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J. Biomed. Sci. 19, 42. Shikonin enhances efficacy of a gene-based cancer vaccine via induction of RANTES. 2012

Chen, H.M., Wang, P.H., Aravindaram, K., Chen, Y.H., Yu, H.H., Yang, W.C., and Yang, N.S.

Notes: In this study, the authors evaluated whether application of the phytochemical shikonin to the skin of mice was able to augment the effect of a DNA-based anti-tumor vaccine by inducing the cytokine RANTES. As part of the study, the AccessQuick™ System was used in RT-PCR analysis to determine expression of RANTES mRNA in treated and control skin samples. (4288)

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Appl. Environ. Microbiol. 78, 5717–5723. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses 2012

Quigley, L., O'Sullivan, O., Beresford, T., Ross, R.P., Fitzgerald, G.F. and Cotter, P.D.

Notes: GoTaq® Green Master Mix was used in the PCR amplification of genomic DNA template for pyrosequencing. (4541)

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PLos ONE 7, e48183. Enhanced expression of vacuolar H+-ATPase subunit E in the roots is associated with the adaptation of Broussonetia papyrifera to salt stress. 2012

Zhang, M., Fang, Y., Liang, Z. and Huang, L.

Notes: The authors examined cellular adaptation to increased salinity in Broussonetia papyrifera by measuring protein and mRNA levels of vacuolar H+-ATPase (V-H+-ATPase) subunits and the activities of V-H+-ATPase and vacuolar H+-pyrophosphatase. Relative expression levels of V-H+-ATPase subunits A, B, E and c in salt-stressed and control plants were determined by RT-PCR using actin as a normalization control gene. cDNA was synthesized using the GoScript™ Reverse Transcription System as described by the manufacturer’s protocol, then amplified by PCR for 25 cycles. The amplification products were analyzed and quantified by agarose gel electrophoresis and ethidium bromide staining. (4258)

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Vet. Parasitol. 188, 160–3. Use of a real time PCR for detecting subspecies of Babesia canis. 2012

Costa, L.M., Jr. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Babesia canis. (4311)

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Viruses 4, 200–10. Clinical characteristics and genetic variability of human rhinovirus in Mexico. 2012

Landa-Cardeña, A., Morales-Romero, J., García-Roman, R., Cobián-Güemes, A.G., Méndez, E., Ortiz-Leon, C., Pitalúa-Cortés, F., Mora, S.I. and Montero, H.

Notes: This study examined the prevalence of strains of human rhinovirus (HRV) that may be causing respiratory infections in Mexican children. Nucleic acids were purified from nasal swabs of two-year-old children, and screened for the presence of HRV by amplifying 20ng of HRV-RNA using the AccessQuick™ RT-PCR System with primers for the 5´ nontranslated region. Products were sequenced and aligned with sequences found in GenBank. (4343)

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J. Immunol. 188(4), 1896–1904. Plac8-dependent and inducible NO synthase-dependent mechanisms clear Chlamydia muridarum infections from the genital tract. 2012

Johnson, R.M., Kerr, M.S. and Slaven, J.E.

Notes: The authors previously showed that there are two independent mechanisms by which Chlamydia-specific CD4 T cells clear infection in epithelial cells; an iNOS-dependent mechanism and a Plac8-dependent mechanism. To further identify the Plac8 mechanism, they used microarrays to identify a second mechanism dependent on Plac8 for terminating Chlamydia replication in epithelial cells.

Several Chlamydia-specific CD4 T cell clones were purified at the end of their culture cycle and grown for 3 days in their usual culture media plus growth factors, without Ag stimulation. Total RNA was isolated from each clone using a protocol that included an RNase-free DNase I treatment step. Specific mRNA gene reverse transcription and amplification were performed using the AccessQuick™ RT-PCR System. (4324)

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J. Wildl. Dis. 48, 416–24. Antibody prevalence and molecular identification of Babesia spp. in roe deer in France. 2012

Bastian, S. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Babesia spp. (4310)

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Am.J.Trop. Med. Hyg. 86(4), 732–735. Identification of Oropouche Orthobunyavirus in the Cerebrospinal Fluid of Three Patients in the Amazonas, Brazil. 2012

Bastos, M.de S., Figueiredo, L.T., Naveca, F.G., Monte, R.L., Lessa, N., Pinto de Figueiredo, R.M., Gimaque, J.B., Pivoto João, G., Ramasawmy, R. and Mourão, M.P.

Notes: Oropouche fever is a arboviral infection in Brazil, surpassed in frequency only by dengue. Oropouche virus (OROV) causes large outbreaks of acute febrile illness in areas along the Amazon and Central-Plateau regions. RNA was extracted from CSF and underwent reverse transcription-polymerase chain reaction and sequencing to identify OROV. Reverse transcription was performed with 5ml of the random primers, using the AccessQuick™ RT-PCR System. (4320)

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Antimicrob. Agents Chemother. 56, 2504–10. Expression of the resistance-nodulation-cell division pump AdelJK in Acinetobacter baumannii is regulated by AdeN, a TetR-type regulator. 2012

Rosenfeld, N. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Acinetobacter baumannii. (4296)

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Proc. Natl. Acad. Sci. USA 109, 13428-13433. CAG expansion induces nucleolar stress in polyglutamine diseases. 2012

Tsoi, H., Lau, T.C., Tsang, S.Y., Lau, K.F., and Chan, H.Y.

Notes: Polyglutamine diseases are neurodegenerative disorders associated with the presence of proteins containing polyglutamine repeats. These authors studied the mechanism of polygluatmine toxicity. Mutant RNAs carrying an expanded CAG repeat were shown to activate the nucleolar stress pathway and induce apoptosis. Expanded CAG RNAs were shown to interact with nucleolin, preventing it from binding to an upstream control element of the rRNA promoter and causing decreased rRNA transcription, which in turn induced apoptosis. Perturbations in rRNA transcription were identified by real-time PCR, and fluorescence in situ hybridization was used to determine that expanded CAG RNAs localized to the nucleolus. Hybridization solutions were supplemented with RNasin® Ribonuclease Inhibitor. ImProm-II™ Reverse Transcriptase was used in RT-qPCR assays. (4228)

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Anal. Biochem. 423(2), 224-228. A bioluminescence assay for DNA methyltransferase activity based on methylation-resistant cleavage. 2012

Jiang, C., Yan, C.Y., Huang, C., Jiang, J.H., and Yu, R.Q.

Notes: This paper describes a bioluminescence-based method for the detection of DNA methyltransferase activity based on methylation-resistant cleavage and protein expression. The authors used Dam methylase as a model enzyme, MboI as the methylation-resistant endonuclease, and luciferase reporter DNA (LR-DNA) as the target. LR-DNA was amplified by PCR and then used as substrate in a Dam methylation reaction. If the target sites in the LR-DNA were fully methylated, they were resistant to subsequent MboI cleavage and expressed luciferase upon in vitro transcription/translation. Incomplete methylation or the absence of methylation resulted in DNA digestion and diminished/absent luciferase activity. TNT® T7 Quick for PCR DNA was used for in vitro translation of the LR-DNA, and the Luciferase Assay System and GloMax® 20/20 Luminometer were used to measure luciferase activity. (4191)

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J. Biotechnol. 157(4), 598-604. Detection of toxic lignin hydrolysate-related compounds using an inaA::luxCDABE fusion strain. 2012

Lee, S., and Mitchell, R.J.

Notes: This study evaluated use of a luciferase reporter construct for detection of hydrolysate related phenolic compounds generated during fermentation of plant products. The authors used a transcriptional fusion of the inaA promoter with the luxCDABE operon to detect phenolic compounds generated in plant hydrolysates. The GloMax® Multi Detection System was used to measure bioluminescence in various bacterial cultures. (4194)

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Appl. Environ. Microbiol. 78, 445–54. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. 2012

Ma, K., Conrad, R. and Lu, Y.

Notes: The authors of this study investigated the microbial mechanisms associated with the reduction of methane production and emission from rice fields observed with intermittent field drainage. They looked in particular at the abundance of mcrA gene copies and transcripts from rice paddy soil fauna. The mcrA gene encodes the alpha subunit of methyl coenzyme M reductase. 

Total nucleic acid was extracted from soil samples using a phenol-chloroform procedure. For RNA analyses, DNA was hydrolyzed using RQ1 RNase-free DNase in the presence of 0.2µl Recombinant RNasin® Ribonuclease Inhibitor and then further purified using a commercial kit. cDNA synthesis was carried out using the Improm-II™ Reverse Transcription System, again in the presence of 1.0µl Recombinant RNasin® Ribonuclease Inhibitor. A clone library of transcripts was generated using the pGEM®-T Easy Vector System. The transcript standard for quantitative mcrA analysis was prepared from the in vitro transcript of a mcrA clone using the Riboprobe® in vitro Transcription Systems. (4241)

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Antimicrob. Agents Chemother. 56, 5332–9. Identification of a novel genomic island conferring resistance to multiple aminoglycoside antibiotics in Campylobacter coli. 2012

Qin, S. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Campylobacter coli. (4316)

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Gene 493, 124-131. A preliminary sketch of horn cancer transcriptome in Indian zebu cattle. 2012

Tripathi ,A.K., Koringa, P.G., Jakhesara, S.J., Ahir, V.B., Ramani, U.V., Bhatt, V.D., Sajnani, M.R., Patel, D.A., Joshi, A.J., Shanmuga, S.J., Rank, D.N., and Joshi, C.G.

Notes: These authors used the Roche 454 next generation sequencing platform to sequence and compare cancerous and normal horn tissue transcripts. mRNA isolated from each sample was fragmented prior to cDNA synthesis. cDNA quality was verified using a high sensitivity DNA Chip kit on the  Bioanalyzer 2100 and the  QuantiFluor™-ST Fluorometer. The transcripts were compared and potential tumor associated genes identified. (4229)

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Gene 507, 152–8. Identification of novel transcripts deregulated in buccal cancer by RNA-seq. 2012

Sajnani, M.R., Patel, A.K., Bhatt, V.D., Tripathi, A.K., Ahir, V.B., Shankar, V., Shah, S., Shah, T.M., Koringa, P.G., Jakhesara, S.J. and Joshi, C.G.

Notes: The authors used the Roche 454 sequencing platform to perform a differential transcriptome analysis and identify genes that are differentially expressed in human buccal cancer and normal tissue. The quantity of first-strand and second-strand cDNA products was estimated using the QuantiFluor™-ST Fluorometer as well as the High Sensitivity DNA Chip kit and Agilent Bioanalyzer 2100. (4238)

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Human Pathology in press. Proliferative glomerulonephritis with monoclonal immunoglobulin G3κ deposits in association with parvovirus B19 infection 2012

Fujita, E., Shimizu, A., Kaneko, T., Masuda, Y., Ishihara, C., Mii, A., Higo, S., Kajimoto, Y., Kanzaki, G., Nagasaka, S., Iino, Y., Katayama, Y. and Fukuda, Y.

Notes: The authors used the ReliaPrep™ FFPE gDNA Miniprep System to isolate DNA from parafin-embedded kidney sections for use in real-time PCR to detect parvovirus B19. (4235)

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J. Clin. Microbiol. 50(5), 1580–5. Sensitive and rapid detection of the New Delhi metallo-beta-lactamase gene by loop-mediated isothermal amplification. 2012

Liu, W. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Acinetobacter baumannii. (4274)

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Biochim. Biophys. Acta 1822, 248-260. MiR-21 is involved in cervical squamous cell tumorigenesis and regulates CCL20. 2012

Yao, T., and Lin, Z.

Notes: This study identified that miR-21 is significantly overexpressed in human cervical squamous cancer tissues and cell lines, and showed that the level of miR-21 correlates with tumor differentiation, and regulates proliferation, apoptosis, and migration of HPV16-positive cells. The authors used gene expression profiling and luciferase reporter assay to identify candidate target genes for miR-21. Wildtype and mutant 3′-UTR sequences from the target gene CCL20 containing putative binding sites for miR-21 were subcloned into the psiCHECK-2 Vector and used to transfect HEK293 cells. The Dual-Luciferase® Reporter Assay System and GloMax® Multi Luminometer were used to measure luciferase activity from both constructs. (4192)

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DNA Research 19, 395-406. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer 2012

Murphy, S.J., Cheville, J.C., Zarei, S., Johnson, S.H., Sikkink, R.A., Kosari, F., Feldman, A.L., Eckloff, B.W., Karnes, R.J. and Vasmatzis, G.

Notes: Genomic rearrangements detected by NGS were mapped and confirmed by PCR. Human Genomic DNA: Male was used as a control for the confirmatory experiments. (4539)

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Cancer Res. 72, 810-820. SMYD3 Promotes Cancer Invasion by Epigenetic Upregulation of the Metalloproteinase MMP-9. 2012

Cock-Rada, A.M., Medjkane, S., Janski, N., Yousfi, N., Perichon, M., Chaussepied, M., Chluba, J., Langsley, G., and Weitzman, J.B.

Notes: These authors investigated the role of matrix metalloproteinase (MMP-9) in a reversible model of cancer that is initiated by infection with intracellular Theileria parasites. They found that gene induction by parasite infection was associated with trimethylation of histone H3K4 (H3K4me3) at the MMP-9 promoter. The H3K4 methyltransferase SMYD3 was the only histone methyltransferase upregulated upon infection. They therefore investigated the role of SMYD3 overexpression on MMP-9 expression and cell migration, identifying SMYD3 as an important new regulator of MMP-9 transcription. During the study they used the GloMax® Multi Luminometer to measure luminescence and absorbance in reporter and cell viability assays. They also used the Dual-Luciferase® Reporter Assay to measure SMYD3 activity in cells transfected with a SMYD3 reporter, and the pGL4-hRluc/TK plasmid for normalization of the experimental reporter activity. GoTaq® DNA polymerase was used in semi-quantitative RT-PCR. (4189)

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J. Virol. 86, 10999–11012. Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces. 2012

Wu, Z., Ren, X., Yang, L., Hu, Y., Yang, J., He, G., Zhang, J., Dong, J., Sun, L., Du, J., Liu, L., Xue, Y., Wang, J., Yang, F., Zhang, S. and Jin, Q.

Notes: Swab samples from 11 species of Chinese bats were vortexed in maintenance medium, filtered through a 0.45µm pore filter, centrifuged and resuspended. Any nonencapsidated (naked) nucleic acid was digested in a cocktail of enzymes including 20U of RNase ONE™ Ribonuclease prior to DNA and RNA purification. Conserved regions of the RNA-dependent RNA polymerase gene of astroviruses were reverse transcribed, amplified and cloned into the pGEM®-T Easy Vector for sequencing. (4552)

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J. Clin. Microbiol. 49, 1628–30. Novel nested direct PCR technique for malaria diagnosis using filter paper samples. 2011

Fuehrer, H.P., Fally, M.A., Habler, V.E., Starzengruber, P., Swoboda, P. and Noedl, H.

Notes: The authors developed a direct-amplification, nested PCR protocol to amplify Plasmodium DNA from 903 filter paper punches containing whole blood. The second round of nested PCR was performed using 2.5µl of PCR products from the first round and GoTaq® PCR Core System. Parallel PCRs were performed using purified DNA from blood, and both rounds of nested PCR were performed using the GoTaq® PCR Core System. (4166)

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Med. Vet. Entomol. 25, 58–63. The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions. 2011

Wanaratana, S., Panyim, S. and Pakpinyo, S.

Notes: To investigate if house flies could act as a vector for avian influenza virus H1N5, flies exposed to the virus were homogenated and the homogenate used to inoculate 10-day-old embryonated chicken eggs (ECEs). Allantoic fluids were collected from the eggs, RNA purified from the samples and the presence of H1N5 assessed using M-specific primers and the AccessQuick™ RT-PCR System and looking for the 276bp amplimer. (4339)

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J. Antimicrob. Chemother. 67, 59-63. Disruption of the blaOXA-51-like gene by ISAba16 and activation of the blaOXA-58 gene leading to carbapenem resistance in Acinetobacter baumannii Ab244.

Lopes. B.S., Evans, B.A., and Amyes, S.G.B.

Notes: This study investigated the genetic basis of carbapenem resistance in the multidrug resistant Acinetobacter baumannii isolate, Ab244. Transposable elements are known to play an important role in multidrug resistance in A. baumannii. The authors used a multiplex PCR approach to detect the presence of known resistance genes and insertion elements, followed by RT-PCR to study expression of the genes identified. For RT-PCR, cDNA was synthesized from 100 ng of RNA using the AccessQuick™ RT-PCR System. Results of the study indicated that the blaOXA-132 gene was inactivated in A. Baumannii AB244 by insertion of ISAba16, and that carbapenem resistance in that isolate was due to an alternate resistance mechanism caused by overexpression of the blaOXA-58 gene. (4344)

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