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Croat. Med. J. 48, 513–519. DNA identification of skeletal remains from the World War II mass graves uncovered in Slovenia. 2007

Marjanovic, D., Durmic-Pasic, A., Bakal, N., Haveric, S., Kalamujic, B., Kovacevic, L., Ramic, J., Pojskic, N., Skaro, V., Projic, P., Bajrovic, K., Hadziselimovic, R., Drobnic, K., Huffine, E., Davoren, J. and Primorac, D.

Notes: The authors used the PowerPlex® 16 System to perform DNA typing of 27 sets of World War II skeletal remains found in two mass graves in Slovenia. Each bone sample was sanded to remove potential contaminants from exterior surfaces, then washed and air-dried. The same procedure was used to process teeth, except that the teeth were not sanded. DNA was isolated from the bone powder using organic extraction, then quantified. DNA was amplified using the PowerPlex® 16 System as per the manufacturer's recommendations; for samples with small amounts of DNA, the number of cycles was increased to 32 and the elongation time extended to 90 seconds. Fifteen sets of remains yielded full profiles, and 12 sets yielded partial profiles, with the least successful profile including 13 loci. DNA was also extracted and amplified from 69 reference buccal swab samples from potential relatives. (3817)

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J. Clin. Microbiol. 45, 3316-3322. Evaluation the Invader Assay with the BACTEC MGIT 960 System for prompt isolation and identification of Mycobacteria from clinical specimens. 2007

Ichimura, S., Nagano, M., Ito, N., Shimojima, M., Egashira, T., Miyamoto, C., Ohkusu, K., and Ezaki, T.

Notes: These authors compared standard culture conditions, DNA isolation and analysis (e.g, sequencing) with a liquid culture, DNA isolation and a homogeneous fluorescent detection system for identifying mycobacterial species. The standard DNA extraction began with a loopful (3–mm3 sphere) of bacterial colony grown on Ogawa slants that used glass beads to mechanically disrupt the cells. The resulting lysate was extracted using phenol/chloroform, and DNA purified from the aqueous phase using a robotic liquid handler AGE-96 (Biotec) and the MagneSil® Blood Genomic, Max Yield System. The DNA extractions were used in PCR and sequencing reactions. (3700)

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Forensic Sci. Int. 48, 478–85. Highly effective DNA extraction method for nuclear short tandem repeat testing of skeletal remains from mass graves. 2007

Davoren, J., Vanek, D., Konjhodzic, R., Crews, J., Huffine, E. and Parsons, T.J.

Notes: The authors compared two DNA extraction methods: the International Commission on Missing Persons silica method and the standard phenol:chloroform method to determine the preferred method for extraction of DNA from skeletal remains. The efficacy of DNA extraction was measured by real-time PCR to quantify DNA and to check for the presence of PCR inhibitors, and by amplification with the PowerPlex® 16 System. DNA was extracted from processed bone powder, and 10µl of the final extract was amplified using the PowerPlex® 16 System and GeneAmp® PCR System 9700 according to the manufacturer's recommendations, except that the extension time was doubled from 30 seconds to 60 seconds for the first 10 cycles and from 45 seconds to 90 seconds for the next 22 cycles. Amplified products were detected using the ABI PRISM® 3100 Genetic Analyzer. The authors concluded that the silica-based method gave better results in autosomal STR typing than the organic extraction method. (3818)

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J. Clin. Invest. 117, 3042–3048. HLA class I polymorphisms are associated with development of infectious mononucleosis upon primary EBV infection. 2007

McAulay, K.A., Higgins, C.D., Macsween, K.F., Lake, A., Jarrett, R.F., Robertson, F.L., Williams, H. and Crawford, D.H.

Notes: The authors examined whether genetic differences at the HLA class I locus affect development of Epstein Barr Virus-associated diseases. Peripheral blood mononuclear cells were isolated from asymptomatic EBV-seropositive and seronegative individuals and patients with acute infectious mononucleosis. DNA was isolated, and genotypes at two HLA class I loci and one HLA class III locus, as a control, were determined by PCR. The 10µl PCRs contained 25ng of DNA, 1X GoTaq® Flexi Reaction Buffer, 2.5mM MgCl2, 200µM dNTP, 0.5 units of GoTaq® Flexi DNA Polymerase and 25µM of forward and reverse primer, one of which was labeled with 6-FAM fluorescent dye. The results show that HLA class I polymorphisms might predispose people to develop infectious mononucleosis upon EBV infection. (3712)

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J. Clin. Microbiol. 45, 1469–1477. Multilocus sequence typing of the pathogenic fungus Aspergillus fumigatus. 2007

Bain, J.M., Tavanti, A., Davidson, A.D., Jacobsen, M.D., Shaw, D., Gow, N.A. and Odds, F.C.

Notes: The authors developed a multilocus sequence typing scheme (MLST) to examine sequence variation and discriminate between Aspergillus fumigatus strains. They also examined the distribution of MAT1-1 and MAT1-2 sexual idiomorphs in 100 clinical and environmental isolates. Sexual idiomorphs were determined using PCR and a reverse primer to both idiomorphs and a forward primer specific to either MAT-1 or MAT-2. PCRs consisted of 2mM MgCl2, 200µM DNTPs and 2.5 units of GoTaq® DNA Polymerase. (3714)

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Hum. Mutat. 0, 1-6. Novel Plexor SNP genotyping technology: comparisons with TaqMan and homogenous MassEXTEND MALDI-TOF mass spectrometry. 2007

Tindall, E.A., Speight, G., Petersen, D.C., Padilla, E.J., and Hayes, V.M.

Notes: This study compared the performance of the Plexor® qPCR System with the TaqMan® and MassEXTEND™ methods for genotyping analysis of 11 SNPs in >2000 DNA samples. All three methods were shown to be equivalent in call rate and accuracy. The Plexor® System is described as a cost-effective, efficient alternative to the TaqMan® technology for medium-throughput SNP analysis. Plexor® qPCR System reactions contained 5ng template DNA, 0.2µl 5µM allele-specific primers, 0.2µl 10µM anchor primer, and 2.5µl 2X Plexor™ Master Mix in a total volume of 5µl. PCR was performed on an ABI PRISM® 7900HT Sequence Detection System using the following cycling conditions: 95°C for 2 minutes; 50°C for 35s; and 40 cycles of 95°C for 5s, 60°C for 35s. Primers were designed using the Plexor® Primer Design Software. (3674)

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Genetics 175, 1047-1058. Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. 2007

Lamb, J.C., Danilova, T., Bauer, M.J., Meyer, J.M., Holland, J.J., Jensen, M.D., and Birchler, J.A.

Notes: These authors generated a set of probes that could be used in fluorescence in situ hybridization (FISH) analyses for karyotyping studies on maize chromosomes. Specific target regions composed of genes or gene clusters and free from repetative elements were identified for each chromosome. Target regions were amplified by PCR, gel purified using the Wizard® SV Gel and PCR Clean-Up System, and tested in a FISH assay. Probes showing low background were selected, subcloned into the pGEM® -T Vector and sequenced to confirm identity. (3627)

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Proc. Natl. Acad. Sci. USA 103, 4552-4557. A dopamine transporter gene functional variant associated with cocaine abuse in a Brazilian sample. 2006

Guindalini, C., Howard, M., Haddley, K., Laranjeira, R., Collier, D., Ammar, N., Craig, I., O'Gara, C., Bubb, V.J., Greenwood, T., Kelsoe, J., Asherson, P., Murray, R.M., Castelo, A., Quinn, J.P., Vallada, H., and Breen, G.

Notes: These authors investigated the effect of various polymorphisms in the dopamine transporter gene (SLC6A3) on susceptibility to cocaine addiction. Genotyping of various polymorphisms in cocaine abusers and control subjects revealed a potential association of the int8 VNTR with cocaine abuse. Seven alleles of the int8 VNTR were sequenced. Various allelic sequences were then cloned into a modified phRL-SV40 Renilla luciferase reporter vector and transfected into the mouse SN4741 cell line, which expresses the dopamine transporter, and the effects on reporter activity were monitored. Sequences of two alleles were then cloned into a pGL3 Promoter Vector construct and transfected into JAP cells. The cells were then challenged with various amounts of cocaine, KCL or KCl and forskolin, and the effect on reporter activity was monitored. The TransFast™ Reagent was used for transfections at a 2:1 reagent:DNA ratio. (3543)

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J. Forensic Sci. 51, 274–281. A proposal for standardization in forensic canine DNA typing: allele nomenclature of six canine-specific STR loci. 2006

Hellmann, A.P., Rohleder, U., Eichmann, C., Pfeiffer, I., Parson, W. and Schleenbecker, U.

Notes: Saliva samples from a total of 142 dogs (36 different pure breeds and several cross breeds) were collected on cotton swabs. Genomic DNA was isolated using the ReadyAmp™ Genomic DNA Purification System. Single amplifications of six canine STR loci were performed using 1–5µl of saliva DNA extract. (3424)

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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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J. Biol. Chem. 281, 13199-13208. Molecular pharmacological phenotyping of EBI2. An orphan seven-transmembrane receptor with constitutive activity. 2006

Rosenkilde, M.M., Benned-Jensen, T., Andersen, H., Holst, P.J., Kledal, T.N., Luttichau, H.R., Larsen, J.K., Christensen, J.P. and Schwartz, T.W.

Notes: The expression level of the seven-transmembrane Epstein-Barr virus-induced receptor 2 (EBI2) was measured in peripheral blood mononuclear cells. Total RNA was isolated from T-lymphocytes, B-lymphocytes, monocytes and NK cells, and reverse transcribed using the ImProm-II™ Reverse Transcription System. The resulting cDNA was quantitated using real-time PCR. (3449)

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Genetics 172, 1867–1876. New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci. 2006

el-Lithy, M.E., Bentsink, L., Hanhart, C.J., Ruys, G.J., Rovito, D., Broekhof, J.L., van der Poel, H.J., van Eijk, M.J., Vreugdenhil, D. and Koornneef, M.

Notes: To examine the flowering time for three new Arabidopsis thaliana recombinant inbred lines (RIL), genomic DNA was isolated from leaves of 92 Arabidopsis accessions and from flower buds of the three RILs using the Wizard® Magnetic 96 DNA Plant System. The purified DNA was used for single sequence length polymorphisms (SSLPs) genotyping. (3417)

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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. Forensic Sci. 51, 740–7. Rapid and high-throughput forensic short tandem repeat typing using a 96-lane microfabricated capillary array electrophoresis microdevice. 2006

Yeung, S.H., Greenspoon, S.A., McGuckian, A., Crouse, C.A., Emrich, C.A., Ban, J. and Mathies, R.A.

Notes: The authors evaluated a 96-channel microfabricated capillary array electrophoresis (µCAE) device for forensic STR typing using the PowerPlex® 16 System and the AmpFlSTR® Profiler Plus® kit. DNA was isolated from one semen (sperm and nonsperm fractions), nine saliva, four blood and two mixed blood stains using either organic extraction or the DNA IQ™ System, then .5–1.0 ng was amplified using the PowerPlex® 16 System and the AmpFlSTR® Profiler Plus® kit according to the manufacturer's instructions. Amplified products were analyzed initially using an ABI PRISM® 310 or Hitachi FMBIO® II instrument, then using the µCAE device. All 48 samples, as well as all minor alleles in 3:1 mixture samples, were accurately typed using the µCAE device. (3772)

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J. Forensic Sci. 51, 351–356. The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains. 2006

Opel, K.L., Chung, D.T., Drábek, J., Tatarek, N.E., Jantz, L.M. and McCord, B.R.

Notes: The authors developed a new set of miniplex primers for DNA typing of degraded DNA from human skeletal remains. The miniplex primers produced smaller amplicons (50–280 base pairs) than standard STR systems. The DNA-typing results obtained with the miniplex primers were compared to results obtained with the PowerPlex® 16 System. The authors determined that larger loci failed to amplify when using degraded DNA and that the degradation cut-off length of template fragments occurred predominantly at 200bp and is not kit-dependent. (3808)

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Int. Congr. Ser. 1288, 249–51. Y-chromosome variation in northeastern Poland. 2006

Pepinski, W., Niemcunowicz-Janica, A., Skawronska, M., Janica, J.R., Koc-Zorawska, E., Janica, J. and Soltyszewski, I.

Notes: The authors generated Y-STR haplotype frequency data for several ethnic populations in Poland using the PowerPlex® Y System. DNA was isolated using Chelex® resin and a proteinase K protocol and amplified, and amplification products were detected using an ABI PRISM® 310 Genetic Analyzer. (3869)

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J. Immunol. 175, 5457–5462. A genetic basis for IFN-gamma production and T-bet expression in humans. 2005

Höhler, T., Reuss, E., Adams, P., Bartsch, B., Weigmann, B., Wörns, M., Galle, P.R., Victor, A. and Neurath, M.F.

Notes: The authors conducted a classical twin study to define the genetic contribution to cytokine production and regulation of T cell-specific transcription factors. Twins were classified as monozygotic and dizygotic by typing 15 short tandem repeat loci using the PowerPlex® 16 System. (3807)

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Legal Med. (Tokyo) 7, 314–318. DNA typing from skeletal remains following an explosion in a military fort--first experience in Ecuador (South-America). 2005

González-Andrade, F. and Sánchez, D.

Notes: On November 20, 2002, an explosion in a munitions facility left 7 people dead, 100 injured and 5 missing. The authors used DNA typing to identify 2 tissue samples and 19 bone samples. These samples, as well as reference samples from relatives of the missing persons, were analyzed using the PowerPlex® 16 System. DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and concentrated, then amplified using 28–30 cycles. For bone samples, the cycle number was increased to 35. The success rate was 90% (19 of 21 samples identified; 2 of 21 samples had a high degree of contamination and could not be identified). (3819)

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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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Vet. Parasitol. 133, 283-287. Genotyping of Giardia intestinalis from domestic and wild animals in Japan using glutamete dehydrogenase gene sequencing. 2005

Itagaki, T., Kinoshita, S., Aoki, M., Itoh, M., Saeki, H., Sato, N., Uetsuki, J., Izumiyama, S., Yagita, K., and Endo, T.

Notes: GoTaq® DNA Polymerase was used in PCR genotyping of Giardia intestinalis. Primers were designed around a 177 bp sequence of the glutamete dehydrogenase gene (gdh). Typing was based on previously reported assemblages of gdh from cats, dogs, cows and monkeys. PCR was performed in a total reaction volume of 25μl using 1.25 units of GoTaq® DNA Polymerase.
(3364)

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Cancer Genet. Cytogenet. 158, 84–7. SKY and genetic fingerprinting reveal a cross-contamination of the putative normal colon epithelial cell line NCOL-1. 2005

Melcher, R., Maisch, S., Koehler, S., Bauer, M., Steinlein, C., Schmid, M., Kudlich, T., Schauber, J., Luehrs, H., Menzel, T. and Scheppach, W.

Notes: The authors performed spectral karyotyping and genetic fingerprinting of the normal colon cell lines NCOL-1a and NCOL-1b. DNA fingerprints covering 11 STR loci and amelogenin were generated using the PowerPlex® ES System and the AmpFlSTR® SGM Plus kit. These two multiplex systems share 7 loci, which served as overlapping controls. The fact that the DNA fingerprints had a matching probability of 99.9995 led the authors to conclude that the NCOL-1 cell lines were derived from the LoVo cell line, probably through contamination. (3838)

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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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J. Bacteriol. 186, 3214-3223. Salmonella enterica Serovar Typhi strains from which SPI7, a 134-kilobase island with genes for Vi exopolysaccharide and other functions, has been deleted. 2004

Nair, S., Alokam, S., Kothapalli, S., Porwollik, S., Proctor, E., Choy, C., McClelland, M., Liu, S.L. and Sanderson, K.E.

Notes: In this study, the Wizard® Genomic DNA Purification Kit was used to isolate chromosomal DNA from Salmonella enterica serovar Typhi. The isolated DNA was used in multiplex PCR to determine the presence or absence of certain DNA regions in various clinical isolates.  (3127)

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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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J. Forensic Sci. 49, 29-39. Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples. 2004

Greenspoon, S.A., Ban, J.D., Sykes, K., Ballard, E.J., Edler, S.S., Baisden, M., and Covington, B.L.

Notes: This paper discusses automated DNA purification from a variety of forensic casework samples using the DNA IQ™ System on a Beckman BioMek® 2000 Laboratory Automated Workstation.  DNA was purified from various forensic casework samples including vaginal swabs, blood stains, tissue and samples.  The researchers also tested diluted and contaminated samples and the ability of the DNA IQ™ System on the Beckman BioMek® 2000 to purify DNA from these samples.  The PowerPlex® 1.1 System was used as a representative forensic laboratory typing system to test the contaminant level in all of the DNA IQ™ purified DNA samples.  (3052)

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