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Proc. Natl. Acad. Sci. USA 109, 2654–9. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice 2012

Ding, J., Lu Q, Ouyang, Y., Mao, H., Zhang, P., Yao, J., Xu, C. Li, X., Xiao, J. and Zhang, Q.

Notes: Genomic DNA was isolated from rice plants and bisulfite treated. Target regions were specifically amplified using bisulfite primers, and the amplified products cloned into the pGEM®-T vector prior to large scale bisulfite sequencing. Sequencing analysis was performed using the Kismeth tool. pGEM®-T was also used as the vector for fragments amplified from cDNA clones of transcripts of interest prior to generating sense and antisense RNA probes for RNA in situ hybridization experiments. Apoptosis of tissue from anthers was assessed using the DeadEnd Fluorometric TUNEL System. (4558)

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Plant Physiol. 148, 479–489. Eukaryotic translation initiation factor 5A is involved in pathogen-induced cell death and development of disease. 2008

Hopkins, M.T., Lampi, Y., Wang, T.W., Liu, Z. and Thompson, J.E.

Notes: Genomic DNA from Arabidopsis thaliana was isolated using the Wizard® Genomic DNA Purification Kit. The extracted DNA was used to amplify the 3´ UTR of AteIF5A-2, A. thaliana translation initiation factor 5A, or the entire gene for creating transgenic plants. Leaf discs from wild-type Arabidopsis were infected with Pseudomonas syringae pv tomato DC3000, a virulent strain regulated by AteIF5A-2, using a syringe. After 24 and 72 hours, 0.4cm leaf discs were fixed, labeled using the DeadEnd™ Fluorometric TUNEL System and stained for AteIF5A-2 protein. (3979)

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Development 135, 541-557. Impaired generation of mature neurons by neural stem cells from hypomorphic Sox2 mutants 2008

Cavallaro, M., Mariani, J., Lancini, C., Latorre, E., Caccia, R., Gullo, F., Valotta, M., DeBiasi, S., Spinardi, L., Ronchi, A., Wanke, E., Brunelli, S., Favaro, r., Ottolenghi, S. and Nicolis, S.K.

Notes: The authors of this paper investigated the role of Sox2 in neuronal differentiation. Neurospheres were derived from the brains of normal and Sox2 hyphomorphic mice and used to generate differentiated neural cells. In astroglia from cultures containing a Sox2-GFP-expressing lentivirus, ectopic expression of Sox2 correlated with reduced GFAP expression. The authors investigated the role of Sox2 by amplifying binding sites upstream of the GFAP promoter and cloning them upstream of the thymidine kinase promoter in the pRL-TK vector. The Dual-Luciferase Assay System was used to analyze the effect of Sox2 expression on the luciferase reporter gene. The DeadEnd™ Fluorometric TUNEL System was also used to assess apoptosis in some of the neurosphere-derived cultures. (3953)

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Proc. Natl. Acad. Sci. USA 103, 6332-7. Nicotine inhibits apoptosis induced by chemotherapeutic drugs by up-regulating XIAP and survivin. 2006

Basgupta, P., Kinkade, R., Joshi, B., DeCook, C., Haura, E. and Chellappan, S.

Notes: RT-PCR was performed to map the subtypes of nicotinic acetylcholine receptors on A549 cells. cDNA was synthesized using the Reverse Transcription System. Northern blotting to assess XIAP and survivin expression was performed, and probes were labeled using the Prime-A-Gene® Labeling System. Apoptosis was assessed in nicotine-stimulated cells using a DeadEnd™ TUNEL Assay. (3382)

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Proc. Natl. Acad. Sci. USA 103, 962-967. Reproductive protein protects functionally sterile honey bee workers from oxidative stress 2006

Seehuus, S-C., Norberg, K., Gimsa, U., Krekling, T. and Amdam, G.V.

Notes: The authors of this paper demonstrate that the pathways controlling lifespan and senescence are linked to the pathways controlling fertility in the honey bee. Using RNAi experiments, the authors demonstrate that vitellogenin protects honey bee workers from oxidative stress. Double-stranded RNA was synthesized from the vitellogenin clone AP4a5 using the RiboMax® T7 System. In additional experiments the authors assessed apoptosis in brain tissue sections using the DeadEND™ Fluorometric TUNEL system. (3636)

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Clin. Can. Res. 11, 5622-30. Antiangiogenic treatment with the three thrombospondin-1 type 1 repeats recombinant protein in an orthopic human pancreatic cancer model. 2005

Zhang, X, et al

Notes: In this study, human pancreatic cancer cells were injected into the pancreas of SCID mice. Mice were treated with thromobospondin-1 three type 1 repeats (3TSR) alone or combined with gemcitabine. The antitumor efficacy of the various treatments was then evaluated. The DeadEnd™ Fluorometric TUNEL System was used to assess apoptosis in tissue sections. (3326)

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Infect. Immun. 72, 5470-5474. Chlamydia trachomatis infection inhibits both Bax and Bak activation induced by staurosporine. 2004

Xiao, Y., Zhong, Y., Greene, W., Dong, F. and Zhong, G.

Notes: The DeadEnd™ Fluorometric TUNEL System was used to label apoptotic Hela cells that were infected with C. trachomatis for 40 hours before treatment with 2μg/ml Staurosporine for an additional 5 hours. Cultures were co-stained with either Anti-ACTIVE® Caspase-3 pAb or Anti-Cytochrome c mAb. Cy®3-conjugated goat anti-rabbit or -mouse IgG was used as a secondary labeling antibody and the cells were visualized by confocal microscopy. (3252)

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Nat. Neurosci. 7, 596-604. Dynein motors transport activated Trks to promote survival of target-dependent neurons. 2004

Heerssen, H.M., Pazyra, M.F. and Segal, R.A.

Notes: This paper describes an assay to test BDNF dissociation from FluoSpheres (amine-modified microspheres, 1μM diameter; Molecular Probes). BDNF was covalently attached to the microspheres. Release of BDNF was tested in supernatants from the BDNF-microspheres in PBS, in complete media, and in culture with rat Dorsal root ganglia. Promega’s BDNF Emax® ImmunoAssay System was used to determine the amounts of BDNF in these samples. The DeadEnd™ Fluorometric TUNEL System was used to examine rat Dorsal root ganglia cells that had been transfected with either dynamitin or β-Galactosidase. In the TUNEL experiments, cells were fixed in 4% paraformaldehyde and counterstained with DAPI. Cells were also stained with Promega’s Anti-β-Galactosidase, Purified Monoclonal Antibody. For these immunocytochemical stains, a 1:500 dilution of Anti-β-Galactosidase antibody and a 1:1,500 dilution of a secondary antibody conjugated to Alexa Fluor-488 (Molecular Probes) were used. The stains were visualized by fluorescence microscopy. (3055)

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Clin. Can. Res. 9, 955-960. Automated quantification of apoptosis after neoadjuvant chemotherapy for breast cancer: Early assessment predicts clinical response 2003

Davis, D.W., Buchholz, T.A., Hess, K.R., Sahin, A.A., Valero, V., McConkey, D.J.

Notes: The authors developed an automated, laser scanning, cytometer-based method to quantify the percentage of tumor cells containing DNA fragmentation characteristic of apoptosis. They used the DeadEnd™ Fluorometric TUNEL System to analyze sections from breast tumor biopsies. (2633)

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Clin. Can. Res. 9, 3183-3189. Epidermal growth factor receptor blockade potentiates apoptosis mediated by paclitaxel and leads to prolonged survival in a murine model of oral cancer 2003

Holsinger, F.C., Doan, D.D., Jasser, S.A., Swan, E.A., Greenberg, J.S., Schiff, B.A., Bekele, B.N., Younes, M.N., Bucana, C.D., Fidler, I.J., Myers, J.N.

Notes: Fuorescent TUNEL analysis was used to determine apoptosis in JMAR cells (human oral squamous cell carcinoma) treated with paclitaxel or paclitaxel plus the EFGR inhibitor PKI166. (2717)

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Cell Death Differ. 10, 175-184. FLIP is expressed in mouse testis and protects germ cells from apoptosis 2003

Giampietri, C., Petrungaro, S., Coluccia, P., D'Alesso, A., Starace, D., Riccioli, A., Padula, F., Srinivasula, S.M., Alnemri, E., Palombi, F., Filippini, A., Ziparo, E., De Cesaris, P.

Notes: TUNEL staining was performed on segments of paraffin embedded seminiferous tubules using the DeadEnd™ Fluorometric TUNEL System. (2666)

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Brain Res. 988, 20-28. Group III secreted phospholipase A2 causes apoptosis in rat primary cortical neuronal cultures. 2003

DeCoster, M.A.

Notes: The DeadEnd™ Fluorometric TUNEL System was used to demonstrate the apoptotic effect of secreted phospholipase A2 (sPLA2) on primary rat cortical neurons in culture. Dual staining with the DeadEnd™ Fluorometric TUNEL System and propidium iodide (PI) allowed quantification of  the TUNEL staining area by analysis of digitized images. (2751)

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Clin. Can. Res. 8, 2413-22. Synergistic therapy of human ovarian carcinoma implanted orthotopically in nude mice by optimal biological doses of pegylated interferon α combined with paclitaxel 2002

Tedjarati, S., Baker, C.H., Apte, S., Huang, S., Wolf, J.K., Killion, J.J., Fidler, I.J.

Notes: TUNEL analysis of tissue sections from the implanted tumors was performed using the DeadEnd™ Fluorometric TUNEL System. (2582)

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Mol. Cell. Neurosci. 19, 359-374. The cyclin-dependent kinase inhibitors p19Ink4d and p27Kip1 are coexpressed in select retinal cells and act cooperatively to control cell cycle exit 2002

Cunningham, J.J., Levine, E.M., Zindy, F., Goloubeva, O., Roussel, M.F., Smeyne, R.J.

Notes: Mouse retinal slices from mice strains deficient for Ink4d, Kip1, or both Ink4d and Kip1, as well as Ink4d/Kip1/p53-triple null mice, were characterized for apoptosis using the DeadEnd Colorimetric TUNEL System. (2442)

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Biotechniques 30, 886-891. Poly (ADP-ribose) polymerase cleavage monitored in situ in apoptotic cells. 2001

O'Brien, M.A., Moravec, R.A., and Riss T.L.

Notes: During apoptosis, Poly (ADP-ribose) polymerase (PARP) is cleaved by caspase-3 to generate an 85 kDa fragment (p85). An affinity-purified polyclonal antibody to the p85 fragment of PARP is characterized. In Western blot analysis with Jurkat cells treated with an anti-Fas antibody and with SH-Sy5Y cells treated with staurosporine, the antibody recognizes the 85-kDa (p85) fragment of PARP but not full-length PARP. The antibody was used at a concentration of 0.75 µg/ml for Western blots and at 2.5µg/ml for immunocytochemistry. TUNEL labeling of apoptotic Jurkat cells was performed with the DeadEnd™ Fluorometric TUNEL System. Immunocytochemistry was also performed using the Anti-β III Tubulin mAb. Good experimental details are given. (2355)

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Plant Cell 13, 1803-1818. The PET1-CMS mitochondrial mutation in sunflower is associated with premature programmed cell death and cytochrome c release. 2001

Balk, J. and Leaver, C.J.

Notes: The DeadEnd™ Fluorometric TUNEL System was used to visualize apoptotic nuclei in sunflower florets. Researchers fixed the florets in 50% (v/v) ethanol, 4% (v/v) formaldehyde and 5% (v/w) glacial acetic acid, and embedded the tissues in polyethylene glycol (PEG), 1500 grade. Sections (7μM) were permeabilized with Proteinase K before proceeding with the DeadEnd™ Fluorometric TUNEL labeling protocol. (2741)

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Proc. Natl. Acad. Sci. USA 97(26), 14376-14381. An alternative, nonapoptotic form of programmed cell death 2000

Sperandio, S., de Belle, I., Bredesen, D.E.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to demonstrate nuclear fragmentation in vitro when 293 cells were transfected with Bax, a known apoptosis inducer. Transfection with the beta subunit of the intracellular domain of the human insulin-like growth factor receptor caused cell death but did not induce nuclear fragmentation. This paraptosis was TUNEL-negative. (2203)

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Proc. Natl. Acad. Sci. USA 97(13), 7561-7566. Antiapoptotic role of the p38 mitogen-activated protein kinase-myocyte enhancer factor 2 transcription factor pathway during neuronal differentiation. 2000

Okamoto, S., Krainc, D., Sherman, K., Lipton, S.A.

Notes: The Apoptosis Detections System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to examine apoptosis in the P19 embryonal carcinoma cells following retinoic acid treatment which causes differentiation of the P19 cells into neuronal cells. (2197)

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J. Neuroimmunol. 104, 58-67. Axonal damage induced by cerebrospinal fluid from patients with relapsing-remitting multiple sclerosis 2000

Alcazar, A., Regidor, I., Masjuan, J., Salinas, M., and Alvarez-Cermeno, J.C.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used as one measure of apoptosis in cultured rat neurons treated with the cerebral spinal fluid (CSF) of multiple sclerosis (MS) patients. CSF from aggressive MS patients induced apoptosis to a greater degree than non-aggressive MS patients. (0043)

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J. Cell Biol. 151(4), 811-824. CaM kinase IV regulates lineage commitment and survival of erythroid progenitors in a non-cell-autonomous manner. 2000

Wayman, G.A., Walters, M.J., Kolibaba, K., Soderling, T.R., Christian, J.L.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to assess apoptotic nuclei in peripheral blood samples collected from Xenopus embryos. The system was used to see whether up-regulation or down-regulation of CaM KIV caused increased apoptotic death of erythroid precursors. (2201)

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Immunity 12, 581-590. Caspase-1 activation of IL-1beta and IL-18 are essential for Shigella flexneri-induced inflammation 2000

Sansonetti, P.J., Phalipon, A., Arondel, J., Thirumalai, K., Banerjee, S., Akira, S., Takeda, K., and Zychlinsky, A.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to label apoptotic cells in 10µm sections of 4% formalin-fixed wildtype and transgenic mouse lung tissue. Wildtype mice infected with Shigella flexneri had TUNEL-positive macrophages within the tissue and the caspase-1 knockout mice had no apparent apoptotic macrophages. (0050)

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FASEB J. 13, 1359-1370. Cholesterol starvation decreases p34cdc2 kinase activity and arrests the cell cycle at G2 2000

Martinez-Botas, J., Suarez, Y., Ferruelo, A.J., Gomez-Coronado, D., and Lasuncion, M.A.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to examine the mode of death of HL-60 cells treated with SKF 104976, an inhibitor of lanosterol 14-alpha demethylase. The cells were labeled and analyzed by flow cytometry. (0048)

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Brain Res. Brain Res. Protoc. 5, 305-311. Combined TUNEL and double immunofluorescent labeling for detection of apoptotic mononuclear phagocytes in autoimmune demyelinating disease. 2000

Ray, S.K., Schaecher, K.E., Shields, D.C., Hogan, E.L., and Banik, N.L.

Notes: Apoptosis was analyzed in 4µm thick frozen rat lumbar spinal cord sections using a modification of the Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System). Instead of using the supplied DNA labeling mix containing flourescein-12-dUTP, the authors substituted an alkali-stable DIG-11-dUTP solution. Detection of TUNEL-positive cells was accomplished with an anti-DIG polyclonal antibody conjugated with 7-amino-4-methylcoumarin-3-acetic acid, which gives bright blue fluorescence. The TUNEL staining was combined with a phagocyte-specific staining with a Texas Red® conjugate. (0045)

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Hum. Gene Ther. 11, 379-388. Deletion of the adenoviral E1b-19kD gene enhances tumor cell killing of a replicating adenoviral vector 2000

Sauthoff, H., Heitner, S., Rom, W.N., Hay, J.G.

Notes: A549 lung adenocarcinoma cells were infected with wildtype adenovirus or a mutant with a deleted E1b-19kD gene. E1b-19kD is a powerful anti-apoptotic agent. Cells infected with the mutant demonstrated more TUNEL positive cells than wildtype or control. The apoptotic effect was heightened with the addition of the chemotherapy drug cisplatin. Excellent detail is provided for cell treatment and preparation. Both adherent and floating cells were affixed to poly-L-lysine coated slides for TUNEL analysis. TUNEL staining was performed with the Apoptosis Detection System, Fluorescein. Update: The Apoptosis Detection System, Fluorescein has been renamed to the DeadEnd™ Fluorometric TUNEL System (Cat.# G3250). (0444)

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Neuroscience 99(2), 333-342. Functional role and therapeutic implications of neuronal caspase-1 and -3 in a mouse model of traumatic spinal cord injury. 2000

Li, M. , Ona, V. O. , Chen, M. , Kaul, M. , Tenneti, L. , Zhang, X. , Stieg, P. E. , Lipton, S. A. , Friedlander, R. M.

Notes: The Apoptosis Detection System, Fluorescein (DeadEnd™ Fluorometric TUNEL System) was used to examine apoptotic nuclei in 10µm paraformaldehyde-fixed, paraffin-embedded rat spinal cord sections. The ability of Z-VAD-FMK was used to determine if apoptotic death could reduce trauma induced apoptosis. Transgenic mice with a dysfunctional caspase-1 showed decreased spinal cord injury as well. (0023)

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