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J. Gen. Virol. 86, 623-630. Mutation of chicken anemia virus VP2 differentially affects serine/threonine and tyrosine protein phosphatase activities. 2005

Peters, M.A., Jackson, D.A., Crabb, B.S. and Browning, G.F.

Notes: This study investigated the role of the dual-specificity protein phosphatase, Viral Protein 2 (VP2) from chicken anemia virus in virus-induced immunosuppression. Mutations were introduced into the VP2 sequence by overlap-expression PCR. Serine/Threonine phosphatase activity of VP2 mutants was investigated using the Serine/Threonine Phosphatase Assay System. (3525)

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Infect. Immun. 73, 7064-7068. Mycobacterial lipomannan induces matrix metalloproteinase-9 expression in human macrophagic cells through a Toll-like receptor 1 (TLR1)/TLR2- and CD14-dependent mechanism. 2005

Elass, E., Aubry, L., Masson, M., Denys, A., Guérardel, Y., Maes, E., Legrand, D., Mazurier, J., and Kremer, L.

Notes: M-MLV Reverse Transcriptase was used to make cDNA from differentiated THP-1 cell total RNA. For these reverse transcription experiments the authors used 5 µg of total RNA, oligo dT and RNasin®. GoTaq® DNA Polymerase was used to amplify the cDNA from the reverse transcription reactions. PCR products were separated by gel electrophoresis and analyzed by ethidium bromide staining and band densitometry. (3357)

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J. Biol. Chem. 280, 1376-1383. PDILT, a divergent testis-specific protein disulfide isomerase with a non-classical SXXC motif that engages in disulfide-dependent interactions in the endoplasmic reticulum. 2005

van Lith, M., Hartigan, N., Hatch, J. and Benham, A.M.

Notes: The tissue-specific patterns of expression of the novel protein disulfide isomerase-like protein of the testis (PDILT) was characterized using the AccessQuick™ RT-PCR System. RNAs isolated from various mouse tissues were amplified to reveal the testis-specific expression. An in vitro PDILT transcript generated using the Riboprobe® System-T7 was used as a positive control. Actin mRNA was also amplified to demonstrate equal RNA input. (3433)

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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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Toxicol. Sci. 85, 632-638. Precision-cut liver slices as a new model to study toxicity-induced hepatic stellate cell activation in a physiologic milieu. 2005

van de Bovenkamp, M., Groothuis, G.M.M., Draaisma, A.L., Merema, M.T., Bezuijen, J.I., van Gils, M.J., Meijer, D.K.F., Friedman, S.L. and Olinga, P.

Notes: Rat liver slices were used to study hepatic stellate cell (HSC) activation and fibrogenesis. The expression of markers of HSC activation and fibrogenesis were analyzed by real-time PCR. To quantitate mRNA levels, total rat liver RNA was reverse transcribed using the Reverse Transcription System, then amplified in the presence of SYBR® Green. (3430)

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J. Clin. Microbiol. 43, 6027-6031. Presence of Rickettsia conorii subsp. israelensis, the causative agent of Israeli spotted fever, in Sicily, Italy, ascertained in a retrospective study. 2005

Giammanco, G.M., Vitale, G., Mansueto, S., Capra, G., Caleca, M.P. and Ammatuna, P.

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)

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RNA 11, 1571-8. Rat1p and Rai1p function with nuclear exosome in the processing and degradation of rRNA precursors. 2005

Fang, F., Phillips, S. and Butler, J.S.

Notes: GoTaq® DNA Polymerase was used in a RT-PCR. The 50μl PCR reactions contained 0.25μl cDNA, 12.5pmol primer, 0.025mM dNTPs, 2.5mM MgCl2 and 0.25μl of GoTaq® DNA Polymerase (5U/μl). PCR was performed using the following conditions: 94°C for 3 minutes followed by 20 cycles (94°C for 30 seconds, 55°C for 30 seconds and 72°C for 30 seconds), followed by 72°C for 7 minutes and held at 4°C. Products were visualized on an agarose gel. (3352)

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RNA 11, 1571–8. Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors. 2005

Fang, F., Phillips, S. and Butler, J.S.

Notes: To examine the effect of the exoribonuclease Rat1p on processing of ribosomal RNAs (rRNA), total RNA was isolated from several yeast strains with altered RAT1 expression. One microgram of DNase-treated total RNA was reverse transcribed in a 20µl reaction. Subsequently, 0.25µl of cDNA product was amplified using 0.25µl of GoTaq® DNA polymerase in a total volume of 50µl. The RT-PCR products were separated on 2% agarose gels and stained using ethidium bromide. (3330)

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Am. J. Med. Genet. 138A, 99–106. Screening for new MTHFR polymorphisms and NTD risk. 2005

O'Leary, V.B., Mills, J.L., Parle-McDermott, A., Pangilinan, F., Molloy, A.M., Cox, C., Weiler, A., Conley, M., Kirke, P.N., Scott, J.M., Brody, L.C. and Birth Defects Research Group.

Notes: The enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR) has at least one polymorphism that is a neural tube defect (NTD) risk factor within the Irish population. To survey for common variations in MTHFR, genomic DNA was extracted from blood, and exons 1–11 of MTHFR were amplified and sequenced with Big Dye® Terminator mix. The Wizard® MagneSil® Sequencing Reaction Clean-Up System was used to purify the sequencing reactions prior to analysis on an ABI PRISM® 377 DNA sequencer. (3444)

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J. Biol. Chem. 280, 36802–8. Structural and genetic analyses reveal a key role in prophage excision for the TorI response regulator inhibitor. 2005

Elantak, L., Ansaldi, M., Guerlesquin, F., Mejean, V. and Morelli, X.

Notes: To test the activity of torI as a prophage excisionase, the chloramphenical aceytltransferase gene was introduced into a non-coding region of the prophage KplE1 in a strain of E. coli containing a torI-encoding plasmid. Expression of torI was induced by IPTG and the cells plated on either chloramphenical or ampicillin. GoTaq® DNA polymerase was used in a PCR test to confirm prophage DNA excision from randomly chosen ampicillin-resistant colonies. (3329)

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J. Biol. Chem. 280, 36802-36808. Structural and genetic analyses reveal a key role in prophage excision for the torl response regulator inhibitor. 2005

ElAntak, L., Ansaldi, M., Guerlesquin, F., Méjean, V. and Morelli, X.

Notes: GoTaq® Polymerase was used in this study investigating the role of TorI (Tor inhibition protein) in prophage DNA excision. PCR products were amplified from E. coli strains carrying a plasmid-encoded torI gene, and were analyzed by gel electrophoresis. (3350)

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J. Bacteriol. 187, 3762-3778. Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403. 2005

Sperandio, B., Polard, P., Ehrlich, D.S., Renault, P. and Guédon, E.

Notes: To study the transcription levels of several genes involved in cysteine and methionine metabolism, Lactococcus lactis strains deficient in these genes were created by double-crossover homologous integration. To do so, PCR was performed to amplify sequences upstream and downstream of the target gene, and the PCR products were ligated and cloned into the pGEM®-T Easy Vector. The resulting vectors were fused to pGhost9, a vector designed for homologous recombination in L. lactis. Once the gene deletions were verified, quantitative real-time RT-PCR was performed to quantitate expression levels of a variety of genes involved in Cys and Met metabolism. (3461)

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Nucl. Acids Res. 33, e41. Targeted ‘knockdown’ of spliceosome function in mammalian cells. 2005

Matter, N. and König, H.

Notes: PCR was performed in 50μl GoTaq® Reaction Buffer containing 5μl of diluted (1:10) reverse transcriptase reactions, 250mM each dNTP, 10 pmol primers and 2.5 U GoTaq® DNA Polymerase. A total of 28 cycles were performed for amplification of P120 minigene transcripts, and 31 cycles were performed for endogenous P120 and ADPRT transcripts. Each cycle consisted of 95°C for 1 min, 59°C (P120) or 58°C (ADPRT) for 1 min and 72°C for 1.5 min. (3353)

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Nucl. Acids Res. 33(4), e41. Targeted 'knockdown' of spliceosome function in mammalian cells. 2005

Matter, N. and Konig, H.

Notes: To examine why there are two splicing systems present in multicellular organisms, the authors used morpholino oligomers complementary to the branch-site recognition elements of U2 or U12 small nuclear RNA to specifically suppress the splicing function in EL4 and Jurkat cells. After transfection with the morpholino oligos, the cells were harvested, and total RNA was isolated followed by DNase-treatment. In a 20µl reverse transcription reaction, 0.8µg total RNA was reverse transcribed with 100ng oligo(dT)15 primer and 200 units of M-MLV Reverse Transcriptase, RNase H Minus. PCR was then performed using 5µl of the diluted (1:10) reverse transcriptase reaction with 2.5 units GoTaq® DNA polymerase in a 50µl reaction for 28–31 cycles. (3278)

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Biol. Reprod. 73, 745–51. The translationally controlled tumor protein is a novel calcium binding protein of the human placenta and regulates calcium handling in trophoblast cells. 2005

Arcuri, F., Papa, S., Meini, A., Carducci, A., Romagnoli, R., Bianchi, L., Riparbelli, M.G., Sanchez, J.C., Palmi, M., Tosi, P., and Cintorino, M.

Notes: These authors examined the role of translationally controlled tumor protein (TPT1) in human placental calcium transport. To test this, expression of TPT1 in the HTR-8/SVneo human trophoblast cell line was silenced by RNA interference. The TPT1 sequence corresponding to nucleotides 317 to 337 was targeted and the corresponding mouse TPT1 sequence was used as a control. The TPT1 sequence oligos for a hairpin siRNA were cloned into the psiSTRIKE™ Puromycin Vector and grown in JM109 cells. The purified plasmids were then transfected into HTR-8/SVneo cells at 60% to 80% confluence with 2µg human or control mouse shRNA vector. The cells were selected for puromycin resistance for two weeks and changes in TPT1 levels were determined by Western blot analysis. (3296)

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Proc. Natl. Acad. Sci. USA 102, 7701-7706. The two-component signal transduction system RR06/HK06 regulates expression of cbpA in Streptococcus pneumoniae. 2005

Standish, A.J., Stroeher, U.H., and Paton, J.C.

Notes: In this study, the binding of the response regulator RR06 to the promoter region of cbpA was investigated. DNA encoding the rr06 gene was cloned into the pGEM®-T Easy vector and transformed into E. coli strain DH5α. Cell lysates were prepared and incubated with a labeled cbpA promoter fragment, and binding was evaluated in an electrophoretic mobility shift assay (EMSA). To further investigate the RR06/cbpA interaction, the cbpA promoter region, or a control rRNA sequence, was biotin labeled and attached to Streptavidin MagneSphere® Paramagnetic Particles. The beads were incubated with E. coli lysates expressing RR06, or with control lysates. After washing, bound proteins were eluted by boiling. Eluted samples were then probed with specific anti-RR06 antisera. (3397)

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Croat. Med. J. 46, 530–539. Twelve-year experience in identification of skeletal remains from mass graves. 2005

Andelinovic, S., Sutlovic, D., Erceg Ivkosic, I., Skaro, V., Ivkosic, A., Paic, F., Rezic, B., Definis-Gojanovic, M. and Primorac D.

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)

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Infect. Immun. 72(2), 629–36. A K+ uptake protein, TrkA, is required for serum, protamine, and polymyxin B resistance in Vibrio vulnificus. 2004

Chen Y.C., Chuang Y.C., Chang C.C., Jeang C.L. and Chang M.C.

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)

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J. Assoc. Lab. Automation 9, 146-149. A novel system for automated RNA isolation: Increasing throughput without increasing footprint. 2004

Laffitte, B., Murray, D., Smith, G., Liacos, J., Siu, A., Finlay, C. and Bruner, J.

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)

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J. Forensic Sci. 49, 754–759. A simple and efficient method for extracting DNA from old and burned bone. 2004

Ye, J., Ji, A., Parra, E.J., Zheng, X., Jiang, C., Zhao, X., Hu, L. and Tu, Z.

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)

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Appl. Environ. Microbiol. 70, 2779–2785. Acquisition of an Agrobacterium Ri plasmid and pathogenicity by other α-Proteobacteria in cucumber and tomato crops affected by root mat. 2004

Weller, S.A., Stead, D.E. and Young, J.P.W.

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)

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Int. Congr. Ser. 1261, 151–3. Analysis of 12 STR loci in Antioquia (Colombia) population sample. 2004

Bravo, M.L.J., Builes, J.J., de Pancorbo, M.M. and Moreno, M.A.

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)

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Toxicol. Sci. 82, 250–258. ARNT2 is not required for TCDD developmental toxicity in Zebrafish. 2004

Prasch, A.L., Heideman, W. and Peterson, R.E.

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)

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Neurosci. Lett. 368, 41-45. Association study of polymorphisms in the 5’ upstream region of human DISC1 gene with schizophrenia. 2004

Kockelkorn, T.T., Arai, M., Matsumoto, H., Fukuda, N., Yamada, K., Minabe, Y., Toyota, T., Ujike, H., Sora, I., Mori, N., Yoshikawa, T. and Itokawa, M.

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)

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Biochem. Biophys. Res. Commun. 321(1), 259-265. Cloning of hOST-PTP: the only example of a protein-tyrosine-phosphatase the function of which has been lost between rodent and human 2004

Cousin, W., Courseaux, A., Ladoux, A., Dani, C., and Peraldi, P.

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)

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