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Infect. Immun. 70, 1984-1990. Helicobacter pylori uses motility for initial colonization and to attain robust infection. 2002

Ottemann, K.M. and Lowenthal, A.C.

Notes: Genomic DNA was isolated from H. pylori with the Wizard® Genomic DNA Purification Kit. The isolated DNA was used in both PCR amplification and Southern blotting. (2292)

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Clin. Chem. 48, 1844-1850. High-throughput detection of submicroscopic deletions and methylation status at 15q11-q13 by a photo-cross-linking oligonucleotide hybridization assay. 2002

Peoples, R., Weltman, H., Van Atta, R., Wang, J., Wood, M., Ferrante-Raimondi, M., Cheng, P. and Huan, B.

Notes: In this paper, biotinylated and fluorescently labeled DNA probes were used simultaneously in hybridization reactions with restriction digested human genomic DNA. Streptavidin-paramagnetic particles were used to capture restriction fragments of interest prior to analysis for CpG methylation and short-nucleotide repeats with an alkaline-phosphatase-conjugated anti-fluorescein antibody.  These immuno-DNA complexes were then analyzed using the AttoPhos® AP Fluorescent Substrate System in 96-well plates. Fluorescence signal was determined using a FluoroCount™ microplate reader. Details of  hybridization conditions, probe concentrations, washes and statistical analysis are provided. (2655)

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J. Am. Soc. Nephrol. 13, 1992–1998. Human CLC-KB gene promoter drives the EGFP expression in the specific distal nephron segments and inner ear. 2002

Kobayashi, K., Uchida, S., Okamura, H.O., Marumo, F. and Sasaki, S.

Notes: The pGEM®-T Easy Vector was used to clone a 12.5 kb fragment containing human kidney specific chloride channel (CLC-KB) gene fused to an enhanced green fluorescence protein (EGFP) created in a long and accurate PCR (LA-PCR) reaction.  The resultant construct was further manipulated and used to make transgenic mice.  (3131)

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Mol. Cell. Neurosci. 21, 546-560. Human glioma cells and undifferentiated primary astrocytes that express aberrant EAAT2 mRNA inhibit normal EAAT2 protein expression and prevent cell death 2002

Guo, H., Lai, L., Butchbach, M.E.R., Lin, C-I.G.

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)

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Physiol. Genomics 10, 181-190. Influence of age, sex, and strength training on human muscle gene expression determined by microarray. 2002

Roth, S.M., Ferrell, R.E., Peters, D.G., Metter, E.J., Hurley, B.F. and Rogers, M.A.

Notes: The SV Total RNA Isolation System was used to isolate total RNA from vastus lateralis muscle biopsies from 20 male and female subjects before and after a nine-week strength-training regime. One microgram of pooled total RNA from each age/sex group was then reverse transcribed to make 33P-labeled cDNAs. Labeled cDNAs from each group were hybridized to GF211 Microarrays (Invitrogen) and analyzed for differential expression patterns. (2759)

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Antimicrob. Agents Chemother. 46, 615-624. Molecular evaluation of the plasma membrane proton pump from Aspergillus fumigatus. 2002

Burghoorn, H.P., Soteropoulos, P., Paderu, P., Kashiwazaki, R., and Perlin, D.S.

Notes: The Wizard® Genomic DNA Purification Kit was used to purify DNA from two strains of Aspergillus fumigatus.  A modified protocol was used for the purification.  Cells were filtered through a 0.2μm SFCA filter, frozen on dry ice and then ground with a mortar and pestle.  The ground cells were then incubated  in Nuclei Lysis Solution at 37°C for 1 h before continuing with the Wizard® Genomic DNA Tissue Culture Cell procedure.  The purified DNA was used in PCR with primers for the A. fumigatus PMA1 gene. (3048)

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Genes Dev. 16, 1890-1905. Molecular mechanisms governign Pcdh-γ gene expression: Evidence for a multiple promoter and cis-alternative splicing model. 2002

Wang, X., Su, H. and Bradley, A.

Notes: Total RNA was isolated from various mouse tissues including brain and cultured cells using the RNAgents® Total RNA Isolation System. The isolated RNA was used for both RACE and RT-PCR analysis. (2579)

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Appl. Environ. Microbiol. 68, 449–455. Multiple Alternate Transcripts Direct the Biosynthesis of Microcystin, a Cyanobacterial Nonribosomal Peptide. 2002

Kaebernick, M., Dittmann, E., Boerner, T., and Neilan, B.A.

Notes: Total RNA was isolated from Microcystis aeruginosa for use in RT-PCR and RACE (Rapid Amplification of cDNA Ends) to characterize transcripts of a gene cluster encoding microcystin synthetase. (2311)

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Mol. Cell. Biol. 22, 5563-5574. NF-kB1 can inhibit v-Abl-induced lymphoid transformation by functioning as a negative regulator of cyclin D1 expression. 2002

Nakamura, Y., Grumont, R.J., and Gerondakis, S.

Notes: In this paper, total RNA isolated from transgenic mouse pre-B cells was used as template for semi-quantitative RT-PCR. The RNA was isolated using the RNAgents® Total RNA Isolation System. Promoter studies were performed in 293T cells with the Dual-Luciferase® Reporter Assay System. Firefly luciferase activity controlled by Renilla luciferase activity was provided by the pRL-TK Vector. (2566)

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Genome Res. 12(3), 487-92. Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. 2002

Doi N., Takashima H., Kinjo M., Sakata K., Kawahashi Y., Oishi Y., Oyama R., Miyamoto-Sato E., Sawasaki T., Endo Y. and Yanagawa H.

Notes: Template DNAs encoding c-Fos (118–211 amino acids) and c-Jun (216–318 amino acids) were generated by PCR, purified and then in vitro transcribed using the RiboMAX™ Large Scale RNA Production System.  Following transcription, the RNA was purified and then translated in a wheat germ extract system supplemented with FluoroTect GreenLys tRNA. The fluorescently labeled proteins generated by the translation reaction were run on a 16.5% Tricine-SDS–PAGE and analyzed with a Molecular Imager FX. Labeling efficiency was calculated by measuring total protein via T7-antibody and determining the amount of fluorescently-labeled protein by fluorescence correlation spectroscopy (FCS). (3084)

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Cancer Res. 62, 4157-4163. Overexpression of epidermal growth factor receptor in urothelium elicits urothelial hyperplasia and promotes bladder tumor growth. 2002

Cheng, J., Huang, H., Zhang, Z.-T., Shapiro, E., Pellicer, A., Sun, T.-T. and Wu, X.-R.

Notes: The RNAgents® Total RNA Isolation System was used to isolate total RNA from urothelial cells scraped from the bladder mucosa of transgenic mice. The RNA was used for both RT-PCR and Northern analysis. (2572)

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Mol. Cell. Neurosci. 21, 205-222. Persephin-overexpressing neural stem cells regulate the function of Nigral dopaminergic neurons and prevent their degeneration in a model of Parkinson's Disease 2002

Åkerud, P., Holm, P.C., Castelo-Branco, G., Sousa, K., Rodriguez, F.J., and Arenas, E.

Notes: Total RNA was isolated from E15, E19, P0, P4 and adult rat brain tissue. RNA was treated with RQ1 RNase-free DNase prior to RT-PCR experiments. (2587)

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J. Clin. Microbiol. 40(2), 501-507. Rapid detection of pyrazinamide-resistant Mycobacterium tuberculosis by a PCR-based in vitro system. 2002

Suzuki, Y., Suzuki, A., Tamaru, A., Katsukawa, C, and Oda, H.

Notes: In this paper, proteins were expressed from PCR-generated template DNA using TNT® Quick for PCR DNA, the TNT® T7 Wheat Germ Extract System and the E.coli T7 S30 Extract System. (2603)

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Clin. Can. Res. 8, 1794–1799. Reverse transcription-polymerase chain reaction detection of prostate-specific antigen, prostate-specific membrane antigen, and prostate stem cell antigen in one milliliter of peripheral blood: Value of the staging of prostate cancer 2002

Hara, N., Kasahara, T., Kawasaki, T., Bilim, V., Obara, K., Takahashi, K., Tomita, Y.

Notes: The authors used the SV Total RNA Isolation System to purify total RNA from 1 ml of whole blood anticoagulated with EDTA for RT-PCR studies of prostate-specific antigens. (2470)

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Infect. Immun. 70, 481-490. Role of the dermonecrotic toxin of Bordetella bronchiseptica in the pathogenesis of respiratory disease in swine. 2002

Brockmeier, S.L., Register, K.B., Magyar, T., Lax, A.J., Pullinger, G.D., and Kunkle, R.A.

Notes: The Wizard® Genomic DNA Purification Kit was used to isolate genomic DNA from wildtype and engineered mutants of B. bronchiseptica. The isolated genomic DNA was used in PCR to analyze the size of the dnt gene. The engineered deletion mutants produced a 1.7kb PCR product and the wildtype gene produced a 2.3kb product. (2293)

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Mol. Cell. Neurosci. 21, 634-644. Smad3-dependent induction of plasminogen activator inhibitor-1 in astrocytes mediates neuroprotective activity of transforming growth factor-β1 against NMDA-induced necrosis 2002

Docagne, F., Nicole, O., Gabriel, C., Fernández-Monreal, M., Lesné, S., Ali, C., Plawinski, L., Carmeliet, P., MacKenzie, E.T., Buisson, A., Vivien, D.

Notes: PAI-1 is an inhibitor of tissue-type plasminogen activator (t-PA) and has been shown to have neuroprotective activity through the TGF-β pathway. The authors performed RTPCR experiments to study PAI-1 expression in cultured neurons and astrocytes. To confirm specificity of PAI-1 amplified products, the products were cloned into pGEMT vectors and sequenced. Wildtype and PAI-1 deficient astrocytes were transfected  (using the cationic lipid reagent, Transfast Transfection Reagent) with a luciferase reporter gene driven by the TGF-β1 response element (CAGA-luc) to determine if PAI-1-/- cells could transduce TGF-β1 signal. Luciferase activity was quantitated using the Luciferase Assay Kit. (2608)

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Int. J. Legal Med. 116, 174–5. STR loci Penta D and Penta E: Austrian Caucasian population data. 2002

Steinlechner, M., Grubwieser, P., Scheithauer, R. and Parson, W.

Notes: The authors determined allele frequencies for the Penta E and Penta D loci in 269 unrelated Austrian Caucasians using the PowerPlex® 16 System. DNA was purified from blood samples using a Qiagen kit, and 1ng of DNA was amplified using a GeneAmp® PCR System 9600 as directed by the manufacturer. Amplified products were detected using an ABI PRISM® 310 Genetic Analyzer. (3851)

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J. Biol. Chem. 277, 17349-17358. Structural Determinants of BRCA1 Translational Regulation 2002

Sobczak, K. and Krzyzosiak, W.J.

Notes: The authors investigated expression of BRCA1 from alternative transcripts possessing different 5′ UTRs. RT-PCR using Promega's AMV reverse transcriptase was performed to generate cDNAs from total RNA isolated from human tissue. Promega's Taq DNA Polymerase was used for the PCR reaction. The authors also prepared two mRNAs that contained one or the other of the 2 alternative 5′ UTRs (ex1a or ex1b) fused with the luciferase coding region. To generate the corresponding DNA for these constructs, the luciferase coding region was amplified from Promega's pGEM® Vector and ligated to PCR-amplified ex1a or exlb. These ligation products served as the template amplifying two cDNA constructs (exla-luc or ex1b-luc). Ten additional cDNAs were made containing a variety of changes to the 5′UTR region of BRCA1. In vitro translation experiments were performed to determine how the composition of the 5′UTR affected protein expression levels (using Promega's RNasin to protect transcribed mRNA; T7 polymerase buffer; and rabbit reticulocyte and wheat germ extracts for translation). The authors conclude that secondary structures associated with elements in the longer 5′UTR reduced translation rates and could be responsible for the reduced expression of BRCA1 often associated with spontaneous ovarian and breast cancers. (2441)

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Plant Cell 14, 2681-2706. The Chlamydomonas reinhardtii organellar genomes respond transcriptionally and post-transcriptionally to abiotic stimuli. 2002

Lilly, J.W., Maul, J.E. and Stern D.B.

Notes: The Access RT-PCR System was used to generate nuclear gene fragments from Chlamydomonas reinhardtii for use as probes for RNA blot hybridization assays and microarrays. RT-PCR reaction products were cloned into the pGEM®-T Easy Vector for sequence verification and to allow easier manipulation. Details of the generation of microarray slides printed on GAPII glass slides (Corning) are provided. (2694)

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J. Clin. Invest. 109, 923-930. The melanin-concentrating hormone receptor 1, a novel target of autoantibody responses in vitiligo 2002

Kemp, E.H., Waterman, E.A., Hawes, B.E., O'Neill, K., Gottumukkala, R.V.S.R.K., Gawkrodger, D.J., Weetman, A.P., and Watson, P.F.

Notes: T4 Polynucleotide Kinase was used to phosphorylate primers before ligating them into a phagemid vector to allow cloning of Sfi I-restricted DNA fragments. Phagemid was prepared from XL1-Blue cells using the Wizard® Minipreps DNA Purification System. Inserts were PCR amplified from the phagemid and purified using the Wizard® PCR Preps DNA Purification System. In separate experiments, the cDNA for the melanin concentrating hormone receptor 1 cDNA was cloned from total melanocyte RNA using MMLV Reverse Transcriptase. In vitro translation of the cDNA was performed using the TnT T7 Coupled Reticulocyte Lysate System and Canine Pancreatic Microsomal Membranes. (2602)

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Clin. Can. Res. 8, 2085-2090. The tumor suppressor gene LKB1 is associated with prognosis in human breast carcinoma 2002

Shen, Z., Wen, X-F., Lan, F., Shen, Z-Z., Shao, Z-M.

Notes: MMLV reverse transcriptase and RNasin Ribonuclease Inhibitor were used to produce cDNA from total RNA isolated from transfected and untransfected human breast cancer cells. The coding region of LKB1 was amplified by PCR using Taq DNA Polymerase and buffer from Promega. (2601)

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J. Biol. Chem. 277, 12023-12031. Transcriptional regulation of Kaposi's sarcoma-associated herpesvirus-encoded oncogene viral interferon regulatory factor by a novel transcriptional silencer, Tis. 2002

Wang, X.-P., Zhang, Y.-J., Deng, J.-H., Pan, H.-Y., Zhou, F.-C., Gao, S.-J.

Notes: Total herpesviral RNA was isolated from HeLa cells, BC-1 cells, 293 cells and human heart tissue using the RNAgents® Total RNA Isolation System. The isolated RNA was used for RT-PCR.  First-strand cDNA synthesis was accomplished using Promega's M-MLV Reverse Transcriptase and Random Hexamer Primers. (2563)

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Forensic Sci. Int. 126, 272–4. Tunisian population data on 15 PCR-based loci. 2002

Brandt-Casadevall, C., Ben Dhiab, M., Taroni, F., Gehrig, C., Dimo-Simonin, N., Zemni, M. and Mangin, P.

Notes: The PowerPlex® 16 System was used to generate population data for 196 unrelated individuals from northern, central and southern Tunisia. Blood was collected on FTA® paper, and DNA was extracted and amplified as directed by the manufacturer. Amplified products were detected using the ABI PRISM® 310 Genetic Analyzer. (3835)

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J. Bacteriol. 184(21), 5880-5893. Yersinia enterocolitica type III secretion: yscM1 and yscM2 regulate yop gene expression by a posttranscriptional mechanism that targets the 5' untranslated region of yop mRNA. 2002

Cambronne, E.D. and Schneewind, O.

Notes: To analyze whether the presence or absence of calcium in Yersinia enterocolitica growth media affected secretion of Yersinia outer proteins (Yops), these researchers used mutational analysis on four gene products that work together to regulate yopQ expression. The various Y. enterocolitica strains were grown in TSB medium supplemented with 5mM CaCl2 or EGTA (+/-Ca2+). After a 2-hour incubation followed by a 2-hour induction, the cultures were centrifuged and the supernatant was separated from the cell pellet. After resuspension in cell lysis buffer, the pellet was subjected to French press and 100µl aliquots were used with the SV Total RNA Isolation System. The eluted total RNA was digested with DNase, phenol/chloroform extracted and ethanol precipitated. Once resuspended, 0.6µg of Yersinia RNA was used in two-step RT-PCR to amplify the yopQ gene and the amplimer was analyzed on an ethidium bromide-stained 2% agarose gel. (3071)

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J. Forensic Sci. 46(4), 998-999. Allele frequencies for the PowerPlex® 16 STR loci in an Albanian population sample from northern Italy. 2001

Robino, C., Gino, S. and Torre, C.

Notes: The authors performed a population study using the PowerPlex® 16 System. (2277)

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