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Soil Biol. Biochem. 64, 18–27. Contrasting Euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns 2013

Wu, H-W., Zhang, L-M, Yuan, C-L. and He, J-Z.

Notes: Products from PCR of the archaeal 16SrRNA gene were purified using the Wizard® SV Gel and PCR Clean-Up Kit before pyrosequencing. (4549)

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Folia Microbiol. 58, 623–30. Detection and quantification of probiotic strain Lactobacillus gasseri K7 in faecal samples by targeting bacteriocin genes. 2013

Treven, P., Turkova, K., Trmčić, A., Obermajer, T., Rogelj, I. and Matijašić, B.B.

Notes: The authors were interested in quantitating the presence as well as the prevalence of Lactobacillus gasseri K7 in humans that did not consume the probiotic bacteria. Fecal samples from 45 healthy adults were collected, frozen, diluted, centrifuged and digested with proteases. After sonication, DNA was extracted using the Maxwell® 16 Tissue DNA Purification kit on the Maxwell® 16 instrument. This same kit and instrument also were used to isolate bacterial DNA from 1ml bacterial cultures. The purified DNA was PCR amplified using primers for gassericin K7 A and K7 B (bacteriocin) genes and GoTaq® Flexi DNA Polymerase in Green GoTaq® Flexi Buffer for 30 cycles. PCR products were analyzed by 1.8 % agarose gel electrophoresis. (4522)

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Epigenetics 8, 534–541. First evidence of DNA methylation in insect Tribolium castaneum: Environmental regulation of DNA methylation with heterochromatin 2013

Feliciello, I., Parazajder, J., Akrap, I. and Ugarović, Ð.

Notes: GoTaq® Green Master Mix was used to amplify Tribolium castaneum  satellite DNA that had been bisulfite treated to detect methylated cytosines. The bisulfite-treated satellite DNA was amplified using methyl-specific primers in a total volume of 30µl using 2X GoTaq® Green Master Mix, 2mM mix of the primer sets, and 1µl of the bisulfite modified DNA.

  (4356)

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PLos ONE 8, e67151. First transcriptome and digital gene expression analysis in Neuroptera with an emphasis on chemoreception genes in Chrysopa pallens (Rambur) 2013

Li, Z.Q., Zhang, S., Ma, Y., Luo, J.Y., Wang, C.Y., Lv, L.M., Dong, S.L. and Cui, J.J.

Notes: RNA was isolated from adult C. pallens (insect) tissues using the SV Total RNA Isolation System prior to cDNA library construction and sequencing on the Illumina HiSeq™ platform. To validate NGS sequence alignment, end-to-end PCR was performed. PCR products were purified using the Wizard® SV Gel and PCR Clean-Up System prior to cloning into a T vector. To verify the identified differentially expressed genes, quantitative real-time PCR (RT-qPCR) was used. Total RNA was extracted and cDNAs synthesized using the Reverse Transcription System prior to qPCR. (4560)

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Proc. Natl. Acad. Sci. USA 110, 18620–5. GATA-1 regulates the generation and function of basophils. 2013

Nei, Y., Obata-Ninomiya, K., Tsutsui, H., Ishiwata, K., Miyasaka, M., Matsumoto, K., Nakae, S., Kanuka, H., Inase, N. and Karasuyama, H.

Notes: RNA was isolated from mouse basophils following fluorescence-activated cell sorting and used in RT-qPCR analysis. (4443)

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PLos ONE 8, e84071. Gene expression profiling of early hepatic stellate cell activation reveals a role for Igfbp3 in cell migration. 2013

Mannaerts, I., Schroyen, B., Verhulst, S., Van Lommel, L., Schuit, F., Nyssen, M. and van Grunsven, L.A.

Notes: Mouse hepatic stellate cells (HSCs) were cultured with valproic acid for various times. Total RNA was isolated and analyzed for multiple transcripts by RT-qPCR using the dye-based GoTaq® RT-qPCR System. Total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System and used for RT-qPCR and expression profiling with an Affymetrix genechip array. (4610)

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J. Biotechnol. 166, 42–50. Molecular characterization of the first transgenic common bean immune to the Bean golden mosaic virus 2013

Aragão, F.J., Noqueira, E.O. Tinoco, M.F. and Faria, J.C.

Notes: PCR products from a tertiary TAIL-PCR were separated by agarose gel electrophoresis and purified using the Wizard® SV Gel and PCR Clean-Up Kit. Purified fragments were cloned into pGEM®-T Easy Vectors, and clones were sequenced. (4547)

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Biomaterials 34, 2005-16. Neural stem cells encapsulated in a functionalized self-assembling peptide hydrogel for brain tissue engineering. 2013

Cheng, T.-Y., Chen, M.-H., Chang, W.-H., Huang, M.-Y., and Wang, T.-W.

Notes: Rat neural stem cells were cultured in a 3D hydrogel for either 7 days or 14 days. The hydrogel was destroyed by pipeting and RNA was isolated from the cells with the ReliaPrep™ RNA Cell Miniprep System. The quantity of RNA was determined with the QuantiFluor® RNA Dye System prior to dye-based real-time amplification with the GoTaq® 1-Step RT-qPCR System. The levels of three targets were compared at the 7 day and 14 day time points. (4595)

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Nucl. Acids Res. 41, 8515–25. Pin1 promotes GR transactivation by enhancing recruitment to target genes. 2013

Poolman, T.M., Farrow, S.N., Matthews, L., Loudon, A.S. and Ray, D.W.

Notes: RNA was extracted from cultured A549 cells and used in RT-qPCR to analyze the effect of transfected siRNAs. (4444)

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Nucl. Acids Res. 41, e112. Reflex: Intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs. 2013

Casbon, J.A., Slatter, A.F., Musgrave-Brown, E., Osborne, R.J., Lichtenstein, C.P. and Brenner, S.

Notes: A 50µl long-range polymerase chain reaction (LRPCR) used 1.25U of GoTaq® Hot Start Polymerase to amplify 250ng of genomic DNA and generate amplicons with multiplex identifier (MID) tags. Reflex extension reactions (25µl) included 1.25U of GoTaq® Hot Start DNA Polymerase in 1X Herculase II Reaction Buffer, 0.5µl of Herculase II Fusion DNA Polymerase) and 0.3pM LRPCR products. (4550)

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Genome Biol. Evol. 5, 1298–1308. Substantial variation in the extent of mitochondrial genome fragmentation among blood-sucking lice of mammals. 2013

Jiang, H., Barker, S.C. and Shao, R.

Notes: PCR products were analyzed on a 1% agarose gel and sized with molecular markers before selection for purification using the Wizard® SV Gel and PCR Clean-Up System. The chosen purified PCR amplicons were then used in NGS. (4557)

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J. Virol. 87, 11945–11949. The Toll and Imd Pathways Are Not Required for Wolbachia-Mediated Dengue Virus Interference 2013

Rancès, E., Johnson, T.K., Popovici, J., Iturbe-Ormaetxe, I., Zakir, T., Warr, C.G. and O’Neil, S.L.

Notes: DNA was extracted from 9 to 15 individual Wolbachia females either 2 or 8 days posteclosion, using the ReliaPrep™ gDNA Tissue MiniPrep System. Wolbachia density was then determined by relative qPCR. (4732)

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Front. Microbiol. 4, 377. Transgenic expression of the human LEDGF/p75 gene relieves the species barrier against HIV-1 infection in mouse cells. 2013

Tada, T., Kadoki, M, Liu, Y., Tokunaga, K., and Iwakura, Y.

Notes: Mouse Endothelial Fibroblast were isolated from transgenic mice and human LEDGF/p75 expression levels were examined by dye-based RT-qPCR. The total RNA was isolated with the ReliaPrep™ RNA Cell Miniprep System. (4605)

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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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mBio. 3(5), e00266–12. A multicenter blinded analysis indicates no association between chronic fatigue syndrome/myalgic encephalomyelitis and either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus. 2012

Alter, H.J., Mikovits, J.A., Switzer, W.M., Ruscetti, F.W., Lo, S.C., Klimas, N., Komaroff, A.L., Montoya, J.G., Bateman, L., Levine, S., Peterson, D., Levin, B., Hanson, M.R., Genfi, A., Bhat, M., Zheng, H., Wang, R., Li, B., Hung, G.C., Lee, L.L., Sameroff, S., Heneine, W., Coffin, J., Hornig, M. and Lipkin, W.I.

Notes: In this report, the original investigators who found XMRV and pMLV (polytropic murine leukemia virus) in blood of subjects with Chronic Fatigue Syndrome (CFS) report that this association is not confirmed in a blinded analysis of samples from rigorously characterized subjects.

The CDC performed nucleic acid testing assays. Plasma was centrifuged and RNA isolated from the pellet. Quantitative real-time RT-PCR assays (qRT-PCR) for generic pMLV/XMRV pro (protease) and gag detection were performed on RNA extracts, using the AccessQuick™ RT-PCR System and an AgPath one-step RT-PCR kit.

ArrayScript RT and AmpliTaq Gold DNA polymerase were used for cDNA synthesis and amplification in the pro and gag qRT-PCR assays, respectively. A third PCR was done using the primers XPOLOF and XPOLOR, followed by a nested PCR with the primers XPOLIF and XPOLIR for the generic detection of MLV/XMRV 216-bp pol sequences. For this reaction, cDNA synthesis and amplification of RNA was done using Promega AMV Reverse Transcriptase and a RobustI RT-PCR kit. Each PCR experiment included 20 water-only reactions to control for contamination. (4300)

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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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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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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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Clin. Chem. 58, 580–9. COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. 2012

Milbury, C.A. et al.

Notes: Human Genomic DNA: Male was used to dilute experimental genomic DNA from cell lines and tumor samples for PCR before sequencing. (4543)

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Food Control 23, 400-404. Development and validation of fast Real-Time PCR assays for species identification in raw and cooked meat mixtures. 2012

Cammà, C., Di Domenico, M., and Monaco, F.

Notes: These authors used the Maxwell® 16 Tissue DNA Purification Kit to extract DNA from 200µl samples of raw meat homogenate from beef, pork, poultry and lamb samples. They also used the Wizard® Genomic DNA Isolation System to extract DNA from cooked meat samples. The extracted DNA was used in real-time, quantitative PCR assays to identify species-specific DNA spiked at 1% in mixed DNA samples. (4353)

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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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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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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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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 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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