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Mol. Biol. Cell 23, 864–80. Caveolin targeting to late endosome/lysosomal membranes is induced by perturbations of lysosomal pH and cholesterol content. 2012

Mundy, D.I., Li, W.P., Luby-Phelps, K. and Anderson, R.G.

Notes: In this paper, FuGENE® HD reagent was used to transiently transfect SV589 Human Fibroblast cells. Transfection conditions were as follows: Cells were grown in 35mm plates and transfected with 2µg DNA at a 3:1 FuGENE® reagent:DNA ratio. (4422)

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J. Virol. 86, 8198–8209. Cellular GCN5 is a Novel Regulator of Human Adenovirus E1A-Conserved Region 3 Transactivation 2012

Ablack, J.N.G., Cohen,M., Thillainadesan, G., Fonseca, G.J., Pelka, P., Torchia, J. and Mymryk, J.S.

Notes: FuGENE HD reagent was used for transient transfection of A549 cells and wild type mouse embryonic fibroblasts. A 3:1 ratio of reagent to DNA was used in the transfection reactions (9µl reagent, 3µg DNA). (4410)

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Proc. Natl. Acad. Sci. USA 109, 12662-12667. Circadian clock protein cryptochrome regulates the expression of proinflammatory cytokines. 2012

Narasimamurthy, R., Hatori, M., Nayak, S.K., Liu, F., Panda, S., and Verma, I.M.

Notes: Sleep deprivation increases susceptibility to diseases such as diabetes and cancer. Because chronic inflammation is a feature of these diseases, the authors of this paper investigated whether the circadian oscillator component Cryptochrome (CRY) has a role in regulating the immune response. They found constitutive NF-κB and protein kinase A (PKA) activation in Cry1(-/-);Cry2(-/-) knockout mice, and high basal levels of cAMP. As part of the study, the effect of CRY overexpression on intracellular cAMP levels was evaluated in 293T cells using the bioluminescence-based GloSensor™ cAMP Assay. Overexpression of CRY1 reduced the cAMP production induced by forskolin, prostaglandin E2 or isoproterenol. Immunoprecipitation analysis with Flag-tagged CRY1 showed that CRY1 binds to adenylyl cyclase and limits cAMP production. The authors suggest that reduced CRY expression in chronic sleep deprivation may result in elevated cAMP levels, leading to increased PKA and NF-κB activation and offering a potential link between sleep deprivation, circadian rhythm disruption and chronic inflammation. (4224)

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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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Appl. Environ. Microbiol. 78, 420–8. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. 2012

Lopez-Siles, M. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Faecalibacterium prausnitzii. (4333)

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Cancer Res. 72, 335-345. Curcumin analogue CDF inhibits pancreatic tumor growth by switching on suppressor microRNAs and attenuating EZH2 expression.
2012

Bao, B., Ali, S., Banerjee, S., Wang, Z., Logna, F., Azmi, A.S., Kong, D., Ahmad, A., Li, Y., Padhye, S., and Sarkar, F.H.

Notes: EZH2 is an epigenetic regulator of cell proliferation that is known to be overexpressed in certain cancers. These authors evaluated the effect of the curcumin analogue CDF on expression of EZH2 in pancreatic cancer cells. The identity of the human pancreatic cancer cell lines used in the study was verified using the PowerPlex® 16 System. (4223)

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Anti-Cancer Drugs 23, 51–64. Cytotoxicity of human recombinant arginase I (Co)-PEG5000 in the presence of supplemental L-citrulline is dependent on decreased argininosuccinate synthetase expression in human cells
2012

Agrawal, V., Woo, J. H., Mauldin, J.P., Jo, C., Stone, E.M., Georgiou, G. and Frankel, A.E.

Notes: The authors used the CellTiter 96® AQueous One Solution Cell Proliferation Assay (MTS) as a third assay (in addition to 3H thymidine and 3H leucine assays) to assess the response of cells to CoArgIPEG and demonstrated not only a decline in cell survival with treatment but also a decline in proliferation and protein synthesis in most cases.

The CellTiter 96® AQueous One Solution Cell Proliferation Assay (MTS) was also used to evaluate the effect of recovery in cancer cells. The authors determined that prolonged treatment resulted in cytotoxicity; however, assessment at 24 hours showed that some cells survived in the short term. Because the authors knew proliferation/protein synthesis inhibition was occurring, evaluation with a cell survival assay like the CellTiter 96® AQueous One Solution Cell Proliferation Assay (MTS) was required for a more complete understanding of cellular health and response. (4511)

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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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J. Biomol. Scr. 17, 993–8. Development of a novel ectonucleotidase assay suitable for high-throughput screening. 2012

Sachsenmeier, K.F., Hay, C., Brand, E., Clarke, L., Rosenthal, K., Guillard, S., Rust, S., Minter, R. and Hollingsworth, R.

Notes: The authors of this paper describe the development of a high-throughput assay to screen for antibody inhibitors of 5´-ectonucleotidase activity (converts AMP to adeonsine plus free phosphate). They used the CellTiter-Glo® Cell Viability Assay to screen for activity. The CellTiter-Glo® luciferase reaction is inhibited by AMP; activity of 5´-ectonucleotidase eliminates AMP, thereby relieving the reaction from inhibition, producing light. The authors demonstrate release of the luciferase reaction from inhibition as a result of 5´-ectonucleotidase activity, and that they were able to show inhibition of 5´-ectonucleotidase activity by anti-5´-ectonucleotidase antibodies. (4261)

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J. Animal Sci. epub . Direct fed microbial supplementation repartitions host energy to the immune system 2012

Qiu, R., Croom, J., Ali, R.A., Ballou, A.L., Smith, C., Ashwell, C.M., Hassan, H.M., Chiang, C.-C. and Koci, M.D.

Notes: The authors of this study investigated the energetic effects of direct fed microbials on 1-day-old broiler chicks. They looked at body weight, feed consumption, whole-body energy expenditure, organ mass, tissue respiration rates and peripheral blood mononuclear cell (PBMC) ATP levels to explore effects on energy metabolism in control-diet chicks versus chicks receiving direct fed microbials. An ATP assay was used because previous attempts to monitor O2 use by PMBCs were inconclusive. PBMC ATP levels were measured using the CellTiter-Glo™ Luminescent Cell Viability Assay in 96-well plates using 10 × 105 cells/well. The authors also looked for differences in ATP depletion in control and experimental chick populations by using an ATP synthase inhibitor and a proton ionophore. In this study, the authors concluded that the PMBC isolated from the direct microbial fed animals consumed more ATP/cell than the controls. (4202)

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156, 278–85. Diversity of spore-forming bacteria and identification of Bacillus amyloliquefaciens as a species frequently associated with the ropy spoilage of bread. 2012

Valerio, F. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Bacillus amyloliquefaciens. (4312)

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ACS Chemical Biology 7(11), 1848-57. Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. 2012

Hall, M.P., Unch, J., Binkowski, B.F., Valley, M.P., Butler, B.L., Wood, M.G., Otto, P., Zimmerman, K., Vidugiris, G., Machleidt, T., Robers, M.B., Benink, H.A., Eggers, C.T., Slater, M.R., Meisenheimer, P.L., Klaubert, D.H., Fan, F., Encell, L.P., and Wood, K.V.

Notes: These authors describe the engineering of an enzyme and substrate to create a novel highly efficient bioluminescence system. The paper introduces NanoLuc™ Luciferase, a small luciferase subunit (19kDa) from the deep-sea shrimp Oplophorus gracilirostris, which provides ∼2.5 millionfold improved luminescence activity in mammalian cells by merging optimization of protein structure with development of a novel imidazopyrazinone substrate (furimazine). The glow-type luminescence (signal half-life >2 hours) produced by the new luciferase has a specific activity ∼150-fold greater than either firefly or Renilla luciferases similarly configured for glow-type assays. In mammalian cells, NanoLuc™ Luciferase shows no evidence of post-translational modifications or subcellular partitioning. The enzyme exhibits high physical stability, retaining activity with incubation up to 55°C or in culture medium for >15 hours at 37°C.
The authors discuss utility of NanoLuc™ Luciferase as a genetic reporter configured for high sensitivity or for response dynamics through addition of a degradation sequence to reduce intracellular accumulation. Data shows the effect of adding a signal sequence to allow export of NanoLuc™ Luciferase to the culture medium, allowing measurement of enzyme activity without cell lysis. (4295)

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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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PLos ONE 7, e47892. Epigenetic disruption of the PIWI pathway in human spermatogenic disorders. 2012

Heyn, H., Ferreira, H.J., Bassas, L., Bonache, S., Sayols, S., Sandoval, J., Esteller, M. and Larriba, S.

Notes: The authors used microarray analysis, bisulfite sequencing and pyrosequencing to examine a possible link between aberrant DNA methylation and abnormal human spermatogenesis and male infertility. They identified almost 600 genes that were differentially methylated in testis tissue of men with secretory male infertility. Genomic DNA used in the microarray analysis was extracted from testicular biopsies using the Wizard® Genomic DNA Purification Kit. For the bisulfite sequencing experiments, genomic DNA was bisulfite-modified, amplified, cloned using the pGEM®-T Easy Vector System, then sequenced. (4257)

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J. Bacteriol. 194, 1885. Escherichia coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage. 2012

Kyle, J.L. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Escherichia coli. (4332)

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PLos ONE 7, e37255. Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11. 2012

Raponi, M., Douglas, A.G., Tammaro, C., Wilson, D.I., and Baralle, D.

Notes: In this study, MCF7 human breast adenocarcinoma cells were transfected with plasmid constructs using FuGENE® 6 transfection reagent. Cells were grown to 50% confluence and transfected with 2µg of DNA at a 3:2 ratio of FuGENE® 6 reagent:DNA. (4358)

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359, 37–43. Expression of heparinase I of Bacteroides stercoris HJ-15 and its degradation tendency toward heparin-like glycosaminoglycans. 2012

Hyun, Y.-J., Jung, I.-H. and Kim, D.-H.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Bacteroides stercoris. (4313)

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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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Sci. Signal. 5, ra64. FAM123A binds to microtubules and inhibits the guanine nucleotide exchange factor ARHGEF2 to decrease actomyosin contractility 2012

Siesser, P.F., Motolese, M., Walker, M.P., Goldfarb, D., Gewain, K., Yan, F., Kulikauskas, R.M., Chien, A.J., Wordeman, L. and Major, M.B.

Notes: To better understand what roles FAM123A may play in signaling, cell behavior and human disease, HT1080 sarcoma cells were plated on MatTek dishes coated with 5mg/ml fibronectin before transfection with Venus (a yellow fluorescent protein)-tagged FAM123A or Venus-WTX, another member of the FAM123 gene family, using FuGENE® HD Transfection Reagent. The cells were imaged the next day for low-resolution analysis. For a higher magnification, dynamic analysis, HT1080 cells were plated onto Delta T dishes coated with 5mg/ml fibronectin and transfected with EGFP-FAM123A and FuGENE® HD Transfection Reagent. The next day, cell images were captured every 10 seconds. Examining the effect of silencing FAM123A, a reporter assay used the pGL4.34[luc2P/SRFRE/Hygro] Vector cotransfected with a CMV-Renilla coreporter and other effector plasmids or siRNA, and luciferase levels assessed using the Dual-Glo® Luciferase Assay System. (4246)

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Veterinary Microbiology 161, 169–78. Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: predominance of a clonal complex. 2012

Siekoula-Nguedia, C. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Flavobacterium psychrophilum. (4334)

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J. Bacteriol. 194, 6950–1. Genome sequence of Clostridium tunisiense TJ, isolated from drain sediment from a pesticide factory. 2012

Sun, L. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Clostridium tunisiense TJ. (4291)

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J. Bacteriol. 194, 4452–3. Genome sequence of the rice pathogen Dickeya zeae strain ZJU1202. 2012

Li, B. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Dickeya zeae. (4327)

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Funt. Integr. Genomics 12, 119–130. Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. 2012

Shin, J.H., Li, R.W., Gao, Y., Baldwin VI, R. and Li, C.J.

Notes: The authors performed ChIP and quantitated immunoprecipitated DNA with the QuantiFluor® dsDNA System prior to NGS on an Illumina Instrument. (4918)

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Funt. Integr. Genomics 12, 119–30. Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. 2012

Shin, J.H., Li, R.W., Gao, Y., Baldwin, R. 6th and Li, C.J.

Notes: The authors studied the effect of butyrate treatment on histone acetylation and characterized how H3 acetylation affects DNA sequence binding specificity. To examine sequence specificity, they performed chromatin immunoprecipitation with butyrate-treated and untreated bovine kidney epithelial cells, quantified the recovered DNA, then sequenced the DNA by Illumina next-generation sequencing. DNA was quantitifed using the QuantiFluor® dsDNA System. (4240)

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