The Wizard® SV 96 Genomic DNA Purification System produced good yields of high quality DNA that displayed sensitivity levels down to 2 genome copies when used as template in fluorescence-based PCR  (3209)

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Antimicrob. Agents Chemother. 47, 27–33. Contributions of MexAB-OprM and an EmrE homolog to intrinsic resistance of Pseudomonas aeruginosa to aminoglycosides and dyes 2003

Li X-Z., Poole K. and Nikaido H.

Notes: The authors examined the putative Pseudomonas aeruginosa homolog to the E. coli small multidrug resistance gene EmrE and its possible role in P. aeruginosa intrinsic drug resistance. Total RNA was isolated from 1-2ml log-phase or overnight stationary-phase P. aeruginosa PAO1 cultures grown in LB using the SV Total RNA Isolation System. After treating the RNA with DNase, 0.1µg RNA was used in the Access RT-PCR System to measure emrEPae expression and the constitutive rpsL gene. The two amplification products were then analyzed on a 1.7% agarose gel. (3074)

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Infect. Immun. 71, 3914–3919. Detection of a luxS-signaling molecule in Bacillus anthracis. 2003

Jones M.B. and Blaser, M.J.

Notes: The Wizard® Genomic DNA Purification Kit was used to purify Bacillus anthracis chromosomal DNA, which was then used in PCR to amplify a luxN ortholog (named open reading frame BA5047). Amplified DNA containing the luxN ortholog region was then cloned into the pGEM®-T Easy Vector. This construct, when transformed into Vibrio harveyi (AI-1-, and AI-2+), allowed the detection of an upregulated signaling system by a bioluminescent assay. (3092)

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Infect. Immun. 71, 3971–8. Development of DNA vaccines against hemolytic-uremic syndrome in a murine model. 2003

Capozzo, A.V.E., Creydt, V.P., Dran, G., Fernández, G., Gómez, S., Bentancor, L.V., Rubel, C., Ibarra, C., Isturiz, M. and Palermo, M.S.

Notes: Researchers used the pGEM®-T Vector System to clone the entire 1.4kb Shiga toxin type 2 gene (Stx2) from E. coli O157-H7 C600 (933W). The resultant construct, named pGEMTStx2, was used as a template in PCR to amplify each region of the gene corresponding to Shiga toxin type 2 subunits A and B. Each PCR product was digested with BamHI and EcoRI before ligation into pCDNA 3.1+ (Invitrogen) to create pStx2ΔA and pStx2B. Mice were then immunized with either one or both of these constructs and another construct expressing murine granulocyte-macrophage colony-stimulating factor. Expression of each subunit in mouse tissue was verified by RT-PCR with specific primers and the AccessQuick™ RT-PCR System. (2701)

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J. Biol. Chem. 278(34), 31895-31901. Down-regulation of hypoxia-inducible factor-2 in PC12 cells by nerve growth factor stimulation. 2003

Naranjo-Suárez, S., Carmen Castellanos, M., Alvarez-Tejado, M., Vara,A., Landázuri, M.O. and del Peso, L.

Notes: In this paper, the authors describe use of ImProm-II™ Reverse Transcriptase to transcribe cDNAs for Quantitative RT-PCR. Reverse transcription (RT) reactions were performed with 1μg total RNA from treated rat PC12 cells. Light Cycler reactions were setup with 1-3μl cDNA from the RT reactions. The researchers incubated cells with EGF and bFGF and analyzed HIF-2α mRNA levels. For these experiments, PC12 cells were incubated with 30ng/ml EGF or 50μM bFGF for 8 hours. Erk1&2 phosphorylation was examined by Western blot using the Anti-ACTIVE® MAPK pAb. Western results were visualized by chemiluminesent detection and analyzed with a digital luminescent image analyzer. The Dual-Luciferase® Reporter Assay System was used to analyze PC12 cell-expressed luciferase from pEpoEm1-luc and pEpoE-luc promoter constructs that were normalized with the pRL-TK vector. Cells were harvested 17-18 hours post transfection and treatment. (2725)

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Gene 315, 43–50. Endonuclease genes up-regulated in tissues undergoing programmed cell death are expressed during male gametogenesis in barley. 2003

Zainaa, G., Morassuttia, C., De Amicisa, F., Fogherb, C., and Marchettia, S.

Notes: Total RNA was isolated from immature barley anthers with the RNAgents® Total RNA Isolation System. Total RNA concentration was determined by spectrophotometric analysis. Next, the authors used the PolyATtract® mRNA Isolation System to isolate poly (A)+ RNA from the total RNA samples. The purified poly (A)+ RNA was used as a template in RT-PCR using the Access RT-PCR System to analyze expression of BEN1 and Bnuc1. (2847)

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Biochem. Biophys. Res. Commun. 306, 756–766. Establishment of a hepatitis C virus subgenomic replicon derived from human hepatocytes infected in vitro. 2003

Kato, N., Sugiyama, K., Namba, K., Dansako, H., Nakamura, T., Takami, M., Naka, K., Nozaki, A. and Shimotohnoe, K.

Notes: In this study, the Wizard® SV Genomic DNA Purification System was used to purify genomic DNA from Hepatitis C (HCV)-infected PH5CH8 hepatic cells. The purified genomic DNA was used in PCR to detect HCV-infected cells.  (3016)

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Int. Congr. Ser. 1239, 673–6. Evaluation of “in house” criteria for PCR-based analysis in immigration casework. 2003

van Eede, P.H., Keller, S. and de Lange, G.G.

Notes: The authors evaluated criteria for using STR analysis to resolve immigration cases by examining 156 one-parent child combinations and 105 two-parent child combinations from 28 families. STR analyses were performed in duplicate using the SMG Plus® kit and a combination of CTTv and FFFL Multiplexes. The authors concluded that the combination of these kits, which analyze a total of 21 STR loci, can be used to successfully resolve immigration casework. However, in 9% of the one-parent cases their criteria of a parental index of 1.000 or more was not met. Additional testing using the PowerPlex® 16 System reduced this from 9% to 1 out of 156 indices. (3858)

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Toxicol. Sci. 73, 423-430. Expression and activity of cytochromes P450 2E1, 2A, and 2B in the mouse ovary: The effect of 4-vinylcyclohexene and its diepoxide metabolite. 2003

Cannady, E.A., Dyer, C.A., Christian, P.J., Sipes, I.G. and Hoyer, P.B.

Notes: These authors characterized cytochrome P450 expression in mouse ovaries treated with the ovotoxin 4-vinylcyclohexene. Total mouse ovary RNA was reverse transcribed using the Reverse Transcription System and random primers, followed by quantitative PCR using primers specific for CYP2E1, 2A and 2B. (3442)

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Clin. Can. Res. 9, 3052-3057. Expression and functional analyses of breast cancer resistance protein in lung cancer 2003

Kawabata, S., Oka, M., Soda, H., Shiozawa, K., Nakatomi, K., Tsurutani, J., Nakamura, Y., Doi, S., Kitazaki, T., Sugahara, K., Yamada, Y., Kamihira, S., Kohno, S.

Notes: Total RNA was obtained from non-small cell lung cancer cell lines and the breast cancer resistance protein message was amplified using real-time quantitative RT-PCR. RT-PCR products were subcloned into the pGEM®-T Easy Vector. (2714)

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Biochem. J. 373, 815–824. Extracellular ATP stimulates the early growth response protein 1 (Egr-1) via a protein kinase C-dependent pathway in the human osteoblastic HOBIT cell line. 2003

Pines, A., Romanello, M., Cestratto, L., Moro, G.L., D’Andrea, P., and Tell, G.

Notes: In this paper, the SV Total RNA Isolation System was used to isolate total RNA from human osteoblast HOBIT cells. One microgram of the purified DNA was used in RT-PCR with a 20mer oligo(dT) and gene-specific primers. (2850)

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Clin. Can. Res. 9, 1057-1062. Genomic instability and tumor-specific alterations in oral squamous cell carcinomas assessed by inter-(simple sequence repeat) PCR 2003

Viswanathan, M., Sangiliyandi, G., Vinod, S.S., Mohanprasad, B.K.C., Shanmugam, G.

Notes: The authors used ISSR PCR to quantitate genomic instability using matched tumor (OSCC) and normal oral squamous cell samples. The inter-repeat region bands of similar molecular size that were altered in more than one case of OSCC were reamplified, gel purified and cloned into the pGEM T Vector for sequencing. (2635)

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J. Biol. Chem. 278 (14), 11985-11994. Genomic organization and evolution of the CX3CR1/CCR8 chemokine receptor locus. 2003

DeVries, M.E., Cao, H., Wang, J., Xu, L., Kelvin, A.A., Ran, L., Chau, L.A., Madrenas, J., Hegele, R.A., and Kelvin, D.J.

Notes: Researchers performed a 5´ RACE analysis on the human CCR8 and mouse CX3CR1 transcripts.  PCR-amplified products from the reactions were cloned in to the pGEM®-T Vector for further analysis.  Also, the human CCR8 and mouse CX3CR1 promoters were cloned into the pGL3-Basic Vector and transfected into THP1 and Jurkat cells. For transfections, 15 x 106 cells in 750μl were used with 15μg of construct in electroporation reactions. Transfectants were grown for 48 hours and analyzed with the Bright-Glo™ Luciferase Assay System. A fourfold increase in activity was observed compared to the pGL3-Basic Vector alone. (2729)

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Biochem. Biophys. Res. Commun. 309, 222–231. Hypoxia induces apoptosis in SV40-immortalized rat proximal tubular cells through the mitochondrial pathways, devoid of HIF1-mediated upregulation of Bax. 2003

Tanaka, T., Hanafusa, N., Ingelfinger, J.R., Ohse, T., Fujita, T., and Nangaku, M.

Notes: ImProm-II™ Reverse Transcriptase was used in real time RT-PCR to measure the ratio of Bax to Bcl-2 in immortalized rat proximal tubular cells (IRPTCs) cultured under normoxic or hypoxic conditions. The researchers used 1μg of total RNA in the reverse transcription reaction. Qiagen’s QuantiTest CYBR Green PCT Kit was used to quantify PCR products. Promega’s terminal deoxynucleotidyl transferase (TdT) was also used for TdT-mediated dUTP nick end labeling (TUNEL) assays on the cells. The TUNEL-stained cells were analyzed by FACS analysis. Data from these experiments was expressed as percent apoptotic cells.  (2849)

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Biochem. J. 371, 443-449. Identification by site-directed mutagenesis of amino acids contributing to ligand-binding specificity or signal transduction properties of the human FP prostanoid receptor. 2003

Neuschäfer-Rube, F., Engemaier, E., Koch, S., Böer U., and Püschel, G.P.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from human placenta. The total RNA was used in RT-PCR to specifically amplify human FP prostanoid receptor 1 cDNAs. The amplified cDNAs were cloned and used in mutagenesis studies. (2852)

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J. Biol. Chem. 278, 28799–28811. Identification of a novel Kruppel-associated box domain protein, Krim-1, that interacts with c-Myc and inhibits its oncogenic activity. 2003

Hennemann, H., Vassen, L., Geisen, C., Eilers, M. and Moroy, T.

Notes: Researchers used M-MLV Reverse Transcriptase, RNase H Minus, Point Mutant, and random hexamers to reverse transcribe total RNA from various rat tissues. The cDNA was then used in real-time PCR reactions with SYBR Green dye and primers specific to Krim-1 or GAPDH sequences.  For reverse transcription, 200 units of M-MLV were used in each 25μl reaction.  Data from real-time PCR was normalized to GAPDH levels and expressed as relative expression levels in various tissues.  (2792)

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J. Clin. Microbiol. 41, 3481–3486. Identification of Streptococcus sanguinis with a PCR-generated species-specific DNA probe. 2003

Li, Y., Pan, Y., Qi, F., and Caufield, P.W.

Notes: The Wizard® Genomic DNA Purification Kit was used to purify genomic DNA from various Streptococcal strains (Streptococcus sanguinis, S. oralis, S. gordonii, S. cristatus, S. mitis, S. parasanguinis, S. pneumoniae, S. mutans, S. salivarius, S. sobrinus, S. ratti, and S. vestibularis), Lactobacillus acidophilus, Actinomyces naeslundii, and E. coli JM109. The genomic DNA was diluted to 50μg/ml and used in Arbitrarily Primed PCR (AP-PCR) experiments to identify common amplimers from clinical Streptococcus sanguinis samples. The authors were able to identify a specific probe that may be helpful in identification of  S. sanguinis clinical isolates. (2836)

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Genes Dev. 17, 1253-1270. In vitro propagation and transcriptional profiling of human mammary stem/progenitor cells. 2003

Dontu, G., Abdallah, W.M., Foley, J.M., Jackson, K.W., Clarke, M.F., Kawamura, M.J. and Wicha, M.S.

Notes: The Wizard® SV Genomic DNA Purification System was used to purify DNA from cultured mammospheres. The mammosphere genomic DNA samples were then used in PCR reactions to amplify Short Tandem Repeats for genetic analysis. (2683)

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J. Bacteriol. 185(17), 5290-5294. Inactivation of ompR promotes precocious swarming and flhDC expression in Xenorhabdus nematophila. 2003

Kim, D.J., Boylan, B., George, N. and Forst, S.

Notes: The swarming behavior of the symbiotic-pathogenic bacterium Xenorhabdus nematophila is examined in this work. To investigate changes in gene expression in different strains at various times, the researchers utilized the AccessQuick™ RT-PCR System to measure the relative amount of gene product. To ensure that the assay was linear, different cycle numbers were used for each gene target ranging from 15 to 21 cycles of amplification. The RT-PCR used approximately 600ng of total RNA that was treated with RQ1 RNase-Free DNase before use.  (2745)

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Nat. Biotechnol. 21(10), 1233-1237. Large-scale genotyping of complex DNA. 2003

Kennedy, G.C., Matsuzaki, H., Dong, S., Liu, W.M., Huang, J., Liu, G., Su, X., Cao, M., Chen, W., Zhang, J., Liu, W., Yang, G., Di, X., Ryder, T., He, Z., Surti, U., Phillips, M.S., Boyce-Jacino, M.T., Fodor, S.P. and Jones, K.W.

Notes: Terminal Deoxynucleotidyl Transferase was used to biotin end-label PCR products generated from adaptor-ligated genomic DNA fragment templates. The labeled probes were then hybridized to microarrays spotted with SNP alleles. The Terminal Deoxynucleotidyl Transferase reaction was performed for 4 hours at 37°C using 15-20 units TdT, TdT reaction buffer and 18μM biotin-ddATP. (2758)

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J. Clin. Microbiol. 41, 4537-4541. Madurella mycetomatis Strains from Mycetoma Lesions in Sudanese Patients Are Clonal. 2003

Ahmed, A., van de Sande, W., Verbrugh, H., Fahal, A., and van Belkum, A.

Notes: Genomic DNA was isolated from Madurella mycetomatis samples.  A modified  Wizard® Genomic DNA Purification Kit protocol was used for the isolations.  Mycelia were sonicated and ground in liquid nitrogen before the addition of Nuclei Lysis Solution. The purified DNA was used in PCR.  (3049)

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