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Cancer Res. 64, 7473-7478. Human polynucleotide phosphorylase (hPNPase0ld-35): A potential link between aging and inflammation 2004

Sarkar, D., Lebedeva, I.V., Emdad, L., Kang, D-c., Baldwin, A.S. and Fisher, P.B.

Notes: Human polynucleotide phosphorylase (hPNPaseold-35) was originally identified as a gene that is upregulated during cellular differentiation and senescence. The authors of this study show that overexpression of hPNPaseold-35 results in the increased production reactive oxygen species (ROS) and the activation of the NF-κB pathway, resulting in expression of the inflammatory cytokines IL-6 and IL-8. HeLa cells were transfected with either empty pGL3-Basic or 3kB-Luc (pGL3-Basic containing three tandem NF-κB binding sites). Transfected cells were infected with an empty adenoviral vector or one containing hPNPaseold-35. Luciferase assays were conducted using the Luciferase Assay System, and signal was normalized to a pSV-βgal control. A 10- to 12-fold increase in luciferase activity was observed in the cells infected with the adenovirus containing hPNPaseold-35 compared to the control cells. This activation was inhibited by compounds that reduced ROS. The authors suggest that hPNPaseold-35 plays an important role in producing age-related inflammation. (3643)

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Am. J. Physiol. Cell Physiol. 287, 1031-1040. Molecular analysis of fiber type-specific expression of murine myostatin promoter. 2004

Salerno, M.S., Thomas, M., Forbes, D., Watson, T., Kambadur, R., and Sharma, M.

Notes: In this article, a 2.5- and a 1.7-kb fragment of the myostatin promoter were amplified by PCR and cloned into the pGEM®-T Easy vector.  These clones were then subcloned into the pGL3-Basic Vector.  Deletion mutants of the constructs were made and used to transient transfect mouse muscle C2C12 cells.  The Luciferase Assay System was then used to analyze transfectants.  The researchers also injected luciferase-reporter constructs into mouse muscle.  Luciferase activity in the mouse muscle was examined by grinding isolated muscles in liquid nitrogen and resuspending them in Cell Culture Lysis Buffer.  Ten micron cryosections of the muscles were also used in immunohistochmical staining experiments.  For these experiments, the researchers used a 1:50 dilution of Promega’s polyclonal anti-luciferase antibody, a secondary antibody and tertiary fluorescein-labeled conjugate.  The slides were counter stained with DAPI. (3147)

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J. Cell Biol. 279, 50069–50077. p51/p63 controls subunit 3 of the major epidermis integrin anchoring the stem cells to the niche. 2004

Kurata, S., Okuyama, T., Osada, M., Watanabe, T., Tomimori, Y., Sato, S., Iwai, A., Tsuji, T., Ikawa, Y. and Katoh, I.

Notes: HeLa and Saos-2 were transiently transfected with luciferase reporter vectors made from the pGL3-Promoter vector containing various intron sequences from the human integrinα3 gene ITGA3.  The first intron sequence was originally cloned by PCR cloning into the pGEM®-T Easy vector. Cell cultures were assessed for luciferase activity by making lysates with the Glo Lysis Buffer and assaying with the Steady-Glo® Assay kit.    (3225)

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Plant Cell 16(5), 1235-1250. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. 2004

Dunoyer P., Lecellier C.H., Parizotto E.A., Himber C. and Voinnet O.

Notes: The authors cloned five distinct silencing suppressor proteins from five different plant viruses in order to examine the pathways involving both small interfering RNA and micro RNA in Arabidopsis thaliana. These viral factors [P1- HcPro of Turnip mosaic virus (TuMV), P38 protein of Turnip crinkle virus (TCV), P19 protein of Tomato bushy stunt virus(TBSV), P25 protein of Potato virus X, and the P15 protein of Peanut clump virus (PCV)] were inserted into a mammalian expression vector and tested for protein production using the TNT® Quick Coupled Transcription/Translation System. The suppression effects of these plant viral proteins were also tested in HeLa cells. The CMV promoter was cloned from pRL-CMV into the pGL3-Basic Vector and both plasmids were transfected at 500ng each plus 1µg of each of the five suppressor-expressing vectors. After one day, 300ng siRNA targeting the firefly luciferase gene was added. Twenty-four hours later, the Dual Luciferase® Reporter Assay System was used to determine the ratio of firefly:Renilla luciferase expression and see if the viral suppressor protein had an effect. (3085)

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Mol. Cell. Biol. 24(8), 3337-46. Recruitment of N-CoR/SMRT-TBLR1 corepressor complex by unliganded thyroid hormone receptor for gene repression during frog development. 2004

Tomita A., Buchholz D.R. and Shi Y.B.

Notes: The authors used Xenopus laevis oocytes to show that unliganded thyroid hormone receptor (TR) recruits N-CoR (nuclear receptor corepressor) to modulate metamorphosis.  To study this influence, the cytoplasm of stage VI oocytes from X. laevis was injected with the indicated mRNAs [TR, retinoic acid receptor (RXR) and FLAG-tagged N-CoR].  The reporter plasmid TRE-Luc (0.33 ng/oocyte; thyroid hormone response elements from a Xenopus promoter driving expression of the firefly luciferase gene) and the control vector phRG-TK (0.03 ng/oocyte) were co-injected into the germinal vesicle (nucleus) after mRNA injection. After overnight incubation at 18°C, oocyte lysates were prepared by lysing six oocytes in 90µL 1X Passive Lysis Buffer. The Dual-Luciferase® Reporter Assay System was then used to assay 7µl of the lysate. The researchers also used an expression vector (based on the pGEM®-4Z Vector) containing the 5’ and 3’ untranslated regions of the X. laevis beta-globin gene flanking the multiple cloning site. (3088)

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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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Mol. Cancer Res. 1, 475-84. Gene expression profiling in prostate cancer cells with Akt activation reveals Fra-1 as an Akt-inducible gene. 2003

Tiwari, G., Sakaue, H., Pollack, J.R., and Roth, R.A.

Notes: These authors analyzed gene expression profiles in the prostate cancer cell line PC3 upon induction of Akt activity to try to identify genes regulated by Akt that participate in the transformation of cells. They identified one mRNA of interest (Fra-1) and cloned its 5' regulatory region into a pGL3-Basic firefly luciferase reporter construct. This construct was used to transiently transfect MCF7 human breast cancer cells along with an Akt plasmid construct and a control vector expressing Renilla luciferase. The firefly construct was induced 4- to 5-fold by co-transfection with Akt3. Transfection conditions were as follows: MCF-7 cells were grown to 70% confluence in six-well plates, then incubated for 15 min with a mixture of 5ng of the control Renilla plasmid, 0.5μg of the Akt-expressing plasmid, and 0.5μg of pFra-luc construct and Fugene® 6 reagent at a 3:1 transfection reagent:DNA ratio. After 48 hours, luciferase activity was assessed using the Dual-Luciferase® Reporter Assay System.


(4361)

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J. Biol. Chem. 278 (22), 19691-19701. Complex transcription and splicing of odorant receptor genes. 2003

Volz, A., Ehlers, A., Younger, R., Forbes, S., Trowsdale, J., Schnorr, D., Beck, S. and Ziegler, A.

Notes: Total RNA was isolated from human testes using the RNAgents® Total RNA Isolation System. The isolated RNA was used in reverse transcription reactions to make cDNAs of HLA-linked OR genes. Promoter regions of HLA-linked OR genes were cloned into the pGL3-Basic Vector. The constructs were then transfected into human embryonic kidney (HEK293) and Odora cells for promoter analysis studies. The Bright-Glo™ Luciferase Assay System was used to generate data from the study.  Results were presented as a comparison to pGL3-Control Vector transfectants. (2730)

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J. Gene Med. 5(8), 723-732. Development of a dual-luciferase fusion gene as a sensitive marker for site-directed DNA repair strategies 2003

Bennett, M. and Schaack, J.

Notes: These authors created a construct encoding a Renilla and firefly luciferase fusion protein to examine the efficiency of site-specific DNA repair. The Renilla gene was taken from the pRL-null Vector and the firefly luciferase gene originated from the pSP-luc+NF Fusion Vector. The fusion construct was created by ligating the C-terminus of the Renilla luciferase gene to the N-terminus of the firefly gene.  The fused proteins were expressed at a constant ratio when transfected into mammalian cells.  Firefly luciferase expression was eliminated by deleting a T at position 213 creating an ochre translational stop codon and placing the downstream sequence out of frame. The mutant protein was then tested for repair using two methods: small fragment homologous replacement and oligonucleotide-mediated repair. The Renilla:firefly expression ratio was tested in several human, murine and simian cell lines and assayed 48 hours post-transfection using the Dual-Luciferase® Reporter Assay System.  In addition, the repaired plasmids were recovered to verify the sequence correction. (3064)

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Cancer Res. 63, 1818-1821. Firefly luciferin-activated Rose Bengal: In vitro photodynamic therapy by
intracellular chemiluminescence in transgenic NIH 3T3 cells.
2003

Theodossiou, T., Hothersall, J.S., Woods, E.A., Okkenhaug, K., Jacobson, J. and MacRobert, A.J.

Notes: NIH 3T3 cells were transfected using Superfect (Qiagen) with Promega's pGL3-Control Vector and a marker for antibiotic resistance at a 5:1 ratio. Transfected cells were visualized after in situ addition of 500μM Beetle Luciferin in 10% FCS medium.  The transfected cells were used to show that light from a luciferase reaction can be used to create targeted cytotoxicity in the presence of the photosensitizer Rose Bengal (RB). This application has specific relevance as a  tumor treatment by photodynamic therapy. (2671)

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Clin. Can. Res. 9, 3167-3175. Fully human anti-interleukin 8 antibody inhibits tumor growth in orthotopic bladder cancer xenografts via down-regulation of matrix metalloproteases and nuclear factor-κB 2003

Mian, B.M., Dinney, C.P.N., Bermejo, C.E., Sweeny, P., Tellez, C., Yang, X.D., Gudas, J.M., McConkey, D.J., Bar-Eli, M.

Notes: Luciferase reporter gene constructs based on the pGL3 vector that contained either MMP-2 or MMP-9 promoters, SV40 promoter (positive control ) or the luciferase basic vectors were transfected into metastatic cells, S53JB-V cells or UMUC-3 cells along with a pβ-actin RL control construct. Cells were treated with an anti-IL-8 antibody, IgG control or no antibody. Dual luciferase reporter assays were performed to determine the effect of the treatments on activity and expression of the MMP-2 and MMP-9 constructs. (2716)

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FEBS Lett. 555, 390-396. Hsp105 but not Hsp70 family proteins suppress the aggregation of heat-denatured protein in the presence of ADP. 2003

Yamagishi, N., Ishihara, K., Saito, Y., and Hatayama, T.

Notes: The pGL3-Control Vector was co-transfected into COS-7 cells with mammalian expression vectors expressing either heat shock protein Hsp70 or Hsp105α.  The cells were ATP-depleted in glucose-free media with 2μM rotenone and 5mM 2-deoxyglucose for up to 3 hours. Afterwards the cells were lysed with the Cell Culture Lysis Reagent and assayed for luciferase activity uaing the Luciferase Assay System. ATP depletion was verified during 2μM rotenone and 5mM 2-deoxyglucose treatment using the CellTiter-Glo® Assay.  (2841)

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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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J. Biol. Chem. 278, 9332-9338. Identification of an upstream enhancer in the mouse laminin α1 gene defining its high level of expression in parietal endoderm cells. 2003

Niimi, T., Hayashi, Y. and Sekiguchi, K.

Notes: The pGL3-basic and pGL3-Promoter vectors were used to make constructs with varying lengths of the mouse LAMA1 promoter. Gene fragments up to 6.1 kb were cloned into the pGL3-promoter vector and analyzed for luciferase expression in a variety of cell lines using the Dual-Luciferase® Reporter Assay System. F9, NIH/3T3, PYS-2 and EHS cells were transiently transfected with 200ng of reporter construct and 20ng of the Renilla luciferase-expressing phRL-null vector in 24-well plates.  Forty-eight hours later, cell lysates were harvested with Passive Lysis Buffer. Site-directed mutagenesis of  the LAMA1 gene promoter was performed with the GeneEditor™ in vitro Site-Directed Mutagenesis System.  (2631)

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J. Virol. 77, 1992-2002. Molecular and functional analysis of an interferon gene from the zebrafish, Danio rerio. 2003

Altmann, S.M., Mellon, M.T., Distel, D.L. and Kim, C.H.

Notes: The pGEM®-T Easy Vector was used to subclone products of a 5´ RACE reaction. A promoter construct, assembled in the pGL3 Basic Vector, was co-transfected with a zebrafish interferon expression vector in the ZF4 zebrafish embryo fibroblast cell line using the TransFast™ Reagent (details provided). Luciferase levels were examined with the BrightGlo™ Luciferase Assay Reagent. Induction of zebrafish mRNA was also examined in zebrafish liver cells (ZFL) following treatment with the known interferon inducer, poly(I)-poly(C). RNA was extracted and reverse transcribed using ImProm-II™ Reverse Transcriptase. The resulting cDNA was used for quantitative, real-time RT-PCR with a SYBR green-based assay. (2627)

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Clin. Can. Res. 9, 5874–5879. Sensitization to the cytotoxicity of cisplatin by transfection with nucleotide excision repair gene Xeroderma Pigmentosun Group A antisense RNA in human lung adenocarcinoma cells. 2003

Wu, X., Fan, W., Xu, S., and Zhou, Y.

Notes: The pGL3-Promoter Vector was treated with various concentrations of the chemotherapeutic cancer and DNA cross-linking agent, cisplatin. The damaged pGL3-Promoter Vector and the pSV-β-Galactosidase Control Vector were then transiently transfected into the human lung adenocarcinoma cell line, A549, and later analyzed for luciferase activity using the Luciferase Assay System with Reporter Lysis Buffer. The researchers also used M-MLV Reverse Transcriptase to clone the antisense sequence to XPA (Xeroderma Pigmentosum group A) mRNA.  The cloned antisense sequence was then expressed in A549 cells for its effect on XPA gene expression. (2833)

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Cancer Res. 63(10), 2658-64. Transactivation of vimentin by beta-catenin in human breast cancer cells. 2003

Gilles C., Polette M., Mestdagt M., Nawrocki-Raby B., Ruggeri P., Birembaut P. and Foidart J.M.

Notes: The authors explored the role of beta-catenin and T-cell factor 4 to transactivate vimentin, a protein involved in gain of mesenchymal characteristics and loss of epithelial characteristics as a precursor to metastasis. The vimentin promoter was cloned into the pGL3-Basic Vector. The beta-catenin/TCF binding sites upstream of a minimal c-fos promoter drove firefly luciferase expression in plasmids called TOP-FLASH (wild-type binding sites) and FOP-FLASH (mutant binding sites).  To examine beta-catenin/TCF-4 induction, several human mammary epithelial cell lines were transfected with a mixture of 0.15µg of various firefly reporter constructs (wild type vimentin promoter, mutant vimentin promoter, TOP-FLASH,or FOP-FLASH), 0.15 µg of the beta-catenin expression vector (or the corresponding empty vector), 0.15 µg of the TCF-4 expression vector and 0.8 ng of the Renilla luciferase vector, phRG-TK.  Twenty-four hours after transfection, the cells were lysed and assayed using the Dual-Luciferase® Reporter Assay System. (3087)

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Am. J. Physiol. Lung Cell. Mol. Physiol. 284(1), L108-18. Transcriptional regulation of CCSP by interferon-gamma in vitro and in vivo. 2003

Ramsay, P.L., Luo, Z., Magdaleno, S.M., Whitbourne, S.K., Cao, X., Park, M.S., Welty, S.E., Yu-Lee, L.Y. and DeMayo, F.J.

Notes: To investigate how interferon gamma stimulates expression of the murine Clara cell secretory protein (CCSP) gene, the 280bp CCSP promoter region was radiolabeled and incubated with nuclear extract from mouse transformed Clara cells (mtCC). Transcription factor binding sites were identified using the Core Footprinting System. A 30bp section of the CCSP promoter containing three transcription factor consensus sites was synthesized with 0, 1 or 2 mutated binding sites and tested in the presence of mtCC nuclear extract. Oligos and nuclear extract were allowed to form complexes with or without interferon gamma in Gel Shift Binding Buffer. A 166bp section of the CCSP promoter was also cloned into the pGL3-Basic Vector and co-transfected with the pRL-TK Vector into mtCC. The cells were subjected to interferon gamma treatment and the cell lysates assayed using the Dual-Luciferase® Reporter Assay System. (3112)

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J. Biol. Chem. 278, 5659-5668. Transcriptional Regulation of the Rat NHE3 Gene. Functional Interactions between GATA-5 and Sp family transcription factors. 2003

Kiela, P.R., LeSueur, J., Collins, J.F. and Ghishan, F.K.

Notes: Researchers created promoter constructs in the pGL3-Basic vector to study NHE3 promoter function in cotransfection experiments with the pRL-null vector.  Transfected Caco-2 cells were analyzed by the Dual-Luciferase® Reporter Assay System. Beta-Galactosidase Assays were also performed on SL2 cells cotransfected with the pRL-null vector. The Renilla Luciferase Assay System was used to normalize these transfectants. (2642)

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J. Biol. Chem. 278, 5156-5162. Y-box-binding protein YB-1 mediates transcriptional repression of human alpha2(I) collagen gene expression by interferon-gamma. 2003

Higashi, K., Inagaki, Y., Suzuki, N., Mitsui, S., Mauviel, A., Kaneko, H. and Nakatsuka, I.

Notes: The Y-box-binding protein YB-1 was examined through the use of a reporter plasmid with wildtype and mutant putative Y-box binding sites. The binding sites were constructed in the pGL3 Basic Vector and measured using the Luciferase Assay System. Studies were performed in normal human dermal fibroblasts.  Expression of YB-1 was found to repress expression of the COL1A2 gene at the transcriptional level. Confirmation of this dose-dependent inhibition was through measurement of the steady-state mRNA levels by quantitative, real-time RT-PCR.  The reverse transcription portion of the quantitative, real-time RT-PCR reactions were performed with ImProm-II™ Reverse Transcriptase followed by a TaqMan-type quantitative PCR step. (2623)

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Mol. Endocrinol. 16(10), 2243-54. Cloning and characterization of a novel endothelial promoter of the human CYP19 (aromatase P450) gene that is up-regulated in breast cancer tissue. 2002

Sebastian, S., Takayama, K., Shozu, M. and Bulun, S.E.

Notes: The promoter region of human CYP19 was amplified from a lambda library and cloned into the pGEM®-T Easy Vector for sequencing. Several mutants of this aromase cytochrome P450 promoter were created and cloned into the pGL3-Basic Vector. One microgram of the various reporter constructs along with 25ng pRL-null Vector (as an internal control) were transfected into HMEC-1 and MCF-7 cells in six-well plates. Luciferase levels were assayed 48 hours post-transfection using the Dual-Luciferase® Reporter Assay System. To further characterize the CYP19 promoter, a 30-mer region with a GATA motif was added to 250ng HMEC-1 nuclear extract in the presence of oligonucleotide competitors or antibodies using the Gel Shift Binding 5X Buffer, then analyzed by gel electrophoresis. (3110)

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Hum. Mol. Genet. 11, 2787-2792. Functional association of the parkin gene promoter with idiopathic Parkinson's disease. 2002

West, A.B., Maraganore, D., Crook, J., Lesnick, T., Lockhart, P.J., Wilkes, K.M., Kapatos, G., Hardy, J.A. and Farrer, M.J.

Notes: BE(2)-M17 and HEK-293T cells (Human dopaminergic neuroblastoma and human embryonic kidney cells, respectively) were cultured in Opti-MEM (Life Technologies) with 10% FBS, penicillin (100 units/ml) and streptomycin (100 mg/ml). Cells were plated at 80% confluence and maintained in an atmosphere of 5% CO2 at 37°C for twenty-four hours prior to transfection in 24-well culture plates. Firefly Luciferase-containing constructs (pGL3) were co-transfected with the phRL-TK synthetic Renilla luciferase vector, at a molar ratio of 1:100 (phRL-TK:pGL3).  These transfections were performed in serum-free media for 12 h using a 1:3 molar ratio of DNA: Fugene reagent (Roche Biochemicals), and 0.2 mg of DNA per well. After forty hours cells were rinsed with PBS and then harvested with Passive Lysis Buffer. The Dual-Luciferase® Reporter Assay System was used to measure firefly and Renilla luciferase activities from the transfected cells using duplicate readings on a Turner Designs 20/20 Single-Injector Luminometer. (2663)

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J. Biol. Chem. 277, 42280–42288. GAGA factor down-regulates its own promoter. 2002

Kosoy, A., Pagans, S., Espina´s, M.L., Azorýn, F. and Bernue´s, J.

Notes: Researchers PCR amplified and cloned the Trl promoter into the pGEM®-T vector. The Trl promoter sequence, as well as the eve promoter sequence and/or a CMV promoter, were used to make luciferase reporter constructs using the pGL3-Basic Vector. Transient transfection experiments were performed with the promoter constructs and GAGA factor expression constructs. Relative luciferase activity from each experiment was measured and compared to that of a control.  (2775)

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J. Biol. Chem. 277, 16456-16463. Identification of essential regions in the cytoplasmic tail of interleukin-1 receptor accessory protein critical for interleukin-1 signaling. 2002

Radons, J., Gabler, S., Wesche, H., Korherr, C., Hofmeister, R. and Falk, W.

Notes: An IL-1 inducible fragment of the murine IL-2 promoter and five tandemly-arranged NFκB binding sites were cloned into the pGL3-Basic Vector, creating the constructs pGL3-IL-2 and pGL3-5xNFκB, respectively. IL2 promoter activation and NFκB activation were measured after rhIL-1α - or PMA-stimulation of EL4D6/76 cells transiently transfected with these constructs. Luciferase activity was measured using the Steady-Glo® Luciferase Assay System. As an internal control, cells were co-transfected with the pRL-SV40 Vector, and expression of firefly and Renilla luciferase was measured using the Dual-Luciferase® Reporter Assay System. (2427)

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J. Biol. Chem. 277, 47014-47021. Identification of Functional Hypoxia Response Elements in the Promoter Region of the DEC1 and DEC2 Genes. 2002

Miyazaki, K., Kawamoto, T., Tanimoto, K., Nishiyama, M., Honda, H., and Kato, Y.

Notes: The researchers used pGL3 basic constructs and the phRL-TK vector in cotransfection studies to examine the effect of hypoxia on promoter regions of DEC1 and DEC2 promoter constructs in ATDC5, 293T, and HeLa cells. The Dual-Luciferase® Assay System was used to examine the expression levels of luciferase from the constructs. (2630)

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