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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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Sci. Signal. 4(180), online. Identification of a lysosomal pathway that modulates glucocorticoid signaling and the inflammatory response 2011

Yuanzheng, H., Xu, Y., Zhang, C., Gao, X., Dykema, K.J., martin, K.R., Ke, J., Hudson, E.A., Khoo, S.K., Resau, J.H., Alberts, A.S., Mackeigan, J.P., Furge, K.A. and Xu, H.E.

Notes: Yuangheng He and colleagues asked how the weak alkaline compound chloroquine (CQ) enhances the anti-inflammatory effects of synthetic glucocorticoids like dexamethasone, which are used to treat a host of inflammatory and autoimmune diseases. In the process they explored the intersection of lysosomal degradation pathways and glucocorticoid receptor signaling. They used Dual-Glo® Luciferase Assay System to look at glucocorticoid receptor-mediated (GR) activation and repression of reporters in AD293 cells under a variety of conditions (presence or absence of CQ; stripped serum, loss of lysosome synthesis, inhibition of V-ATPase, etc). They also used HaloTag® protein fusions to observe the fate of GR populations in the presence or absence of CQ and in the presence or absence of compounds that impair proteasome function. Live-cell imaging of GR-HaloTag® protein fusions revealed a dynamic association of the GR with lysosomes. The authors showed that glucocorticoid signaling is regulated by lysosomes. (4203)

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J. Biomol. Scr. 16(9), 995–1006. A biochemical screen for identification of small-molecule regulators of the wnt pathway using Xenopus egg extracts. 2011

Thorne, C.A., Lafleur, B., Lewis, M., Hanson, A.J., Jernigan, K.K., Weaver, D.C., Huppert, K.A., Chen, T.W., Wichaidit, C., Cselenyi, C.S., Tahinci, E., Meyers, K.C., Waskow, E., Orton, D., Salic, A., Lee, L.A., Robbins, D.J., Huppert, S.S. and Lee, E.

Notes: The authors used a biochemical assay using Xenopus egg extracts to monitor degradation levels of two Wnt pathway components, Axin and ß-catenin, and identify modulators of the Wnt pathway. ß-catenin and Axin were expressed in vitro as firefly and Renilla luciferase fusion proteins, respectively, using the TNT® SP6 High-Yield Protein Expression System and shown to behave in Xenopus extracts in a similar way to wildtype proteins, which were expressed as radiolabled proteins in rabbit reticulocyte lysate. Degradation of labeled proteins was monitored by SDS polyacrylamide gel electrophoresis and autoradiography, and degradation of luciferase fusion proteins was examined using the Dual-Glo® Luciferase Assay. Using the Xenopus extract-based assay, the authors screened chemical libraries to identify two modulators of the Wnt pathway, then confirmed this inhibition in HEK 293 cells by demonstrating a decrease in ß-catenin expression with increasing concentrations of the inhibitors. This decrease in ß-catenin-Fluc levels was measured using the Steady-Glo™ Luciferase Assay, and luciferase activity was normalized to cell viability, as determined using the CellTiter-Glo® Assay. (4181)

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J. Infectious Diseases 204, 1011–20. VP24 is a molecular determinant of Ebola virus virulence in guinea pigs. 2011

Mateo, M., Carbonnelle, C., Reynard, O., Kolesnikova, L., Nemirov, K., Page, A., Volchkova, V.A. and Volchkov, V.E.

Notes: The authors used Dual-Glo® Luciferase Assay to measure a pISG54 promoter-driven firefly luciferase gene (0.5µg) and pRL-TK plasmid constitutively expressing Renilla luciferase (0.1µg), and either a plasmid (0.5µg) expressing the corresponding variants of Ebola virus (EBOV) structural protein VP24 construct (phCMV-EBOV-VP24) or empty phCMV in HEK 293T and GPC-16 transfected cells. A total of 1.1µg of DNA was transfected. Cells were stimulated with interferon (IFN) 24 hours post-transfection, harvested 16 hours later, and assayed for dual-luciferase activity. Data indicated that mutations in the V24 protein were associated with EBOV virulence but that this virulence was not linked to the IFN-antagonist function of V24 protein. (4178)

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Cancer Res. 70, 9641–9. An illegitimate microRNA target site within the 3' UTR of MDM4 affects ovarian cancer progression and chemosensitivity. 2010

Wynendaele, J., Böhnke, A., Leucci, E., Nielsen, S.J., Lambertz, I., Hammer, S., Sbrzesny, N., Kubitza, D., Wolf, A., Gradhand, E., Balschun, K., Braicu, I., Sehouli, J., Darb-Esfahani, S., Denkert, C., Thomssen, C., Hauptmann, S., Lund, A., Marine, J.C. and Bartel, F.

Notes: The authors identified a single nucleotide polymorphism (SNP) in the 3´ untranslated region (3´ UTR) of MDM4, which promotes tumorigenesis by decreasing p53 tumor suppressor function, in ovarian cancer cells. This A to C transversion creates a putative target site for the hsa-miR-191 microRNA in the MDM4-C allele, but not the wildtype MDM4-A allele. To determine if this SNP affects MDM4 translation efficiency or mRNA stability, the authors cloned a 224-bp fragment of the MDM4 3´UTRs into the psiCHECK™-2 Vector and transfected the ovarian cancer cell line A2780 with the 224A or 224C variants of the MDM4 3´ UTR. The authors used the luciferase-based psiCHECK™-2 Vector and Dual-Glo® Luciferase Assay System to show that the C variant dramatically reduces translation efficiency and/or mRNA stability. They also assessed MDM4 expression levels in A/A, A/C and C/C ovarian cancer cells and tissues using RT-qPCR. qPCR primers for MDM4 were designed using the Plexor® Primer Design Software, and assays were performed using the Plexor® qPCR System. (4157)

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J. Lipid Res. 51, 2211–2222. Pioglitazone increases apolipoprotein A-I production by directly enhancing PPRE-dependent transcription in HepG2 cells. 2010

Zhang, L.H., Kamanna, V.S., Ganji, S.H., Xiong, X-M. and Kashyap, M.L.

Notes: The authors investigated the role of pioglitazone on transcriptional regulation of the apoA-I gene and looked at the biological properties of pioglitazone-induced apoA-I-containing high-density lipoprotein particles (HDL). To investigate the biological properties of the HDL particles, the authors treated THP-1 cells with conditioned medium from HepG2 cultures treated or untreated with pioglitazone and looked at adhesion to human aortic endothelial cells (HAEC). During the experiment, HAEC viability and proliferation were monitored using the CellTiter-Glo® Luminescent Cell Viability Assay. Additionally, to determine whether pioglitazone stimulates apoA-I transcription, a luciferase reporter construct was made containing the apoA-I gene promoter. Transfected cells were treated with pioglitazone, and luciferase expression was monitored using the Dual-Luciferase® Reporter Assay System. (4173)

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J. Biol. Chem. 284, 20946–20955. B cell lymphoma (Bcl)-2 protein is the major determinant in bcl-2 adenine-uridine-rich element turnover overcoming HuR activity. 2009

Ghisolfi, L., Calastretti, A., Franzi, S., Canti, G., Donnini, M., Capaccioli, S., Nicolin, A. and Bevilacqua, A.

Notes: To examine post-transcriptional regulation of B cell lymphoma (bcl)-2 mRNA in human cell lines, the bcl-2 open reading frame was cloned into the pCI-neo Mammalian Expression Vector with a FLAG tag. This construct was transfected into U2OS human osteosarcoma cells, lysed, immunoprecipitated on Anti-FLAG-coated beads and analyzed by SDS-PAGE. A 260bp fragment containing the human c-myc 3´UTR adenine-uridine(AU)-rich element (ARE) was cloned into the pGL4.71 [hRlucP] Vector above to produce the pGL4.71PmARE plasmid. For transient expression, SK-N-BE and HEK293 cells in 96-well plates were cotransfected with 200ng of the pGL4.71 constructs (carrying c-myc or bcl-2 ARE) and 200ng of the pGL3-Control Vector. Luciferase expression was assessed using the Dual-Glo® Luciferase Reporter Assay System. HEK293 cells were also stably cotransfected with the same pGL4.71 constructs and a vector carrying G418 resistance. Renilla luciferase expression was assessed and clones chosen with similar expression levels. (4071)

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Cancer Res. 69, 896–904. Prostaglandin E2 stimulates human lung carcinoma cell growth through induction of integrin-linked kinase: the involvement of EP4 and Sp1. 2009

Zheng, Y., Ritzenthaler, J.D., Sun, X., Roman, J. and Han, S.

Notes: In this paper, the role of prostaglandin E2 (PGE2) stimulation of integrin-linked kinase (ILK) in human lung carcinoma was explored. Mutations of Sp1 and NF-κB cis-acting elements in an ILK promoter-pGL3-Basic Vector construct were created using the GeneEditor™ in vitro Site-Directed Mutagenesis System. The mutations were confirmed via sequencing. Human non–small cell lung carcinoma (NSCLC) cells were plated at a density of 5 × 105 cells per well in six-well plates and transfected with 2µg of ILK promoter reporter vectors with or without 0.2µg of the phRL-TK Renilla Luciferase Reporter Vector. After 24 hours, the transfected cells were exposed to PGE2 and the cells lysed for assessment using the Dual-Luciferase® Reporter Assay System. NSCLC cells were transfected with inactive (ILK-S343A) and superactive ILK (ILK-S343D) cDNA, incubated for 24 hours, treated with or without exogenous PGE2 or with an Sp1 inhibitor for 2 hours. The numbers of viable cells were measured using the CellTiter-Glo® Luminescent Cell Viability Assay. (4026)

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J. Biol. Chem. 283, 30650–7. Cyclin-dependent kinase 2 negatively regulates human pregnane X receptor-mediated CYP34A gene expression in HepG2 liver carcinoma cells. 2008

Lin, W., Wu, J., Dong, H., Bouck, D., Zeng, F.Y and Chen, T.

Notes: HepG2 cells in a T-25 culture flask (3 million cells at 70ndash;80% confluency) were transfected with CYP3A4 reporter plasmid (a pGL3 reporter construct) and a CMV-Renilla control plasmid (a total of 2.5µg of plasmid mix was used) using FuGENE® 6 Reagent for transient transfection assays. Reporter activities were measured using the Dual-Glo® Luciferase Assay System. (4268)

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DNA Research 15, 137-149. Exploration of human ORFeome: High-throughput preparation of ORF clones and efficient characterization of their protein products. 2008

Nagase, T., Yamakawa, H., Tadokoro, S., Nakajima, D., Inoue, S., Yamaguchi, K., Itokawa, Y., Kikuno, R.F., Koga, H. and Ohara, O.

Notes: These authors used the Flexi® Vector System to prepare ORF clones encoding 1929 human genes and to transfer a subset of these clones to various expression vectors for further analysis. They created HaloTag® fusion proteins and examined expression of these proteins in vitro and in COS7 and HEK293 cells. They also performed comparisons between the Flexi® System and Gateway® cloning system, specifically examining the effects of flanking sequences on protein expression in in vitro translation systems and confirming that the cellular localization of the HaloTag® fusion proteins was consistent with results obtained using GFP-fusions. (3800)

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Assay Drug Dev. Technol. 5, 127–136. Bioluminescent assays for high-throughput screening 2007

Fan, F. and Wood, K.V.

Notes: The authors of this paper review bioluminescent assay technologies, discussing HTS reporter, cell-based and luciferase biosensor assays. They divide luminescent assays into three basic categories: assays that measure ATP concentration (cell viability and kinase assays), assays that measure changes in luciferase levels (reporter assays, GPCR assays), and assays that measure changes in luciferin levels (protease [including caspase], P450 and MAO assays). (3737)

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J. Virol. 81, 558–567. Hijacking components of the cellular secretory pathway for replication of poliovirus RNA. 2007

Belov, G.A., Altan-Bonnet, N., Kovtunovych, G., Jackson, C.L., Lippincott-Schwartz, J. and Ehrenfeld, E.

Notes: In this study, the Renilla luciferase gene from the phRL-CMV Vector was incorporated into polioviral RNA in place of a structural protein-coding region. Renilla luciferase activity was then monitored as a convenient indicator of viral replication. Specifically, these authors tested whether the guanine nucleotide exchange factors GBF1 and BIG2 could rescue brefeldin A (BFA)-induced inhibition of polioviral replication in HeLa cells. Cells were transfected with plasmids encoding either GBF1 or BIG2, together with the firefly-luciferase-encoding pGL4.13 Vector, which was used as a control to monitor transfection efficiency. Eighteen hours post-transfection, the cells were transfected with polioviral replicon RNA containing the Renilla luciferase gene. One hour later, normal growth medium containing EnduRen® Live Cell Substrate and either BFA or solvent alone, was added and Renilla luciferase activity was monitored at hourly intervals for 7 hours. Cells were then lysed and firefly luciferase activity was measured to assess transfection efficiency using the Dual-Glo® Luciferase Assay System System. In the presence of BFA, GBF1 was able to partially rescue viral replication. In the presence of BIG2 and BFA, no viral replication occurred. (3562)

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Proc. Natl. Acad. Sci. USA 104, 19256-19261. Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein. 2007

Betzi S, Restouin A, Opi S, Arold ST, Parrot I, Guerlesquin F, Morelli X, Collette Y.

Notes: The authors wanted to screen inhibitory compounds for the HIV-1 accessory protein Nef using both computer modeling and experimental methods. Using a structure-based program for the SH3 binding surface of Nef, drug compounds were screened in silico and then further analyzed using a cell-based assay. The Nef gene and SH3 domain were cloned into the pACT and pBIND Vectors of the CheckMate™ Mammalian Two-Hybrid System, transfected into COS-7 cells, and 18 hours later, the cells exposed to potential inhibitors. After 24 hours, luciferase activity was assessed using either the Dual-Glo™ or the Steady-Glo® Luciferase Assay Systems. (3751)

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J. Biol. Chem. 282, 15284–15293. Synergism of accessory factors in functional expression of mammalian odorant receptors. 2007

Zhuang, H. and Matsunami, H.

Notes: To explore the role that accessory proteins may play in successfully expressing odorant receptors (ORs) on the cell surface of heterologous cells, the authors explored cotransfecting receptor-transporting proteins RTP1S, Ric8b and Gαolf with an N-terminally tagged OR to generate a functional and ligand-specific expression system. Three tags (Rho, FLAG or HA) were inserted into the NheI and EcoRI sites of the pCI Mammalian Expression Vector. Amplified OR orfs were cloned into the MluI and NotI sites of the tagged pCI Mammalian Expression Vector. The accessory proteins were subcloned into HA-pCI (RTP1S) or pCI (RTP1S, Ric8b, Hsc70t and Gαolf). For cotransfection, the N-terminal tagged OR vectors (0.8µg) and the assessory proteins (individually or in combination; 0.8µg) were transfected into HEK293T or Hana3A cells. The transfected cells were then subjected to immunocytochemistry, live-cell surface staining, permeabilized staining or FACS analysis. The Dual-Glo™ Luciferase Assay System was used to assess OR activation via CRE elements on a firefly luciferase vector. pRL-SV40 Vector was the internal control for cell viability and transfection efficiency. HEK293T or Hana3A cells were plated on 96-well plates, transfected with 1µg of CRE-Luc vector, 1µg of pRL-SV40 Vector, 5µg of OR and 1µg total for all accessory proteins (0.25µg each protein with pCI Mammalian Expression Vector to keep amount of plasmid constant). Twenty-four hours posttransfection, the medium was changed to CD293 chemically defined medium, incubated for 30 minutes at 37°C then replaced with 25µl of odorant solution in CD293 for a second incubation of 4 hours at 4°C. Then the reporter protein expression levels were measured by luminescence. (3687)

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Proc. Natl. Acad. Sci. USA 103, 16834-16839. A genetic variant that disrupts MET transcription is associated with autism. 2006

Campbell, D.B., Sufcliffe, J.S., Ebert, P.J., Militerni, R., Bravaccio, C., Trillo, S., Elia, M., Schneider, C., Melmed, R., Sacco, R., Persico, A.M. and Levitt, P.

Notes: In this family-based study of 1,231 autism cases, a genetic association of a common C allele in the promoter of the MET gene and autism was identified. Initial sequencing of the MET genes from 86 individuals with autism was used to identify several candidate variants in the MET promoter and 3´ untranslated region. Family-based analyses were then performed to determine whether an association could be demonstrated between any of these variants and autism. A G/C variant 20bp 5´ of the MET transcription start site was found to be overrepresented among individuals with autism, particularly among families where more than on child was affected. Once the candidate variant was identified, the effect of the G/C change on transcription of the MET gene was investigated in a reporter assay. Two 762 bp fragments of the MET promoter region, differing only in the G/C nucleotide, were cloned into pGL4.10 firefly luciferase reporter vectors. These vectors were then transfected into mouse neural cell lines, and luciferase production was monitored using the Dual-Glo™ Assay. The construct containing the C allele produced less than half of the luciferase activity of construct containing the G allele. (3579)

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Cancer Res. 66, 9731–9735. Identification of a chemical inhibitor of the oncogenic transcription factor forkhead box M1. 2006

Radhakrishnan, S.K., Bhat, U.G., Hughes, D.E., Wang, I.C., Costa, R.H. and Gartel, A.L.

Notes: To screen a compound library for an inhibitor of FoxM1 transcriptional activity, U2OS cells with doxycyclin-inducible FoxM1-green fluorescent protein (GFP) fusion protein were stably transfected with a firefly luciferase construct driven by a 6× FoxM1 responsive promoter and the pRL-CMV Vector. These cells were grown overnight in 96-well plates, treated with doxycyclin and test compounds. Firefly and Renilla luciferase expression was assessed using the Dual-Glo™ Luciferase Assay System. (3730)

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J. Biol. Chem. 281, 9030-9037. The plasma membrane lactate transporter MCT4, but not MCT1, is up-regulated by hypoxia through a HIF-1alpha-dependent mechanism. 2006

Ullah, M.S., Davies, A.J. and Halestrap, A.P.

Notes: Monocarboxylate transporters (MCT) transport lactic acid across the cell membrane. The promoters of 4 MCT family members (MCT1, MCT2, MCT3 and MCT4), were amplified by PCR and cloned into the pGEM®-T Easy Vector. The sequences were confirmed, and the promoters were cloned into the pGL3-Basic Vector. The Dual-Glo™ Luciferase Assay System was used to quantitate promoter activity under basal and hypoxic conditions in HeLa cells. The pRL-SV40 Vector was used to normalize for differences in transfection efficiency. (3463)

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J. Immunol. 175, 5981–5985. Transcriptional activators of helper T cell fate are required for establishment but not maintenance of signature cytokine expression. 2005

Martins, G.A., Hutchins, A.S. and Reiner, S.L.

Notes: To determine the potential role that T-bet, a T-box transcription factor that specifies Th1 lineage commitment, and Hlx, a homeobox gene, may have in helper T cell differentiation, the physical interaction between the two proteins was tested using the CheckMate™ Mammalian Two-Hybrid System. The pACT-T-bet and pBIND-Hlx fusion vectors were co-transfected with pG5luc into 293T cells. After 48 hours, the firefly and Renilla luciferase activities were measured using the Dual-Glo® Luciferase Assay System. (3493)

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J. Immunol. 172, 5512–5521. Human CD1D gene has TATA boxless dual promoters: An SP1-binding element determines the function of the proximal promoter. 2004

Chen, Q.Y. and Jackson, N.

Notes: These authors demonstrated that the human CD1D gene has distal and proximal TATA boxless promoter sequences. Distal and proximal promoters to CD1D were cloned into the pGL3-Basic Vector to create reporter constructs. One construct contained the entire 4,986 base pair region containing distal and proximal CD1D promoter.  Transient transfections were performed using 5 x 105 Jurkat cells in 24-well plates, 0.8 μg of pGL3 Basic Vector with the insert of interest, and 30ng of pRL-CMV Vector as a transfection normalization control. The Dual-Glo™ Luciferase Assay System was used to assay luciferase activities.  (3061)

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RNA 10, 277–286. Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. 2004

Verge´, V., VonLanthenm, M., Masson, J.M., Trachsel, H., and Altmann, M.

Notes: Researchers cloned the Photinus and Renilla luciferase ORFs into the pSP64 Poly(A) Vector to create a dual-reporter vector named SP6P. A similar vector, SP6R.4G(-508/-3).P, was created in which a 5´ untranslated region from the Saccharomyces cerevisiae TIF4631 gene was cloned between the two reporter genes. These two vectors were used to transform yeast strains. The resultant transformants were lysed using Passive Lysis Buffer and a modified lysis procedure.   Lysates were analyzed for luciferase activities using the Dual-Luciferase® Reporter Assay System and a TD20/20 luminometer. The researchers also cloned and sequenced the 5´  untranslated region of TIF4631 by using a RACE-PCR technique followed by cloning the PCR amplimers into the pGEM®-T Vector. (2845)

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Hum. Mol. Genet. 13, 2221-2231. SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. 2004

Shirasawa, S., Harada, H., Furugaki, K., Akamizu, T., Ishikawa, N., Ito, K., Ito, K., Tamai, H., Kuma, K., Kubota, S., Hiratani, H., Tsuchiya, T., Baba, I., Ishikawa, M., Tanaka, M., Sakai, K., Aoki, M., Yamamoto, K. and Sasazuki, T.

Notes: Real-time TaqMan® amplification reactions were cleaned up using the Wizard® MagneSil® Sequencing Reaction Clean-Up System.  The purified products were then used in sequencing reactions.  This paper also describes use of the Dual-Luciferase® Reporter Assay System to analyze HEK293 cells transfected with a pGL3-Enhancer vector construct.  (3181)

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J. Virol. 77, 4588-4596. Human Cytomegalovirus activates inflammatory cytokine responses via CD14 and Toll-like Receptor 2. 2003

Compton, T., Kurt-Jones, E.A., Boehme, K.W., Belko, J., Latz, E., Golenbock, D.T., and Finberg, R.W.

Notes: Researchers used Promega's pGL3-Basic Vector to create a NF-κB promoter-driven firefly luciferase reporter vector for use in transient transfections with the phRL-TK Vector. The two vectors, along with pUC18, were transiently transfected into HEK293 cells using GeneJuice Transfection Reagent (Novagen). Transfections were performed oversnight using 80ng NF-κB-pGL3-Basic construct, and 20ng of phRL-TK and pUC18 vectors in 96-well plates containing 2.5 x 104 cells/well. The following day, the cells were exposed to various treatments. Luciferase activity was measured using the Dual-Glo™ Luciferase Assay System.   (2672)

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Mol. Cell. Biol. 22, 5182-5193. Drosophila Mi-2 Negatively Regulates dDREF by Inhibiting Its DNA-Binding Activity. 2002

Hirose, F., Ohshima, N., Kwon, E.-J., Yoshida, H., and Yamaguchi, M.

Notes: Drosophila Mi-2 was discovered to specifically bind the DNA binding domain of dDREF (DNA replication-related element factor) by yeast two hybrid screen. This binding was shown to inhibit dDREF’s transcriptional regulatory action on a DNA replication-related element (DRE). Analysis of dDREF binding to the DRE was performed by examination of expression from –168DPCNAluc, –168mutΔPCNAluc, and pRL-actin5C reporter genes in Schneider cells using the Dual-Glo™ Luciferase Assay System. (2622)

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